Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Coesel, S. N., Durham, B. P., Groussman, R. D., Hu, S. K., Caron, D. A., Morales, R. L., Ribalet, F., & Armbrust, E. V. Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities. Proceedings of the National Academy of Sciences of the United States of America, 118(6), (2021): e2011038118, https://doi.org/10.1073./pnas.2011038118.The 24-h cycle of light and darkness governs daily rhythms of complex behaviors across all domains of life. Intracellular photoreceptors sense specific wavelengths of light that can reset the internal circadian clock and/or elicit distinct phenotypic responses. In the surface ocean, microbial communities additionally modulate nonrhythmic changes in light quality and quantity as they are mixed to different depths. Here, we show that eukaryotic plankton in the North Pacific Subtropical Gyre transcribe genes encoding light-sensitive proteins that may serve as light-activated transcription factors, elicit light-driven electrical/chemical cascades, or initiate secondary messenger-signaling cascades. Overall, the protistan community relies on blue light-sensitive photoreceptors of the cryptochrome/photolyase family, and proteins containing the Light-Oxygen-Voltage (LOV) domain. The greatest diversification occurred within Haptophyta and photosynthetic stramenopiles where the LOV domain was combined with different DNA-binding domains and secondary signal-transduction motifs. Flagellated protists utilize green-light sensory rhodopsins and blue-light helmchromes, potentially underlying phototactic/photophobic and other behaviors toward specific wavelengths of light. Photoreceptors such as phytochromes appear to play minor roles in the North Pacific Subtropical Gyre. Transcript abundance of environmental light-sensitive protein-encoding genes that display diel patterns are found to primarily peak at dawn. The exceptions are the LOV-domain transcription factors with peaks in transcript abundances at different times and putative phototaxis photoreceptors transcribed throughout the day. Together, these data illustrate the diversity of light-sensitive proteins that may allow disparate groups of protists to respond to light and potentially synchronize patterns of growth, division, and mortality within the dynamic ocean environment.This work was supported by a grant from the Simons Foundation (SCOPE Award 329108 [to E.V.A.]) and XSEDE Grant Allocation OCE160019 (to R.D.G.)

Daily changes in phytoplankton lipidomes reveal mechanisms of energy storage in the open ocean

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 9 (2018): 5179, doi:10.1038/s41467-018-07346-z.Sunlight is the dominant control on phytoplankton biosynthetic activity, and darkness deprives them of their primary external energy source. Changes in the biochemical composition of phytoplankton communities over diel light cycles and attendant consequences for carbon and energy flux in environments remain poorly elucidated. Here we use lipidomic data from the North Pacific subtropical gyre to show that biosynthesis of energy-rich triacylglycerols (TAGs) by eukaryotic nanophytoplankton during the day and their subsequent consumption at night drives a large and previously uncharacterized daily carbon cycle. Diel oscillations in TAG concentration comprise 23 ± 11% of primary production by eukaryotic nanophytoplankton representing a global flux of about 2.4 Pg C yr−1. Metatranscriptomic analyses of genes required for TAG biosynthesis indicate that haptophytes and dinoflagellates are active members in TAG production. Estimates suggest that these organisms could contain as much as 40% more calories at sunset than at sunrise due to TAG production.This work was supported by a grant from the Simons Foundation, and is a contribution of the Simons Collaboration on Ocean Processes and Ecology (SCOPE award # 329108, B.A.S.V.M.). K.W.B. was further supported by the Postdoctoral Scholarship Program at Woods Hole Oceanographic Institution & U.S. Geological Survey

Several species of diatoms show a putative plastid localization sequence on <i>petF</i>.

<p>Representative <i>PETF</i> sequences that possess putative chloroplast transit peptides as identified in the nuclear-encoded <i>T</i>. <i>oceanica PETF</i> (top, NC) and plastid-encoded <i>petF</i> from <i>O</i>. <i>sinensis</i>, <i>T</i>. <i>weissogii</i>, <i>T</i>. <i>pseudonana</i> and <i>P</i>. <i>tricornutum</i> (bottom, CP). Residues corresponding to <i>T</i>. <i>oceanica</i> transit peptides highlighted in blue box. The orange box marks the ASAFAP motif, with potential cleavage site between A/G and F marked by an orange arrow. Red arrows mark Fe-coordinating cysteine residues. Twenty-eight unmatched amino acids unique to the N-terminus of <i>Grammatophora oceanica</i> (MMETSP0009) were omitted for brevity. MMETSP and Accession IDs: <i>Thalassiosira oceanica</i>, [GenBank:EJK54785.1]; <i>Thalassiosira miniscula</i> 1, MMETSP0737, [CAMERA:0183720344]; <i>Thalassiosira miniscula</i> 2, MMETSP0737, [CAMERA:0183726686]; <i>Thalassiosira</i> sp., MMETSP1071, [CAMERA:0181112606]; <i>Skeletonema costatum</i>, MMETSP0013, [CAMERA:0113387486]; <i>Skeletonema marinoi</i>, MMETSP0319, [CAMERA:0115919778]; <i>Skeletonema menzelii</i> 1, MMETSP0604, [CAMERA:0183674844]; <i>Skeletonema menzelii</i>, MMETSP0603, [CAMERA:0183648216]; <i>Minutocellus polymorphus</i>, MMETSP1070, [CAMERA:0181038080]; <i>Odontella aurita</i>, MMETSP0015, [CAMERA:0113537566]; <i>Grammatophora oceanica</i>, MMETSP0009, [CAMPEP:0194032050]; <i>Thalassionema frauenfeldii</i>, MMETSP0786, [CAMERA:0178915392]; <i>Thalassionema frauenfeldii</i>, MMETSP0786, [CAMERA:0178916612]; <i>Odontella sinensis</i> (CP), [Swiss-Prot:P49522]; <i>Thalassiosira weissflogii</i> (CP), [Swiss-Prot:O98450]; <i>Thalassiosira pseudonana</i> (CP), [GenBank:YP_874492], <i>Phaeodactylum tricornutum</i> (CP), [GenBank:YP_874403].</p

Presence or absence of detected transcripts in diatoms per species or subspecies.

<p>Sampled diatoms are shown with three select outgroups. Numbers indicate total unique copy variants as defined by the number of independently clustering paralogs. Abbreviations: ferritin, FTN; flavodoxin, FLAV; ferredoxin, FER; plastocyanin, PCYN; cytochrome c6, CytC6; superoxide dismutase, SOD. Eukaryote-only 18S sequences curated and aligned by SILVA (<a href="http://www.arb-silva.de" target="_blank">www.arb-silva.de</a>) were re-aligned with the 18S sequences available for all MMETSP samples and for genomes and non-MMETSP transcriptomes included in our analyses (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129081#sec014" target="_blank">Methods</a>). Tree drawn with FastTree. Diatoms all fell within a single clade; all other eukaryote branches except for select outgroups are not shown.</p

Diversity and Evolutionary History of Iron Metabolism Genes in Diatoms

<div><p>Ferroproteins arose early in Earth’s history, prior to the emergence of oxygenic photosynthesis and the subsequent reduction of bioavailable iron. Today, iron availability limits primary productivity in about 30% of the world’s oceans. Diatoms, responsible for nearly half of oceanic primary production, have evolved molecular strategies for coping with variable iron concentrations. Our understanding of the evolutionary breadth of these strategies has been restricted by the limited number of species for which molecular sequence data is available. To uncover the diversity of strategies marine diatoms employ to meet cellular iron demands, we analyzed 367 newly released marine microbial eukaryotic transcriptomes, which include 47 diatom species. We focused on genes encoding proteins previously identified as having a role in iron management: iron uptake (high-affinity ferric reductase, multi-copper oxidase, and Fe(III) permease); iron storage (ferritin); iron-induced protein substitutions (flavodoxin/ferredoxin, and plastocyanin/cytochrome c6) and defense against reactive oxygen species (superoxide dismutases). Homologs encoding the high-affinity iron uptake system components were detected across the four diatom Classes suggesting an ancient origin for this pathway. Ferritin transcripts were also detected in all Classes, revealing a more widespread utilization of ferritin throughout diatoms than previously recognized. Flavodoxin and plastocyanin transcripts indicate possible alternative redox metal strategies. Predicted localization signals for ferredoxin identify multiple examples of gene transfer from the plastid to the nuclear genome. Transcripts encoding four superoxide dismutase metalloforms were detected, including a putative nickel-coordinating isozyme. Taken together, our results suggest that the majority of iron metabolism genes in diatoms appear to be vertically inherited with functional diversity achieved via possible neofunctionalization of paralogs. This refined view of iron use strategies in diatoms elucidates the history of these adaptations, and provides potential molecular markers for determining the iron nutritional status of different diatom species in environmental samples.</p></div

The three components of the reductive uptake system in diatoms.

<p>Frequency of detected transcripts for ferric reductase (FRE), multi-copper oxidase (MCO) and iron(III) permease (FTR). Bars show proportion of strains within Bacillariophyceae (B), Fragilariophyceae (F), Mediophyceae (M) and Coscinodiscophyceae (C) where 1 or more transcripts were detected versus total strains.</p

Ferritin phylogenetic tree of diatom clade.

<p>Maximum likelihood (ML) tree generated with RAxML using PROTGAMMAWAG model. Numbers beside branches indicate bootstrap support values from 1,000 trees; values under 50 removed for clarity. At major nodes, where the branching structure is in agreement with Bayesian inference, posterior probabilities are listed to the right of bootstrap values following a forward slash. Consensus trees were generated with MrBayes v3.1.2 from 1,000,000 generations, with trees sampled every 500 generations. Branches colored by organismal phylogeny: diatoms, orange; unclassified pedinellid, light green; dinoflagellates, blue. Genus and species are given followed by sequence source and ID. Multiple adjacent tips from the same taxonomic unit were collapsed, with number of members given in brackets.</p

Phylogenetic tree of Fe and Mn SOD from diatoms only.

<p>Midpoint-rooted approximately-maximum-likelihood tree of putative and known Fe and Mn SOD amino acid sequences. Sequences with less than 95% similarity in aligned residues shown. Node support values are calculated from 1,000 resamples, only values over 0.5 are shown. At major nodes, where the branching structure is in agreement with Bayesian inference, posterior probabilities are listed to the right of bootstrap values following a forward slash. Consensus trees were generated with MrBayes v3.1.2 from 1,700,000 generations, with trees sampled every 500 generations.</p

The Ubiquitin-NiSOD fusion protein.

<p>Section of a multiple sequence alignment of verified NiSOD, verified ubiquitin (UBQ), and putative UBQ-NiSOD fusion genes. Trimmed to show terminal 23 residues of UBQ, and first 29 residues of NiSOD. Accession numbers: Bacterial NiSOD (SodN) sequences (top four rows, blue side bar: <i>Streptomyces coelicolor</i>, [Swiss-Prot:P80735]; <i>Streptomyces seoulensis</i>, [Swiss-Prot:P80734]; <i>Prochlorococcus marinus</i>, [Swiss-Prot:Q7V8K4]; <i>Synechococcus</i> sp. WH8102, [Swiss-Prot:Q7U5S1]) aligned with putative UBQ-NiSOD fusion protein from one representative of each diatom class (middle four rows, purple bar: <i>Pseudo-nitzschia multiseries</i>, [JGI:206387]; <i>Striatella unipunctata</i>, MMETSP0800, [CAMERA:0118699990]; <i>Ditylum brightwellii</i>, MMETSP1063, [CAMERA:0180982606]; <i>Rhizosolenia setigera</i>, MMETSP0789, [CAMERA:0178952988]) and the terminal UBQ from four model eukaryotes (bottom four rows, red bar: <i>Tetrahymena pyriformis</i>, [Swiss-Prot:P0CG82]; <i>Phytophthora infestans</i>, [Swiss-Prot:P22589]; <i>Arabidopsis thaliana</i>, [Swiss-Prot:Q1EC66]; <i>Saccharomyces cerevisiae</i>, [Swiss-Prot:P0CG63]). Black arrow indicates cleavage site for NiSOD in bacteria, cleavage site for UBQ in eukaryotes, and proposed cleavage site for UBQ-NiSOD fusion protein.</p

Relationship of diatom PCYN to other phytoplankton.

<p>Midpoint-rooted approximately-maximum-likelihood tree of putative and known PCYN. Support values shown for deep nodes, with values under 0.5 removed for clarity. Branches outside of diatom clade are collapsed; with dominant phylogenetic composition, ratio of dominant taxa to total taxa, number of species in the collapsed clade, and number of sequences. At major nodes, where the branching structure is in agreement with Bayesian inference, posterior probabilities are listed to the right of bootstrap values following a forward slash. Consensus trees were generated with MrBayes v3.1.2 from 2,400,000 generations, with trees sampled every 500 generations. One representative is shown from groups sharing greater than 95% similarity in aligned sequence identity. Branches colored by organismal phylogeny: diatoms, orange; chlorophytes, green; haptophytes and cryptophytes, lavender; non-diatom stramenopiles, magenta; alveolates, blue; opisthokonts and amoebozoa, brown, mixed clades, gray. Previously identified PCYN from <i>Thalassiosira oceanica</i> noted in bold. Distinct <i>P</i>. <i>heimii</i> and <i>F</i>. <i>kerguelensis</i> paralogs shown with red or blue dots, respectively. Top to bottom, diatom labels: <i>Coscinodiscus wailesii</i>, [CAMERA:0172483904]; <i>Pseudo-nitzschia heimii</i>, [CAMPEP:0197183406]; <i>Pseudo-nitzschia arenysensis</i>, [CAMERA:0116141514]; <i>Pseudo-nitzschia granii</i>, IH deg7180000014200 frame0; <i>Corethron hystrix</i>, [CAMERA:0113306274]; <i>Fragilariopsis kerguelensis</i>, [CAMERA:0170793268]; <i>Fragilariopsis kerguelensis</i>, [CAMERA:0170902168]; <i>Proboscia inermis</i>, [CAMERA:0171306160]; <i>Striatella unipunctata</i>, [CAMERA:0118690216]; <i>Ditylum brightwellii</i>, [CAMERA:0180970060]; <i>Fragilariopsis cylindrus</i>, [JGI:272258]; <i>Fragilariopsis kerguelensis</i>, [CAMERA:0170771410]; <i>Pseudo-nitzschia heimii</i>, [CAMPEP:0197180752]; <i>Rhizosolenia setigera</i>, [CAMERA:0178972290]; <i>Thalassiosira oceanica</i>, [EMBL:D2Z0I2]; <i>Fragilariopsis kerguelensis</i>, [CAMERA:0170889260]; <i>Pseudo-nitzschia heimii</i>, [CAMPEP:0197182106].</p