In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii.
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| Title: | In situ transcriptomic analysis of the globally important keystone N |
|---|---|
| Authors: | Hewson, Ian1 hewson@cornell.edu, Poretsky, Rachel S.2, Beinart, Roxanne A.1,3, White, Angelicque E.4, Tuo Shi1,5, Bench, Shellie R.1, Moisander, Pia H.1, Paerl, Ryan W.1, Tripp, H. James1, Montoya, Joseph P.6, Moran, Mary Ann2, Zehr, Jonathan P.1 |
| Source: | ISME Journal: Multidisciplinary Journal of Microbial Ecology. May2009, Vol. 3 Issue 5, p618-631. 14p. 3 Charts, 5 Graphs. |
| Subjects: | Cyanobacteria, Heterogeneity, Ecophysiology, Gene expression, Nitrogen cycle, Genomes, Cyanobacterial toxins |
| Geographic Terms: | Pacific Ocean |
| Abstract: | The diazotrophic cyanobacterium Crocosphaera watsonii supplies fixed nitrogen (N) to N-depleted surface waters of the tropical oceans, but the factors that determine its distribution and contribution to global N2 fixation are not well constrained for natural populations. Despite the heterogeneity of the marine environment, the genome of C. watsonii is highly conserved in nucleotide sequence in contrast to sympatric planktonic cyanobacteria. We applied a whole assemblage shotgun transcript sequencing approach to samples collected from a bloom of C. watsonii observed in the South Pacific to understand the genomic mechanisms that may lead to high population densities. We obtained 999 C. watsonii transcript reads from two metatranscriptomes prepared from mixed assemblage RNA collected in the day and at night. The C. watsonii population had unexpectedly high transcription of hypothetical protein genes (31% of protein-encoding genes) and transposases (12%). Furthermore, genes were expressed that are necessary for living in the oligotrophic ocean, including the nitrogenase cluster and the iron-stress-induced protein A (isiA) that functions to protect photosystem I from high-light-induced damage. C. watsonii transcripts retrieved from metatranscriptomes at other locations in the southwest Pacific Ocean, station ALOHA and the equatorial Atlantic Ocean were similar in composition to those recovered in the enriched population. Quantitative PCR and quantitative reverse transcriptase PCR were used to confirm the high expression of these genes within the bloom, but transcription patterns varied at shallower and deeper horizons. These data represent the first transcript study of a rare individual microorganism in situ and provide insight into the mechanisms of genome diversification and the ecophysiology of natural populations of keystone organisms that are important in global nitrogen cycling.The ISME Journal (2009) 3, 618–631; doi:10.1038/ismej.2009.8; published online 19 February 2009 [ABSTRACT FROM AUTHOR] |
| Copyright of ISME Journal: Multidisciplinary Journal of Microbial Ecology is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Text: Availability: 0 |
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| Header | DbId: egs DbLabel: Engineering Source An: 37820913 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: In situ transcriptomic analysis of the globally important keystone N<subscript>2</subscript>-fixing taxon Crocosphaera watsonii. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Hewson%2C+Ian%22">Hewson, Ian</searchLink><relatesTo>1</relatesTo><i> hewson@cornell.edu</i><br /><searchLink fieldCode="AR" term="%22Poretsky%2C+Rachel+S%2E%22">Poretsky, Rachel S.</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22Beinart%2C+Roxanne+A%2E%22">Beinart, Roxanne A.</searchLink><relatesTo>1,3</relatesTo><br /><searchLink fieldCode="AR" term="%22White%2C+Angelicque+E%2E%22">White, Angelicque E.</searchLink><relatesTo>4</relatesTo><br /><searchLink fieldCode="AR" term="%22Tuo+Shi%22">Tuo Shi</searchLink><relatesTo>1,5</relatesTo><br /><searchLink fieldCode="AR" term="%22Bench%2C+Shellie+R%2E%22">Bench, Shellie R.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Moisander%2C+Pia+H%2E%22">Moisander, Pia H.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Paerl%2C+Ryan+W%2E%22">Paerl, Ryan W.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Tripp%2C+H%2E+James%22">Tripp, H. James</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Montoya%2C+Joseph+P%2E%22">Montoya, Joseph P.</searchLink><relatesTo>6</relatesTo><br /><searchLink fieldCode="AR" term="%22Moran%2C+Mary+Ann%22">Moran, Mary Ann</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22Zehr%2C+Jonathan+P%2E%22">Zehr, Jonathan P.</searchLink><relatesTo>1</relatesTo> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22ISME+Journal%3A+Multidisciplinary+Journal+of+Microbial+Ecology%22">ISME Journal: Multidisciplinary Journal of Microbial Ecology</searchLink>. May2009, Vol. 3 Issue 5, p618-631. 14p. 3 Charts, 5 Graphs. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Cyanobacteria%22">Cyanobacteria</searchLink><br /><searchLink fieldCode="DE" term="%22Heterogeneity%22">Heterogeneity</searchLink><br /><searchLink fieldCode="DE" term="%22Ecophysiology%22">Ecophysiology</searchLink><br /><searchLink fieldCode="DE" term="%22Gene+expression%22">Gene expression</searchLink><br /><searchLink fieldCode="DE" term="%22Nitrogen+cycle%22">Nitrogen cycle</searchLink><br /><searchLink fieldCode="DE" term="%22Genomes%22">Genomes</searchLink><br /><searchLink fieldCode="DE" term="%22Cyanobacterial+toxins%22">Cyanobacterial toxins</searchLink> – Name: SubjectGeographic Label: Geographic Terms Group: Su Data: <searchLink fieldCode="DE" term="%22Pacific+Ocean%22">Pacific Ocean</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: The diazotrophic cyanobacterium Crocosphaera watsonii supplies fixed nitrogen (N) to N-depleted surface waters of the tropical oceans, but the factors that determine its distribution and contribution to global N2 fixation are not well constrained for natural populations. Despite the heterogeneity of the marine environment, the genome of C. watsonii is highly conserved in nucleotide sequence in contrast to sympatric planktonic cyanobacteria. We applied a whole assemblage shotgun transcript sequencing approach to samples collected from a bloom of C. watsonii observed in the South Pacific to understand the genomic mechanisms that may lead to high population densities. We obtained 999 C. watsonii transcript reads from two metatranscriptomes prepared from mixed assemblage RNA collected in the day and at night. The C. watsonii population had unexpectedly high transcription of hypothetical protein genes (31% of protein-encoding genes) and transposases (12%). Furthermore, genes were expressed that are necessary for living in the oligotrophic ocean, including the nitrogenase cluster and the iron-stress-induced protein A (isiA) that functions to protect photosystem I from high-light-induced damage. C. watsonii transcripts retrieved from metatranscriptomes at other locations in the southwest Pacific Ocean, station ALOHA and the equatorial Atlantic Ocean were similar in composition to those recovered in the enriched population. Quantitative PCR and quantitative reverse transcriptase PCR were used to confirm the high expression of these genes within the bloom, but transcription patterns varied at shallower and deeper horizons. These data represent the first transcript study of a rare individual microorganism in situ and provide insight into the mechanisms of genome diversification and the ecophysiology of natural populations of keystone organisms that are important in global nitrogen cycling.The ISME Journal (2009) 3, 618–631; doi:10.1038/ismej.2009.8; published online 19 February 2009 [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of ISME Journal: Multidisciplinary Journal of Microbial Ecology is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1038/ismej.2009.8 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 14 StartPage: 618 Subjects: – SubjectFull: Cyanobacteria Type: general – SubjectFull: Heterogeneity Type: general – SubjectFull: Ecophysiology Type: general – SubjectFull: Gene expression Type: general – SubjectFull: Nitrogen cycle Type: general – SubjectFull: Genomes Type: general – SubjectFull: Cyanobacterial toxins Type: general – SubjectFull: Pacific Ocean Type: general Titles: – TitleFull: In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Hewson, Ian – PersonEntity: Name: NameFull: Poretsky, Rachel S. – PersonEntity: Name: NameFull: Beinart, Roxanne A. – PersonEntity: Name: NameFull: White, Angelicque E. – PersonEntity: Name: NameFull: Tuo Shi – PersonEntity: Name: NameFull: Bench, Shellie R. – PersonEntity: Name: NameFull: Moisander, Pia H. – PersonEntity: Name: NameFull: Paerl, Ryan W. – PersonEntity: Name: NameFull: Tripp, H. James – PersonEntity: Name: NameFull: Montoya, Joseph P. – PersonEntity: Name: NameFull: Moran, Mary Ann – PersonEntity: Name: NameFull: Zehr, Jonathan P. IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 05 Text: May2009 Type: published Y: 2009 Identifiers: – Type: issn-print Value: 17517362 Numbering: – Type: volume Value: 3 – Type: issue Value: 5 Titles: – TitleFull: ISME Journal: Multidisciplinary Journal of Microbial Ecology Type: main |
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