Biology subjects

Evans, J. T.

Publications and source records attributed to Evans, J. T..

3 recordsLinked to original sources

bioRxiv2022

The Western Lake Erie Culture Collection: A promising resource for evaluating the physiological and genetic diversity of Microcystis and its associated microbiome

Cyanobacteria harmful algal blooms (cyanoHABs) dominated by Microcystis spp. have significant public health and economic implications in freshwater bodies around the world. These blooms are capable of producing a variety of cyanotoxins, including microcystins, that affect fishing and tourism industries, human and environmental health, and access to drinking water. In this study, we isolated and sequenced the genomes of 21 unialgal Microcystis cultures collected from western Lake Erie between 2017-2019. While some cultures isolated in different years have a high degree of genetic similarity (Average Nucleotide Identity >99%), genomic data shows that these cultures also represent much of the breadth of known Microcystis diversity in natural populations. Only 5 isolates contained all the genes required for microcystin synthesis while 2 isolates contained a previously described partial mcy operon. Microcystin production within cultures was also assessed using Enzyme-Linked Immunosorbent Assay (ELISA) and supported genomic results with high concentrations (up to 900 g L-1) in cultures with complete mcy operons and no or low toxin detected otherwise. These xenic cultures also contained a substantial diversity of bacteria associated with Microcystis, which has become increasingly recognized as an essential component of cyanoHAB community dynamics. These results highlight the genomic diversity among Microcystis strains and associated bacteria in Lake Erie, and their potential impacts on bloom development, toxin production, and toxin degradation. This collection significantly increases the availability of environmentally relevant Microcystis strains from temperate North America, which is changing rapidly due to climate change. HighlightsO_LITwenty one xenic Microcystis cultures were isolated from western Lake Erie and capture the diversity of Microcystis strains observed in natural populations as well as their associated bacteria C_LIO_LIMicrocystis strains show variability in core and accessory gene content, and genetically similar strains produce varying concentrations and congeners of microcystins C_LIO_LIThis collection is a valuable resource for studying strain diversity and interactions between Microcystis and associated bacteria C_LIO_LIOur collection increases the availability of environmentally relevant strains from temperate North America, which is historically underrepresented in culture collections. C_LI

microbiology↗

bioRxiv2022

Long-term population decline of a genetically homogenous continental-wide top Arctic predator

Genetic analysis can provide valuable information for conservation programs by unraveling the demographic trajectory of populations, by estimating effective population size, or by inferring genetic differentiation between populations. Here, we investigated the genetic differentiation within the Snowy Owl (Bubo scandiacus), a species identified as vulnerable by the IUCN, to (i) quantify connectivity among wintering areas, (ii) to evaluate current genetic diversity and effective population size and (iii) to infer changes in the historical effective population size changes from the last millennia to the recent past. The Snowy Owl, a highly mobile top predator, breeds across the Arctic tundra which is a region especially sensitive to current climate change. Using SNP-based analyses on Snowy Owls sampled across the North American nonbreeding range, we found an absence of genetic differentiation among individuals located up to 4,650 km apart. Our results suggest high genetic intermixing and effective dispersal at the continental scale despite documented philopatry to nonbreeding sites in winter. Reconstructing the population demographic indicated that North American Snowy Owls have been steadily declining since the Last Glacial Maximum ca 20,000 years ago and concurrently with global increases in temperature. Conservation programs should now consider North American Snowy Owls as a single, genetically homogenous continental-wide population which is most likely sensitive to the long-term global warming occurring since the Last Glacial Maximum.

ecology↗

bioRxiv2019

To dereplicate or not to dereplicate?

Our ability to reconstruct genomes from metagenomic datasets has rapidly evolved over the past decade, leading to publications presenting 1,000s, and even more than 100,000 metagenome-assembled genomes (MAGs) from 1,000s of samples. While this wealth of genomic data is critical to expand our understanding of microbial diversity, evolution, and ecology, various issues have been observed in some of these datasets that risk obfuscating scientific inquiry. In this perspective we focus on the issue of identical or highly similar genomes assembled from independent datasets. While obtaining multiple genomic representatives for a species is highly valuable, multiple copies of the same or highly similar genomes complicates downstream analysis. We analyzed data from recent studies to show the levels of redundancy within these datasets, the highly variable performance of commonly used dereplication tools, and to point to existing approaches to account and leverage repeated sampling of the same/similar populations.

microbiology↗