Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula
Abstract Functional genomics of diatom-dominated communities from the Antarctic Peninsula was studied using comparative metatranscriptomics. Samples obtained from diatom-rich communities in the Bransfield Strait, the western Weddell Sea and sea ice in the Bellingshausen Sea/Wilkins Ice Shelf yielded...
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Oxford University Press (OUP)
2015
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croxfordunivpr:10.1038/ismej.2015.40 2024-04-07T07:48:14+00:00 Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula Pearson, Gareth A Lago-Leston, Asuncion Cánovas, Fernando Cox, Cymon J Verret, Frederic Lasternas, Sebastian Duarte, Carlos M Agusti, Susana Serrão, Ester A 2015 http://dx.doi.org/10.1038/ismej.2015.40 http://www.nature.com/articles/ismej201540.pdf http://www.nature.com/articles/ismej201540 https://academic.oup.com/ismej/article-pdf/9/10/2275/56371522/41396_2015_article_bfismej201540.pdf en eng Oxford University Press (OUP) https://academic.oup.com/pages/standard-publication-reuse-rights http://www.springer.com/tdm The ISME Journal volume 9, issue 10, page 2275-2289 ISSN 1751-7362 1751-7370 Ecology, Evolution, Behavior and Systematics Microbiology journal-article 2015 croxfordunivpr https://doi.org/10.1038/ismej.2015.40 2024-03-08T03:02:52Z Abstract Functional genomics of diatom-dominated communities from the Antarctic Peninsula was studied using comparative metatranscriptomics. Samples obtained from diatom-rich communities in the Bransfield Strait, the western Weddell Sea and sea ice in the Bellingshausen Sea/Wilkins Ice Shelf yielded more than 500K pyrosequencing reads that were combined to produce a global metatranscriptome assembly. Multi-gene phylogenies recovered three distinct communities, and diatom-assigned contigs further indicated little read-sharing between communities, validating an assembly-based annotation and analysis approach. Although functional analysis recovered a core of abundant shared annotations that were expressed across the three diatom communities, over 40% of annotations (but accounting for <10% of sequences) were community-specific. The two pelagic communities differed in their expression of N-metabolism and acquisition genes, which was almost absent in post-bloom conditions in the Weddell Sea community, while enrichment of transporters for ammonia and urea in Bransfield Strait diatoms suggests a physiological stance towards acquisition of reduced N-sources. The depletion of carbohydrate and energy metabolism pathways in sea ice relative to pelagic communities, together with increased light energy dissipation (via LHCSR proteins), photorespiration, and NO3− uptake and utilization all pointed to irradiance stress and/or inorganic carbon limitation within sea ice. Ice-binding proteins and cold-shock transcription factors were also enriched in sea ice diatoms. Surprisingly, the abundance of gene transcripts for the translational machinery tracked decreasing environmental temperature across only a 4 °C range, possibly reflecting constraints on translational efficiency and protein production in cold environments. Article in Journal/Newspaper Antarc* Antarctic Antarctic Peninsula Bellingshausen Sea Bransfield Strait Ice Shelf Sea ice Weddell Sea Wilkins Ice Shelf Oxford University Press Antarctic The Antarctic Antarctic Peninsula Weddell Sea Bellingshausen Sea Bransfield Strait Weddell Wilkins ENVELOPE(59.326,59.326,-67.248,-67.248) Wilkins Ice Shelf ENVELOPE(-72.500,-72.500,-70.416,-70.416) The ISME Journal 9 10 2275 2289 |
institution |
Open Polar |
collection |
Oxford University Press |
op_collection_id |
croxfordunivpr |
language |
English |
topic |
Ecology, Evolution, Behavior and Systematics Microbiology |
spellingShingle |
Ecology, Evolution, Behavior and Systematics Microbiology Pearson, Gareth A Lago-Leston, Asuncion Cánovas, Fernando Cox, Cymon J Verret, Frederic Lasternas, Sebastian Duarte, Carlos M Agusti, Susana Serrão, Ester A Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula |
topic_facet |
Ecology, Evolution, Behavior and Systematics Microbiology |
description |
Abstract Functional genomics of diatom-dominated communities from the Antarctic Peninsula was studied using comparative metatranscriptomics. Samples obtained from diatom-rich communities in the Bransfield Strait, the western Weddell Sea and sea ice in the Bellingshausen Sea/Wilkins Ice Shelf yielded more than 500K pyrosequencing reads that were combined to produce a global metatranscriptome assembly. Multi-gene phylogenies recovered three distinct communities, and diatom-assigned contigs further indicated little read-sharing between communities, validating an assembly-based annotation and analysis approach. Although functional analysis recovered a core of abundant shared annotations that were expressed across the three diatom communities, over 40% of annotations (but accounting for <10% of sequences) were community-specific. The two pelagic communities differed in their expression of N-metabolism and acquisition genes, which was almost absent in post-bloom conditions in the Weddell Sea community, while enrichment of transporters for ammonia and urea in Bransfield Strait diatoms suggests a physiological stance towards acquisition of reduced N-sources. The depletion of carbohydrate and energy metabolism pathways in sea ice relative to pelagic communities, together with increased light energy dissipation (via LHCSR proteins), photorespiration, and NO3− uptake and utilization all pointed to irradiance stress and/or inorganic carbon limitation within sea ice. Ice-binding proteins and cold-shock transcription factors were also enriched in sea ice diatoms. Surprisingly, the abundance of gene transcripts for the translational machinery tracked decreasing environmental temperature across only a 4 °C range, possibly reflecting constraints on translational efficiency and protein production in cold environments. |
format |
Article in Journal/Newspaper |
author |
Pearson, Gareth A Lago-Leston, Asuncion Cánovas, Fernando Cox, Cymon J Verret, Frederic Lasternas, Sebastian Duarte, Carlos M Agusti, Susana Serrão, Ester A |
author_facet |
Pearson, Gareth A Lago-Leston, Asuncion Cánovas, Fernando Cox, Cymon J Verret, Frederic Lasternas, Sebastian Duarte, Carlos M Agusti, Susana Serrão, Ester A |
author_sort |
Pearson, Gareth A |
title |
Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula |
title_short |
Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula |
title_full |
Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula |
title_fullStr |
Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula |
title_full_unstemmed |
Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula |
title_sort |
metatranscriptomes reveal functional variation in diatom communities from the antarctic peninsula |
publisher |
Oxford University Press (OUP) |
publishDate |
2015 |
url |
http://dx.doi.org/10.1038/ismej.2015.40 http://www.nature.com/articles/ismej201540.pdf http://www.nature.com/articles/ismej201540 https://academic.oup.com/ismej/article-pdf/9/10/2275/56371522/41396_2015_article_bfismej201540.pdf |
long_lat |
ENVELOPE(59.326,59.326,-67.248,-67.248) ENVELOPE(-72.500,-72.500,-70.416,-70.416) |
geographic |
Antarctic The Antarctic Antarctic Peninsula Weddell Sea Bellingshausen Sea Bransfield Strait Weddell Wilkins Wilkins Ice Shelf |
geographic_facet |
Antarctic The Antarctic Antarctic Peninsula Weddell Sea Bellingshausen Sea Bransfield Strait Weddell Wilkins Wilkins Ice Shelf |
genre |
Antarc* Antarctic Antarctic Peninsula Bellingshausen Sea Bransfield Strait Ice Shelf Sea ice Weddell Sea Wilkins Ice Shelf |
genre_facet |
Antarc* Antarctic Antarctic Peninsula Bellingshausen Sea Bransfield Strait Ice Shelf Sea ice Weddell Sea Wilkins Ice Shelf |
op_source |
The ISME Journal volume 9, issue 10, page 2275-2289 ISSN 1751-7362 1751-7370 |
op_rights |
https://academic.oup.com/pages/standard-publication-reuse-rights http://www.springer.com/tdm |
op_doi |
https://doi.org/10.1038/ismej.2015.40 |
container_title |
The ISME Journal |
container_volume |
9 |
container_issue |
10 |
container_start_page |
2275 |
op_container_end_page |
2289 |
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1795662156952240128 |