Christine Martineau

• PhD
• Researcher at Natural Resources Canada

Plant species shape soil microbiome composition through species-specific interactions. However, it is less clear how these host-microbe interactions vary across populations of genetically structured species, particularly those spanning diverse climatic and soil gradients. In this study, we explore the influence of host genetic composition and edaph...

Oil sands process‐affected water (OSPW) is a by‐product of bitumen extraction from oil sands surface mining in Alberta, Canada. A major group of organics in OSPW known as naphthenic acid fraction compounds (NAFCs) are of concern due to their persistence and toxicity. Constructed wetland treatment systems have emerged as potential biological treatme...

The study of microbial communities of the plant phyllosphere in remote locations using DNA-based approaches is limited by the challenges associated with their preservation in the field and during transportation. Freezing is a common DNA preservation strategy, but it may be unsuitable for leaf samples, or inaccessible in some locations. Other method...

In conservation strategies, getting precise and repeatable information on the species’ diet and health without relying on invasive or laborious methods is challenging. Here, we developed an efficient and non-invasive workflow for the sequencing and analysis of four taxonomic markers from fecal DNA to characterize the gut microbiota, parasites, and...

The soil supports many ecosystem services (ES) essential to human well‐being. Rapid developments in digital soil mapping (DSM) allow the mapping of soil types and soil properties with improved resolution and accuracy. However, the potential of DSM to improve the assessment and mapping of ES is not fully exploited. To better understand this potentia...

Earthworms influence soil properties and element cycling, notably through the formation of casts. These biogenic structures are hotspots of microbial activity and play a role in soil carbon and nutrient dynamics. Previous research revealed that earthworm casts harbour distinct microbiomes from mineral soils under controlled laboratory conditions. B...

In conservation strategies, getting precise and repeatable information on the species’ diet and health without relying on invasive or laborious methods is challenging. Here, we developed an efficient and non-invasive workflow for the sequencing and analysis of four taxonomic markers from fecal DNA to characterize the gut microbiota, parasites, and...

In conservation strategies, getting precise and repeatable information on the species’ diet and health without relying on invasive or laborious methods is challenging. Here, we developed an efficient and non-invasive workflow for the sequencing and analysis of four taxonomic markers from fecal DNA to characterize the gut microbiota, parasites, and...

In recent years, plant–microorganism interactions and their impact on plant growth and health, and in turn on plant-driven ecosystem services (e.g., carbon storage, phytoremediation) have gained a lot of interest in the scientific community. This interest has been stimulated by the development of high-throughput sequencing technologies that greatly...

In eastern Canada, boreal forests are locally experiencing a shift between two alternative stable states, productive closed-canopy feather moss (Pleurozium schreberi (Brid.) Mitt.) forests to low-productivity open lichen (Cladonia spp.) woodlands. While this shift has important consequences for ecosystem structure and productivity, little is known...

Soil sampling for environmental DNA in remote and semi-remote locations is often limited due to logistical constraints surrounding sample preservation, including no or limited access to a freezer. Freezing at − 20 °C is a common DNA preservation strategy, however, other methods such as desiccation, ethanol or commercial preservatives are available...

Soils are losing increasing amounts of carbon annually to freshwaters as dissolved organic matter (DOM), which, if degraded, can offset their carbon sink capacity. However, the processes underlying DOM degradation across environments are poorly understood. Here we show DOM changes similarly along soil-aquatic gradients irrespective of environmental...

Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in...

Naphthenic acids (NAs) are a complex mixture of organic compounds released during bitumen extraction from mined oil sands that are important contaminants of oil sands process-affected water (OSPW). NAs can be toxic to aquatic organisms and, therefore, are a main target compound for OSPW. The ability of microorganisms to degrade NAs can be exploited...

Earthworm invasion in North American forests has the potential to greatly impact soil microbial communities by altering soil physicochemical properties, including structure, pH, nutrient availability, and soil organic matter (SOM) dynamics. While most research on the topic has been carried out in northern temperate forests, little is known about th...

The oil sands mining operations in Alberta have produced billions of m³ of tailings which must be reclaimed and integrated into various mine closure landforms, including terrestrial landforms. Microorganisms play a central role in nutrient cycling during the reclamation of disturbed landscapes, contributing to successful vegetation restoration and...

Trembling aspen (Populus tremuloïdes) is the most widely distributed fast-growing tree species in the eastern Canadian boreal mixed forest. The ability of this species to invade disturbed environments is related to its ability to reproduce easily by suckering. This phenomenon whereby genetically identical individuals appear in a clonal way could le...

Metagenomics and stable isotope probing insights into naphthenic acids degradation in constructed wetland treatment systems

Introduction Reforestation of degraded lands in the boreal forest is challenging and depends on the direction and strength of the plant-soil feedback (PSF). Methods Using a gradient in tree productivity (null, low and high) from a long-term, spatially replicated reforestation experiment of borrow pits in the boreal forest, we investigated the inte...

Plant-microbe interactions play a crucial role in maintaining biodiversity and ecological services in boreal forest biomes. Mining for minerals, and especially the emission of heavy metal-enriched dust from mine sites, is a potential threat to biodiversity in offsite landscapes. Understanding the impacts of mining on surrounding phyllosphere microb...

Earthworm invasion in North American forests has the potential to greatly impact soil microbial communities by altering soil physicochemical properties, including structure, pH, nutrient availability, and soil organic matter (SOM) dynamics. While most research on the topic has been carried out in northern temperate forests, little is known on the i...

Threats from mining to the biodiversity and ecological services of boreal forests are increasing as demand for minerals increases globally. However, much less is known about how offsite effects of mines affect understory communities as they occur outside the immediate location of mining and are often overlooked during ecological evaluations. We con...

Soils are losing increasing amounts of carbon annually to freshwaters as dissolved organic matter (DOM), which, if degraded, can accelerate climate change. DOM is more susceptible to degradation closer to its source and becomes increasingly dominated by the same, difficult-to-degrade compounds as degradation proceeds. However, the processes underly...

Global change is shifting ecosystem type relative abundance in boreal forests, while the green energy transition results in increased mining activities around the globe. The interaction and consequent effects of these two trends on biodiversity have not been examined in depth. Bryophytes species can be used as indicators to measure these effects be...

Avalaible online : https://couvertboreal.com/publications/automne-2022/

One of the reclamation objectives for treated oil sands tailings (OST) is to establish boreal forest communities that can integrate with the surrounding area. Hence, selection of appropriate soil reclamation cover designs and plant species for revegetation are important aspects of tailings landform reclamation and closure. Research and monitoring o...

Conservation genomics is an important tool to manage threatened species under current biodiversity loss. Recent advances in sequencing technology mean that we can now use whole genomes to investigate demographic history, local adaptation, inbreeding, and more in unprecedented detail. However, for many rare and elusive species only non-invasive samp...

The integration of winter cover crop (WCC) in culture rotations promotes multiple ecosystem services, but concomitant microbial diversity and functioning responses in soil have received less attention. A field trial was established to test the hypothesis that enhanced crop diversity with the integration of WCC in a conventional maize-soy rotation p...

23e colloque annuel de la Chaire AFD

The relationship between soil microbial diversity and agroecosystem functioning is controversial due to the elevated diversity level and the functional redundancy of microorganisms. A field trial was established to test the hypothesis that enhanced crop diversity with the integration of winter cover crops (WCC) in a conventional maize-soy rotation...

The ability of plantations to provide ecosystem services relies on interdependent actions, notably the control of competing vegetation to provide planted seedlings with adequate resource levels. While short-term results from silviculture trials can inform about resource acquisition and use by planted seedlings during the establishment phase, longer...

Oak wilt is caused by the fungus Bretziella fagacearum which develops in the outer sapwood of oak trees. Being one of the most problematic forest diseases in North America, the causal pathogen is present in 28 eastern states of the USA, including infection centers along the Canadian border. Despite significant importation of oak logs from northeast...

To provide essential knowledge for the development of woodland caribou recovery plans, the Canadian Forest Service initiated an integrative research project in collaboration with the Pessamit Innu community (QC North Shore). The first objective is to mobilize science and indigenous knowledge and perspectives to inform the North Shore caribou recove...

In Alberta’s Athabasca oil sands region (AOSR), over 1.25 billion m3 of tailings waste from the bitumen extraction process are stored in tailings ponds. Fugitive emissions associated with residual hydrocarbons in tailings ponds pose an environmental concern and include greenhouse gases (GHGs), reduced sulphur compounds (RSCs), and volatile organic...

The development of rare earth element (REE) production in Canada could generate significant economic benefits but also poses serious potential risks to the environment. Rare earth elements have been widely used in modern life and industries and are even indispensable in some crucial advanced technologies (e.g., permanent magnets). Increasing demand...

Anthropogenic N emissions represent a potential threat for forest ecosystems, and environmental indicators that provide insight into the changing forest N cycle are needed. Tree ring N isotopic ratios (δ¹⁵N) appear as a contentious choice for this role as the exact mechanisms behind tree-ring δ¹⁵N changes seldom benefit from a scrutiny of the soil-...

Unharvested hardwoods are abundant in eastern Canada, due to the low quality of their fiber and the absence of outlets in conventional wood transformation industries. The objective of this study was to assess the biochemical and thermochemical energy conversion potential of decaying hardwoods and compare their relationships with external and intern...

Abandoned unrestored mines are an important environmental concern as they typically remain unvegetated for decades, exposing vast amounts of mine waste to erosion. Several factors limit the revegetation of these sites, including extreme abiotic and unfavorable biotic conditions. However, some pioneer tree species having high levels of genetic diver...

Abandoned unrestored mines are an important environmental issue since they typically remain unvegetated for decades, exposing vast amounts of mine waste to erosion. Several factors limit the revegetation of these sites, including extreme abiotic conditions and unfavorable biotic conditions. However, some pioneer tree species having high level of ge...

Nutrient cycling generally recovers rapidly following disturbance in forest ecosystems. Concerns have been expressed that the resilience of this function may be altered by enhanced disturbance frequency, and especially by the use of salvage logging. A sudden hemlock looper (Lambdina fiscellaria) outbreak in a boreal forest leading to tree mortality...

We describe a strain of Legionella quinlivanii isolated from a bronchoalveolar lavage specimen from an 83-year-old patient in the province of Québec. Identification was done using 16S rRNA sequencing. The strain could replicate efficiently in human THP-1 macrophages and maintained a low level of cytotoxicity. Upon analyzing the whole genome sequenc...

Objectives: Azole resistance among Aspergillus fumigatus isolates is a growing concern worldwide. Induction of mutations during azole therapy, environment-acquired mutations caused by azole fungicides and intrinsic resistance of cryptic Fumigati species all contribute to the burden of resistance. However, there is a lack of data in Canada on this...

Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous diversity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the biodiversity exchanges between these two reser...

Background: HIV-1 transmitted/founder viruses (TF) are selected during the acute phase of infection from a multitude of virions present during transmission. They possess the capacity to establish infection and viral dissemination in a new host. Deciphering the discrete genetic determinant of infectivity in their envelope may provide clues for vacc...

Background The biofilm of a methanol-fed denitrification system that treated a marine effluent is composed of multi-species microorganisms, among which Hyphomicrobium nitrativorans strain NL23 and Methylophaga nitratireducenticrescens strain JAM1 are the principal bacteria involved in the denitrifying activities. Here, we report the capacity of the...

Background The biofilm of a methanol-fed, marine denitrification system is composed of a multi-species microbial community, among which Hyphomicrobium nitrativorans and Methylophaga nitratireducenticrescens are the principal bacteria involved in the denitrifying activities. To assess its resilience to environmental changes, the biofilm was cultivat...

The identification of transmission clusters (TCs) of HIV-1 using phylogenetic analyses can provide insights into viral transmission network and help improve prevention strategies. We compared the use of partial HIV-1 envelope fragment of 1,070 bp with its loop 3 (108 bp) to determine its utility in inferring HIV-1 transmission clustering. Serum sam...

West Nile virus (WNV) was introduced for the first time in the western hemisphere in 1999 in New York City. In 2002, a phenotype-modifying mutation (Env-V159A) defined the first North American genotype WN02. So far, three genotypes has been described in North America but little is known about WNV evolution in Canada. We report the phylogenetic char...

Background: The biofilm of a continuous, methanol-fed, fluidized denitrification system that treated a marine effluent at the Montreal Biodome is composed of a multi-species microbial community, among which Hyphomicrobium nitrativorans NL23 and Methylophaga nitratireducenticrescens JAM1 are the principal bacteria involved in the denitrifying activi...

IntroductionFindings from the community-based Canadian Sentinel Practitioner Surveillance Network (SPSN) suggest children were more affected by the 2018/19 influenza A(H1N1)pdm09 epidemic.AimTo compare the age distribution of A(H1N1)pdm09 cases in 2018/19 to prior seasonal influenza epidemics in Canada.Methods The age distribution of unvaccinated i...

Background. The biofilm of a continuous, methanol-fed, fluidized denitrification system that treated a marine effluent is composed of multi-species microorganisms, among which Hyphomicrobium nitrativorans NL23 and Methylophaga nitratireducenticrescens JAM1 are the principal bacteria involved in the denitrifying activities. This biofilm can be cultu...

We analysed 254 Shigella spp., isolates collected in Québec, Canada, during 2013-2014. Overall, 23.6% of isolates showed reduced susceptibility to azithromycin (RSA) encoded by mphA (11.6%), ermB (1.7%) or by both genes (86.7%). Shigella strains with RSA were mostly isolated from men who have sex with men (68.8% or higher) from the Montreal region....

Here, we present the draft genome sequence of Aspergillus thermomutatus (formerly known as Neosartorya pseudofischeri ; strain HMR-AF-39/LSPQ-01276), a cryptic species of Aspergillus section Fumigati . This species is intrinsically resistant to antifungal azoles and is recognized as an agent of invasive aspergillosis among immunocompromised hosts.

We present the draft genome sequences of two clinical strains of Aspergillus turcosus , one azole-susceptible (strain HMR-AF-23/LSPQ-01275) and the other azole-resistant (strain HMR-AF-1038/LSPQ-01280), isolated from bronchoalveolar lavage fluid of two adult patients. These two strains are the first reported clinical isolates of A. turcosus .

Globally increasing anthropogenic airborne emissions of reactive nitrogen (N) generate several environmental issues that require investigating how N accumulation modifies the N cycle. Tree-ring δ ¹⁵ N series may help understanding past and current perturbations in the forest N cycle. Although several studies have addressed this issue, most of them...

Vaccine effectiveness (VE) against influenza B was derived separately for Victoria and Yamagata lineages across eight seasons (2010-11 to 2017-18) in Canada when trivalent influenza vaccine was predominantly used. VE was ≥50% regardless of lineage match to circulating viruses, except when the vaccine strain was unchanged from the prior season.

We investigated sex as a potential modifier of influenza vaccine effectiveness (VE) between 2010-11 and 2016-17 in Canada. Overall VE was 49% (95%CI=43-55%) for females and 38% (95%CI=28-46%) for males (absolute difference [AD]=11%, p-value=0.03). Sex differences were greatest for influenza A(H3N2) (AD=17%, p=0.07) and B(Victoria) (AD=20%, p=0.08)...

Serratia marcescens is an environmental bacterium commonly associated with outbreaks in neonatal intensive care units (NICU). Investigation of S. marcescens outbreaks requires efficient recovery and typing of clinical and environmental isolates. In this study, we described how the use of next-generation sequencing applications, such as bacterial wh...

Methods: We performed a secondary analysis of the Determinants of Oral Corticosteroid Responsiveness in Wheezing Asthmatic Youth (DOORWAY) study, a prospective cohort study of children (aged 1-17 years) presenting to the emergency department with moderate or severe exacerbations. Nasopharyngeal specimens were analyzed by RT-PCR for 27 respiratory...

Background: Lymphogranuloma venereum (LGV) is a sexually transmitted infection (STI) caused by Chlamydia trachomatis genotypes L1, L2 and L3. This LGV is associated with significant morbidity and increased risk of HIV transmission. While fewer than two cases per year were reported in Quebec before 2005, LGV emerged in 2005-2006 with 69 cases, foll...

Identifying recent HIV-1 infections is crucial for monitoring HIV-1 incidence and optimizing public health prevention efforts. To identify recent HIV-1 infections, we evaluated and compared the performance of 4 sequence-based diversity measures including percent diversity, percent complexity, Shannon entropy and number of haplotypes targeting 13 ge...

Sequence-based diversity measures expressed as the median/IQR and calculated from NGS of 7 segments representing 4 selected HIV-1 env GP120 conserved subdomains. (PDF)

Viral sequences data qualifiers. (XLSX)

Sequence based diversity measures calculation methods. (PDF)

Sequence-based diversity measures expressed as the median/IQR and calculated from NGS of 5 segments representing 5 selected HIV-1 env GP120 variable loops and 1 segment for a part of the gp41ectodomain. (PDF)

Sequence-based diversity measures expressed as the mean with student t-test results comparing recent versus chronic HIV infected sequences by 13 env segments. (PDF)

Streptococcus pneumoniae is one of the major causes of pneumonia, meningitis and other pneumococcal infections in young children and elders. Determination of circulating S. pneumoniae serotypes is an essential service by public health laboratories for the monitoring of putative serotype replacement following the introduction of pneumococcal conjuga...

WGS and assembly quality metrics. (XLSX)

Serotypes and identification level determined with WGS methods. For PneumoCaT, the serotype chosen after the capsule variant analysis step is represented in bold. (XLSX)

Impact of N50 and coverage on identification quality. This test was realized using a two-way Wilcoxon-Mann-Whitney test with an alpha value set to 0.05. (XLSX)

S. pneumoniae isolates and serotypes included in this study. (XLSX)

Serotypes and identification level determined using the multiplex PCR and sequetyping methods. (XLSX)

Background: Vaccine effectiveness (VE) estimates are reported from Canada's Sentinel Practitioner Surveillance Network (SPSN) for the 2015-16 influenza season, characterized by a delayed A(H1N1)pdm09 epidemic and concurrent B(Victoria) activity. Potential influences beyond antigenic match are explored including viral genomic variation, birth cohor...

Age-related differences in influenza B lineage detection were explored in the community-based Canadian Sentinel Practitioner Surveillance Network (SPSN) from 2010-2011 to 2015-2016. Whereas >80% of B(Victoria) cases were <40 years old, B(Yamagata) cases showed a bimodal age distribution with 27% who were <20 years old and 61% who were 30-64 years o...