skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Vampirovibrio chlorellavorus draft genome sequence, annotation, and preliminary characterization of pathogenicity determinants

Abstract

Vampirovibrio chlorellavorus is recognized as a pathogen of commercially-relevant Chlorella species. Algal infection and total loss of productivity (biomass) often occurs when susceptible algal hosts are cultivated in outdoor open pond systems. The pathogenic life cycle of this bacterium has been inferred from laboratory and field observations, and corroborated in part by the genomic analyses for two Arizona isolates recovered from an open algal reactor. V. chlorellavorus predation has been reported to occur in geographically-and environmentally-diverse conditions. Genomic analyses of these and additional field isolates is expected to reveal new information about the extent of ecological diversity and genes involved in host-pathogen interactions. The draft genome sequences for two isolates of the predatory V. chlorellavorus (Cyanobacteria; Ca. Melainabacteria) from an outdoor cultivation system located in the Arizona Sonoran Desert were assembled and annotated. The genomes were sequenced and analyzed to identify genes (proteins) with predicted involvement in predation, infection, and cell death of Chlorella host species prioritized for biofuel production at sites identified as highly suitable for algal production in the southwestern USA. Genomic analyses identified several predicted genes encoding secreted proteins that are potentially involved in pathogenicity, and at least three apparently complete sets of virulence (Vir) genes, characteristicmore » of the VirB-VirD type system encoding the canonical VirB1-11 and VirD4 proteins, respectively. Additional protein functions were predicted suggesting their involvement in quorum sensing and motility. The genomes of two previously uncharacterized V. chlorellavorus isolates reveal nucleotide and protein level divergence between each other, and a previously sequenced V. chlorellavorus genome. This new knowledge will enhance the fundamental understanding of trans-kingdom interactions between a unique cosmopolitan cyanobacterial pathogen and its green microalgal host, of broad interest as a source of harvestable biomass for biofuels or bioproducts.« less

Authors:
ORCiD logo [1];  [2]; ORCiD logo [1];  [2]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  2. Univ. of Arizona, Tucson, AZ (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Office of Energy Efficiency and Renewable Energy (EERE)
OSTI Identifier:
1557759
Report Number(s):
LA-UR-19-20027
Journal ID: ISSN 1322-0829
Grant/Contract Number:  
89233218CNA000001
Resource Type:
Accepted Manuscript
Journal Name:
Phycological Research
Additional Journal Information:
Journal Name: Phycological Research; Journal ID: ISSN 1322-0829
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biological Science; Algae pathogens; algal pathogen; chlorella; melainabacteria; VirB

Citation Formats

Hovde, Blake T., Steichen, Seth A., Starkenburg, Shawn R., and Brown, Judith K. Vampirovibrio chlorellavorus draft genome sequence, annotation, and preliminary characterization of pathogenicity determinants. United States: N. p., 2019. Web. doi:10.1111/pre.12392.
Hovde, Blake T., Steichen, Seth A., Starkenburg, Shawn R., & Brown, Judith K. Vampirovibrio chlorellavorus draft genome sequence, annotation, and preliminary characterization of pathogenicity determinants. United States. doi:10.1111/pre.12392.
Hovde, Blake T., Steichen, Seth A., Starkenburg, Shawn R., and Brown, Judith K. Wed . "Vampirovibrio chlorellavorus draft genome sequence, annotation, and preliminary characterization of pathogenicity determinants". United States. doi:10.1111/pre.12392. https://www.osti.gov/servlets/purl/1557759.
@article{osti_1557759,
title = {Vampirovibrio chlorellavorus draft genome sequence, annotation, and preliminary characterization of pathogenicity determinants},
author = {Hovde, Blake T. and Steichen, Seth A. and Starkenburg, Shawn R. and Brown, Judith K.},
abstractNote = {Vampirovibrio chlorellavorus is recognized as a pathogen of commercially-relevant Chlorella species. Algal infection and total loss of productivity (biomass) often occurs when susceptible algal hosts are cultivated in outdoor open pond systems. The pathogenic life cycle of this bacterium has been inferred from laboratory and field observations, and corroborated in part by the genomic analyses for two Arizona isolates recovered from an open algal reactor. V. chlorellavorus predation has been reported to occur in geographically-and environmentally-diverse conditions. Genomic analyses of these and additional field isolates is expected to reveal new information about the extent of ecological diversity and genes involved in host-pathogen interactions. The draft genome sequences for two isolates of the predatory V. chlorellavorus (Cyanobacteria; Ca. Melainabacteria) from an outdoor cultivation system located in the Arizona Sonoran Desert were assembled and annotated. The genomes were sequenced and analyzed to identify genes (proteins) with predicted involvement in predation, infection, and cell death of Chlorella host species prioritized for biofuel production at sites identified as highly suitable for algal production in the southwestern USA. Genomic analyses identified several predicted genes encoding secreted proteins that are potentially involved in pathogenicity, and at least three apparently complete sets of virulence (Vir) genes, characteristic of the VirB-VirD type system encoding the canonical VirB1-11 and VirD4 proteins, respectively. Additional protein functions were predicted suggesting their involvement in quorum sensing and motility. The genomes of two previously uncharacterized V. chlorellavorus isolates reveal nucleotide and protein level divergence between each other, and a previously sequenced V. chlorellavorus genome. This new knowledge will enhance the fundamental understanding of trans-kingdom interactions between a unique cosmopolitan cyanobacterial pathogen and its green microalgal host, of broad interest as a source of harvestable biomass for biofuels or bioproducts.},
doi = {10.1111/pre.12392},
journal = {Phycological Research},
number = ,
volume = ,
place = {United States},
year = {2019},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

The host Range of the Chlorellavorous Bacterium ("Vampirovibrio Chlorellvorus")
journal, December 1986


Association of Vampirovibrio chlorellavorus with decline and death of Chlorella sorokiniana in outdoor reactors
journal, October 2018

  • Park, Sang-Hyuck; Steichen, Seth A.; Li, Xuehui
  • Journal of Applied Phycology, Vol. 31, Issue 2
  • DOI: 10.1007/s10811-018-1633-9

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
journal, April 2012


Prokka: rapid prokaryotic genome annotation
journal, March 2014


BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
journal, June 2015


A Greedy Algorithm for Aligning DNA Sequences
journal, February 2000

  • Zhang, Zheng; Schwartz, Scott; Wagner, Lukas
  • Journal of Computational Biology, Vol. 7, Issue 1-2
  • DOI: 10.1089/10665270050081478

QGB: Combined Use of Sequence Similarity and Codon Bias for Coding Region Identification
journal, January 1994

  • States, David J.; Gish, Warren
  • Journal of Computational Biology, Vol. 1, Issue 1
  • DOI: 10.1089/cmb.1994.1.39

VirB1* Promotes T-Pilus Formation in the vir-Type IV Secretion System of Agrobacterium tumefaciens
journal, July 2007

  • Zupan, J.; Hackworth, C. A.; Aguilar, J.
  • Journal of Bacteriology, Vol. 189, Issue 18
  • DOI: 10.1128/JB.00480-07

ABC transporter-mediated uptake of iron, siderophores, heme and vitamin B12
journal, April 2001


Real-time quantitative detection of Vampirovibrio chlorellavorus, an obligate bacterial pathogen of Chlorella sorokiniana
journal, October 2018


Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus
journal, January 2015

  • Soo, Rochelle M.; Woodcroft, Ben J.; Parks, Donovan H.
  • PeerJ, Vol. 3
  • DOI: 10.7717/peerj.968

A large-scale evaluation of algorithms to calculate average nucleotide identity
journal, February 2017


Antagonistic association of the chlorellavorus bacterium (“Bdellovibrio” chlorellavorus) withChlorella vulgaris
journal, January 1978

  • Coder, David M.; Starr, Mortimer P.
  • Current Microbiology, Vol. 1, Issue 1
  • DOI: 10.1007/BF02601710

ATP-Binding Cassette Transporters in Bacteria
journal, June 2004


The Mosaic Type IV Secretion Systems
journal, January 2016


A novel predatory bacterium infecting the eukaryotic alga Nannochloropsis
journal, June 2018


Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
journal, April 2017

  • Huerta-Cepas, Jaime; Forslund, Kristoffer; Coelho, Luis Pedro
  • Molecular Biology and Evolution, Vol. 34, Issue 8
  • DOI: 10.1093/molbev/msx148

Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements
journal, June 2004


Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform
journal, November 2016

  • Li, Po-E; Lo, Chien-Chi; Anderson, Joseph J.
  • Nucleic Acids Research, Vol. 45, Issue 1
  • DOI: 10.1093/nar/gkw1027

The ABC of ABCs: a phylogenetic and functional classification of ABC systems in living organisms
journal, April 2001


CDD/SPARCLE: functional classification of proteins via subfamily domain architectures
journal, November 2016

  • Marchler-Bauer, Aron; Bo, Yu; Han, Lianyi
  • Nucleic Acids Research, Vol. 45, Issue D1
  • DOI: 10.1093/nar/gkw1129