Biology subjects

Chase, E. E.

Publications and source records attributed to Chase, E. E..

7 recordsLinked to original sources

bioRxiv2026

Three catalase-peroxidases promote extended stationary phase survival of Vibrio natriegens during ecologically relevant exposures to exogenous hydrogen peroxide

Vibrio natriegens is an emerging model organism in laboratory and biotechnology research that is known for its fast growth rate and diverse metabolic capabilities. However, little is known about its response to oxidative stress. Reactive oxygen species (ROS) are ubiquitous stressors for most aerobic life and without mitigation can lead to cellular damage and sometimes death. V. natriegens is unusual amongst the Vibrio genus and Proteobacterial phylum in having three copies of katG encoding the bifunctional ROS defense enzyme catalase-peroxidase. The biological significance of having three copies of this protective gene was investigated with phylogenetics and gene inactivation studies. We determined that two of the katG copies arose recently via duplication and subsequent divergence. Analysis of single, double, and triple {Delta}katG constructs revealed each katG gene product contributes to survival during exposure to ecologically relevant concentrations of exogenous hydrogen peroxide (HOOH) under stationary phase conditions but found the genes were dispensable for HOOH resistance during exponential growth. We also demonstrated the involvement of the RpoS regulon in V. natriegens oxidative stress response in stationary phase. As an outcome of this investigation, we identified and repaired several spontaneous loss-of-function mutations of rpoS in laboratory cultures of the V. natriegens type strain ATCC 14048. Together, these results provide physiological and evolutionary insights into V. natriegens ROS response.

microbiology↗

bioRxiv2025

The ornithine-arginine cycle supported a toxic, metalimnic Planktothrix rubescens bloom

Planktothrix rubescens is distinct from other cyanobacterial harmful algal bloom (cHAB) genera: the crimson-red cHAB thrives in the cold, low-light, nutrient-limited metalimnion. Studies have attributed this ecological success to buoyancy regulation, low-light adaptations, and the uptake of nitrogen-rich amino acids. Yet, it remains to be mechanistically determined how this cHAB maintains physiological nutrient quotas in the metalimnion due to limited in situ molecular studies. We employed metagenomics and metabolomics to investigate a toxigenic P. rubescens bloom in Meads Quarry (Knoxville, TN, USA) observed in two separate years. Our results suggest a perennial, metalimnic P. rubescens population may exist, with spring turnover facilitating seasonal migration to the epilimnion. Although P. rubescens dominated the epilimnion and metalimnion, intracellular metabolite pools grouped by depth and suggested depth-discrete partitioning of the arginine deiminase-mediated ornithine-arginine cycle (OAC, i.e., urea cycle). While the arginine influx driving the OAC is unclear, we hypothesize this input is provided via the uptake of urea or nitrogen-rich amino acids. Further, we demonstrate arginine deiminase (argE) is broadly distributed in Planktothrix genera and known microcystin producers, suggesting argE-mediated arginine recycling via the OAC may influence the fitness of toxigenic cHAB genera which require ample nitrogen to synthesize microcystins. Cumulatively, our results serve as a case study to provide insight on the metabolic pathways driving the ecological success of metalimnic P. rubescens blooms. On a broader scale, this work strengthens the case that alternative nitrogen metabolism - including urea utilization, amino acid uptake, and the OAC - is a driver of toxigenic cyanobacterial blooms in fresh waters.

bioinformatics↗

bioRxiv2025

Lysogen formation governs colonies while lytic infection is more prevalent in single cells of the bloom-forming cyanobacterium, Microcystis

While the bloom-forming cyanobacterium Microcystis can exist as free-living single cells or within dense mucilaginous colonies, the drivers and consequences of colony formation remain unclear. Here, we integrated metatranscriptomic datasets from two Microcystis bloom events in Lake Taihu, China, to analyze and validate the functional differences between colonial and single-cell Microcystis. Our results confirmed colony expression profiles were disproportionately enriched in Microcystis transcripts (and functions) compared to other prokaryotic taxa. Concomitantly, viral infection strategies diverged by Microcystis community morphology: colony-associated cells expressed lysogeny-associated genes, while single cells exhibited increased signatures of lytic infection. These data are consistent with the hypothesis that Microcystis colonies foster conditions favorable to lysogen formation--likely due to local high cell densities and the resulting advantage of superinfection immunity--whereas solitary cells experience stronger lytic pressure. On a broader scale, our findings refine the understanding of bloom dynamics by identifying how community morphological states coincide with distinct host-virus interactions. Cumulatively, this work underscores the importance of colony formation in shaping Microcystis ecology and highlights the need for mechanistic studies that disentangle the interplay between phage infection modes, colony formation, and microbial community structure.

microbiology↗

bioRxiv2024

Time of day of infection shapes development of a eukaryotic algal-Nucleocytoviricota virocell

Aureococcus anophagefferens represents one component of a model host-virus system (with the "giant virus" Kratosvirus quantuckense). Studies to define its ribocell (uninfected cells) and virocell (virus-infected cells) forms are needed, as both are abundant during algal blooms. A linkage between light-derived energy, virus particle production and virocell formation has been noted. We explored how the time of day (morning, afternoon, late day) of virus-host contact shaped virocell ontogeny. In parallel, we explored the need for light derived energy in this mixotrophic plankter by inhibiting photosystem II (PSII). Using flow cytometry and photochemical assessments, we examined the physiology of infected cells and controls, and estimated virus particle production by virocells. We observed distinct differences between ribocell and virocell response to treatments, including reductions in virus particle production during reduced light (i.e., duration) and PSII inhibition. Collectively this work demonstrates the importance of light in shaping the fate of infected cells and provides insight into the factors that constrain in situ blooms. Most significantly, we show that time of day when a virus and host come into contact influences viral particle production, and therefore bloom dynamics; a factor that needs to be considered in future bloom modeling work.

microbiology↗

bioRxiv2024

The diel disconnect between cell growth and division in Aureococcus is interrupted by giant virus infection

Viruses of eukaryotic algae have become an important topic due to their roles in nutrient cycling and top-down control of algal blooms. Omics-based studies have identified a boon of genomic and transcriptional potential among the Nucleocytoviricota, a phylum of large dsDNA viruses which have been shown to infect algal and non-algal eukaryotes. However, little is still understood regarding the infection cycle of these viruses, particularly in how they take over a metabolically active host and convert it into a virocell state. Of particular interest are the roles light and the diel cycle in virocell development. Yet despite such a large proportion of Nucleocytoviricota infecting phototrophs, little work has been done to tie infection dynamics to the presence, and absence, of light. Here, we examine the role of the diel cycle on the physiological and transcriptional state of the pelagophyte Aureococcus anophagefferens while undergoing infection by Kratosvirus quantuckense. Our observations demonstrate how infection by the virus interrupts the diel growth and division of this cell line, and that infection further complicates the system by enhancing export of cell biomass.

microbiology↗

bioRxiv2023

Declines in ice cover induce light limitation in freshwater diatoms

The rediscovery of diatom blooms embedded within and beneath Lake Erie ice cover (2007-2012) ignited an intense interest in psychrophilic adaptations and winter limnology. Subsequent studies determined ice plays a vital role in winter diatom ecophysiology, as diatoms partition to the underside of ice thereby fixing their location within the photic zone. Yet, climate change has led to widespread ice decline across the Great Lakes, with Lake Erie presenting a nearly ice-free state in several recent winters. It has been hypothesized the resultant turbid, isothermal water column will induce light limitation amongst winter diatoms, serving as a detrimental competitive disadvantage. Here, we conducted a physiochemical and metatranscriptomic survey of the winter Lake Erie water column (2019-2020) that spanned spatial, temporal, and climatic gradients to investigate this hypothesis. We determined ice-free conditions decreased diatom bloom magnitude and altered diatom community composition. Diatoms increased the expression of various photosynthetic genes and iron transporters, suggesting they are attempting to increase their quantity of photosystems and light-harvesting components (a well-defined indicator of light limitation). Notably, we identified two gene families which serve to increase diatom fitness in the turbid ice-free water column: proton-pumping rhodopsins (a second means of light-driven energy acquisition) and fasciclins (a means to "raft" together to increase buoyancy and co-locate to the surface to optimize light acquisition). With large-scale climatic changes already underway, our observations provide insight into how diatoms respond to the dynamic ice conditions of today and shed light on how they will fare in a climatically altered tomorrow.

ecology↗

bioRxiv2022

"Quasigenus" among Phycodnaviridae: A diversity of chlorophyte-infecting viruses in response to a dense algal culture in a high-rate algal pond.

This study approaches a high rate algal pond (HRAP) culture by metagenomic sequencing of the viral DNA fraction, this includes the so-called giant virus fraction (phylum Nucleocytoviricota), with the goal of revealing viruses coexisting within an intensified algal culture. A wealth of interesting novel viruses is revealed, including members of Nucleocytoviricota, Lavidaviridae, and polinton-like viruses, which are taxa containing previously characterized algal viruses. Our sequencing results are coupled with a virus targeted qPCR study and 18S rDNA metabarcoding to elucidate potential virus-host interactions. Several species of green algae are identified (Chlorophyta), likely representing the alternating dominant populations during the year of study. Finally, we observe a bloom of viral diversity within the family Phycodnaviridae (Nucleocytoviricota), including highly related but non-identical genotypes, appearing in the HRAP in September and October 2018. This bloom is most likely the cause of a mass mortality event of the cultured algae that occurred during these same months. We hypothesize that these related Phycodnaviridae lineages selectively infect different strains of the same algal species of the Genus Picochlorum that have been identified in the HRAP by metabarcoding and coined this phenomenon a "quasigenus" by analogy to the RNA virus quasispecies concept.

evolutionary biology↗