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Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems

Marine planktonic protists are critical components of ocean ecosystems and are highly diverse. Molecular sequencing methods are being used to describe this diversity and reveal new associations and metabolisms that are important to how these ecosystems function. We describe here the use of the singl...

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Autores principales: Sieracki, M. E., Poulton, N. J., Jaillon, O., Wincker, P., de Vargas, C., Rubinat-Ripoll, L., Stepanauskas, R., Logares, R., Massana, R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6465268/
https://www.ncbi.nlm.nih.gov/pubmed/30988337
http://dx.doi.org/10.1038/s41598-019-42487-1
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author Sieracki, M. E.
Poulton, N. J.
Jaillon, O.
Wincker, P.
de Vargas, C.
Rubinat-Ripoll, L.
Stepanauskas, R.
Logares, R.
Massana, R.
author_facet Sieracki, M. E.
Poulton, N. J.
Jaillon, O.
Wincker, P.
de Vargas, C.
Rubinat-Ripoll, L.
Stepanauskas, R.
Logares, R.
Massana, R.
author_sort Sieracki, M. E.
collection PubMed
description Marine planktonic protists are critical components of ocean ecosystems and are highly diverse. Molecular sequencing methods are being used to describe this diversity and reveal new associations and metabolisms that are important to how these ecosystems function. We describe here the use of the single cell genomics approach to sample and interrogate the diversity of the smaller (pico- and nano-sized) protists from a range of oceanic samples. We created over 900 single amplified genomes (SAGs) from 8 Tara Ocean samples across the Indian Ocean and the Mediterranean Sea. We show that flow cytometric sorting of single cells effectively distinguishes plastidic and aplastidic cell types that agree with our understanding of protist phylogeny. Yields of genomic DNA with PCR-identifiable 18S rRNA gene sequence from single cells was low (15% of aplastidic cell sorts, and 7% of plastidic sorts) and tests with alternate primers and comparisons to metabarcoding did not reveal phylogenetic bias in the major protist groups. There was little evidence of significant bias against or in favor of any phylogenetic group expected or known to be present. The four open ocean stations in the Indian Ocean had similar communities, despite ranging from 14°N to 20°S latitude, and they differed from the Mediterranean station. Single cell genomics of protists suggests that the taxonomic diversity of the dominant taxa found in only several hundreds of microliters of surface seawater is similar to that found in molecular surveys where liters of sample are filtered.
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spelling pubmed-64652682019-04-18 Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems Sieracki, M. E. Poulton, N. J. Jaillon, O. Wincker, P. de Vargas, C. Rubinat-Ripoll, L. Stepanauskas, R. Logares, R. Massana, R. Sci Rep Article Marine planktonic protists are critical components of ocean ecosystems and are highly diverse. Molecular sequencing methods are being used to describe this diversity and reveal new associations and metabolisms that are important to how these ecosystems function. We describe here the use of the single cell genomics approach to sample and interrogate the diversity of the smaller (pico- and nano-sized) protists from a range of oceanic samples. We created over 900 single amplified genomes (SAGs) from 8 Tara Ocean samples across the Indian Ocean and the Mediterranean Sea. We show that flow cytometric sorting of single cells effectively distinguishes plastidic and aplastidic cell types that agree with our understanding of protist phylogeny. Yields of genomic DNA with PCR-identifiable 18S rRNA gene sequence from single cells was low (15% of aplastidic cell sorts, and 7% of plastidic sorts) and tests with alternate primers and comparisons to metabarcoding did not reveal phylogenetic bias in the major protist groups. There was little evidence of significant bias against or in favor of any phylogenetic group expected or known to be present. The four open ocean stations in the Indian Ocean had similar communities, despite ranging from 14°N to 20°S latitude, and they differed from the Mediterranean station. Single cell genomics of protists suggests that the taxonomic diversity of the dominant taxa found in only several hundreds of microliters of surface seawater is similar to that found in molecular surveys where liters of sample are filtered. Nature Publishing Group UK 2019-04-15 /pmc/articles/PMC6465268/ /pubmed/30988337 http://dx.doi.org/10.1038/s41598-019-42487-1 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Sieracki, M. E.
Poulton, N. J.
Jaillon, O.
Wincker, P.
de Vargas, C.
Rubinat-Ripoll, L.
Stepanauskas, R.
Logares, R.
Massana, R.
Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems
title Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems
title_full Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems
title_fullStr Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems
title_full_unstemmed Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems
title_short Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems
title_sort single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6465268/
https://www.ncbi.nlm.nih.gov/pubmed/30988337
http://dx.doi.org/10.1038/s41598-019-42487-1
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