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Citation: Orsi, William D.: Contigs from metatranscriptomes from Namibian sediments (doi.org/10.1101/2020.03.26.009324). 29. March 2020. Open Data LMU. 10.5282/ubm/data.187

Contigs from metatranscriptomes from Namibian sediments (doi.org/10.1101/2020.03.26.009324)
Contigs from metatranscriptomes from Namibian sediments (doi.org/10.1101/2020.03.26.009324)

Foraminifera are single-celled eukaryotes (protists) of large ecological importance, as well as environmental and paleoenvironmental indicators and biostratigraphic tools. In addition, they are capable of surviving in anoxic marine environments where they represent a major component of the benthic community. However, the cellular adaptations of Foraminifera to the anoxic environment remain poorly constrained. We sampled an oxic-anoxic transition zone in marine sediments from the Namibian shelf, where the genera Bolivina and Stainforthia dominated the Foraminifera community, and use metatranscriptomics to characterize Foraminifera metabolism across the different geochemical conditions. The relative abundance of Foraminifera gene expression in anoxic sediment depths increased an order of magnitude, which was confirmed in a ten-day incubation experiment where the development of anoxia coincided with a 27-fold increase in the relative abundance of Foraminifera protein encoding transcripts. This indicates that many Foraminifera were not only surviving, but thriving under the anoxic conditions. The anaerobic energy metabolism of these active Foraminifera was characterized by fermentation of sugars and amino acids, dissimilatory nitrate reduction, fumarate reduction, and dephosphorylation of creatine phosphate. This was co-expressed alongside genes involved in production of reticulopodia, phagocytosis, calcification, and clathrin-mediated-endocytosis (CME). Thus, Foraminifera may use CME under anoxic conditions to utilize dissolved organic matter as a carbon and energy source, in addition to ingestion of prey cells via phagocytosis. These mechanisms help explain how some Foraminifera can thrive under anoxia, which would help to explain their ecological success documented in the fossil record since the Cambrian period more than 500 million years ago.

Foraminifera, Transcriptomics, Gene expression, RNA-seq, RNA
Orsi, William D.
2020

[img] Text (contigs 12 cm A)
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[img] Text (contigs 12 cm B)
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[img] Text (contigs 12 cm A)
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[img] Text (contigs 28 cm A)
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[img] Text (contigs 28 cm B)
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[img] Text (contigs 28 cm C)
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[img] Text (core top A)
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[img] Text (contigs 3 days incubation A)
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[img] Text (contigs 3 days incubation B)
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[img] Text (contigs 7 days)
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[img] Text (contigs 10 days A)
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[img] Text (contigs 10 days B)
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[img] Text (18 hours A)
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DOI: 10.5282/ubm/data.187

This dataset is available unter the terms of the following Creative Commons LicenseCC BY-NC-ND 4.0

Abstract

Foraminifera are single-celled eukaryotes (protists) of large ecological importance, as well as environmental and paleoenvironmental indicators and biostratigraphic tools. In addition, they are capable of surviving in anoxic marine environments where they represent a major component of the benthic community. However, the cellular adaptations of Foraminifera to the anoxic environment remain poorly constrained. We sampled an oxic-anoxic transition zone in marine sediments from the Namibian shelf, where the genera Bolivina and Stainforthia dominated the Foraminifera community, and use metatranscriptomics to characterize Foraminifera metabolism across the different geochemical conditions. The relative abundance of Foraminifera gene expression in anoxic sediment depths increased an order of magnitude, which was confirmed in a ten-day incubation experiment where the development of anoxia coincided with a 27-fold increase in the relative abundance of Foraminifera protein encoding transcripts. This indicates that many Foraminifera were not only surviving, but thriving under the anoxic conditions. The anaerobic energy metabolism of these active Foraminifera was characterized by fermentation of sugars and amino acids, dissimilatory nitrate reduction, fumarate reduction, and dephosphorylation of creatine phosphate. This was co-expressed alongside genes involved in production of reticulopodia, phagocytosis, calcification, and clathrin-mediated-endocytosis (CME). Thus, Foraminifera may use CME under anoxic conditions to utilize dissolved organic matter as a carbon and energy source, in addition to ingestion of prey cells via phagocytosis. These mechanisms help explain how some Foraminifera can thrive under anoxia, which would help to explain their ecological success documented in the fossil record since the Cambrian period more than 500 million years ago.

Keywords

Foraminifera, Transcriptomics, Gene expression, RNA-seq, RNA

References

Anaerobic metabolism of Foraminifera thriving below the seafloor

William D. Orsi, Raphaël Morard, Aurele Vuillemin, Michael Eitel, Gert Wörheide, Jana Milucka, Michal Kucera

doi: https://doi.org/10.1101/2020.03.26.009324

Item Type:Data
Contact Person:Orsi, William D.
E-Mail of Contact:w.orsi at lrz.uni-muenchen.de
Subjects:Faculty of Geosciences
Dewey Decimal Classification:600 Natural sciences and mathematics > 550 Earth sciences
600 Natural sciences and mathematics > 560 Paleontology, Paleozoology
600 Natural sciences and mathematics > 570 Life sciences
ID Code:187
Deposited By: Prof. Dr. William D. Orsi
Deposited On:29. Apr 2020 09:01
Last Modified:29. Apr 2020 09:01

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