Experimental identification and in silico prediction of bacterivory in green algae

Bock, Nicholas A.; Charvet, Sophie; Burns, John A.; Gyaltshen, Yangtsho; Rozenberg, Andrey; Duhamel, Solange; Kim, Eunsoo

doi:10.1038/s41396-021-00899-w

Cited by 31 publications

(40 citation statements)

References 87 publications

(119 reference statements)

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“…We predict the trophic modes of B. bigelowii and a mixotrophic haptophyte Haptolina brevifila using the transcriptomes, based on the methods by Burns et al (2018) and Bock et al (2021) . In this model-based analysis, the probability of potential phagocytosis of organisms is evaluated with the scores of 0 to 1.…”

Section: Methodsmentioning

confidence: 99%

Unstable Relationship Between Braarudosphaera bigelowii (= Chrysochromulina parkeae) and Its Nitrogen-Fixing Endosymbiont

et al. 2021

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Marine phytoplankton are major primary producers, and their growth is primarily limited by nitrogen in the oligotrophic ocean environment. The haptophyte Braarudosphaera bigelowii possesses a cyanobacterial endosymbiont (UCYN-A), which plays a major role in nitrogen fixation in the ocean. However, host-symbiont interactions are poorly understood because B. bigelowii was unculturable. In this study, we sequenced the complete genome of the B. bigelowii endosymbiont and showed that it was highly reductive and closely related to UCYN-A2 (an ecotype of UCYN-A). We succeeded in establishing B. bigelowii strains and performed microscopic observations. The detailed observations showed that the cyanobacterial endosymbiont was surrounded by a single host derived membrane and divided synchronously with the host cell division. The transcriptome of B. bigelowii revealed that B. bigelowii lacked the expression of many essential genes associated with the uptake of most nitrogen compounds, except ammonia. During cultivation, some of the strains completely lost the endosymbiont. Moreover, we did not find any evidence of endosymbiotic gene transfer from the endosymbiont to the host. These findings illustrate an unstable morphological, metabolic, and genetic relationship between B. bigelowii and its endosymbiont.

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Section: Methodsmentioning

confidence: 99%

Unstable Relationship Between Braarudosphaera bigelowii (= Chrysochromulina parkeae) and Its Nitrogen-Fixing Endosymbiont

et al. 2021

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“…Earlier studies revealed the possibility of bacterivory activity of H. akashiwo (31)(32)(33), while the ecophysiological feature of the species has been rarely discussed in depth since then. A recent study predicted the bacterivory potentials of several green algae based on their gene sets and confirmed the activity experimentally (45),suggesting that the usage of both photosynthesis and phagocytosis for survival may be more common than previously considered. Phagocytotic and photosynthetic capabilities of the organisms were computationally predicted using the predictTrophicMode tool using default mode (38,45).…”

Section: Resultsmentioning

confidence: 60%

“…A recent study predicted the bacterivory potentials of several green algae based on their gene sets and confirmed the activity experimentally (45),suggesting that the usage of both photosynthesis and phagocytosis for survival may be more common than previously considered. Phagocytotic and photosynthetic capabilities of the organisms were computationally predicted using the predictTrophicMode tool using default mode (38,45). We analyzed the gene models predicted based on the transcriptomes of various algal species presented in Table 3 and ourH.…”

Section: Resultsmentioning

confidence: 60%

“…To predict the trophic mode ofH. akashiwo, the predicted protein sequences based on the transcriptome were tested for phagocytotic and prototrophic potentials using a gene-based Trophic Mode Prediction tool using default mode (38,45). The gene models of a non-photosynthetic ciliate, Paramecium tetraurelia (NCBI BioProject PRJNA19409) as well as phytosyntheticEmiliania huxleyi (NCBI AHAL00000000.1) and Chlamydomonas reinhardtii (https://www.uniprot.org/uniprot/?query=proteome:UP000006906 ), and conditionally symbiotic and photosynthetic Breviolum minutum(Previously termed Symbiodinium minutum, https://marinegenomics.oist.jp/symb/viewer/download?project id=21 , ( 46)), were also analyzed.…”

Section: Annotation Go Analyses and Trophic Mode Predictionmentioning

confidence: 99%

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De novo assembly and inferred functional annotation of the transcriptome of Heterosigma akashiwo

Sato

Seki

Suzuki

et al. 2022

Preprint

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Heterosigma akashiwo is a eukaryotic, cosmopolitan, and unicellular alga (class: Raphidophyceae), and produces fish-killing blooms. There is a substantial scientific and practical interest in its ecophysiological characteristics that determine bloom dynamics and its adaptation to broad climate zones. A well-annotated genomic/genetic sequence information enables researchers to characterize organisms using modern molecular technology. The Chloroplast and the mitochondrial genome sequences and transcriptome sequence assembly (TSA) datasets with limited sizes for H. akashiwo are available in NCBI nucleotide database on December 2021: there is no doubt that more genetic information of the species will greatly enhance the progress of biological characterization of the species. Here, we conducted H. akashiwo RNA sequencing, a de novo transcriptome assembly (NCBI TSA ICRV01) of a large number of high-quality short-read sequences, and the functional annotation of predicted genes. Based on our transcriptome, we confirmed that the organism possesses genes that were predicted to function in phagocytosis, supporting the earlier observations of H. akashiwo bacterivory. Along with its capability for photosynthesis, the mixotrophy of H. akashiwo may partially explain its high adaptability to various environmental conditions. Our study here will provide an important toehold to decipher H. akashiwo ecophysiology at a molecular level.

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“…However, from the late spring onwards, freshwater from river runoff and ice melt enforce vertical stratification of the Arctic Ocean, keeping inorganic nutrients below the photic zone. Low nutrient conditions favour smaller species with high surface-to-volume ratios and photo-mixotrophic life strategies (Bock et al, 2021; Jeong et al, 2021; Lie et al, 2018; McKie-Krisberg & Sanders, 2014). Ice-dwelling species are also exposed to salinity fluctuations, nutrient pulses and depletion, and have the ability to maintain viable cells during ice-free periods.…”

Section: Introductionmentioning

confidence: 99%

Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related microalgae

Dorrell

Kuo

Füssy

et al. 2021

Preprint

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The Arctic Ocean is being impacted by warming temperatures, increasing freshwater and highly variable ice conditions. The microalgal communities underpinning Arctic marine food webs, once thought to be dominated by diatoms, include a phylogenetically diverse range of small algal species, whose biology remains poorly understood. Here, we present genome sequences of a cryptomonad, a haptophyte, a chrysophyte, and a pelagophyte, isolated from the Arctic water column and ice. Comparing protein family distributions and sequence similarity across a densely-sampled set of algal genomes and transcriptomes, we note striking convergences in the biology of distantly related small Arctic algae, compared to non-Arctic relatives; although this convergence is largely exclusive of Arctic diatoms. Using high-throughput phylogenetic approaches, incorporating environmental sequence data from Tara Oceans, we demonstrate that this convergence was partly explained by horizontal gene transfers (HGT) between Arctic species, in over at least 30 other discrete gene families, and most notably in ice-binding domains (IBD). These Arctic-specific genes have been repeatedly transferred between Arctic algae, and are independent of equivalent HGTs in the Antarctic Southern Ocean. Our data provide insights into the specialised Arctic marine microbiome, and underlines the role of geographically-limited HGT as a driver of environmental adaptation in eukaryotic algae.

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Experimental identification and in silico prediction of bacterivory in green algae

Cited by 31 publications

References 87 publications

Unstable Relationship Between Braarudosphaera bigelowii (= Chrysochromulina parkeae) and Its Nitrogen-Fixing Endosymbiont

Unstable Relationship Between Braarudosphaera bigelowii (= Chrysochromulina parkeae) and Its Nitrogen-Fixing Endosymbiont

De novo assembly and inferred functional annotation of the transcriptome of Heterosigma akashiwo

Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related microalgae

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