Biology subjects

Cameron, E. S.

Publications and source records attributed to Cameron, E. S..

9 recordsLinked to original sources

bioRxiv2026

Transposable Element Diversification and the Evolution of Peltigerales Lichen Symbionts

Lichens are composite organisms formed through the symbiotic association between fungi, algae and/or bacteria. Multiple independent origins of the lichenized lifestyle have been reported in both fungal and algal lineages, but the molecular mechanisms and evolution underpinning these symbiotic relationships remain largely unknown. In this study, we performed long-read metagenomic sequencing on 11 Peltigerales lichen species to characterize the genomic content of lichen symbionts via metagenome assembled genomes (MAGs). Peltigerales genomes generated in this work represent the largest Lecanoromycetes genome sequenced to date, driven by high transposable element content. Transposable elements (TEs) are known to drive genome evolution in other symbioses but have been underexplored in lichen symbionts due technological limitations. Transcriptomics revealed that many genes associated with adaptations to the lichenized lifestyle are associated with TEs suggesting that they may play a key role in the evolution of lichenization.

genomics↗

bioRxiv2025

Tangerine: a Starship-like element in the genomes of Xanthoria lichen-forming fungi

Lichens are symbiotic associations between filamentous fungi and photosynthetic micro-organisms, such as green algae and/or cyanobacteria, that result in a single anatomically-complex structure that can thrive in environments inhospitable to most organisms, including arctic tundra, high mountains, and deserts. Recent evidence suggests that lichens may be even more complex than previously appreciated, containing multiple microbial constituents, but how genomes of the principal fungal symbiont (which provides the majority of biomass in lichen tissue) have been shaped during evolution is largely unexplored. Recently, giant transposable elements called Starships have been found in many genomes of filamentous fungi, but to which extent they occur in lichen-forming fungi is not known. In this report, we describe a Starship element from the lichen fungus Xanthoria parietina. This element, named Tangerine, contains several genes that have signatures of horizontal gene transfer from non-lichen-forming fungi, most likely from black yeasts of the Chaetothyriales, that are often lichen-associated. Repetitive sequences carried by Tangerine, and found in other sites in Xanthoria genomes, are affected by repeat-induced point mutation (RIP), a mechanism of genome defense against transposable elements, consistent with fungal sexual reproduction which always precedes new lichen formation by Xanthoria. Tangerines "captain" belongs to a newly defined family of tyrosine recombinases specific to lichen-forming Lecanoromycetes. Several other captain clades have signatures of horizontal gene transfer between distantly related lichen-forming fungi and non-mycobiont lichen-associated fungi. We speculate that Starships may play a significant, yet hitherto unrecognized role, in lichen genome evolution and provide a roadmap for further investigation.

genomics↗

bioRxiv2024

Specialization in Molecular Functions and Secondary Metabolite Production Potential in Cyanobacterial Symbionts

Cyanobacteria are globally occurring photosynthetic bacteria notable for their contribution to primary production and their production of toxins which have detrimental impacts on ecosystems. Beyond this, cyanobacteria can form mutualistic symbiotic relationships with a diverse set of eukaryotes, ranging from land plants to fungi. Nevertheless, not all cyanobacteria are found in symbiotic associations suggesting symbiotic cyanobacteria have evolved specializations that facilitate host-interactions. Photosynthetic capabilities, nitrogen fixation, and the production of complex biochemicals are key functions provided by host-associated cyanobacterial symbionts. To explore if additional specializations are associated with such lifestyles in cyanobacteria, we have conducted comparative phylogenomics of molecular functions and of biosynthetic gene clusters (BGCs) in 977 cyanobacterial genomes. Cyanobacteria with host-associated and symbiotic lifestyles were concentrated in the family Nostocaceae, where eight monophyletic clades correspond to specific host taxa. In agreement with previous studies, symbionts are likely to provide fixed nitrogen to their eukaryotic partners. Additionally, our analyses identified chitin metabolising pathways in cyanobacteria associated with specific host groups, while obligate symbionts had fewer BGCs. The conservation of molecular functions and BGCs between closely related symbiotic and free-living cyanobacteria suggests that there is the potential for additional cyanobacteria to form symbiotic relationships than is currently known.

genomics↗

bioRxiv2023

Evidence for a core set of microbial lichen symbionts from a global survey of metagenomes

Lichens are the archetypal symbiosis and the one for which the term was coined. Although application of shotgun sequencing techniques has shown that many lichen symbioses can harbour more symbionts than the canonically recognized fungus and photobiont, no global census of lichen organismal composition has been undertaken. Here, we analyze the genome content of 437 lichen metagenomes from six continents, and show that four bacterial lineages occur in the majority of lichen symbioses, at a frequency on par with algal photobionts. A single bacterial genus, Lichenihabitans, occurs in nearly one-third of all lichens sampled. Genome annotations from the most common lichen bacterial symbionts suggest they are aerobic anoxygenic photoheterotrophs and produce essential vitamins, but do not fix nitrogen. We also detected secondary basidiomycete symbionts in about two-thirds of analyzed metagenomes. Our survey suggests a core set of four to seven microbial symbionts are involved in forming and maintaining lichen symbioses.

microbiology↗

bioRxiv2022

plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets

The use of culture independent molecular methods, often referred to as metagenomics, have revolutionized the ability to explore and characterize microbial communities from diverse environmental sources. Most metagenomic workflows have been developed for identification of prokaryotic and eukaryotic community constituents, but tools for identification of plastid genomes are lacking. The endosymbiotic origin of plastids also poses challenges where plastid metagenomic assembled genomes (MAGs) may be misidentified as low-quality bacterial MAGs. Current tools are limited to classification of contigs as plastid and do not provide further assessment or characterization of plastid MAGs. plastiC is a workflow that allows users to identify plastid genomes in metagenome assemblies, assess completeness, and predict taxonomic association from diverse environmental sources. plastiC is a Snakemake workflow available at https://github.com/Finn-Lab/plastiC. We demonstrate the utility of this workflow with the successful recover of algal plastid MAGs from publicly available lichen metagenomes.

bioinformatics↗

bioRxiv2022

Early Seasonal Increases and Persistence in Relative Abundance of Potentially Toxic Cyanobacteria: Concerning Impacts of Extended Ice-Free Periods in Northern Temperate Lakes

Cyanobacteria threaten public and ecosystem health globally through the production of secondary metabolites including potent toxins, and disruption of water treatment processes. Warmer water temperatures and high nutrient availability are key characteristics associated with the occurrence of cyanobacteria. There is typically concern of cyanobacteria blooms (e.g., visible biomass accumulations) occurring in the summer season of eutrophic systems. However, in this study, the proliferation of cyanobacteria in lakes across all seasons and in absence of visual biomass indicators of bloom condition was observed in three oligotrophic lakes of the Turkey Lakes Watershed (TLW) in Ontario, located within a sugar maple dominated forest on the Canadian Shield. Almost 40 years of ice phenology data showed that rising temperatures have led to significantly longer ice-free periods and aquatic growing seasons in TLW. Warming is especially evident in the autumn, with the onset of ice-on periods commencing significantly later in the year. Cyanobacterial communities in three interconnected temperate, oligotrophic lakes were characterized over an 18-month period from July 2018 to January 2020 (across 10 synoptic sampling events) using amplicon sequencing of the V4 region of the 16S rRNA gene. During the winter, there was low abundance or occasional absence of cyanobacteria; however, a non-photosynthetic basal lineage of cyanobacteria (Melainabacteria) was present during periods of ice cover. Notably, photosynthetic populations reappeared in the water column immediately following the loss of ice-cover--they were especially abundant in lakes with surficial geology and lake morphometry that favor greater availability of fine sediment and associated nutrients. Thus, this collective analysis demonstrates that the convergence of key abiotic and biotic factors--climate forcing of hydrological and biogeochemical processes, and intrinsic landscape features--enable increases in the relative abundance of potentially toxic cyanobacteria within the temperate forest biome of Canada over increasingly longer periods of time.

ecology↗

bioRxiv2022

Characterization of Cyanobacterial Communities in Lakes Requires Consideration of Diurnal and Spatial Variation

Continental-scale increases in aquatic system eutrophication are linked with increased cyanobacteria threats to recreational water use and drinking water resources globally. Increasing evidence suggests that diurnal vertical migration of cyanobacteria are key factors that must be considered in cyanobacterial bloom risk management. While this has been discussed in marine and eutrophic freshwater contexts, reports of diurnal vertical migration of cyanobacteria in oligotrophic freshwater lakes are scant. Typical monitoring protocols do not reflect these dynamics and frequently focus only on surface water sampling approaches, and either ignore sampling time or recommend large midday timeframes (e.g., 10AM-3PM), thereby preventing accurate characterization of cyanobacterial community dynamics. To evaluate the impact of diurnal migrations and water column stratification on cyanobacterial abundance and composition, communities were characterized in a shallow well-mixed lake interconnected to a thermally stratified lake in the Turkey Lakes Watershed (Ontario, Canada) using amplicon sequencing of the 16S rRNA gene across a multi-time point sampling series in 2018 and 2022. This work showed that cyanobacteria are present in oligotrophic lakes and their community structure varies (i) diurnally, (ii) across the depth of the water column, (iii) interannually within the same lake and (iv) between different lakes that are closely interconnected within the same watershed. It underscored the need for integrating multi-timepoint, multi-depth discrete sampling guidance into lake and reservoir monitoring programs to describe cyanobacteria community dynamics and signal change to inform risk management associated with the potential for cyanotoxin production. Ignoring variability in cyanobacterial community dynamics (such as that reported herein) and reducing sample numbers can lead to a false sense of security and missed opportunities to identify and mitigate changes in trophic status and associated risks such as toxin or taste and odor production, especially in sensitive, oligotrophic systems. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/478008v2_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@14ea7aorg.highwire.dtl.DTLVardef@12e0217org.highwire.dtl.DTLVardef@18b61beorg.highwire.dtl.DTLVardef@1be2fe6_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights{blacksquare} Cyanobacterial populations fluctuate sporadically across diurnal cycles {blacksquare}Cyanobacterial communities can vary significantly between interconnected lakes {blacksquare}Significant annual shifts in communities signal higher risk and need for monitoring {blacksquare}Cyanobacteria monitoring for risk management should incorporate time and depth

ecology↗

bioRxiv2021

Ensuring that fundamentals of quantitative microbiology are reflected in microbial diversity analyses based on next-generation sequencing

Diversity analysis of amplicon sequencing data is mainly limited to plug-in estimates calculated using normalized data to obtain a single value of an alpha diversity metric or a single point on a beta diversity ordination plot for each sample. As recognized for count data generated using classical microbiological methods, read counts obtained from a sample are random data linked to source properties by a probabilistic process. Thus, diversity analysis has focused on diversity of (normalized) samples rather than probabilistic inference about source diversity. This study applies fundamentals of statistical analysis for quantitative microbiology (e.g., microscopy, plating, most probable number methods) to sample collection and processing procedures of amplicon sequencing methods to facilitate inference reflecting the probabilistic nature of such data and evaluation of uncertainty in diversity metrics. Types of random error are described and clustering of microorganisms in the source, differential analytical recovery during sample processing, and amplification are found to invalidate a multinomial relative abundance model. The zeros often abounding in amplicon sequencing data and their implications are addressed, and Bayesian analysis is applied to estimate the source Shannon index given unnormalized data (both simulated and real). Inference about source diversity is found to require knowledge of the exact number of unique variants in the source, which is practically unknowable due to library size limitations and the inability to differentiate zeros corresponding to variants that are actually absent in the source from zeros corresponding to variants that were merely not detected. Given these problems with estimation of diversity in the source even when the basic multinomial model is valid, sample-level diversity analysis approaches are discussed. HighlightsO_LIRandom error in amplicon sequencing method should be considered in diversity analysis C_LIO_LIClustering, amplification, and differential recovery distort sample diversity C_LIO_LIThe multinomial model for compositional count data is compromised by amplification C_LIO_LIThere are three types of zeros in amplicon sequencing data, including missing zeros C_LIO_LISource alpha diversity estimates are biased by unknown number of unique variants C_LI

bioinformatics↗

bioRxiv2020

To rarefy or not to rarefy: Enhancing microbial community analysis through next-generation sequencing

Amplicon sequencing has revolutionized our ability to study DNA collected from environmental samples by providing a rapid and sensitive technique for microbial community analysis that eliminates the challenges associated with lab cultivation and taxonomic identification through microscopy. In water resources management, it can be especially useful to evaluate ecosystem shifts in response to natural and anthropogenic landscape disturbances to signal potential water quality concerns, such as the detection of toxic cyanobacteria or pathogenic bacteria. Amplicon sequencing data consist of discrete counts of sequence reads, the sum of which is the library size. Groups of samples typically have different library sizes that are not representative of biological variation; library size normalization is required to meaningfully compare diversity between them. Rarefaction is a widely used normalization technique that involves the random subsampling of sequences from the initial sample library to a selected normalized library size. Rarefying is often dismissed as statistically invalid because subsampling effectively discards a portion of the observed sequences. Nonetheless, it remains prevalent in practice. Notably, the superiority of rarefying relative to many other normalization approaches has been argued in diversity analysis. Here, repeated rarefying is proposed as a tool for diversity analyses to normalize library sizes. This enables (i) proportionate representation of all observed sequences and (ii) characterization of the random variation introduced to diversity analyses by rarefying to a smaller library size shared by all samples. While many deterministic data transformations are not tailored to produce equal library sizes, repeatedly rarefying reflects the probabilistic process by which amplicon sequencing data are obtained as a representation of the source microbial community. Specifically, it evaluates which data might have been obtained if a particular samples library size had been smaller and allows graphical representation of the effects of this library size normalization process upon diversity analysis results.

bioinformatics↗