Exploring winter diet, gut microbiota and parasitism in caribou using multi-marker metabarcoding of fecal DNA.

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 plants and lichens composing the winter diet of caribou (Rangifer tarandus), Canada's most iconic endangered species. Sequencing of the 18S rRNA gene of eukaryotes from seven locations in Manitoba and Saskatchewan, Canada, allowed for the detection of five genera of parasites in caribou feces (including Nematodirella and Parelaphostrongylus) with variable frequency of occurrence depending on sampling location and sex.

How tree traits modulate tree methane fluxes: A review.

Trees can play different roles in the regulation of fluxes of methane (CH), a greenhouse gas with a warming potential 83 times greater than that of carbon dioxide. Forest soils have the greatest potential for methane uptake compared to other land uses. In addition to their influence on soil CH fluxes, trees can act directly as a source or sink of CH, by transporting CH produced in the soil and harbouring the key microorganisms involved in CH production and consumption (methanogens and methanotrophs).

Drying as an effective method to store soil samples for DNA-based microbial community analyses: a comparative study.

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 as potential alternative DNA preservation methods for room temperature storage. In this study, we assessed five preservation methods (CD1 solution, 95% Ethanol, Dry & Dry silica gel packs, RNAlater, LifeGuard) along with freezing at - 20 °C, against immediate extraction on organic and mineral soils for up to three weeks of preservation.

Universal microbial reworking of dissolved organic matter along environmental gradients.

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 differences.

Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems.

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 boreal, temperate, and Mediterranean forest soils.

Microbial degradation of naphthenic acids using constructed wetland treatment systems: metabolic and genomic insights for improved bioremediation of process-affected water.

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 for bioremediation of OSPW using constructed wetland treatment systems (CWTS), which represent a possible low energy and low-cost option for scalable in situ NA removal.

Microbial community structural and functional differentiation in capped thickened oil sands tailings planted with native boreal species.

The oil sands mining operations in Alberta have produced billions of m 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 long-term sustainability. However, microbial community succession and response in reconstructed and revegetated tailings remain largely unexplored.

Does wood mulch trigger microbially mediated positive plant-soil feedback in degraded boreal forest sites? A study.

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 interplay between microbial communities and soil and tree nutrient stocks and concentrations in relation to a positive PSF induced by wood mulch amendment.

Results: Three levels of mulch amendment underlie the observed gradient in tree productivity, and plots that had been amended with a continuous layer of mulch 17 years earlier showed a positive PSF with trees up to 6 m tall, a closed canopy, and a developing humus layer.

Out of site, out of mind: Changes in feather moss phyllosphere microbiota in mine offsite boreal landscapes.

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 microbiota is especially lacking.

Management of adverse events related to first-generation tyrosine receptor kinase inhibitors in adults: a narrative review.

Objective: The aim of this article is to conduct a literature review on first-generation TRK inhibitors (TRKi), namely entrectinib and larotrectinib, to describe the most common adverse events (AEs) and their management in adults.

Methods: A search strategy was conducted in MEDLINE, EMBASE, and Google Scholar using a list of predetermined keywords. Peer-reviewed articles written in English and published through June 2021 were included.

Understanding Willow Transcriptional Response in the Context of Oil Sands Tailings Reclamation.

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 of the long term and immediate impacts of capped OST on the growth and survival of native boreal plant species are currently underway.

The biological sink of atmospheric H is more sensitive to spatial variation of microbial diversity than NO and CO emissions in a winter cover crop field trial.

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 promotes microbial diversity and the biological sink of H in soil, while reducing NO emissions to the atmosphere. Vicia villosa (hairy vetch), Avena sativa (oat), and Raphanus sativus (Daikon radish) were cultivated alone or in combinations and flux measurements were performed throughout two subsequent growing seasons.

A Deep Look into the Microbiology and Chemistry of Froth Treatment Tailings: A Review.

In Alberta's Athabasca oil sands region (AOSR), over 1.25 billion m 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 compounds (VOCs).

Nitrogen isotopes in the soil-to-tree continuum - Tree rings express the soil biogeochemistry of boreal forests exposed to moderate airborne emissions.

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 (δN) appear as a contentious choice for this role as the exact mechanisms behind tree-ring δN changes seldom benefit from a scrutiny of the soil-to-tree N continuum. This study integrates the results from the analysis of soil chemistry, soil microbiome genomics, and δN values of soil N compounds, roots, ectomycorrhizal (EcM) fungi and recent tree rings of thirteen white spruce trees sampled in five stands, from two regions exposed to moderate anthropogenic N emissions (3.

Plant Genotype Influences Physicochemical Properties of Substrate as Well as Bacterial and Fungal Assemblages in the Rhizosphere of Balsam Poplar.

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 diversity, such as balsam poplar , can naturally colonize these sites and initiate plant succession.

strain isolated from a human: A case report and whole genome sequencing analysis.

We describe a strain of 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.

The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada.

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 reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.

Prevalence and mechanisms of azole resistance in clinical isolates of Aspergillus section Fumigati species in a Canadian tertiary care centre, 2000 to 2013.

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 emerging threat.

HIV-1 Envelope Glycoprotein Amino Acids Signatures Associated with Clade B Transmitted/Founder and Recent Viruses.

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 vaccine design.

Phylogenetic analysis of West Nile virus in Quebec, Canada, 2004-2016: Co-circulation of distinct variants harbouring conserved amino acid motifs in North America.

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.

Dynamics of a methanol-fed marine denitrifying biofilm: 1-Impact of environmental changes on the denitrification and the co-occurrence of and .

Background: The biofilm of a methanol-fed denitrification system that treated a marine effluent is composed of multi-species microorganisms, among which strain NL23 and strain JAM1 are the principal bacteria involved in the denitrifying activities. Here, we report the capacity of the denitrifying biofilm to sustain environmental changes, and the impact of these changes on the co-occurrence of and .

Methods: In a first set of assays, the original biofilm (OB) was cultivated in an artificial seawater (ASW) medium under anoxic conditions to colonize new carriers.

Dynamics of a methanol-fed marine denitrifying biofilm: 2-impact of environmental changes on the microbial community.

Background: The biofilm of a methanol-fed, marine denitrification system is composed of a multi-species microbial community, among which and are the principal bacteria involved in the denitrifying activities. To assess its resilience to environmental changes, the biofilm was cultivated in artificial seawater (ASW) under anoxic conditions and exposed to a range of specific environmental conditions. We previously reported the impact of these changes on the denitrifying activities and the co-occurrence of strain NL23 and in the biofilm cultures.

A Short-Term Assessment of Nascent HIV-1 Transmission Clusters Among Newly Diagnosed Individuals Using Envelope Sequence-Based Phylogenetic Analyses.

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 samples of recently ( = 106) and chronically ( = 156) HIV-1-infected patients with status confirmed were sequenced.

Children under 10 years of age were more affected by the 2018/19 influenza A(H1N1)pdm09 epidemic in Canada: ‎possible cohort effect following the 2009 influenza pandemic.

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.MethodsThe age distribution of unvaccinated influenza A(H1N1)pdm09 cases and test-negative controls were compared across A(H1N1)pdm09-dominant epidemics in 2018/19, 2015/16 and 2013/14 and with the general population of SPSN provinces.

Draft Genome Sequences of Azole-Resistant and Azole-Susceptible Aspergillus turcosus Clinical Isolates Recovered from Bronchoalveolar Lavage Fluid Samples.

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.