Biology subjects

Latimer, J.

Publications and source records attributed to Latimer, J..

5 recordsLinked to original sources

bioRxiv2026

Skiaviridae: a large DNA virus family that persistently infects thraustochytrid protists

Genomics and metagenomics have transformed our understanding of the diversity of large DNA viruses infecting eukaryotic microorganisms. Using long-read sequencing, we discovered ubiquitous, co-culturing nucleocytoviruses in several thraustochytrid protists. These viruses are closely related to SmDNAV, an 'orphan' virus of the thraustochytrid Sicyoidochytrium minutum. Transcriptomics, proteomics and electron microscopy demonstrate viral gene expression and particle formation in these cultures without obvious defects in culture growth. We also found SmDNAV-type viruses associated with previously sequenced thraustochytrids. Phylogenetic analysis reveals that the SmDNAV and SmDNAV-like genomes belong to a hitherto unrecognized order of Nucleocytoviricota, here named "Skiavirales". All fifteen identified skiavirus genomes lack numerous viral hallmark genes including DNA-dependent RNA polymerase; all but three also lack DNA polymerase family B (PolB). PolB phylogeny suggests a specific relationship between Skiavirales and the recently discovered mirusviruses, which belong to a different viral realm. Gene exchange between skiaviruses, co-occurring mirusviruses, and host nuclear genomes shows that persistent infection by diverse large DNA viruses provides an opportunity for virus-virus and virus-host co-evolution in thraustochytrids and, perhaps, other microbial eukaryotes.

evolutionary biology↗

bioRxiv2026

Full-length 16S ribosomal RNA gene sequencing reveals dynamics of tick-adapted and environmentally derived bacteria in the microbiome of the black-legged tick, Ixodes scapularis in Nova Scotia, Canada

Lyme disease is a tick-borne illness caused by the spirochaete bacterium Borrelia (Borreliella) burgdorferi. The black-legged tick Ixodes scapularis, which transmits B. burgdorferi and several other human pathogens, is endemic to the eastern United States and, due to climate change, is rapidly expanding into central and eastern Canada. Amplification and sequencing of bacterial DNA from I. scapularis is increasingly used to monitor the presence and abundance of B. burgdorferi and associated bacteria. However, variation in the nature of molecular data collected across studies presents challenges for analysis and interpretation. Here we use full-length Oxford Nanopore 16S ribosomal RNA gene amplicon sequencing to characterize the microbiome of I. scapularis, with an explicit focus on distinguishing between tick-adapted bacteria (endosymbionts and pathogens) and environmentally acquired bacteria (external sources, including soil, vegetation or vertebrate hosts). We show that environmental dominance strength differs between these two ecological classes of bacteria, and that environmental dominance does not appear to represent stochastic background alone; environmentally derived bacterial taxa detected in tick microbiomes are not mere contaminants. Paired soil microbiome profiling from tick collection sites will be required to test whether environmental dominance and associated co-occurrence structure track with seasonal changes in exposure and environmental microbial populations.

microbiology↗

bioRxiv2026

Phylogeny and morphology of novel Labyrinthulomycetes in Nova Scotia, Canada

Labyrinthulomycetes are ubiquitous marine decomposers and include the thraustochytrids, a lineage known for their extensive production of polyunsaturated fatty acids and biotechnology applications. Despite historical taxonomic confusion, environmental surveys have begun to expand the known diversity within labyrinthulomycetes. Here we present 18S ribosomal DNA (rDNA) sequences from 17 novel labyrinthulomycetes strains established as axenic cultures from natural samples taken from three locations in Nova Scotia, Canada. We also present light and transmission electron microscopic analysis for three of these isolates. The combination of phylogenetic and morphological analysis suggests that these isolates belong to three different genera, Thraustochytrium, Ulkenia and Oblongichytrium. Our results expand the known genetic diversity of labyrinthulomycetes in Atlantic Canadian waters, contributing new strains to understudied genera for future comparative genomic investigations, including Ulkenia and Oblongichytrium for which very few genomic resources are available.

evolutionary biology↗

bioRxiv2025

Warming and elevated CO2 cause greater and deeper root growth by shrubs in a boreal bog

1Boreal bogs sequester large stores of terrestrial carbon in waterlogged peat occupied by extensive networks of vascular plant roots. Historically, cold temperatures and shallow water tables in bogs have favored the growth of Sphagnum over vascular plants. Seasonally variable water tables in bogs constrain woody shrub and tree root production to shallow, oxic acrotelm peat horizons while herbs with aerenchymous root tissue can grow below the water table. Warming and elevated CO2 are altering ecosystem functioning in nutrient-limited, rain-fed (ombrotrophic) bogs, via direct impacts on physiology and indirectly via altering water table levels. The environmental changes are shifting interactions between vascular plant fine-roots and the surrounding peat horizons and increasingly favoring vascular plant growth relative to Sphagnum sp. Altered functioning of fine-roots may dramatically affect the role of plants in these ecosystems because of the importance of these organs for plant resource acquisition. We examined how fine-roots across vascular PFTs differentially respond to warming & elevated CO2 manipulations and the consequent water table depression in a forested, boreal bog. We used minirhizotrons (cameras inserted belowground) to measure fine-root production, depth distribution, and standing crop from 2015-2021 for each PFT. We found that daily rates of fine-root production accelerated more for shrubs than for trees or herbs. Shrubs and trees grew their roots more deeply with depressed water table levels and shrub fine-roots became narrower. On an annual basis, fine-root production increased with warming, though these rates varied among PFTs and exhibited interactions with elevated CO2. Standing crop of fine-roots increased with warming temperatures, most strongly for shrubs under elevated CO2, because of these productivity responses. From these results, we expect boreal bogs will become increasingly dominated by shrubs under future warmer temperatures, higher atmospheric CO2 concentrations, and lower water table levels.

ecology↗

bioRxiv2020

Somatic chromosomal number alterations affecting driver genes inform in-vitro and clinical drug response in high-grade serous ovarian cancer

The genomic complexity and heterogeneity of high-grade serous ovarian cancer (HGSOC) has hampered the realisation of successful therapies and effective personalised treatment is an unmet clinical need. Here we show that primary HGSOC spheroid models can be used to predict drug response and use them to demonstrate that somatic copy number alterations (SCNAs) in frequently amplified HGSOC cancer genes significantly correlate with gene expression and drug response. These genes are often located in areas of the genome with frequent clonal SCNAs. MYC chromosomal copy number is associated with ex-vivo and clinical response to paclitaxel and ex-vivo response to mTORC1/2 inhibition. Activation of the mTOR survival pathway in the context to MYC-amplified HGSOC is mostly due to increased prevalence of SCNAs in genes from the PI3K pathway. These results suggest that SCNAs encompassing driver genes could be used to inform therapeutic response in the context of clinical trials testing personalised medicines.

cancer biology↗