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Prokaryotes

Genome Sequence of Hydrogenovibrio sp. Strain SC-1, a Chemolithoautotrophic Sulfur and Iron Oxidizer

Christopher Neely, Charbel Bou Khalil, Alex Cervantes, Raquel Diaz, Angelica Escobar, Karen Ho, Stephen Hoefler, Hillary H. Smith, Karla Abuyen, Pratixaben Savalia, Kenneth H. Nealson, David Emerson, Benjamin Tully, Roman A. Barco, Jan Amend
Christopher Neely
fRio Hondo Community College, Whittier, California, USA
mCommunity College Cultivation Cohort, University of Southern California, Los Angeles, California, USA
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Charbel Bou Khalil
jOrange Coast College, Costa Mesa, California, USA
mCommunity College Cultivation Cohort, University of Southern California, Los Angeles, California, USA
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Alex Cervantes
fRio Hondo Community College, Whittier, California, USA
mCommunity College Cultivation Cohort, University of Southern California, Los Angeles, California, USA
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Raquel Diaz
hBrookdale Community College, Middletown, New Jersey, USA
mCommunity College Cultivation Cohort, University of Southern California, Los Angeles, California, USA
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Angelica Escobar
kSantiago Canyon College, Orange, California, USA
mCommunity College Cultivation Cohort, University of Southern California, Los Angeles, California, USA
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Karen Ho
gPasadena City College, Pasadena, California, USA
mCommunity College Cultivation Cohort, University of Southern California, Los Angeles, California, USA
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Stephen Hoefler
iMission College, Santa Clara, California, USA
mCommunity College Cultivation Cohort, University of Southern California, Los Angeles, California, USA
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Hillary H. Smith
lWaubonsee Community College, Sugar Grove, Illinois, USA
mCommunity College Cultivation Cohort, University of Southern California, Los Angeles, California, USA
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Karla Abuyen
cDepartment of Environmental Studies, University of Southern California, Los Angeles, California, USA
dCenter for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, California, USA
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Pratixaben Savalia
aDepartment of Earth Sciences, University of Southern California, Los Angeles, California, USA
dCenter for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, California, USA
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Kenneth H. Nealson
aDepartment of Earth Sciences, University of Southern California, Los Angeles, California, USA
bDepartment of Biological Sciences, University of Southern California, Los Angeles, California, USA
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David Emerson
eBigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
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Benjamin Tully
bDepartment of Biological Sciences, University of Southern California, Los Angeles, California, USA
dCenter for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, California, USA
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Roman A. Barco
aDepartment of Earth Sciences, University of Southern California, Los Angeles, California, USA
dCenter for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, California, USA
eBigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
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Jan Amend
aDepartment of Earth Sciences, University of Southern California, Los Angeles, California, USA
bDepartment of Biological Sciences, University of Southern California, Los Angeles, California, USA
dCenter for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, California, USA
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DOI: 10.1128/genomeA.01581-17
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ABSTRACT

Hydrogenovibrio sp. strain SC-1 was isolated from pyrrhotite incubated in situ in the marine surface sediment of Catalina Island, CA. Strain SC-1 has demonstrated autotrophic growth through the oxidation of thiosulfate and iron. Here, we present the 2.45-Mb genome sequence of SC-1, which contains 2,262 protein-coding genes.

GENOME ANNOUNCEMENT

Iron is an essential trace element that limits primary productivity in surface marine waters (1). Microaerophilic neutrophilic iron-oxidizing bacteria are involved in the cycling of iron in the marine environment; however, this biological function has so far been predominantly associated with representatives of the class Zetaproteobacteria (2) and with other uncharacterized isolates (3). Here, we present the genome sequence of Hydrogenovibrio sp. strain SC-1, which was isolated from pyrrhotite coupons that were incubated in situ on surface marine sediments of Big Fisherman’s Cove, Catalina Island, CA. SC-1 is the only known iron-oxidizing bacterium within the family Piscirickettsiaceae (4). Similar to the iron-oxidizing Zetaproteobacteria, SC-1 is able to use the energy from iron to grow autotrophically (5). Strain SC-1 is a member of the Thiomicrospira-Hydrogenovibrio-Thiomicrorhabdus group of bacteria, which is known for autotrophic thiosulfate oxidation and obligate chemolithoautotrophy (6).

SC-1 genomic DNA was extracted by bead beating using the FastDNA Spin soil kit (MP Biomedical, Santa Ana, CA, USA) per the manufacturer’s protocol. DNA was sequenced at the Single Cell Genomics Center at the Bigelow Laboratory for Ocean Sciences using a NextSeq instrument (Illumina, USA). A total of 6,336,875 raw paired-end sequences were generated and processed using Trimmomatic version 0.32 (7) to trim the last 5 bp of each sequence, regions with low quality scores (Q < 15), and reads less than 36 bp in length, resulting in 5,349,014 quality-controlled sequences. As part of the standard operating procedure for the Single Cell Genomics Center, quality-controlled sequences were processed prior to assembly using a complexity filter threshold of 0.05, normalization with kmernorm version 1.05 (parameters: k = 21; t = 30; c = 3) (http://sourceforge.net/projects/kmernorm/), and a contamination filter with an identity threshold of 1, yielding 2,313,229 high-quality paired-end sequences (8). These sequences were de novo assembled using the SPAdes genome assembler version 3.0.0 (9), generating 41 contigs. The maximum contig length was 263,867 bp. The Hydrogenovibrio sp. SC-1 genome was 2.45 Mb in length, with a GC content of 42.9% and an N50 value of 131,404 bp. Annotation was performed by the Joint Genome Institute (JGI) Integrated Microbial Genomes system (10), resulting in 2,262 protein-coding genes, 2 rRNAs (1 copy each of the 16S and 23S rRNA genes), and 36 tRNA genes.

Analysis revealed genes that encode proteins for the tricarboxylic acid cycle, pentose phosphate cycle, glycolysis, and carbon fixation via the Calvin cycle and for the oxidations of thiosulfate (soxABCXYZ) and sulfide (sulfide-quinone reductase). Genes coding for flagellum biosynthesis and chemotaxis indicate that SC-1 bacteria have the potential for motility, but this has not been observed under culture conditions. Genes that show the potential for the oxidation of molecular hydrogen (hydAB and hypABCDEF) were detected.

Accession number(s).This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession no. PKGB00000000. The version associated with this submission is version PKGB01000000. Also, the SC-1 genome sequence described in this paper has been deposited in the JGI Integrated Microbial Genomes and Microbiomes system and in the JGI Genome Portal under IMG Genome ID 2627853948.

ACKNOWLEDGMENTS

This research was funded as part of the 2017 NSF Community College Cultivation Cohort (C4) Research Experience for Undergraduates (grant OCE-1460892), performed in conjunction with the NSF Science and Technology Center for Dark Energy Biosphere Investigations (grant OCE-0939654) and the NASA Astrobiology Institute–Life Underground (grant NNA-13AA92A). Sequencing was supported by NASA Exobiology grant NNX15AM11G. R.A.B. was supported by the NSF Postdoctoral Research Fellowship in Biology (award 1523639).

We thank Liz Fergusson (Bigelow Laboratory) for setting up sequencing reactions.

This is C-DEBI contribution no. 409.

FOOTNOTES

    • Received 2 January 2018.
    • Accepted 5 January 2018.
    • Published 1 February 2018.
  • Copyright © 2018 Neely et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

REFERENCES

  1. 1.↵
    1. Gledhill M,
    2. Buck KN
    . 2012. The organic complexation of iron in the marine environment: a review. Front Microbiol 3:69. doi:10.3389/fmicb.2012.00069.
    OpenUrlCrossRefPubMed
  2. 2.↵
    1. Emerson D,
    2. Fleming EJ,
    3. McBeth JM
    . 2010. Iron-oxidizing bacteria: an environmental and genomic perspective. Annu Rev Microbiol 64:561–583. doi:10.1146/annurev.micro.112408.134208.
    OpenUrlCrossRefPubMedWeb of Science
  3. 3.↵
    1. Edwards KJ,
    2. Rogers DR,
    3. Wirsen CO,
    4. McCollom TM
    . 2003. Isolation and characterization of novel psychrophilic, neutrophilic, Fe-oxidizing, chemolithoautotrophic α- and γ-proteobacteria from the deep sea. Appl Environ 69:2906–2913. doi:10.1128/AEM.69.5.2906-2913.2003.
    OpenUrlCrossRef
  4. 4.↵
    1. Barco RA,
    2. Hoffman CL,
    3. Ramírez GA,
    4. Toner BM,
    5. Edwards KJ,
    6. Sylvan JB
    . 2017. In-situ incubation of iron-sulfur mineral reveals a diverse chemolithoautotrophic community and a new biogeochemical role for Thiomicrospira. Environ Microbiol 19:1322–1337. doi:10.1111/1462-2920.13666.
    OpenUrlCrossRef
  5. 5.↵
    1. Emerson D,
    2. Rentz JA,
    3. Lilburn TG,
    4. Davis RE,
    5. Aldrich H,
    6. Chan C,
    7. Moyer CL
    . 2007. A novel lineage of Proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities. PLoS One 2:e667–e669. doi:10.1371/journal.pone.0000667.
    OpenUrlCrossRefPubMed
  6. 6.↵
    1. Boden R,
    2. Scott KM,
    3. Williams J,
    4. Russel S,
    5. Antonen K,
    6. Rae AW,
    7. Hutt LP
    . 2017. An evaluation of Thiomicrospira, Hydrogenovibrio and Thioalkalimicrobium: reclassification of four species of Thiomicrospira to each Thiomicrorhabdus gen. nov. and Hydrogenovibrio, and reclassification of all four species of Thioalkalimicrobium to Thiomicrospira. Int J Syst Evol Microbiol 67:1140–1151. doi:10.1099/ijsem.0.001855.
    OpenUrlCrossRef
  7. 7.↵
    1. Bolger AM,
    2. Lohse M,
    3. Usadel B
    . 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi:10.1093/bioinformatics/btu170.
    OpenUrlCrossRefPubMedWeb of Science
  8. 8.↵
    1. Stepanauskas R,
    2. Fergusson EA,
    3. Brown J,
    4. Poulton NJ,
    5. Tupper B,
    6. Labonté JM,
    7. Becraft ED,
    8. Brown JM,
    9. Pachiadaki MG,
    10. Povilaitis T,
    11. Thompson BP,
    12. Mascena CJ,
    13. Bellows WK,
    14. Lubys A
    . 2017. Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles. Nat Commun 8:84. doi:10.1038/s41467-017-00128-z.
    OpenUrlCrossRefPubMed
  9. 9.↵
    1. Bankevich A,
    2. Nurk S,
    3. Antipov D,
    4. Gurevich AA,
    5. Dvorkin M,
    6. Kulikov AS,
    7. Lesin VM,
    8. Nikolenko SI,
    9. Pham S,
    10. Prjibelski AD,
    11. Pyshkin AV,
    12. Sirotkin AV,
    13. Vyahhi N,
    14. Tesler G,
    15. Alekseyev MA,
    16. Pevzner PA
    . 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi:10.1089/cmb.2012.0021.
    OpenUrlCrossRefPubMed
  10. 10.↵
    1. Markowitz VM,
    2. Korzeniewski F,
    3. Palaniappan K,
    4. Szeto E,
    5. Werner G,
    6. Padki A,
    7. Zhao X,
    8. Dubchak I,
    9. Hugenholtz P,
    10. Anderson I,
    11. Lykidis A,
    12. Mavromatis K,
    13. Ivanova N,
    14. Kyrpides NC
    . 2006. The integrated microbial genomes (IMG) system. Nucleic Acids Res 34:D344–D348. doi:10.1093/nar/gkj024.
    OpenUrlCrossRefPubMedWeb of Science
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Genome Sequence of Hydrogenovibrio sp. Strain SC-1, a Chemolithoautotrophic Sulfur and Iron Oxidizer
Christopher Neely, Charbel Bou Khalil, Alex Cervantes, Raquel Diaz, Angelica Escobar, Karen Ho, Stephen Hoefler, Hillary H. Smith, Karla Abuyen, Pratixaben Savalia, Kenneth H. Nealson, David Emerson, Benjamin Tully, Roman A. Barco, Jan Amend
Genome Announcements Feb 2018, 6 (5) e01581-17; DOI: 10.1128/genomeA.01581-17

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Genome Sequence of Hydrogenovibrio sp. Strain SC-1, a Chemolithoautotrophic Sulfur and Iron Oxidizer
Christopher Neely, Charbel Bou Khalil, Alex Cervantes, Raquel Diaz, Angelica Escobar, Karen Ho, Stephen Hoefler, Hillary H. Smith, Karla Abuyen, Pratixaben Savalia, Kenneth H. Nealson, David Emerson, Benjamin Tully, Roman A. Barco, Jan Amend
Genome Announcements Feb 2018, 6 (5) e01581-17; DOI: 10.1128/genomeA.01581-17
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