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:
-
- NASA Ames Research Center, Moffett Field, CA (United States); Bay Area Environmental Research Institute, Petaluma, CA (United States)
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- NASA Ames Research Center, Moffett Field, CA (United States)
- NASA Ames Research Center, Moffett Field, CA (United States); Univ. of Vienna, Vienna (Austria)
- Publication Date:
- Research Org.:
- Lawrence Livermore National Laboratory (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:
- 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. https://doi.org/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. https://doi.org/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}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 4 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Revisiting N2 fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach
journal, October 2014
- Woebken, Dagmar; Burow, Luke C.; Behnam, Faris
- The ISME Journal, Vol. 9, Issue 2
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
journal, March 2010
- Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent
- Systematic Biology, Vol. 59, Issue 3
Coastal Strains of Marine Synechococcus Species Exhibit Increased Tolerance to Copper Shock and a Distinctive Transcriptional Response Relative to Those of Open-Ocean Strains
journal, June 2009
- Stuart, R. K.; Dupont, C. L.; Johnson, D. A.
- Applied and Environmental Microbiology, Vol. 75, Issue 15
Cyanobacterial reuse of extracellular organic carbon in microbial mats
journal, October 2015
- Stuart, Rhona K.; Mayali, Xavier; Lee, Jackson Z.
- The ISME Journal, Vol. 10, Issue 5
An Improved General Amino Acid Replacement Matrix
journal, April 2008
- Le, S. Q.; Gascuel, O.
- Molecular Biology and Evolution, Vol. 25, Issue 7
Physiological ecology of cyanobacteria in microbial mats and other communities
journal, September 1995
- Stal, Lucas J.
- New Phytologist, Vol. 131, Issue 1
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment
journal, March 1998
- Ewing, Brent; Hillier, LaDeana; Wendl, Michael C.
- Genome Research, Vol. 8, Issue 3
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008
- Zerbino, D. R.; Birney, E.
- Genome Research, Vol. 18, Issue 5
Diel Interactions of Oxygenic Photosynthesis and N2 Fixation (Acetylene Reduction) in a Marine Microbial Mat Community
journal, January 1987
- Bebout, Brad M.; Paerl, Hans W.; Crocker, Kenneth M.
- Applied and Environmental Microbiology, Vol. 53, Issue 10
Hydrogenases and Hydrogen Metabolism of Cyanobacteria
journal, March 2002
- Tamagnini, P.; Axelsson, R.; Lindberg, P.
- Microbiology and Molecular Biology Reviews, Vol. 66, Issue 1
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
journal, October 2003
- Guindon, Stéphane; Gascuel, Olivier
- Systematic Biology, Vol. 52, Issue 5
The minimum information about a genome sequence (MIGS) specification
journal, May 2008
- Field, Dawn; Garrity, George; Gray, Tanya
- Nature Biotechnology, Vol. 26, Issue 5
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons
journal, August 2011
- Alikhan, Nabil-Fareed; Petty, Nicola K.; Ben Zakour, Nouri L.
- BMC Genomics, Vol. 12, Issue 1
Draft Genome Sequence of an Oscillatorian Cyanobacterium, Strain ESFC-1
journal, June 2013
- Everroad, R. C.; Woebken, D.; Singer, S. W.
- Genome Announcements, Vol. 1, Issue 4
GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
journal, June 2001
- Besemer, J.
- Nucleic Acids Research, Vol. 29, Issue 12
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990
- Woese, C. R.; Kandler, O.; Wheelis, M. L.
- Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990
- Woese, C. R.; Kandler, O.; Wheelis, M. L.
- Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
Physiological ecology of cyanobacteria in microbial mats and other communities
journal, September 1995
- Stal, Lucas J.
- New Phytologist, Vol. 131, Issue 1
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
The bidirectional hydrogenase of Synechocystis sp. PCC 6803 works as an electron valve during photosynthesis
journal, March 2000
- Appel, Jens; Phunpruch, Saranya; Steinmüller, Klaus
- Archives of Microbiology, Vol. 173, Issue 5-6
The integrated microbial genomes (IMG) system
journal, January 2006
- Markowitz, V. M.
- Nucleic Acids Research, Vol. 34, Issue 90001
Cyanobacterial reuse of extracellular organic carbon in microbial mats
journal, October 2015
- Stuart, Rhona K.; Mayali, Xavier; Lee, Jackson Z.
- The ISME Journal, Vol. 10, Issue 5
Sulphide-dependent anoxygenic photosynthesis in the cyanobacterium Oscillatoria limnetica
journal, October 1975
- Cohen, Y.; JØRgensen, B. B.; Padan, E.
- Nature, Vol. 257, Issue 5526
Multiplex profiling of serum proteins in solution using barcoded antibody fragments and next generation sequencing
journal, July 2020
- Brofelth, Mattias; Ekstrand, Anna Isinger; Gour, Shashank
- Communications Biology, Vol. 3, Issue 1
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
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008
- Zerbino, D. R.; Birney, E.
- Genome Research, Vol. 18, Issue 5
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
journal, March 1998
- Ewing, Brent; Green, Phil
- Genome Research, Vol. 8, Issue 3
Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis
journal, January 2012
- Woebken, Dagmar; Burow, Luke C.; Prufert-Bebout, Leslie
- The ISME Journal, Vol. 6, Issue 7
Generation of Long Insert Pairs Using a Cre-LoxP Inverse PCR Approach
journal, January 2012
- Peng, Ze; Zhao, Zhiying; Nath, Nandita
- PLoS ONE, Vol. 7, Issue 1
The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008
- Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.
- BMC Genomics, Vol. 9, Issue 1, Article No. 75
Fermentation in cyanobacteria
journal, September 1997
- Stal, L.
- FEMS Microbiology Reviews, Vol. 21, Issue 2
Diurnal Cycle of Oxygen and Sulfide Microgradients and Microbial Photosynthesis in a Cyanobacterial Mat Sediment
journal, January 1979
- Jørgensen, Bo B.; Revsbech, Niels P.; Blackburn, T. Henry
- Applied and Environmental Microbiology, Vol. 38, Issue 1
Occurrence of Hydrogenases in Cyanobacteria and Anoxygenic Photosynthetic Bacteria: Implications for the Phylogenetic Origin of Cyanobacterial and Algal Hydrogenases
journal, November 2006
- Ludwig, Marcus; Schulz-Friedrich, Rüdiger; Appel, Jens
- Journal of Molecular Evolution, Vol. 63, Issue 6
Occurrence of Hydrogenases in Cyanobacteria and Anoxygenic Photosynthetic Bacteria: Implications for the Phylogenetic Origin of Cyanobacterial and Algal Hydrogenases
journal, November 2006
- Ludwig, Marcus; Schulz-Friedrich, Rüdiger; Appel, Jens
- Journal of Molecular Evolution, Vol. 63, Issue 6
A simple, fast, and accurate method of phylogenomic inference
journal, January 2008
- Wu, Martin; Eisen, Jonathan A.
- Genome Biology, Vol. 9, Issue 10
Cyanobacterial hydrogenases: diversity, regulation and applications
journal, November 2007
- Tamagnini, Paula; Leitão, Elsa; Oliveira, Paulo
- FEMS Microbiology Reviews, Vol. 31, Issue 6
Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics
journal, November 2012
- Burow, Luke C.; Woebken, Dagmar; Marshall, Ian PG
- The ISME Journal, Vol. 7, Issue 4
Diversity in hydrogen evolution from bidirectional hydrogenases in cyanobacteria from terrestrial, freshwater and marine intertidal environments
journal, November 2012
- Kothari, Ankita; Potrafka, Ruth; Garcia-Pichel, Ferran
- Journal of Biotechnology, Vol. 162, Issue 1
Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics
journal, November 2012
- Burow, Luke C.; Woebken, Dagmar; Marshall, Ian PG
- The ISME Journal, Vol. 7, Issue 4
ALLPATHS: De novo assembly of whole-genome shotgun microreads
journal, February 2008
- Butler, J.; MacCallum, I.; Kleber, M.
- Genome Research, Vol. 18, Issue 5
Cyanobacterial hydrogenases: diversity, regulation and applications
journal, November 2007
- Tamagnini, Paula; Leitão, Elsa; Oliveira, Paulo
- FEMS Microbiology Reviews, Vol. 31, Issue 6
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
Molecular and morphological characterization of cyanobacterial diversity in the stromatolites of Highborne Cay, Bahamas
journal, January 2009
- Foster, Jamie S.; Green, Stefan J.; Ahrendt, Steven R.
- The ISME Journal, Vol. 3, Issue 5
The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008
- Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.
- BMC Genomics, Vol. 9, Issue 1, Article No. 75
Generation of Long Insert Pairs Using a Cre-LoxP Inverse PCR Approach
journal, January 2012
- Peng, Ze; Zhao, Zhiying; Nath, Nandita
- PLoS ONE, Vol. 7, Issue 1
ALLPATHS: De novo assembly of whole-genome shotgun microreads
journal, February 2008
- Butler, J.; MacCallum, I.; Kleber, M.
- Genome Research, Vol. 18, Issue 5
Hydrogen metabolism in organisms with oxygenic photosynthesis: hydrogenases as important regulatory devices for a proper redox poising?
journal, November 1998
- Appel, Jens; Schulz, Rüdiger
- Journal of Photochemistry and Photobiology B: Biology, Vol. 47, Issue 1
Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay
journal, October 2011
- Burow, Luke C.; Woebken, Dagmar; Bebout, Brad M.
- The ISME Journal, Vol. 6, Issue 4
Diversity in hydrogen evolution from bidirectional hydrogenases in cyanobacteria from terrestrial, freshwater and marine intertidal environments
journal, November 2012
- Kothari, Ankita; Potrafka, Ruth; Garcia-Pichel, Ferran
- Journal of Biotechnology, Vol. 162, Issue 1
Consed: A Graphical Tool for Sequence Finishing
journal, March 1998
- Gordon, David; Abajian, Chris; Green, Phil
- Genome Research, Vol. 8, Issue 3
A simple, fast, and accurate method of phylogenomic inference
journal, January 2008
- Wu, Martin; Eisen, Jonathan A.
- Genome Biology, Vol. 9, Issue 10
Complexity of cyanobacterial exopolysaccharides: composition, structures, inducing factors and putative genes involved in their biosynthesis and assembly
journal, September 2009
- Pereira, Sara; Zille, Andrea; Micheletti, Ernesto
- FEMS Microbiology Reviews, Vol. 33, Issue 5
The minimum information about a genome sequence (MIGS) specification
journal, May 2008
- Field, Dawn; Garrity, George; Gray, Tanya
- Nature Biotechnology, Vol. 26, Issue 5
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons
journal, August 2011
- Alikhan, Nabil-Fareed; Petty, Nicola K.; Ben Zakour, Nouri L.
- BMC Genomics, Vol. 12, Issue 1
The integrated microbial genomes (IMG) system
journal, January 2006
- Markowitz, V. M.
- Nucleic Acids Research, Vol. 34, Issue 90001
GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
journal, June 2001
- Besemer, J.
- Nucleic Acids Research, Vol. 29, Issue 12
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
journal, March 1998
- Ewing, Brent; Green, Phil
- Genome Research, Vol. 8, Issue 3
Sulphide-dependent anoxygenic photosynthesis in the cyanobacterium Oscillatoria limnetica
journal, October 1975
- Cohen, Y.; JØRgensen, B. B.; Padan, E.
- Nature, Vol. 257, Issue 5526
Photoproduction of H2 by wildtype Anabaena PCC 7120 and a hydrogen uptake deficient mutant: from laboratory experiments to outdoor culture
journal, November 2002
- Lindblad, P.
- International Journal of Hydrogen Energy, Vol. 27, Issue 11-12
Consed: A Graphical Tool for Sequence Finishing
journal, March 1998
- Gordon, David; Abajian, Chris; Green, Phil
- Genome Research, Vol. 8, Issue 3
Molecular and morphological characterization of cyanobacterial diversity in the stromatolites of Highborne Cay, Bahamas
journal, January 2009
- Foster, Jamie S.; Green, Stefan J.; Ahrendt, Steven R.
- The ISME Journal, Vol. 3, Issue 5
The bidirectional hydrogenase of Synechocystis sp. PCC 6803 works as an electron valve during photosynthesis
journal, March 2000
- Appel, Jens; Phunpruch, Saranya; Steinmüller, Klaus
- Archives of Microbiology, Vol. 173, Issue 5-6
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
journal, October 2003
- Guindon, Stéphane; Gascuel, Olivier
- Systematic Biology, Vol. 52, Issue 5
Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay
journal, October 2011
- Burow, Luke C.; Woebken, Dagmar; Bebout, Brad M.
- The ISME Journal, Vol. 6, Issue 4
Culture-dependent characterization of cyanobacterial diversity in the intertidal zones of the Portuguese coast: A polyphasic study
journal, March 2012
- Brito, Ângela; Ramos, Vitor; Seabra, Rui
- Systematic and Applied Microbiology, Vol. 35, Issue 2
Diel Interactions of Oxygenic Photosynthesis and N2 Fixation (Acetylene Reduction) in a Marine Microbial Mat Community
journal, January 1987
- Bebout, Brad M.; Paerl, Hans W.; Crocker, Kenneth M.
- Applied and Environmental Microbiology, Vol. 53, Issue 10
Diurnal Cycle of Oxygen and Sulfide Microgradients and Microbial Photosynthesis in a Cyanobacterial Mat Sediment
journal, January 1979
- Jørgensen, Bo B.; Revsbech, Niels P.; Blackburn, T. Henry
- Applied and Environmental Microbiology, Vol. 38, Issue 1
Works referencing / citing this record:
Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat
journal, September 2018
- Lee, Jackson Z.; Everroad, R. Craig; Karaoz, Ulas
- PLOS ONE, Vol. 13, Issue 9