Metatranscriptomic Sequencing of Winter and Spring Planktonic Communities from Lake Erie, a Laurentian Great Lake

Zepernick, Brittany N.; Denison, Elizabeth R; Chaffin, Justin D.; Bullerjahn, George S.; Pennacchio, Christa; Frenken, Thijs; Peck, Daniel H.; Anderson, James T.; Niles, Derek; Zastepa, Arthur; McKay, R. Michael L.; Wilhelm, Steven W.; Rokas, ed.

doi:10.1128/mra.00351-22

Cited by 5 publications

(9 citation statements)

References 9 publications

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“…Samples of opportunity ( n = 77) from the Lake Erie planktonic community were collected across temporal, spatial, and climatic gradients throughout the winter of 2019 and 2020 [ 36 , 37 ]. This large-scale collaborative effort included multiple surveys conducted by the US Coast Guard Cutter Neah Bay , Canadian Coast Guard Ship Limnos and merchant vessel Orange Apex , resulting in a large metatranscriptomic dataset [ 36 ]. Prior to sample collection, water column physiochemical parameters were recorded along with meteorological conditions and ice cover observations.…”

Section: Methodsmentioning

confidence: 99%

“…We employed in situ analyses and metatranscriptomics to explore the hypothesis that winter diatoms are light limited in the ice-free water column. Facilitated by collaborative efforts with the US and Canadian Coast Guards [ 35 ], opportunistic samples were collected throughout 2019 and 2020, yielding samples collected from both ice-covered (2019) and ice-free (2020) water columns [ 36 ]. The survey also included spring samples, which we include for additional comparison.…”

Section: Introductionmentioning

confidence: 99%

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Declines in ice cover are accompanied by light limitation responses and community change in freshwater diatoms

Zepernick,

Chase,

Denison

et al. 2024

The ISME Journal

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The rediscovery of diatom blooms embedded within and beneath Lake Erie ice cover (2007-2012) ignited 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. Our results suggest ice-free conditions decreased planktonic 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). We identified two gene families which serve to increase diatom fitness in the turbid ice-free water column: proton-pumping rhodopsins (PPRs; a potential 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.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Declines in ice cover are accompanied by light limitation responses and community change in freshwater diatoms

Zepernick,

Chase,

Denison

et al. 2024

The ISME Journal

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“…Samples intended for RNA extraction were passed through 0.22-µm nominal pore-size filters, flash-frozen, and stored at -80 °C until further processing. Details regarding RNA extraction and sequence processing can be found in an associated Microbiology Resource Announcement (47). Sample metadata can be accessed through the Biological and Chemical Oceanography Data Management Office (BCO-DMO) under dataset number 809945 (48).…”

Section: Methodsmentioning

confidence: 99%

“…Opportunistic surface water samples were collected by USCGC Neah Bay between February and March of two consecutive years (2019 and 2020) (47). The winter of 2019 was considered a high-ice year (95% mean maximum ice cover) while the winter of 2020 was largely ice-free (15% mean maximum ice cover) (46).…”

Section: Methodsmentioning

confidence: 99%

Metatranscriptomics reveals declines in ice cover influence winter viral community activity

Denison,

Zepernick,

McKay

et al. 2024

Preprint

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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.

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“…Residual DNA in samples was digested using a modified version of the Turbo DNase protocol and the Turbo DNA-free kit (Ambion, Austin, TX, USA). Removal of genomic DNA was confirmed via the absence of an amplicon band in an agarose gel after 30 cycles of PCR amplification using 519F/785R 16s rRNA primers as reported previously (Zepernick et al, 2022a). Final RNA concentrations were determined using the HS Qubit RNA assay (Invitrogen, Wltham, MA, USA).…”

Section: Ph Effects On Fragilaria Crotonensis Transcriptionmentioning

confidence: 99%

Morphological, physiological, and transcriptional responses of the freshwater diatom Fragilaria crotonensis to elevated pH conditions

Zepernick

Stark

et al. 2022

Front. Microbiol.

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Harmful algal blooms (HABs) caused by the toxin-producing cyanobacteria Microcystis spp., can increase water column pH. While the effect(s) of these basified conditions on the bloom formers are a high research priority, how these pH shifts affect other biota remains understudied. Recently, it was shown these high pH levels decrease growth and Si deposition rates in the freshwater diatom Fragilaria crotonensis and natural Lake Erie (Canada-US) diatom populations. However, the physiological mechanisms and transcriptional responses of diatoms associated with these observations remain to be documented. Here, we examined F. crotonensis with a set of morphological, physiological, and transcriptomic tools to identify cellular responses to high pH. We suggest 2 potential mechanisms that may contribute to morphological and physiological pH effects observed in F. crotonensis. Moreover, we identified a significant upregulation of mobile genetic elements in the F. crotonensis genome which appear to be an extreme transcriptional response to this abiotic stress to enhance cellular evolution rates–a process we have termed “genomic roulette.” We discuss the ecological and biogeochemical effects high pH conditions impose on fresh waters and suggest a means by which freshwater diatoms such as F. crotonensis may evade high pH stress to survive in a “basified” future.

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Metatranscriptomic Sequencing of Winter and Spring Planktonic Communities from Lake Erie, a Laurentian Great Lake

Cited by 5 publications

References 9 publications

Declines in ice cover are accompanied by light limitation responses and community change in freshwater diatoms

Declines in ice cover are accompanied by light limitation responses and community change in freshwater diatoms

Metatranscriptomics reveals declines in ice cover influence winter viral community activity

Morphological, physiological, and transcriptional responses of the freshwater diatom Fragilaria crotonensis to elevated pH conditions

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