Biology subjects

Walsh, D. A.

Publications and source records attributed to Walsh, D. A..

15 recordsLinked to original sources

bioRxiv2026

Evidence of an acetone carboxylation pathway in photoheterotrophic bacteria from the Arctic Ocean

Carboxylases are among the most important enzymes in nature as they catalyze the fixation of inorganic carbon (CO2), a central step in the global carbon cycle. In addition to their well-known function in autotrophic CO2 fixation, many carboxylases play a role in the heterotrophic assimilation of organic compounds. In this study, we provide genomic evidence for an assimilatory carboxylation pathway involved in acetone degradation in photoheterotrophic bacteria from metagenomes collected along a latitudinal transect of the Arctic Ocean. This curious metabolism was linked to a single population of Gammaproteobacteria (Porticoccus arcticus). P. arcticus has a streamlined genome compared to Porticoccus relatives but has maintained a complete acetone carboxylation pathway while acquiring multiple proteorhodopsin genes by lateral gene transfer. Arctic Ocean metatranscriptomes revealed the acetone carboxylase and rhodopsins genes were among the most highly expressed P. arcticus genes in oligotrophic Arctic surface waters. P. arcticus sequences were consistently detected, and often abundant (up to 9%), in a multiyear Arctic Ocean 16S rRNA time-series, supporting its ecological significance in Arctic marine systems. Overall, this work reports a metabolic module (acetone carboxylation) in the ocean that may allow photoheterotrophic bacteria to enhance their biosynthetic capacity via CO2 assimilation.

microbiology↗

bioRxiv2026

Metagenomic Discovery of Neutral Lipid Metabolism Pathways in the Arctic Ocean Microbiomes Suggests a Potential New Role in Survival and Oceanic Carbon Cycling

The Arctic Ocean microbiomes experience extreme seasonal fluctuations in light, nutrient availability, and organic carbon supply. In this environment, neutral lipid storage may provide a key survival strategy. Here, we investigated the diversity, distribution, and ecological role of neutral lipid metabolism in Arctic microbiomes using metagenome-resolved analyses and global ocean comparisons. Arctic photic-zone microbiomes were strongly enriched in triacylglycerol (TAG) biosynthesis genes relative to other oceans, primarily due to picoeukaryotic phytoplankton, including the ecologically dominant Micromonas and Bathycoccus. In contrast, prokaryotic communities exhibited diverse TAG-degrading taxa and fatty acid transport systems, supporting a previously unrecognized lipotrophic bacterial guild exploiting phytoplankton-derived lipids as carbon and energy sources. Genome-resolved analyses further revealed distinct bacterial lipid-storage strategies: TAG-producing taxa preferentially encoded fatty acid uptake and carbohydrate utilization pathways, whereas polyhydroxyalkanoate-producing taxa were associated with aromatic compound degradation, linking terrestrial organic matter to lipid storage. Our results expand the known diversity of marine microbes capable of neutral lipid metabolism and identify microbial lipid cycling as a previously overlooked component of the Arctic carbon cycle. We propose that neutral lipid storage and turnover support microbial survival through the polar night while enhancing carbon transfer within Arctic microbial food webs under ongoing climate change.

microbiology↗

bioRxiv2026

Changing Pacific salmon nursery lake ecosystem dynamics over centuries to millennia: insights from sedimentary DNA metabarcoding

Pacific salmon are keystone species to North Pacific freshwater, coastal, and oceanic ecosystems, but many populations have declined or become more variable in recent decades due to anthropogenic impacts and climate change. Long-term records are needed to understand past changes, identify ecosystem stressors, and guide restoration. We used sedimentary DNA (sedDNA), an emerging paleoecological approach offering broader taxonomic information than traditional methods, to reconstruct ecosystem changes across five Pacific salmon nursery lakes in British Columbia (Canada). DNA metabarcoding targeting the 18S ribosomal RNA gene V7 region was used to track shifts in eukaryotic communities including algae and invertebrates over centuries to millennia. Most lakes showed notable algal community shifts over the past two centuries, with declining green algae and rising diatom relative abundances. Chrysophytes and dinoflagellates also increased over the past century in most lakes, likely driven by stronger thermal stratification, which favored these motile and mixotrophic algae that are capable of vertical migration and flexible nutrient acquisition. We contextualized the trajectories of each core through an ordination analysis based on 98 lakes distributed across British Columbia, which identified land-use changes and longer growing seasons as potential drivers. Network analyses of the sedDNA time series revealed decreasing modularity and increasing connection across lakes, suggesting a shift in resilience mechanisms from between-module buffering by compartmentalized specialists to within-guild insurance via functional overlap among generalists. Our findings demonstrate that sedDNA provides taxonomically rich, long-term insights into aquatic ecological dynamics, which are foundational for understanding and protecting Pacific salmon nursery habitats.

ecology↗

bioRxiv2023

Multiplexed Amplicon Sequencing Reveals High Sequence Diversity of Antibiotic Resistance Genes in Quebec Sewers

The United Nations Environment Assembly (UNEA-3) have recognised the importance of the environment in the development, spread and transmission of antimicrobial resistance (AMR) to humans and animals. Such recognition calls for wider surveillance of antimicrobial resistance genes (ARG) in wastewater and other environmental reservoirs. For ARG surveillance to be valuable to regulators, it must enable source tracking and risk assessment. Adequate surveillance also requires the processing of a large number of samples at a relatively low cost, and a low detection limit to allow quantification of the riskiest ARGs. However, current methods for tracking ARGs have various limitations. The current study presents a multiplexed targeted amplicon sequencing approach for the detection of sequence variants of ARGs in environmental samples. To demonstrate the application of this technique, wastewater samples collected from the inlet to 16 treatment plants located along a 440-km transect of the St-Lawrence river in the province of Quebec (Canada) were analysed. Among the ARGs examined, between 3 and 45 nucleic acid sequence variants were detected demonstrating the high sequence diversity that occurs within genes originating from a single sample type and the information that is missed using traditional techniques. Using the PLSDB and Comprehensive Antibiotic Resistance Database (CARD), the risk of ARG sequence variants was inferred based upon their reported mobility and detection in pathogens. Results suggest that sequence variants within a single ARG class present different risks to public health. In the future, targeted amplicon sequencing could be a valuable tool in environmental studies for both risk assessment purposes and in AMR source tracking.

microbiology↗

bioRxiv2022

Degradation pathways for organic matter of terrestrial origin are widespread and expressed in Arctic Ocean microbiomes

BackgroundThe Arctic Ocean receives massive freshwater input and a correspondingly large amount of humic-rich organic matter of terrestrial origin. Global warming, permafrost melt, and a changing hydrological cycle will contribute to an intensification of terrestrial organic matter release to the Arctic Ocean. Although considered recalcitrant to degradation due to complex aromatic structures, humic substances can serve as substrate for microbial growth in terrestrial environments. However, the capacity of marine microbiomes to process aromatic-rich humic substances, and how this processing may contribute to carbon and nutrient cycling in a changing Arctic Ocean, is relatively unexplored. Here, we used a combination of metagenomics and metatranscriptomics to assess the prevalence and diversity of metabolic pathways and bacterial taxa involved in aromatic compound degradation in the salinity-stratified summer waters of the Canada Basin in the western Arctic Ocean. ResultsCommunity-scale meta-omics profiling revealed that 22 complete pathways for processing aromatic compounds were present and expressed in the Canada Basin, including those for aromatic ring fission and upstream funnelling pathways to access diverse aromatic compounds of terrestrial origin. A phylogenetically diverse set of functional marker genes and transcripts were associated with fluorescent dissolved organic matter, a component of which is of terrestrial origin. Pathways were common throughout global ocean microbiomes, but were more abundant in the Canada Basin. Genome-resolved analyses identified 12 clades of Alphaproteobacteria, including Rhodospirillales, as central contributors to aromatic compound processing. These genomes were mostly restricted in their biogeographical distribution to the Arctic Ocean, and were enriched in aromatic compound processing genes compared to their closest relatives from other oceans. ConclusionOverall, the detection of a phylogenetically diverse set of genes and transcripts implicated in aromatic compound processing supports the view that Arctic Ocean microbiomes have the capacity to metabolize humic substances of terrestrial origin. In addition, the demonstration that bacterial genomes replete with aromatic compound degradation genes exhibit a limited distribution outside of the Arctic Ocean suggests that processing humic substances is an adaptive trait of the Arctic Ocean microbiome. Future increases in terrestrial organic matter input to the Arctic Ocean may increase the prominence of aromatic compound processing bacteria and their contribution to Arctic carbon and nutrient cycles.

microbiology↗

bioRxiv2022

Genome-resolved community structure and function of freshwater bacteria at a continental scale

Lakes are heterogenous ecosystems inhabited by a rich microbiome whose genomic diversity is poorly defined. We present a continental-scale study of metagenomes representing 6.5 million km2 of the most lake-rich landscape on Earth. Analysis of 308 Canadian lakes resulted in a metagenome-assembled genome (MAG) catalogue of 1,008 mostly novel bacterial genomospecies. Lake trophic state was a leading driver of taxonomic and functional diversity among MAG assemblages, reflecting the responses of communities profiled by 16S rRNA amplicons and gene-centric metagenomics. Coupling the MAG catalogue with watershed geomatics revealed terrestrial influences of soils and land use on assemblages. Agriculture and human population density were drivers of turnover, indicating detectable anthropogenic imprints on lake bacteria at the continental scale. The sensitivity of bacterial assemblages to human impact reinforces lakes as sentinels of environmental change. Overall, the LakePulse MAG catalogue greatly expands the freshwater genomic landscape, advancing an integrative view of diversity across Earths microbiomes.

microbiology↗

bioRxiv2022

A resistome survey across hundreds of freshwater bacterial communities reveals the impacts of veterinary and human antibiotics use

Our decreasing ability to fight bacterial infections is a major health concern. It is arising due to the evolution of antimicrobial resistance (AMR) in response to the mis- and overuse of antibiotics in both human and veterinary medicine. Lakes integrate watershed processes and thus may act as receptors and reservoirs of antibiotic resistance genes (ARGs) introduced into the watershed by human activities. The resistome - the diversity of ARGs - under varying anthropogenic watershed pressures has been previously studied either focused on few select genes or few lakes. Here, we link the resistome of [~]350 lakes sampled across Canada to human watershed activity, trophic status, as well as point sources of ARG pollution. A high percentage of the resistance genes detected was either unimpacted by human activity or highly prevalent in pristine lakes, highlighting the role of AMR in microbial ecology in aquatic systems, as well as a pool of genes available for potential horizontal gene transfer to pathogenic species. Nonetheless, watershed agricultural and pasture area significantly impacted the resistome. Moreover, the number of hospitals and the population density in a watershed, the volume of wastewater entering the lake, as well as the fraction of manure applied in the watershed as fertilizer significantly impacted ARG diversity. Together, these findings indicate that lake resistomes are regularly stocked with resistance genes evolved in the context of both veterinary and human antibiotics use and represent reservoirs of ARGs that require further monitoring.

genomics↗

bioRxiv2022

Protist diversity and metabolic strategy in freshwater lakes are shaped by trophic state and watershed land use at a continental scale

Protists play key roles in aquatic food webs as primary producers, predators, nutrient recyclers, and symbionts. Yet, a comprehensive view of protist diversity in freshwaters has been challenged by the immense environmental heterogeneity among lakes worldwide. We assessed protist diversity in the surface waters of 366 freshwater lakes across a north temperate to subarctic extent covering nearly 8.4 million km2 of Canada. Sampled lakes represented broad gradients in size, trophic state, and watershed land use. Hypereutrophic lakes contained the least diverse and most distinct protist communities relative to nutrient-poor lakes. Greater taxonomic variation among eutrophic lakes was mainly a product of heterotroph and mixotroph diversity, whereas phototroph assemblages were more similar under high- nutrient conditions. Overall, local physicochemical factors, particularly ion and nutrient concentrations, elicited the strongest responses in community structure, far outweighing the effects of geographic gradients. Despite their contrasting distribution patterns, obligate phototroph and heterotroph turnover was predicted by an overlapping set of environmental factors, while the metabolic plasticity of mixotrophs may have made them less predictable. Notably, protist diversity was associated with variation in watershed soil pH and agricultural crop coverage, pointing to human impact on the land-water interface that has not been previously identified in studies at smaller scales. Our study exposes the importance of both within-lake and external watershed characteristics in explaining protist diversity and biogeography, critical information in further developing an understanding of how freshwater lakes and their watersheds are impacted by anthropogenic stressors. ImportanceFreshwater lakes are experiencing rapid changes under accelerated anthropogenic stress and a warming climate. Microorganisms underpin aquatic food webs, yet little is known about how freshwater microbial communities are responding to human impact. Here, we assessed the diversity of protists and their myriad ecological roles in lakes varying in size across watersheds experiencing a range of land use pressures by leveraging data from a continental-scale survey of Canadian lakes. We found evidence of human impact on protist assemblages through an association with lake trophic state and extending to agricultural activity and soil characteristics in the surrounding watershed. Furthermore, trophic state appeared to explain the distributions of phototrophic and heterotrophic protists in contrasting ways. Our findings highlight the vulnerability of lake ecosystems to increased land use and the importance of assessing terrestrial interfaces to elucidate freshwater ecosystem dynamics.

ecology↗

bioRxiv2022

A consensus protocol for the recovery of mercury methylation genes from metagenomes

Mercury methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-MATE (Hg-cycling Microorganisms in Aquatic and Terrestrial Ecosystems) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on co-assembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a co-assembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

microbiology↗

bioRxiv2021

Comparative analysis of zooplankton diversity in freshwaters: What can we gain from metagenomic analysis?

Molecular genetic approaches applied to environmental DNA have great potential for biodiversity research and ecosystem monitoring. A metagenome contains genetic information from all organisms captured in an environmental sample. It has been primarily used to study bacteria and archaea, but promising reports focusing on metazoan diversity are emerging. However, methodological uncertainties remain, and studies are required to validate the power and the limitations of such an approach when applied to macro-eukaryotes. Here, we analyzed water sample metagenomes to estimate zooplankton diversity in 22 freshwater lakes across Eastern Canada. We tested the coherence of data based on morphologically identified zooplankton taxa and molecular genetic data derived from shotgun sequencing of environmental DNA collected at the same time. RV coefficients showed a significant correlation between the relative abundance of zooplankton families derived from small subunit rRNA genes extracted from the metagenomes and morphologically identified zooplankton. However, differences in congruence with morphological counts were detected when varied bioinformatic approaches were applied to presence-absence data. This study presents one of the first diversity assessments of a group of aquatic metazoans using metagenomes and validates the coherence of the community composition derived from genetic and classical species surveys. Overall, our results suggest that metagenomics has the potential to be further developed to describe metazoan biodiversity in aquatic ecosystems, and to advance this area we provide key recommendations for workflow improvement.

ecology↗

bioRxiv2021

A metagenomic-based stufy of two sites from the Barbadian reef system

We study the microbiome of sea water collected from two locations of the Barbadian coral reefs. The two sites differ in several environmental and ecological variables including their endogenous benthic community in addition to their proximity to urban development and runoffs from inland watersheds. The composition of the microbial community was estimated using whole genome DNA shotgun sequencing. Although both sites exhibit a similar degree of richness, the less urbanized site (Maycocks reef at Hangmans Bay) is strongly concentrated with phototrophs. In comparison, the more urbanized location (Bellairs Research Institute) is enriched for copiotrophs, macroalgal symbionts and marine-related disease-bearing organisms from taxa scattered across the tree of life. Overall, our samples and associated measurements of chemical and environmental qualities of the water are in line with previous marine microbiome profiles of warm ocean surface waters. This suggests our approach captures salient information regarding the state of each coral reef site and sets the stage for larger longitudinal studies of coral reef dynamics in Barbados.

microbiology↗

bioRxiv2020

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

Microbial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs for oxidation of sulfur and thiosulfate (dsrA, dsrC/tusE, soxC, soxD and soxYZ). Evidence for retention of AMGs during niche-differentiation of diverse phage populations provided evidence that auxiliary metabolism imparts measurable fitness benefits to phages with ramifications for ecosystem biogeochemistry. Gene abundance and expression profiles of AMGs suggested significant contributions by phages to sulfur and thiosulfate oxidation in freshwater lakes and oceans, and a sensitive response to changing sulfur concentrations in hydrothermal environments. Overall, our study provides novel insights on the distribution, diversity and ecology of phage auxiliary metabolism associated with sulfur and reinforces the necessity of incorporating viral contributions into biogeochemical configurations.

microbiology↗

bioRxiv2020

Anxiety enhances pain in a model of osteoarthritis and is associated with altered endogenous opioid function and reduced opioid analgesia

Chronic pain states such as osteoarthritis (OA) are often associated with negative affect, including anxiety and depression. This is, in turn, associated with greater opioid analgesic use, potentially contributing to current and future opioid crises. We utilise an animal model to investigate the neurobiological mechanisms underlying increased opioid use associated with high anxiety and chronic pain. Combining a genetic model of negative affect, the Wistar Kyoto (WKY) rat, and intra-articular injection of monosodium iodoacetate (MIA; 1mg), our model of high anxiety and augmented OA-like pain behaviour mirrors the clinical problem. Effects of morphine (0.5-6mg.kg-1) on pain behaviour and spinal nociceptive neuronal activity were determined in WKY rats, and normo-anxiety Wistar rats, 3 weeks after MIA injection. WKY rats developed augmented OA-like pain, and had blunted inhibitory responses to morphine, when compared to Wistar rats. Potential alterations in endogenous opioid function were probed via systemic blockade of opioid receptors with naloxone (0.1-1mg.kg-1), quantification of circulating levels of {beta}-endorphin, and determination of spinal expression of the mu-opioid receptor (MOR). These studies revealed increased opioidergic tone, and increased spinal desensitization of MORs via the master phosphorylation site at serine residue 375, in this model. We demonstrate attenuated MOR function in the absence of previous exogenous opioid ligand exposure in our model of high anxiety and OA-like pain, which may account for reduced analgesic effect of morphine and provide a potential explanation for increased opioid analgesic intake in high anxiety chronic pain patients. Significance StatementChronic pain affects large numbers of people, and pain management often relies on poorly effective opioid analgesics, the iatrogenic effects of which are increasingly recognised. The endogenous opioid system - the target for exogenous opioid analgesics - plays key roles in emotional affective states and pain control, but the complex interplay between anxiety, chronic pain, and endogenous opioid system function is challenging to study in people. Here, we have addressed this using a clinically-relevant experimental model. Anxiety-like behaviour was associated with increased chronic arthritis-like pain behaviour, altered opioid receptor function, and reduced efficacy of opioid analgesics. We provide new evidence, which may explain why chronic pain patients with comorbid high anxiety have higher opioid analgesic use.

neuroscience↗

bioRxiv2019

Anthropogenic impact on lake bacterial communities across Eastern Canada

Lakes play a pivotal role in ecological and biogeochemical processes and have been described as sentinels of environmental change. Assessing lake health across large geographic scales is critical to predict the stability of their ecosystem services and their vulnerability to anthropogenic disturbances. The LakePulse research network is tasked with the assessment of lake health across gradients of land use on a continental scale. Bacterial communities are an integral and rapidly responding component of lake ecosystems, yet large-scale responses to anthropogenic activity remain elusive. Here, we assess the ecological impact of land use on bacterial communities from 220 lakes covering more than 660 000 km2 across Eastern Canada. Alteration of communities was found on every level examined including richness, community composition, community network structure and indicator taxa of high or low lake water quality. Specifically, increasing anthropogenic impact within the watershed lowered richness mediated by changes in salinity. Likewise, community composition was significantly correlated with agriculture and urban development within a watershed. Interaction networks showed decreasing complexity and fewer keystone taxa in impacted lakes. Together, these findings point to vast bacterial community changes of largely unknown consequences induced by human activity within lake watersheds. Significance StatementLakes play central roles in Earths ecosystems and are sentinels of climate change and other watershed alterations. Assessing lake health across large geographic scales is therefore critical to predict ecosystem stability and lake vulnerability to anthropogenic disturbances. In this context, the LakePulse research network is tasked with a large-scale assessment of lake health across Canada. Bacterial communities are an integral and rapidly responding component of lake ecosystems, yet their large-scale responses to anthropogenic activity remain unknown. Here, we assessed the anthropogenic impact on bacterial communities of over 200 lakes located across large environmental gradients. We found communities to be impacted on every level investigated, indicating that human activities within watersheds cause vast bacterial community changes of largely unknown consequences.

ecology↗

bioRxiv2019

Neurophysiological alterations in the nucleus reuniens of a mouse model of Alzheimer’s disease

Transgenic mice that overproduce beta-amyloid (A{beta}) peptides exhibit neurophysiological alterations at the cellular, synaptic and network levels. Recently, increased neuronal activity in nucleus reuniens (Re), has been linked to hyperexcitability within hippocampal-thalamo-cortical networks in the J20 mouse model of amyloidopathy. Here in vitro whole-cell patch clamp recordings were used to compare old pathology-bearing J20 mice and wild-type controls to examine whether alterations to the intrinsic electrophysiological properties of Re neurons could contribute to the amyloidopathy-associated Re hyperactivity. A greater proportion of Re neurons displayed a hyperpolarised membrane potential in J20 mice without changes to the incidence or frequency of spontaneous action potential (AP) generation. Passive membrane properties were independent of transgene expression. Re neurons recorded from J20 mice did not exhibit increased AP generation in response to depolarising current stimuli but did exhibit an increased propensity to rebound burst following hyperpolarising current stimuli. This increase in rebound firing does not appear to result from alterations to T-type calcium channels. Finally, in J20 mice there was an [~]8% reduction in spike width, similar to what we and others have reported in CA1 pyramidal neurons from multiple amyloidopathy mice. We conclude that alterations to the intrinsic properties of Re neurons may contribute to the hyperexcitability observed in hippocampal-thalmo-cortical circuits under pathological A{beta} load.\n\nKey PointsO_LIAlterations in the neurophysiology of hippocampal and cortical neurons has been linked to network hyperexcitability in mouse models of amyloidopathy.\nC_LIO_LIThe nucleus reuniens (Re) is part of a cognitive network involving the hippocampal formation and prefrontal cortex. Increased cellular activity in Re has been linked to the generation of hippocampal-thalamo-cortical seizure activity in J20 mice.\nC_LIO_LIRe neurons display hyperpolarised resting membrane potentials in J20 mice. Passive membrane properties are unaffected by transgene expression. Re neurons recorded from J20 mice did not exhibit increased excitability in response to depolarising current stimuli but did exhibit an increased propensity to rebound burst following hyperpolarising current stimuli. This increased rebound firing was not a result of changes in T-type Ca2+ conductances. Finally we observed a decrease in AP width.\nC_LIO_LIThese results help us understand how altered Re cellular neurophysiology may contribute to hippocampal-thalamo-cortical hyperexcitability in J20 mice.\nC_LI

neuroscience↗