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Title: Permanent draft genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria

Abstract

The nonheterocystous filamentous cyanobacterium, strain ESFC-1, is a recently described member of the order Oscillatoriales within the Cyanobacteria. ESFC-1 has been shown to be a major diazotroph in the intertidal microbial mat system at Elkhorn Slough, CA, USA. Based on phylogenetic analyses of the 16S RNA gene, ESFC-1 appears to belong to a unique, genus-level divergence; the draft genome sequence of this strain has now been determined. Here we report features of this genome as they relate to the ecological functions and capabilities of strain ESFC-1. The 5,632,035 bp genome sequence encodes 4914 protein-coding genes and 92 RNA genes. One striking feature of this cyanobacterium is the apparent lack of either uptake or bi-directional hydrogenases typically expected within a diazotroph. In addition, a large genomic island is found that contains numerous low GC-content genes and genes related to extracellular polysaccharide production and cell wall synthesis and maintenance.

Authors:
 [1];  [2];  [3];  [1];  [1];  [4];  [3];  [2]
  1. NASA Ames Research Center, Moffett Field, CA (United States); Bay Area Environmental Research Institute, Petaluma, CA (United States)
  2. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  3. NASA Ames Research Center, Moffett Field, CA (United States)
  4. NASA Ames Research Center, Moffett Field, CA (United States); Univ. of Vienna, Vienna (Austria)
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1367987
Report Number(s):
LLNL-JRNL-700959
Journal ID: ISSN 1944-3277
Grant/Contract Number:  
AC52-07NA27344
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Cyanobacteria; Nitrogen fixation; Hydrogenase; Intertidal microbial mat

Citation Formats

Everroad, R. Craig, Stuart, Rhona K., Bebout, Brad M., Detweiler, Angela M., Lee, Jackson Z., Woebken, Dagmar, Prufert-Bebout, Leslie, and Pett-Ridge, Jennifer. Permanent draft genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria. United States: N. p., 2016. Web. doi:10.1186/s40793-016-0174-6.
Everroad, R. Craig, Stuart, Rhona K., Bebout, Brad M., Detweiler, Angela M., Lee, Jackson Z., Woebken, Dagmar, Prufert-Bebout, Leslie, & Pett-Ridge, Jennifer. Permanent draft genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria. United States. doi:10.1186/s40793-016-0174-6.
Everroad, R. Craig, Stuart, Rhona K., Bebout, Brad M., Detweiler, Angela M., Lee, Jackson Z., Woebken, Dagmar, Prufert-Bebout, Leslie, and Pett-Ridge, Jennifer. Wed . "Permanent draft genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria". United States. doi:10.1186/s40793-016-0174-6. https://www.osti.gov/servlets/purl/1367987.
@article{osti_1367987,
title = {Permanent draft genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria},
author = {Everroad, R. Craig and Stuart, Rhona K. and Bebout, Brad M. and Detweiler, Angela M. and Lee, Jackson Z. and Woebken, Dagmar and Prufert-Bebout, Leslie and Pett-Ridge, Jennifer},
abstractNote = {The nonheterocystous filamentous cyanobacterium, strain ESFC-1, is a recently described member of the order Oscillatoriales within the Cyanobacteria. ESFC-1 has been shown to be a major diazotroph in the intertidal microbial mat system at Elkhorn Slough, CA, USA. Based on phylogenetic analyses of the 16S RNA gene, ESFC-1 appears to belong to a unique, genus-level divergence; the draft genome sequence of this strain has now been determined. Here we report features of this genome as they relate to the ecological functions and capabilities of strain ESFC-1. The 5,632,035 bp genome sequence encodes 4914 protein-coding genes and 92 RNA genes. One striking feature of this cyanobacterium is the apparent lack of either uptake or bi-directional hydrogenases typically expected within a diazotroph. In addition, a large genomic island is found that contains numerous low GC-content genes and genes related to extracellular polysaccharide production and cell wall synthesis and maintenance.},
doi = {10.1186/s40793-016-0174-6},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 11,
place = {United States},
year = {Wed Aug 24 00:00:00 EDT 2016},
month = {Wed Aug 24 00:00:00 EDT 2016}
}

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Works referenced in this record:

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing
journal, December 2012

  • Shih, P. M.; Wu, D.; Latifi, A.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 3, p. 1053-1058
  • DOI: 10.1073/pnas.1217107110