Draft Genome Sequence of the Freshwater Diatom Fragilaria crotonensis SAG 28.96

Zepernick, Brittany N.; Truchon, Alexander R.; Gann, Eric R.; Wilhelm, Steven W.

doi:10.1128/mra.00289-22

Cited by 5 publications

(3 citation statements)

References 30 publications

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“…Further analysis revealed 33% of the polar centric DE genes were annotated as Chaetoceros -like ( Supplemental Figure 13B ), despite Chaetoceros -like genes forming \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $\le$\end{document} 10% of mapped reads throughout the winter libraries ( Supplemental Figure 7 ). Here, the “ Chaetoceros -like” label arises because the transcriptomes were annotated with largely marine-comprised databases due to a lack of comprehensive freshwater taxonomic sequencing [ 9 , 63 ]. Hence, diatom classes are reported in the text and genera are reported in the Supplemental Figures and Supplemental Table 1 .…”

Section: Resultsmentioning

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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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: Resultsmentioning

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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“…BBMap.sh 10.3389/fmicb.2022.1044464 (default settings) was used to remove residual rRNA reads and BBMap.repair (default settings) was used to validate pairedend reads (Bushnell, 2014). Sorted reads were mapped to the annotated F. crotonensis reference genome (Zepernick et al, 2022b) in CLC (default settings: length fraction: 0.5, similarity fraction 0.8) (Supplementary Data Sheet 1a), and normalized to transcripts per million (TPM). To calculate similarity (Bray-Curtis) and identify contributors to gene-expression differences between samples, non-metric multi-dimensional scaling (nMDS) and Similarity Percentage (SIMPER) analyses were performed on normalized expression values (TPM) using PRIMER (v.7) (Clarke and Gorley, 2015).…”

Section: Ph Effects On Fragilaria Crotonensis Transcriptionmentioning

confidence: 99%

“…Data are available under BioProject accession number: PRJNA807324 and BioSample accession number: SAMN25978007. Further information concerning the genome may be accessed in Zepernick et al (2022b). The transcriptome raw reads that were mapped to the F. crotonensis genome were deposited in the NCBI sequence read archive under BioProject accession number: PRJNA866361.…”

Section: Data Availability Statementmentioning

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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Declines in ice cover induce light limitation in freshwater diatoms

Zepernick

Chase

Denison

et al. 2023

Preprint

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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.

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Draft Genome Sequence of the Freshwater Diatom Fragilaria crotonensis SAG 28.96

Abstract: Here, we report the assembled and annotated genome of the freshwater diatom Fragilaria crotonensis SAG 28.96. The 61.85-Mb nuclear genome was assembled into 879 contigs, has a GC content of 47.40%, contains 26,015 predicted genes, and shows completeness of 81%.

Cited by 5 publications

References 30 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

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

Declines in ice cover induce light limitation in freshwater diatoms

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