Publications by authors named "Philippe Constant"

27 Publications

  • Page 1 of 1

Gut microbiome of the emerald ash borer, Agrilus planipennis Fairmaire, and its relationship with insect population density.

FEMS Microbiol Ecol 2020 08;96(8)

Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, QC, H7V 1B7, Canada.

The gut microbial communities of beetles play crucial roles in their adaptive capacities. Environmental factors such as temperature or nutrition naturally affect the insect microbiome, but a shift in local conditions like the population density on a host tree could also lead to changes in the microbiota. The emerald ash borer (EAB), Agrilus planipennis Fairmaire, is an exotic wood borer that causes environmental and economic damage to ash trees in North America. This study aimed to describe the taxonomic structure of the EAB gut microbiome and explore its potential relationship with borer population size. The number of EAB adults collected per tree through a 75 km transect from an epicenter allowed the creation of distinct classes of population density. The Gammaproteobacteria and Ascomycota predominated in bacterial and fungal communities respectively, as determined by sequencing of the bacterial 16S rRNA gene and the fungal internal transcribed spacer ITS2. Species richness and diversity of the bacterial community showed significant dependence on population density. Moreover, α-diversity and β-diversity analysis revealed some indicator amplicon sequence variants suggesting that the plasticity of the gut microbiome could be related to the EAB population density in host trees.
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http://dx.doi.org/10.1093/femsec/fiaa141DOI Listing
August 2020

Natural Variation in Physicochemical Profiles and Bacterial Communities Associated with Aedes aegypti Breeding Sites and Larvae on Guadeloupe and French Guiana.

Microb Ecol 2021 Jan 3;81(1):93-109. Epub 2020 Jul 3.

Laboratory of Vector Control Research, Transmission Reservoir and Pathogens Diversity Unit, Institut Pasteur of Guadeloupe, Morne Jolivière, Guadeloupe, France.

Aedes aegypti develop in aquatic habitats in which mosquito larvae are exposed to physicochemical elements and microorganisms that may influence their life cycle and their ability to transmit arboviruses. Little is known about the natural bacterial communities associated with A. aegypti or their relation to the biotic and abiotic characteristics of their aquatic habitats. We characterized the physicochemical properties and bacterial microbiota of A. aegypti breeding sites and larvae on Guadeloupe and in French Guiana. In addition, we explored whether geographic location, the type of breeding site and physicochemical parameters influenced the microbiota associated with this mosquito species. We used large-scale 16S rRNA gene sequencing of 160 breeding sites and 147 pools of A. aegypti larvae and recorded 12 physicochemical parameters at the sampled breeding sites. Ordination plots and multiple linear regression were used to assess the influence of environmental factors on the bacterial microbiota of water and larvae. We found territory-specific differences in physicochemical properties (dissolved oxygen, conductivity) and the composition of bacterial communities in A. aegypti breeding sites that influenced the relative abundance of several bacteria genera (e.g., Methylobacterium, Roseoccocus) on the corresponding larvae. A significant fraction of the bacterial communities identified on larvae, dominated by Herbiconiux and Microvirga genera, were consistently enriched in mosquitoes regardless the location. In conclusion, territory-specific differences observed in the biotic and abiotic properties of A. aegypti breeding sites raise concern about the impact of these changes on pathogen transmission by different A. aegypti populations.
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http://dx.doi.org/10.1007/s00248-020-01544-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7794107PMC
January 2021

A Gaseous Milieu: Extending the Boundaries of the Rhizosphere.

Trends Microbiol 2020 07 26;28(7):536-542. Epub 2020 Mar 26.

Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, H7V 1B7, Canada; Quebec Center for Biodiversity Sciences (QCBS), Montreal, H3A 1B1, Canada.

Plant root activities shape microbial community functioning in the soil, making the rhizosphere the epicenter of soil biogeochemical processes. With this opinion article, we argue to rethink the rhizosphere boundaries: as gases can diffuse several centimeters away from the roots into the soil, the portion of soil influenced by root activities is larger than the strictly root-adhering soil. Indeed, gases are key drivers of biogeochemical processes due to their roles as energy sources or communication molecules, which has the potential to modify microbial community structure and functioning. In order to get a more holistic perspective on this key environment, we advocate for interdisciplinarity in rhizosphere research by combining knowledge of soluble compounds with gas dynamics.
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http://dx.doi.org/10.1016/j.tim.2020.02.016DOI Listing
July 2020

Gamma irradiation triggers a global stress response in Escherichia coli O157:H7 including base and nucleotides excision repair pathways.

Microb Pathog 2020 Dec 10;149:104342. Epub 2020 Jun 10.

INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, Québec, H7V 1B7, Canada; Research Laboratories in Sciences Applied to Food, Canadian Irradiation Centre, INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, Québec, H7V 1B7, Canada. Electronic address:

Shiga toxin-producing Escherichia coli O157:H7, one of the most severe human foodborne pathogens, can withstand several stresses, including some levels of γ-irradiation. In this study, the response of E. coli O157:H7 to a sensitization irradiation dose of 0.4 kGy was assessed using RNA-seq transcriptomic at 10 (t10) and 60 (t60) min post-irradiation, combined with an isobaric tags for relative and absolute quantitation (iTRAQ) proteomic analysis at 60 min post-irradiation. Several functions were induced by the treatment, such as base excision repair and nucleotide excision repair pathways; sulfur and histidine metabolism, and virulence mechanisms. Additionally, the sulA gene, coding for the cell division repressor, together with other genes involved in SOS response and repair mechanism (including recA, recN, recJ, recQ, mutM and uvrB) were up-regulated at t60. As the early response to irradiation stress (t10), dnaK, groEL, ibpA, sulfur metabolism genes, as well as those related to oxidative stress were up-regulated, while histidine biosynthesis genes were down-regulated. Acid stress, heat shock, UV resistance and several virulence genes, especially stx2A/stx2b which code for the Shiga toxins characteristic of O157:H7, were upregulated at 60 min post-irradiation. The treatment was also found to increase the levels of CysN, MutM, DinG and DnaC in the cells, proteins involved respectively in sulfur metabolism, base excision repair, recombinational DNA repair and chromosome replication. Our results provide insights into the resistance response of E. coli O157:H7 to a non-lethal irradiation dose. Our findings indicate that E. coli O157:H7 can resist to γ-irradiation through important modifications in genes expression and proteins profiles.
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http://dx.doi.org/10.1016/j.micpath.2020.104342DOI Listing
December 2020

Biological H and CO oxidation activities are sensitive to compositional change of soil microbial communities.

Can J Microbiol 2020 Apr 30;66(4):263-273. Epub 2020 Jan 30.

Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada.

Trace gas uptake by microorganisms controls the oxidative capacity of the troposphere, but little is known about how this important function is affected by changes in soil microbial diversity. This article bridges that knowledge gap by examining the response of the microbial community-level physiological profiles (CLPPs), carbon dioxide (CO) production, and molecular hydrogen (H) and carbon monoxide (CO) oxidation activities to manipulation of microbial diversity in soil microcosms. Microbial diversity was manipulated by mixing nonsterile and sterile soil with and without the addition of antibiotics. Nonsterile soil without antibiotics was used as a reference. Species composition changed significantly in soil microcosms as a result of dilution and antibiotic treatments, but there was no difference in species richness, according to PCR amplicon sequencing of the bacterial 16S rRNA gene. The CLPP was 15% higher in all dilution and antibiotic treatments than in reference microcosms, but the dilution treatment had no effect on CO production. Soil microcosms with dilution treatments had 58%-98% less H oxidation and 54%-99% lower CO oxidation, relative to reference microcosms, but did not differ among the antibiotic treatments. These results indicate that H and CO oxidation activities respond to compositional changes of microbial community in soil.
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http://dx.doi.org/10.1139/cjm-2019-0412DOI Listing
April 2020

Physiological traits and relative abundance of species as explanatory variables of co-occurrence pattern of cultivable bacteria associated with chia seeds.

Can J Microbiol 2019 Sep 3;65(9):668-680. Epub 2019 Jun 3.

Institut National de la Recherche Scientifique-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada.

Deciphering the rules defining microbial community assemblage is envisioned as a promising strategy to improve predictions of pathogens colonization and proliferation in food. Despite the increasing number of studies reporting microbial co-occurrence patterns, only a few attempts have been made to challenge them in experimental or theoretical frameworks. Here, we tested the hypothesis that observed variations in co-occurrence patterns can be explained by taxonomy, relative abundance, and physiological traits of microbial species. We used PCR amplicon sequencing of taxonomic markers to assess distribution and co-occurrence patterns of bacterial and fungal species found in 25 chia ( L.) samples originating from eight different sources. The use of nutrient-rich and oligotrophic media enabled isolation of 71 strains encompassing 16 bacterial species, of which five corresponded to phylotypes represented in the molecular survey. Tolerance to different growth inhibitors and antibiotics was tested to assess the physiological traits of these isolates. Divergence of physiological traits and relative abundance of each pair of species explained 69% of the co-occurrence profile displayed by cultivable bacterial phylotypes in chia. Validation of this ecological network conceptualization approach to more food products is required to integrate microbial species co-occurrence patterns in predictive microbiology.
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http://dx.doi.org/10.1139/cjm-2019-0052DOI Listing
September 2019

Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes.

Appl Environ Microbiol 2019 03 6;85(6). Epub 2019 Mar 6.

INRS-Institut Armand-Frappier, Laval, Québec, Canada.

The atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H). H has been proposed as the first electron donor leading to ATP synthesis due to its ubiquity throughout the biosphere as well as its ability to easily diffuse through microbial cells and its low activation energy requirement. Even today, hydrogenase enzymes enabling the production and oxidation of H are found in thousands of genomes spanning the three domains of life across aquatic, terrestrial, and even host-associated ecosystems. Even though H has already been proposed as a universal growth and maintenance energy source, its potential contribution as a driver of biogeochemical cycles has received little attention. Here, we bridge this knowledge gap by providing an overview of the classification, distribution, and physiological role of hydrogenases. Distribution of these enzymes in various microbial functional groups and recent experimental evidence are finally integrated to support the hypothesis that H-oxidizing microbes are keystone species driving C cycling along O concentration gradients found in H-rich soil ecosystems. In conclusion, we suggest focusing on the metabolic flexibility of H-oxidizing microbes by combining community-level and individual-level approaches aiming to decipher the impact of H on C cycling and the C-cycling potential of H-oxidizing microbes, via both culture-dependent and culture-independent methods, to give us more insight into the role of H as a driver of biogeochemical processes.
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http://dx.doi.org/10.1128/AEM.02418-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6414374PMC
March 2019

Strain-level genetic diversity of confers plasticity to denitrification capacity in a methylotrophic marine denitrifying biofilm.

PeerJ 2018 23;6:e4679. Epub 2018 Apr 23.

Institut Armand-Frappier, Institut National de la Recherche Scientifique, Laval, Québec, Canada.

Background: The biofilm of a methanol-fed, fluidized denitrification system treating a marine effluent is composed of multi-species microorganisms, among which NL23 and JAM1 are the principal bacteria involved in the denitrifying activities. Strain NL23 can carry complete nitrate (NO[Formula: see text]) reduction to N, whereas strain JAM1 can perform 3 out of the 4 reduction steps. A small proportion of other denitrifiers exists in the biofilm, suggesting the potential plasticity of the biofilm in adapting to environmental changes. Here, we report the acclimation of the denitrifying biofilm from continuous operating mode to batch operating mode, and the isolation and characterization from the acclimated biofilm of a new denitrifying bacterial strain, named GP59.

Methods: The denitrifying biofilm was batch-cultured under anoxic conditions. The acclimated biofilm was plated on specific medium to isolate denitrifying isolates. Planktonic cultures of strains GP59 and JAM1 were performed, and the growth and the dynamics of NO[Formula: see text], nitrite (NO[Formula: see text]) and NO were determined. The genomes of strains GP59 and JAM1 were sequenced and compared. The transcriptomes of strains GP59 and JAM1 were derived from anoxic cultures.

Results: During batch cultures of the biofilm, we observed the disappearance of NL23 without affecting the denitrification performance. From the acclimated biofilm, we isolated strain GP59 that can perform, like NL23, the complete denitrification pathway. The GP59 cell concentration in the acclimated biofilm was 2-3 orders of magnitude higher than JAM1 and NL23. Genome analyses revealed that strain GP59 belongs to the species . The GP59 genome shares more than 85% of its coding sequences with those of strain JAM1. Based on transcriptomic analyses of anoxic cultures, most of these common genes in strain GP59 were expressed at similar level than their counterparts in strain JAM1. In contrast to strain JAM1, strain GP59 cannot reduce NO[Formula: see text] under oxic culture conditions, and has a 24-h lag time before growth and NO[Formula: see text] reduction start to occur in anoxic cultures, suggesting that both strains regulate differently the expression of their denitrification genes. Strain GP59 has the ability to reduce NO[Formula: see text] as it carries a gene encoding a NirK-type NO[Formula: see text] reductase. Based on the CRISPR sequences, strain GP59 did not emerge from strain JAM1 during the biofilm batch cultures but rather was present in the original biofilm and was enriched during this process.

Discussion: These results reinforce the unique trait of the species among the genus as facultative anaerobic bacterium. These findings also showed the plasticity of denitrifying population of the biofilm in adapting to anoxic marine environments of the bioreactor.
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http://dx.doi.org/10.7717/peerj.4679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5918138PMC
April 2018

Denitrifying metabolism of the methylotrophic marine bacterium strain JAM1.

PeerJ 2017 28;5:e4098. Epub 2017 Nov 28.

INRS-Institut Armand-Frappier, Laval, Québec, Canada.

Background: strain JAM1 is a methylotrophic, marine bacterium that was isolated from a denitrification reactor treating a closed-circuit seawater aquarium. It can sustain growth under anoxic conditions by reducing nitrate ([Formula: see text]) to nitrite ([Formula: see text]). These physiological traits are attributed to gene clusters that encode two dissimilatory nitrate reductases (Nar). Strain JAM1 also contains gene clusters encoding two nitric oxide (NO) reductases and one nitrous oxide (NO) reductase, suggesting that NO and NO can be reduced by strain JAM1. Here we characterized further the denitrifying activities of JAM1.

Methods: Series of oxic and anoxic cultures of strain JAM1 were performed with NO, [Formula: see text] or sodium nitroprusside, and growth and NO, [Formula: see text], [Formula: see text] and N concentrations were measured. Ammonium ([Formula: see text])-free cultures were also tested to assess the dynamics of NO, [Formula: see text] and [Formula: see text]. Isotopic labeling of NO was performed in NH-amended cultures. Cultures with the JAM1Δ double mutant were performed to assess the involvement of the Nar systems on NO production. Finally, RT-qPCR was used to measure the gene expression levels of the denitrification genes cytochrome -type nitric oxide reductase ( and ) and nitrous oxide reductase (), and also and that encode NO-sensitive regulators.

Results: Strain JAM1 can reduce NO to NO and NO to N and can sustain growth under anoxic conditions by reducing NO as the sole electron acceptor. Although strain JAM1 lacks a gene encoding a dissimilatory [Formula: see text] reductase, [Formula: see text]-amended cultures produce NO, representing up to 6% of the N-input. [Formula: see text] was shown to be the key intermediate of this production process. Upregulation in the expression of c, and during the growth and the NO accumulation phases suggests NO production in strain JAM1 cultures.

Discussion: By showing that all the three denitrification reductases are active, this demonstrates that JAM1 is one of many bacteria species that maintain genes associated primarily with denitrification, but not necessarily related to the maintenance of the entire pathway. The reason to maintain such an incomplete pathway could be related to the specific role of strain JAM1 in the denitrifying biofilm of the denitrification reactor from which it originates. The production of NO in strain JAM1 did not involve Nar, contrary to what was demonstrated in . JAM1 is the only reported species that has the capacity to grow under anoxic conditions by using [Formula: see text] and NO as sole electron acceptors for its growth. It is also one of a few marine methylotrophs that is studied at the physiological and genetic levels in relation to its capacity to perform denitrifying activities.
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http://dx.doi.org/10.7717/peerj.4098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5710167PMC
November 2017

Survey of High-Affinity H-Oxidizing Bacteria in Soil Reveals Their Vast Diversity Yet Underrepresentation in Genomic Databases.

Microb Ecol 2017 11 17;74(4):771-775. Epub 2017 Jun 17.

INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, Québec, H7V 1B7, Canada.

While high-affinity H-oxidizing bacteria (HA-HOB) serve as the main sink of atmospheric H, the ecology of this specialist functional group is rather unknown due to its recent discovery. The main purpose of our study is to provide the first extensive survey of HA-HOB in farmland, larch, and poplar soils exposed to 0.5 and 10,000 ppmv H. Using qPCR and qRT-PCR assays along with PCR amplicon high-throughput sequencing of hhyL gene encoding for the large subunit of high-affinity [NiFe]-hydrogenases (HAH), we found that hhyL gene expression ratio explained better variation in measured H oxidation rates than HA-HOB species richness. Carbon, nitrogen, pH, and bacterial species richness appeared as the most important drivers of HA-HOB community structure. Our study also highlights the need to cultivate HA-HOB due to the huge gap in current genomic databases.
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http://dx.doi.org/10.1007/s00248-017-1011-1DOI Listing
November 2017

The Tale of a Neglected Energy Source: Elevated Hydrogen Exposure Affects both Microbial Diversity and Function in Soil.

Appl Environ Microbiol 2017 06 17;83(11). Epub 2017 May 17.

INRS-Institut Armand-Frappier, Laval, Québec, Canada

The enrichment of H-oxidizing bacteria (HOB) by H generated by nitrogen-fixing nodules has been shown to have a fertilization effect on several different crops. The benefit of HOB is attributed to their production of plant growth-promoting factors, yet their interactions with other members of soil microbial communities have received little attention. Here we report that the energy potential of H, when supplied to soil, alters ecological niche partitioning of bacteria and fungi, with multifaceted consequences for both generalist and specialist microbial functions. We used dynamic microcosms to expose soil to the typical atmospheric H mixing ratio (0.5 ppmv) permeating soils, as well as mixing ratios comparable to those found at the soil-nodule interface (10,000 ppmv). Elevated H exposure exerted direct effects on two HOB subpopulations distinguished by their affinity for H while enhancing community level carbon substrate utilization potential and lowering CH uptake activity in soil. We found that H triggered changes in the abundance of microorganisms that were reproducible yet inconsistent across soils at the taxonomic level and even among HOB. Overall, H exposure altered microbial process rates at an intensity that depends upon soil abiotic and biotic features. We argue that further examination of direct and indirect effects of H on soil microbial communities will lead to a better understanding of the H fertilization effect and soil biogeochemical processes. An innovative dynamic microcosm chamber system was used to demonstrate that H diffusing in soil triggers changes in the distribution of HOB and non-HOB. Although the response was uneven at the taxonomic level, an unexpected coordinated response of microbial functions was observed, including abatement of CH oxidation activity and stimulation of carbon turnover. Our work suggests that elevated H rewires soil biogeochemical structure through a combination of direct effects on the growth and persistence of HOB and indirect effects on a variety of microbial processes involving HOB and non-HOB.
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http://dx.doi.org/10.1128/AEM.00275-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5440700PMC
June 2017

H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups.

PeerJ 2016 10;4:e1782. Epub 2016 Mar 10.

INRS-Institut Armand-Frappier , Laval, Quebec , Canada.

Soil microbial communities are continuously exposed to H2 diffusing into the soil from the atmosphere. N2-fixing nodules represent a peculiar microniche in soil where H2 can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). In this study, we investigated the impact of H2 exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil H2 exposure from the atmosphere and N2-fixing nodules. Biphasic kinetic parameters governing H2 oxidation activity in soil changed drastically upon elevated H2 exposure, corresponding to a slight but significant decay of high affinity H2-oxidizing bacteria population, accompanied by an enrichment or activation of microorganisms displaying low-affinity for H2. In contrast to previous studies that unveiled limited response by a few species, the relative abundance of 958 bacterial ribotypes distributed among various taxonomic groups, rather than a few distinct taxa, was influenced by H2 exposure. Furthermore, correlation networks showed important alterations of ribotype covariation in response to H2 exposure, suggesting that H2 affects microbe-microbe interactions in soil. Taken together, our results demonstrate that H2-rich environments exert a direct influence on soil H2-oxidizing bacteria in addition to indirect effects on other members of the bacterial communities.
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http://dx.doi.org/10.7717/peerj.1782DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793312PMC
March 2016

Towards the development of multifunctional molecular indicators combining soil biogeochemical and microbiological variables to predict the ecological integrity of silvicultural practices.

Microb Biotechnol 2016 May 8;9(3):316-29. Epub 2016 Feb 8.

INRS-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, Québec, Canada, H7V 1B7.

The impact of mechanical site preparation (MSP) on soil biogeochemical structure in young larch plantations was investigated. Soil samples were collected in replicated plots comprising simple trenching, double trenching, mounding and inverting site preparation. Unlogged natural mixed forest areas were used as a reference. Analysis of soil nutrients, abundance of bacteria and gas exchanges unveiled no significant difference among the plots. However, inverting site preparation resulted in higher variations of gas exchanges when compared with trenching, mounding and unlogged natural forest. A combination of the biological and physicochemical variables was used to define a multifunctional classification of the soil samples into four distinct groups categorized as a function of their deviation from baseline ecological conditions. According to this classification model, simple trenching was the approach that represented the lowest ecological risk potential at the microsite level. No relationship was observed between MSP method and soil bacterial community structure as assessed by high-throughput sequencing of bacterial 16S rRNA gene; however, indicator genotypes were identified for each multifunctional soil class. This is the first identification of multifunctional molecular indicators for baseline and disturbed ecological conditions in soil, demonstrating the potential of applied microbial ecology to guide silvicultural practices and ecological risk assessment.
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http://dx.doi.org/10.1111/1751-7915.12348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4835570PMC
May 2016

Identification of Unknown Carboxydovore Bacteria Dominant in Deciduous Forest Soil via Succession of Bacterial Communities, coxL Genotypes, and Carbon Monoxide Oxidation Activity in Soil Microcosms.

Appl Environ Microbiol 2016 02 18;82(4):1324-1333. Epub 2015 Dec 18.

INRS-Institut Armand-Frappier, Laval, Québec, Canada

Surveys of the coxL gene, encoding the large subunit of the CO dehydrogenase, are used as a standard approach in ecological studies of carboxydovore bacteria scavenging atmospheric CO. Recent soil surveys unveiled that the distribution of coxL sequences encompassing the atypical genotype coxL type I group x was correlated to the CO oxidation activity. Based on phylogenetic analysis including the available coxL reference genome sequences, this unusual genotype was assigned to an unknown member of the Deltaproteobacteria, with the coxL sequence from Haliangium ochraceum being the sole and closest reference sequence. Here we seek to challenge the proposed taxonomic assignation of the coxL group x genotype through the monitoring of CO consumption activity and microbial community successions during the colonization of sterile soil microcosms inoculated with indigenous microorganisms. In our study, we established that the estimated population density of Deltaproteobacteria was too small to account for the abundance of the coxL group x genotype detected in soil. Furthermore, we computed a correlation network to relate 16S rRNA gene profiles with the succession of coxL genotypes and CO uptake activity in soil. We found that most of the coxL genotypes for which the colonization profile displayed covariance with CO uptake activity were related to potential carboxydovore bacteria belonging to Actinobacteria and Alphaproteobacteria. Our analysis did not provide any evidence that coxL group x genotypes belonged to Deltaproteobacteria. Considering the colonization profile of CO-oxidizing bacteria and the theoretical energy yield of measured CO oxidation rates in soil microcosms, we propose that unknown carboxydovore bacteria harboring the atypical coxL group x genotype are mixotrophic K-strategists.
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http://dx.doi.org/10.1128/AEM.03595-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4751856PMC
February 2016

Detection and isolation of plant-associated bacteria scavenging atmospheric molecular hydrogen.

Environ Microbiol 2016 09 21;18(8):2495-506. Epub 2016 Jan 21.

Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8562, Japan.

High-affinity hydrogen (H2 )-oxidizing bacteria possessing group 5 [NiFe]-hydrogenase genes are important contributors to atmospheric H2 uptake in soil environments. Although previous studies reported the occurrence of a significant H2 uptake activity in vegetation, there has been no report on the identification and diversity of the responsible microorganisms. Here, we show the existence of plant-associated bacteria with the ability to consume atmospheric H2 that may be a potential energy source required for their persistence in plants. Detection of the gene hhyL - encoding the large subunit of group 5 [NiFe]-hydrogenase - in plant tissues showed that plant-associated high-affinity H2 -oxidizing bacteria are widely distributed in herbaceous plants. Among a collection of 145 endophytic isolates, seven Streptomyces strains were shown to possess hhyL gene and exhibit high- or intermediate-affinity H2 uptake activity. Inoculation of Arabidopsis thaliana (thale cress) and Oryza sativa (rice) seedlings with selected isolates resulted in an internalization of the bacteria in plant tissues. H2 uptake activity per bacterial cells was comparable between plant and soil, demonstrating that both environments are favourable for the H2 uptake activity of streptomycetes. This study first demonstrated the occurrence of plant-associated high-affinity H2 -oxidizing bacteria and proposed their potential contribution as atmospheric H2 sink.
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http://dx.doi.org/10.1111/1462-2920.13162DOI Listing
September 2016

Surveying the endomicrobiome and ectomicrobiome of bark beetles: The case of Dendroctonus simplex.

Sci Rep 2015 Nov 26;5:17190. Epub 2015 Nov 26.

INRS-Institut Armand-Frappier, Laval, QC, H7V1B7, Canada.

Many bark beetles belonging to the Dendroctonus genus carry bacterial and fungal microbiota, forming a symbiotic complex that helps the insect to colonize the subcortical environment of the host tree. However, the biodiversity of those bacteria at the surface of the cuticle or inside the body parts of bark beetles is not well established. The aim of this study was to characterize the bacterial microbiome associated with the eastern larch beetle, Dendroctonus simplex, using bacterial 16S rRNA gene pyrosequencing. The ecto- and endomicrobiome and the subcortical galleries were investigated. Several bacterial genera were identified, among which Pseudomonas, Serratia and Yersinia are associated with the surface of the beetle cuticle, and genera belonging to Enterobacteriaceae and Gammaproteobacteria with the interior of the insect body. The index of dissimilarity indicates that the bacterial microbiome associated with each environment constitutes exclusive groups. These results suggest the presence of distinct bacterial microbiota on the surface of the cuticle and the interior of D. simplex body. Additionally, the bacterial diversity identified in the galleries is substantially different from the ectomicrobiome, which could indicate a selection by the insect. This study reports for the first time the identification of the eastern larch beetle microbiome.
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http://dx.doi.org/10.1038/srep17190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4660424PMC
November 2015

Breathing air to save energy--new insights into the ecophysiological role of high-affinity [NiFe]-hydrogenase in Streptomyces avermitilis.

Microbiologyopen 2016 Feb 5;5(1):47-59. Epub 2015 Nov 5.

INRS-Institut Armand Frappier, Laval, Québec, Canada.

The Streptomyces avermitilis genome encodes a putative high-affinity [NiFe]-hydrogenase conferring the ability to oxidize tropospheric H2 in mature spores. Here, we used a combination of transcriptomic and mutagenesis approaches to shed light on the potential ecophysiological role of the enzyme. First, S. avermitilis was either exposed to low or hydrogenase-saturating levels of H2 to investigate the impact of H2 on spore transcriptome. In total, 1293 genes were differentially expressed, with 1127 and 166 showing lower and higher expression under elevated H2 concentration, respectively. High H2 exposure lowered the expression of the Sec protein secretion pathway and ATP-binding cassette-transporters, with increased expression of genes encoding proteins directing carbon metabolism toward sugar anabolism and lower expression of NADH dehydrogenase in the respiratory chain. Overall, the expression of relA responsible for the synthesis of the pleiotropic alarmone ppGpp decreased upon elevated H2 exposure, which likely explained the reduced expression of antibiotic synthesis and stress response genes. Finally, deletion of hhySL genes resulted in a loss of H2 uptake activity and a dramatic loss of viability in spores. We propose that H2 is restricted to support the seed bank of Streptomyces under a unique survival-mixotrophic energy mode and discuss important ecological implications of this finding.
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http://dx.doi.org/10.1002/mbo3.310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4767420PMC
February 2016

Atmospheric hydrogen scavenging: from enzymes to ecosystems.

Appl Environ Microbiol 2015 Feb;81(4):1190-9

We have known for 40 years that soils can consume the trace amounts of molecular hydrogen (H2) found in the Earth’s atmosphere.This process is predicted to be the most significant term in the global hydrogen cycle. However, the organisms and enzymes responsible for this process were only recently identified. Pure culture experiments demonstrated that several species of Actinobacteria, including streptomycetes and mycobacteria, can couple the oxidation of atmospheric H2 to the reduction of ambient O2. A combination of genetic, biochemical, and phenotypic studies suggest that these organisms primarily use this fuel source to sustain electron input into the respiratory chain during energy starvation. This process is mediated by a specialized enzyme, the group 5 [NiFe]-hydrogenase, which is unusual for its high affinity, oxygen insensitivity, and thermostability. Atmospheric hydrogen scavenging is a particularly dependable mode of energy generation, given both the ubiquity of the substrate and the stress tolerance of its catalyst. This minireview summarizes the recent progress in understanding how and why certain organisms scavenge atmospheric H2. In addition, it provides insight into the wider significance of hydrogen scavenging in global H2 cycling and soil microbial ecology.
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http://dx.doi.org/10.1128/AEM.03364-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4309691PMC
February 2015

Land-use influences the distribution and activity of high affinity CO-oxidizing bacteria associated to type I-coxL genotype in soil.

Front Microbiol 2014 12;5:271. Epub 2014 Jun 12.

Institut National de la Recherche Scientifique-Institut Armand-Frappier Laval, QC, Canada.

Soil carboxydovore bacteria are the biological sink of atmospheric carbon monoxide (CO). The initial oxidation of CO is catalyzed by a CO-dehydrogenase (CODH), and the gene coxL encodes the large subunit of the enzyme. Only a few carboxydovore isolates were shown to oxidize atmospheric CO and little is known about the potential impact of global change on the ecophysiology of this functional group. The main objective of this study was to assess the impact of land-use and soil properties on coxL gene diversity and identify molecular indicators for the soil uptake of atmospheric CO. Soil samples were collected in three neighboring sites encompassing different land-use types, namely deciduous forest, larch plantation and maize field. CO uptake activity was related to total carbon and nitrogen content in soil, with the highest activity observed in deciduous forest. An extensive coxL database was assembled to optimize a PCR detection assay targeting sequences belonging to functional type I-CODH and hypothetical type II-CODH. Fully replicated coxL gene libraries unveiled a unique molecular signature in deciduous forest soil, with enrichment of type I sequences. Genetic profiles of larch and maize monocultures were not statistically different and showed higher level of coxL gene richness than deciduous forest. Soil water content and CO uptake activity explained 38% of the variation of coxL gene profiles in a canonical ordination analysis, leading to the identification of sequences belonging to the δ-Proteobacteria cluster as indicator for high affinity CO uptake activity. Enrichment of type I and δ-Proteobacteria coxL sequences in deciduous forest were confirmed by qPCR in an independent soil survey. CO uptake activity in model carboxydovore bacteria suggested that a significant fraction of detected putative high affinity CO oxidizers were active in soil. Land-use was a driving force separating coxL diversity in deciduous forest from monocultures.
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http://dx.doi.org/10.3389/fmicb.2014.00271DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053681PMC
June 2014

Genome data mining and soil survey for the novel group 5 [NiFe]-hydrogenase to explore the diversity and ecological importance of presumptive high-affinity H(2)-oxidizing bacteria.

Appl Environ Microbiol 2011 Sep 8;77(17):6027-35. Epub 2011 Jul 8.

Max Planck Institute for Terrestrial Microbiology, Department of Biogeochemistry, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany.

Streptomyces soil isolates exhibiting the unique ability to oxidize atmospheric H(2) possess genes specifying a putative high-affinity [NiFe]-hydrogenase. This study was undertaken to explore the taxonomic diversity and the ecological importance of this novel functional group. We propose to designate the genes encoding the small and large subunits of the putative high-affinity hydrogenase hhyS and hhyL, respectively. Genome data mining revealed that the hhyL gene is unevenly distributed in the phyla Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. The hhyL gene sequences comprised a phylogenetically distinct group, namely, the group 5 [NiFe]-hydrogenase genes. The presumptive high-affinity H(2)-oxidizing bacteria constituting group 5 were shown to possess a hydrogenase gene cluster, including the genes encoding auxiliary and structural components of the enzyme and four additional open reading frames (ORFs) of unknown function. A soil survey confirmed that both high-affinity H(2) oxidation activity and the hhyL gene are ubiquitous. A quantitative PCR assay revealed that soil contained 10(6) to 10(8) hhyL gene copies g (dry weight)(-1). Assuming one hhyL gene copy per genome, the abundance of presumptive high-affinity H(2)-oxidizing bacteria was higher than the maximal population size for which maintenance energy requirements would be fully supplied through the H(2) oxidation activity measured in soil. Our data indicate that the abundance of the hhyL gene should not be taken as a reliable proxy for the uptake of atmospheric H(2) by soil, because high-affinity H(2) oxidation is a facultatively mixotrophic metabolism, and microorganisms harboring a nonfunctional group 5 [NiFe]-hydrogenase may occur.
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http://dx.doi.org/10.1128/AEM.00673-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3165403PMC
September 2011

Streptomycetes contributing to atmospheric molecular hydrogen soil uptake are widespread and encode a putative high-affinity [NiFe]-hydrogenase.

Environ Microbiol 2010 Mar 27;12(3):821-9. Epub 2009 Dec 27.

Max Planck Institute for Terrestrial Microbiology, Department of Biogeochemistry, Karl-von-Frisch-Strasse, 35043 Marburg, Germany.

Uptake of molecular hydrogen (H2) by soil is a biological reaction responsible for approximately 80% of the global loss of atmospheric H2. Indirect evidence obtained over the last decades suggests that free soil hydrogenases with an unusually high affinity for H2 are carrying out the reaction. This assumption has recently been challenged by the isolation of Streptomyces sp. PCB7, displaying the high-affinity H2 uptake activity previously attributed to free soil enzymes. While this finding suggests that actinobacteria could be responsible for atmospheric H2 soil uptake, the ecological importance of H2-oxidizing streptomycetes remains to be investigated. Here, we show that high-affinity H2 uptake activity is widespread among the streptomycetes. Among 14 streptomycetes strains isolated from temperate forest and agricultural soils, six exhibited a high-affinity H2 uptake activity. The gene encoding the large subunit of a putative high-affinity [NiFe]-hydrogenase (hydB-like gene sequence) was detected exclusively in the isolates exhibiting high-affinity H2 uptake. Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH) experiments targeting hydB-like gene transcripts and H2 uptake assays performed with strain PCB7 suggested that streptomycetes spores catalysed the H2 uptake activity. Expression of the activity in term of biomass revealed that 10(6)-10(7) H2-oxidizing bacteria per gram of soil should be sufficient to explain in situ H2 uptake by soil. We propose that specialized H2-oxidizing actinobacteria are responsible for the most important sink term in the atmospheric H2 budget.
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http://dx.doi.org/10.1111/j.1462-2920.2009.02130.xDOI Listing
March 2010

Tropospheric H(2) budget and the response of its soil uptake under the changing environment.

Sci Total Environ 2009 Mar 19;407(6):1809-23. Epub 2009 Jan 19.

INRS-Institut Armand-Frappier, 531 boul. des Prairies, Laval, Québec, Canada H7V 1B7.

Molecular hydrogen (H(2)) is an indirect greenhouse gas present at the trace level in the atmosphere. So far, the sum of its sources and sinks is close to equilibrium, but its large-scale utilization as an alternative energy carrier would alter its atmospheric burden. The magnitude of the emissions associated with a future H(2)-based economy is difficult to predict and remains a matter of debate. Previous attempts to predict the impact that a future H(2)-based economy would exert on tropospheric chemistry were realized by considering a steady rate of microbial-mediated soil uptake, which is currently responsible of ~80% of the tropospheric H(2) losses. Although soil uptake, also known as dry deposition is the most important sink for tropospheric H(2), microorganisms involved in the activity remain elusive. Given that microbial-mediated H(2) soil uptake is influenced by several environmental factors, global change should exert a significant effect on the activity and then, assuming a steady H(2) soil uptake rate for the future may be mistaken. Here, we present an overview of tropospheric H(2) sources and sinks with an emphasis on microbial-mediated soil uptake process. Future researches are proposed to investigate the influence that global change would exert on H(2) dry deposition and to identify microorganisms involved H(2) soil uptake activity.
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http://dx.doi.org/10.1016/j.scitotenv.2008.10.064DOI Listing
March 2009

Critical review of mercury fates and contamination in the Arctic tundra ecosystem.

Sci Total Environ 2008 Aug 15;400(1-3):173-211. Epub 2008 Aug 15.

Environment Canada, Science and Technology branch Montréal, Québec, Canada.

Mercury (Hg) contamination in tundra region has raised substantial concerns, especially since the first report of atmospheric mercury depletion events (AMDEs) in the Polar Regions. During the past decade, steady progress has been made in the research of Hg cycling in the Polar Regions. This has generated a unique opportunity to survey the whole Arctic in respect to Hg issue and to find out new discoveries. However, there are still considerable knowledge gaps and debates on the fate of Hg in the Arctic and Antarctica, especially regarding the importance and significance of AMDEs vs. net Hg loadings and other processes that burden Hg in the Arctic. Some studies argued that climate warming since the last century has exerted profound effects on the limnology of High Arctic lakes, including substantial increases in autochthonous primary productivity which increased in sedimentary Hg, whereas some others pointed out the importance of the formation and postdeposition crystallographic history of the snow and ice crystals in determining the fate and concentration of mercury in the cryosphere in addition to AMDEs. Is mercury re-emitted back to the atmosphere after AMDEs? Is Hg methylation effective in the Arctic tundra? Where the sources of MeHg are? What is its fate? Is this stimulated by human made? This paper presents a critical review about the fate of Hg in the Arctic tundra, such as pathways and process of Hg delivery into the Arctic ecosystem; Hg concentrations in freshwater and marine ecosystems; Hg concentrations in terrestrial biota; trophic transfer of Hg and bioaccumulation of Hg through food chain. This critical review of mercury fates and contamination in the Arctic tundra ecosystem is assessing the impacts and potential risks of Hg contamination on the health of Arctic people and the global northern environment by highlighting and "perspectiving" the various mercury processes and concentrations found in the Arctic tundra.
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http://dx.doi.org/10.1016/j.scitotenv.2008.06.050DOI Listing
August 2008

Isolation of Streptomyces sp. PCB7, the first microorganism demonstrating high-affinity uptake of tropospheric H2.

ISME J 2008 Oct 12;2(10):1066-76. Epub 2008 Jun 12.

INRS-Institut Armand-Frappier, Laval, Québec, Canada.

Microbial-mediated soil uptake accounts for approximately 80% of the global tropospheric dihydrogen (H(2)) sinks. Studies conducted over the last three decades provide indirect evidences that H(2) soil uptake is mediated by free soil hydrogenases or by unknown microorganisms that have a high affinity for H(2). The exact nature of these hypothetical free soil enzymes or of H(2)-consuming microorganisms remains elusive because the activity has never been observed in pure culture. Here, we present the first aerobic microorganism able to consume tropospheric H(2) at ambient levels. A dynamic microcosm chamber was developed to enrich a microbial consortium with a high affinity for H(2), from which selected bacterial and fungal strains were isolated and tested for H(2) uptake. Strain PCB7 had a H(2) consumption activity that followed a Michaelis-Menten kinetics, with an apparent K(m) of 11 p.p.m.v. and a H(2) threshold concentration <0.100 p.p.m.v., corresponding to the high-affinity uptake of tropospheric H(2) observed in soil. 16S ribosomal RNA gene sequences showed that strain PCB7 is highly related to several Streptomyces species. H(2) consumption occurred during the sporulation period of the bacterium. Addition of nickel increased the activity, suggesting that the enzymes involved in H(2) consumption belong to the NiFe uptake class of hydrogenases. Because this is the first microorganism showing a high-affinity uptake of tropospheric H(2), we anticipate that Streptomyces sp. PCB7 will become a model organism for the understanding of the environmental factors influencing H(2) soil uptake.
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http://dx.doi.org/10.1038/ismej.2008.59DOI Listing
October 2008

The ebullition of hydrogen, carbon monoxide, methane, carbon dioxide and total gaseous mercury from the Cornwall Area of Concern.

Sci Total Environ 2007 Aug 17;381(1-3):256-62. Epub 2007 May 17.

Science and Technology Branch, Environment Canada, 105 McGill street, 7th floor (Youville), Montréal, Québec, Canada H2Y 2E7.

This paper reports the first ebullitive fluxes of hydrogen (H2), carbon monoxide (CO), methane (CH4), carbon dioxide (CO2) and total gaseous mercury (TGM) from the Cornwall Area of Concern (CAC). Although sediments were contaminated with mercury, bubbling was a negligible source of mercury for the global atmosphere. Indeed, the average emission of TGM through ebullition was 0.04 pg m(-2) h(-1). Measurements of H2, CO, CH4 and CO2 trapped gas concentrations and fluxes were used as indicators of diagenesis processes. The CAC represented a significant regional source of CH4 since the estimated ebullitive fluxes (3.5 mg m(-2) h(-1)) were similar to the CH4 emissions measured above typical flooded freshwater wetlands. As molecular diffusion is known as the main pathway of CO2 transport from water to the atmosphere, CO2 ebullitive fluxes were weak (0.39 mg m(-2) h(-1)). Bubbling of CO (1.6 microg m(-2) h(-1)) was 10 folds less important than CO fluxes measured over flooded freshwater wetlands. Finally, H2 emissions (0.001 microg m(-2) h(-1)) were negligible since the level of this trace gas is tightly regulated by microorganisms in anaerobic environments.
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http://dx.doi.org/10.1016/j.scitotenv.2007.03.029DOI Listing
August 2007

Heterogeneity between 16S ribosomal RNA gene copies borne by one Desulfitobacterium strain is caused by different 100-200 bp insertions in the 5' region.

Can J Microbiol 2007 Jan;53(1):116-28

INRS-Insitut Armand-Frappier, Laval, QC, Canada.

Strains of Desulfitobacterium hafniense, such as strains PCP-1, DP7, TCE1, and TCP-A, have unusual long 16S ribosomal RNA (rRNA) genes due to an insertion of approximately 100 bp in the 5' region. In this report, we analyzed the 16S rRNA genes of different Desulfitobacterium strains to determine if such an insertion is a common feature of desulfitobacteria. We amplified this region by polymerase chain reaction (PCR) from eight Desulfitobacterium strains (D. hafniense strains PCP-1, DP7, TCP-A, TCE1, and DCB-2; D. dehalogenans; D. chlororespirans; and Desulfitobacterium sp. PCE1) and resolved each PCR product by denaturing gradient gel electrophoresis (DGGE). All strains had from two to seven DGGE- migrating bands, suggesting heterogeneity in their 16S rRNA gene copies. For each strain, the 5' region of the 16S rRNA genes was amplified and a clone library was derived. Clones corresponding to most PCR-DGGE migration bands were isolated. Sequencing of representative clones revealed that the heterogeneity was generated by insertions of 100-200 bp. An insertion was found in at least one copy of the 16S rRNA gene in all examined strains. In total, we found eight different types of insertions (INS1-INS8) that varied from 123 to 193 nt in length. Two-dimensional structural analyses of transcribed sequences predicted that all insertions would form an energetically stable loop. Reverse transcriptase-PCR experiments revealed that most of the observed insertions in the Desulfitobacterium strains were excised from the mature 16S rRNA transcripts. Insertions were not commonly found in bacterial 16S rRNA genes, and having a different insertion in several 16S rRNA gene copies borne by a single bacterial species was rarely observed. The function of these insertions is not known, but their occurrence can have an important impact in deriving 16S rRNA oligonucleotidic fluorescence in situ hybridization probes, as these insertions can be excised from 16S rRNA transcripts.
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http://dx.doi.org/10.1139/w06-111DOI Listing
January 2007

Abiotic source of reactive organic halogens in the sub-arctic atmosphere?

Environ Sci Technol 2005 Nov;39(22):8812-6

Department of Chemistry, University of York, York YO10 5DD, UK.

Recent theoretical studies indicate that reactive organic iodocarbons such as CH2I2 would be extremely effective agents for tropospheric Arctic ozone depletion and that iodine compounds added to a Br2/BrCl mixture have a significantly greater ozone (and mercury) depletion effect than additional Br2 and BrCl molecules. Here we report the first observations of CH2I2, CH2IBr, and CH2ICl in Arctic air, as well as other reactive halocarbons including CHBr3, during spring at Kuujjuarapik, Hudson Bay. The organoiodine compounds were present atthe highest levels yet reported in air. The occurrence of the halocarbons was associated with northwesterly winds from the frozen bay, and, in the case of CHBr3, was anticorrelated with ozone and total gaseous mercury (TGM), suggesting a link between inorganic and organic halogens. The absence of local leads coupled with the extremely short atmospheric lifetime of CH2I2 indicates that production occurred in the surface of the sea-ice/overlying snowpack over the bay. We propose an abiotic mechanism for the production of polyhalogenated iodo- and bromocarbons, via reaction of HOI and/or HOBr with organic material on the quasi-liquid layer above sea-ice/snowpack, and report laboratory data to support this mechanism. CH2I2, CH2IBr, and other organic iodine compounds may therefore be a ubiquitous component of air above sea ice where they will increase the efficiency of bromine-initiated ozone and mercury depletion.
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http://dx.doi.org/10.1021/es050918wDOI Listing
November 2005
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