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Lovejoy, Connie

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Lovejoy

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Connie

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Université Laval. Département de biologie

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ncf11850007

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  • PublicationAccès libre
    Genomic evidence of functional diversity in DPANN archaea, from oxic species to anoxic vampiristic consortia
    (Springer Nature on behalf of the International Society for Microbial Ecology, 2022-01-20) Vigneron, Adrien; Cruaud, Perrine; Lovejoy, Connie; Vincent, Warwick F.
    DPANN archaea account for half of the archaeal diversity of the biosphere, but with few cultivated representatives, their metabolic potential and environmental functions are poorly understood. The extreme geochemical and environmental conditions in meromictic ice-capped Lake A, in the Canadian High Arctic, provided an isolated, stratified model ecosystem to resolve the distribution and metabolism of uncultured aquatic DPANN archaea living across extreme redox and salinity gradients, from freshwater oxygenated conditions, to saline, anoxic, sulfidic waters. We recovered 28 metagenome-assembled genomes (MAGs) of DPANN archaea that provided genetic insights into their ecological function. Thiosulfate oxidation potential was detected in aerobic Woesearchaeota, whereas diverse metabolic functions were identified in anaerobic DPANN archaea, including degradation and fermentation of cellular compounds, and sulfide and polysulfide reduction. We also found evidence for “vampiristic” metabolism in several MAGs, with genes coding for pore-forming toxins, peptidoglycan degradation, and RNA scavenging. The vampiristic MAGs co-occurred with other DPANNs having complementary metabolic capacities, leading to the possibility that DPANN form interspecific consortia that recycle microbial carbon, nutrients and complex molecules through a DPANN archaeal shunt, adding hidden novel complexity to anaerobic microbial food webs.
  • PublicationAccès libre
    Salinity tolerance mechanisms of an Arctic Pelagophyte using comparative transcriptomic and gene expression analysis
    (Springer Nature, 2022-05-25) Lovejoy, Connie; Kuo, Alan; Freyria, Nastasia J.; Chovatia, Mansi; Johnson, Jenifer; Lipzen, Anna; Barry, Kerrie W.; Grigoriev, Igor V.
    Little is known at the transcriptional level about microbial eukaryotic adaptations to short-term salinity change. Arctic microalgae are exposed to low salinity due to sea-ice melt and higher salinity with brine channel formation during freeze-up. Here, we investigate the transcriptional response of an ice-associated microalgae over salinities from 45 to 8. Our results show a bracketed response of differential gene expression when the cultures were exposed to progressively decreasing salinity. Key genes associated with salinity changes were involved in specific metabolic pathways, transcription factors and regulators, protein kinases, carbohydrate active enzymes, and inorganic ion transporters. The pelagophyte seemed to use a strategy involving overexpression of Na+-H+ antiporters and Na+ -Pi symporters as salinity decreases, but the K+ channel complex at higher salinities. Specific adaptation to cold saline arctic conditions was seen with differential expression of several antifreeze proteins, an ice-binding protein and an acyl-esterase involved in cold adaptation.
  • PublicationAccès libre
    A decadal perspective on north water microbial eukaryotes as Arctic Ocean sentinels
    (Nature Publishing Group, 2021-04-16) Lovejoy, Connie; Freyria, Nastasia J.; Joli, Nathalie
    The North Water region, between Greenland and Ellesmere Island, with high populations of marine birds and mammals, is an Arctic icon. Due to climate related changes, seasonal patterns in water column primary production are changing but the implications for the planktonic microbial eukaryote communities that support the ecosystem are unknown. Here we report microbial community phenology in samples collected over 12 years (2005–2018) from July to October and analysed using high throughput 18S rRNA V4 amplicon sequencing. Community composition was tied to seasonality with summer communities more variable than distinct October communities. In summer, sentinel pan-Arctic species, including a diatom in the Chaetoceros socialis-gelidus complex and the picochlorophyte Micromonas polaris dominated phytoplankton and were summer specialists. In autumn, uncultured undescribed open water dinoflagellates were favored, and their ubiquity suggests they are sentinels of arctic autumn conditions. Despite the input of nutrients into surface waters, autumn chlorophyll concentrations remained low, refuting projected scenarios that longer ice-free seasons are synonymous with high autumn production and a diatom dominated bloom. Overall, the summer sentinel microbial taxa are persisting, and a subset oceanic dinoflagellate should be monitored for possible ecosystem shifts as later autumn ice formation becomes prevalent elsewhere.
  • PublicationRestreint
    Two versions of short-term phytoplankton ecophysiology and taxonomic assemblages in the Arctic Ocean’s North Water (Canada, Greenland)
    (Oxford University Press, 2021-03-17) Lovejoy, Connie; Lacour, Thomas; Royer, Sarah-Jeanne; Freyria, Nastasia J; Babin, Marcel; Joli, Nathalie
    Photosynthetic performance in open marine waters is determined by how well phytoplankton species are adapted to their immediate environment and available light. Although there is light for 24 h a day during the Arctic summer, little is known about short-term (h) temporal variability of phytoplankton photosynthetic performance in Arctic waters. To address this, we sampled the North Water (76.5°N) every 4 h over 24 h at two stations on the East and West sides that are influenced by different water masses and current conditions. We specifically investigated phytoplankton pigments, the xanthophyll cycle (XC), which is an indication of photoprotective capacity, and photosynthesis–irradiance (PE) response curves, at the surface and 20 m depth. The photophysiological parameters on the two sides differed along with the taxonomic signal derived from accessory pigments. On both sides, surface XC pigments showed high photoprotection capacity with the dinodinoxanthin–diatoxanthin (DD) and the violaxanthin, antheraxanthin and zeaxanthin cycles correlated with incoming radiation. The PE results showed that communities dominated by small flagellates on the western side performed better compared to diatom dominated communities on the eastern side. We conclude that phytoplankton and photosynthetic capacity differed consistent with known hydrography, with implications for a changing Arctic.
  • PublicationAccès libre
    Chlorovirus and myovirus diversity in permafrost thaw ponds
    (Inter-Research Science Publisher, 2018-12-17) Culley, Alexander; Lovejoy, Connie; Comte, Jérôme; Vincent, Warwick F.; Lévesque, Alice
    Permafrost thaw ponds occur in high abundance across the northern landscape of Canada and are sites of intense microbial activity, resulting in carbon dioxide and methane emissions to the atmosphere. In this study, we focused on viruses as largely unstudied agents of top-down control in these high-latitude microbial ecosystems. Specifically, we compared the diversity of myovirus, chlorovirus and host microbial communities in an organic soil palsa valley pond and a mineral soil lithalsa valley pond. These 2 subarctic permafrost landscapes are both common in northern Québec, Canada. Sequence analysis of ribosomal small subunit RNA genes showed that the community structure of bacteria and microbial eukaryotes differed significantly between the 2 ponds, which both differed from microbial communities in a rock-basin lake (whose formation was not related to permafrost thawing and which we used as a reference pond) in the same region. The viral assemblages included 439 OTUs in the uncultured Myoviridae category and 41 OTUs in the family Phycodnaviridae. Phylogenetic analysis of the latter based on an amino acid sequence alignment revealed a single large clade related to chloroviruses, consistent with the abundant presence of chlorophytes in these waters. As there was for the bacterial and eukaryotic communities, there were also significant differences in the community structure of these viral groups among the 3 ponds. These results suggest that host community composition is influenced by environmental filtering, which in turn contributes to driving viral diversity across landscape types.
  • PublicationAccès libre
    Size-fractionated microbiome structure in subarctic rivers and a coastal plume across DOC and salinity gradients
    (Frontiers Media, 2022-01-03) Matveev, Alex; Lovejoy, Connie; Vincent, Warwick F.; Blais, Marie-Amélie
    Little is known about the microbial diversity of rivers that flow across the changing subarctic landscape. Using amplicon sequencing (rRNA and rRNA genes) combined with HPLC pigment analysis and physicochemical measurements, we investigated the diversity of two size fractions of planktonic Bacteria, Archaea and microbial eukaryotes along environmental gradients in the Great Whale River (GWR), Canada. This large subarctic river drains an extensive watershed that includes areas of thawing permafrost, and discharges into southeastern Hudson Bay as an extensive plume that gradually mixes with the coastal marine waters. The microbial communities differed by size-fraction (separated with a 3-μm filter), and clustered into three distinct environmental groups: (1) the GWR sites throughout a 150-km sampling transect; (2) the GWR plume in Hudson Bay; and (3) small rivers that flow through degraded permafrost landscapes. There was a downstream increase in taxonomic richness along the GWR, suggesting that sub-catchment inputs influence microbial community structure in the absence of sharp environmental gradients. Microbial community structure shifted across the salinity gradient within the plume, with changes in taxonomic composition and diversity. Rivers flowing through degraded permafrost had distinct physicochemical and microbiome characteristics, with allochthonous dissolved organic carbon explaining part of the variation in community structure. Finally, our analyses of the core microbiome indicated that while a substantial part of all communities consisted of generalists, most taxa had a more limited environmental range and may therefore be sensitive to ongoing change.
  • PublicationAccès libre
    Contrasting sea ice conditions shape microbial food webs in Hudson Bay (Canadian Arctic)
    (Nature Publishing Group, 2022-10-23) Jacquemot, Loïc; Vigneron, Adrien; Tremblay, Jean-Éric; Lovejoy, Connie
    The transition from ice-covered to open water is a recurring feature of the Arctic and sub-Arctic, but microbial diversity and cascading effects on the microbial food webs is poorly known. Here, we investigated microbial eukaryote, bacterial and archaeal communities in Hudson Bay (sub-Arctic, Canada) under sea-ice cover and open waters conditions. Co-occurrence networks revealed a <3 µm pico‒phytoplankton-based food web under the ice and a >3 µm nano‒microphytoplankton-based food web in the open waters. The ice-edge communities were characteristic of post-bloom conditions with high proportions of the picophytoplankton Micromonas and Bathycoccus. Nano‒ to micro‒phytoplankton and ice associated diatoms were detected throughout the water column, with the sympagic Melosira arctica exclusive to ice-covered central Hudson Bay and Thalassiosira in open northwestern Hudson Bay. Heterotrophic microbial eukaryotes and prokaryotes also differed by ice-state, suggesting a linkage between microbes at depth and surface phytoplankton bloom state. The findings suggest that a longer open water season may favor the establishment of a large phytoplankton-based food web at the subsurface chlorophyll maxima (SCM), increasing carbon export from pelagic diatoms to deeper waters and affect higher trophic levels in the deep Hudson Bay.
  • PublicationAccès libre
    Genomic insights into cryptic cycles of microbial hydrocarbon production and degradation in contiguous freshwater and marine microbiomes
    (BioMed Central, 2023-05-12) Vigneron, Adrien; Cruaud, Perrine; Lovejoy, Connie; Vincent, Warwick F.
    Background: Cyanobacteria and eukaryotic phytoplankton produce long-chain alkanes and generate around 100 times greater quantities of hydrocarbons in the ocean compared to natural seeps and anthropogenic sources. Yet, these compounds do not accumulate in the water column, suggesting rapid biodegradation by co-localized microbial populations. Despite their ecological importance, the identities of microbes involved in this cryptic hydrocarbon cycle are mostly unknown. Here, we identifed genes encoding enzymes involved in the hydrocarbon cycle across the salinity gradient of a remote, vertically stratifed, seawater-containing High Arctic lake that is isolated from anthropogenic petroleum sources and natural seeps. Metagenomic analysis revealed diverse hydrocarbon cycling genes and populations, with patterns of variation along gradients of light, salinity, oxygen, and sulfur that are relevant to freshwater, oceanic, hadal, and anoxic deep sea ecosystems. Results Analyzing genes and metagenome-assembled genomes down the water column of Lake A in the Canadian High Arctic, we detected microbial hydrocarbon production and degradation pathways at all depths, from surface freshwaters to dark, saline, anoxic waters. In addition to Cyanobacteria, members of the phyla Flavobacteria, Nitrospina, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia had pathways for alkane and alkene production, providing additional sources of biogenic hydrocarbons. Known oil-degrading microorganisms were poorly represented in the system, while long-chain hydrocarbon degradation genes were identifed in various freshwater and marine lineages such as Actinobacteria, Schleiferiaceae, and Marinimicrobia. Genes involved in sulfur and nitrogen compound transformations were abundant in hydrocarbon producing and degrading lineages, suggesting strong interconnections with nitrogen and sulfur cycles and a potential for widespread distribution in the ocean. Conclusions Our detailed metagenomic analyses across water column gradients in a remote petroleum-free lake derived from the Arctic Ocean suggest that the current estimation of bacterial hydrocarbon production in the ocean could be substantially underestimated by neglecting non-phototrophic production and by not taking low oxygen zones into account. Our fndings also suggest that biogenic hydrocarbons may sustain a large fraction of freshwater and oceanic microbiomes, with global biogeochemical implications for carbon, sulfur, and nitrogen cycles.
  • PublicationAccès libre
    Genomic evidence for sulfur intermediates as new biogeochemical hubs in a model aquatic microbial ecosystem
    (2021-02-16) Culley, Alexander; Lovejoy, Connie; Vincent, Warwick F.; Vigneron, Adrien; Couture, Raoul-Marie; Cruaud, Perrine
    Background The sulfur cycle encompasses a series of complex aerobic and anaerobic transformations of S-containing molecules and plays a fundamental role in cellular and ecosystem-level processes, influencing biological carbon transfers and other biogeochemical cycles. Despite their importance, the microbial communities and metabolic pathways involved in these transformations remain poorly understood, especially for inorganic sulfur compounds of intermediate oxidation states (thiosulfate, tetrathionate, sulfite, polysulfides). Isolated and highly stratified, the extreme geochemical and environmental features of meromictic ice-capped Lake A, in the Canadian High Arctic, provided an ideal model ecosystem to resolve the distribution and metabolism of aquatic sulfur cycling microorganisms along redox and salinity gradients. Results Applying complementary molecular approaches, we identified sharply contrasting microbial communities and metabolic potentials among the markedly distinct water layers of Lake A, with similarities to diverse fresh, brackish and saline water microbiomes. Sulfur cycling genes were abundant at all depths and covaried with bacterial abundance. Genes for oxidative processes occurred in samples from the oxic freshwater layers, reductive reactions in the anoxic and sulfidic bottom waters and genes for both transformations at the chemocline. Up to 154 different genomic bins with potential for sulfur transformation were recovered, revealing a panoply of taxonomically diverse microorganisms with complex metabolic pathways for biogeochemical sulfur reactions. Genes for the utilization of sulfur cycle intermediates were widespread throughout the water column, co-occurring with sulfate reduction or sulfide oxidation pathways. The genomic bin composition suggested that in addition to chemical oxidation, these intermediate sulfur compounds were likely produced by the predominant sulfur chemo- and photo-oxidisers at the chemocline and by diverse microbial degraders of organic sulfur molecules. Conclusions The Lake A microbial ecosystem provided an ideal opportunity to identify new features of the biogeochemical sulfur cycle. Our detailed metagenomic analyses across the broad physico-chemical gradients of this permanently stratified lake extend the known diversity of microorganisms involved in sulfur transformations over a wide range of environmental conditions. The results indicate that sulfur cycle intermediates and organic sulfur molecules are major sources of electron donors and acceptors for aquatic and sedimentary microbial communities in association with the classical sulfur cycle.
  • PublicationAccès libre
    Stratification and summer protist communities in the Arctic influenced coastal systems of Nunavik (Québec, Canada)
    (Frontiers Research Foundation, 2024-01-29) Jacquemot, Loïc; Tremblay, Jean-Éric; Morency, Carlee; Lovejoy, Connie
    Phytoplankton and other protists in the 3 µm to 50 µm size fraction are grazed on by zooplankton and form the base of Arctic marine food webs essential for local indigenous communities. Anthropogenic climate change is increasing stratification over much of the Arctic Ocean and surrounding seas, but the influence of stratification on protist communities in more coastal regions along Eastern Hudson Bay, Hudson Strait and Ungava Bay is little known. We used 18S rRNA and rDNA amplicon sequencing during two consecutive summers (2017 and 2018) and detailed water column properties to compare the 3 µm to 50 µm protist communities under contrasting stratification regimes in the Eastern Hudson Bay Complex. We found that the surface mixed layer in Eastern Hudson Bay, which is under the influence of river runoff, was strongly stratified and dominated by mixotrophic and bacterivorous taxa, mostly the dinoflagellates Heterocapsa rotundata and Gymnodiniales spp., and a more diatom-dominated community at the Subsurface Chlorophyll Maximum (SCM), which persisted in deeper colder and more saline water. The massive sequencing effort retrieved seven putative toxic algae from the upper warmer waters of eastern Hudson Bay. These included Pseudo-nitzschia spp. and potentially harmful dinoflagellates, most notably Alexandrium sp. The persistent weaker stratification conditions in Hudson Strait and Ungava Bay in summer favored a different diatom community, dominated by Chaetoceros spp. and Thalassiosira spp., and small photosynthetic flagellates including Phaeocystis pouchetii and Micromonas polaris. As freshwater input increases and stratification intensifies in the Arctic, our findings suggest the summer dinoflagellate-based community seen in coastal Hudson Bay may also be favored in other regions receiving increased river runoff. These conditions could also favor harmful algal events. The Hudson Strait and Ungava Bay protist communities were found nearer the surface and consisted of diverse species able to profit from ongoing nutrient input due to tidal mixing. These results suggest greater resilience in this and other tidally influenced coastal Arctic Bays lacking larger rivers inputs.