Biology subjects

Zepernick, B. N.

Publications and source records attributed to Zepernick, B. N..

5 recordsLinked to original sources

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

Metatranscriptomics reveals declines in ice cover influence winter viral community activity

Freshwater lakes are sentinels of environmental change, and climate change-driven declines in ice cover have been shown to disrupt aquatic communities and jeopardize ecosystem services. Viruses shape microbial communities and regulate biogeochemical cycles by acting as top-down controls, yet there is relatively little known about how declining ice cover will influence viral community activity. Lake Erie is a critical freshwater ecosystem and serves as a model system to assess how ice cover extent will affect winter limnology. We surveyed size selected surface water metatranscriptomes for conserved viral hallmark genes as a proxy for active virus populations and compared activity profiles between ice-covered and ice-free conditions from two contrasting winters. Active virus communities were present in both conditions, spanning diverse phylogenetic clades of bacteriophage (Caudovirales), giant viruses (Nucleocytoviricota), and RNA viruses (Orthornavirae). However, viral activity was significantly shaped by the extent of ice cover. Notably, viral richness and relative transcript abundance in the surface waters were reduced under ice relative to the ice-free conditions. Correlations with microbial community metrics suggest the differences in viral communities are at least in part driven by the decreased winter diatom bloom associated with declines in ice cover. Overall, our data suggest viral community activity is influenced by ice cover extent, and viruses may serve as sentinels of environmental disturbance and ecosystem response(s) to climate change. IMPORTANCEAs ice cover is projected to become increasingly rare on large temperate lakes, there is a need to understand how microbial communities during winter months might respond to these changing ice-cover conditions. Despite the documented controls viruses have on microbial communities, little is known regarding the relationship between virus activity and ice cover extent. By using metatranscriptomics to investigate virus communities, we show that viral community activity is sensitive to ice cover extent, likely due in part to ice cover-driven shifts in host community structure. This work serves to build our understanding of how viral communities will function in a future, potentially ice-free, climate.

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↗

bioRxiv2019

Flaming as part of aseptic technique increases CO2(g) and decreases pH in freshwater culture media

Aseptic technique has historically served as a fundamental practice in microbiology, helping maintain culture purity and integrity. This technique has been widely encouraged and employed for use with cultures of heterotrophic bacteria as well as freshwater and marine algae. Yet, recent observations have suggested these approaches may bring their own influences. We observed variations in growth amongst replicate experimental cyanobacterial cultures upon flaming of the culture tube opening during sample transfer and collection. Investigation revealed the pH of culture media had decreased from the initial pH established during media preparation. Flaming of sterile culture media alone confirmed a significant decrease, by as much as 1.7 pH units, and correlated with increased flaming events over time. We hypothesized that the causative factor was the introduction of carbon dioxide into the media. To test this hypothesis, qualitative and quantitative analyses were used to identify the primary driver of pH decline. We further assessed the direct effects of flaming and subsequent pH changes on Microcystis aeruginosa cultures, showing flame-driven pH changes and/or the introduction of carbon dioxide influenced experimental results. Our observations provide a cautionary tale of how classic and well-accepted approaches may not always provide the results promised, suggesting new approaches may be necessary in research areas assessing pH or carbon related-effects on microbial communities.

microbiology↗