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Genome Sequences

Metagenome-Assembled Genome Sequence of Dolichospermum circinale Strain Clear-D4, Assembled from a Harmful Cyanobacterial Bloom Enrichment Culture

Kyra M. Florea, J. Cameron Thrash, Eric A. Webb
Frank J. Stewart, Editor
Kyra M. Florea
aDepartment of Biological Sciences, University of Southern California, Los Angeles, California, USA
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J. Cameron Thrash
aDepartment of Biological Sciences, University of Southern California, Los Angeles, California, USA
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Eric A. Webb
aDepartment of Biological Sciences, University of Southern California, Los Angeles, California, USA
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Frank J. Stewart
Georgia Institute of Technology
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DOI: 10.1128/MRA.01123-20
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ABSTRACT

Dolichospermum circinale (formerly Anabaena circinale) is a significant harmful algal bloom species. We report the draft metagenome-assembled genome (MAG) for a strain of D. circinale (Clear-D4) obtained from an enrichment culture. The genome sequence comprises 5,029,933 bp in 560 contigs with a GC content of 37%.

ANNOUNCEMENT

Cyanobacterial harmful algal blooms (cyanoHABs) pose environmental, ecological, and economic threats to freshwaters. Species of Dolichospermum, a diazotrophic, bloom-forming, heterocystous, cyanobacterial genus, have the potential to produce cyanotoxins, including microcystin, anatoxin, and saxitoxin (1–3). Increasing Dolichospermum bloom frequency in recent decades necessitates an improved understanding of this prolific cyanoHAB genus (4). Clear Lake, CA, is 303d-listed for nutrients and experiences annual cyanoHABs (5). To better understand the microbial communities involved in Dolichospermum cyanoHABs, we performed metagenomic sequencing on a Dolichospermum enrichment culture, resulting in a new metagenome-assembled genome (MAG) for Dolichospermum circinale.

Bucket tow surface water samples were collected from Clear Lake (lat 38.973166, long 122.72809) in August 2019. Free Dolichospermum trichomes, visualized with a dissecting scope, were pipettor hand-picked and enriched in 50% BG-110 medium at 25°C with 100 μmol Q/m2/s light on a 12:12-h light/dark cycle. Additions of 50% BG-110 were introduced every other week to maintain growth. Prior to sequencing, we identified the genus Dolichospermum morphologically in the above enrichments with a Zeiss AxioStar epifluorescence microscope (Oberkochen, Germany) (6). A single enrichment culture (Clear-D4) was chosen for metagenomic sequencing. Cell material from the Clear-D4 enrichment (50 ml) was filtered onto 8-μm polycarbonate filters and rinsed into 2-ml bead-beating tubes using lysing solution from the Qiagen DNeasy PowerBiofilm kit (Hilden, Germany). The cells were lysed using 5 liquid N2 freeze-thaw cycles, followed by the addition of proteinase K and incubation at 55°C overnight. Genomic DNA was then extracted using the aforementioned Qiagen kit protocol. The quality of isolated DNA was verified using Tris-borate-EDTA (TBE) gel electrophoresis and quantified via NanoDrop UV-visible (UV-Vis) spectroscopy and Qubit spectrofluorimetry (Thermo Fisher Scientific, Waltham, MA). Library preparation (i.e., NEBNext DNA library prep kit via the manufacturer’s recommendations) and 1 Gbp of Illumina paired-end (PE) 2 × 150-bp sequencing were conducted by Novogene (Nanjing, China) with 300-bp size-selected inserts, generating 19,844,532 reads. KBase and modules therein were used for de novo assembly with default settings unless otherwise noted (7). Prior to de novo assembly, the quality of the paired-end reads was checked with FastQC v0.11.5 (8), and the reads were trimmed to enhance quality using Trimmomatic v0.36 (9). De novo genome assembly was done using metaSPAdes v3.13.0 (10). Binning was completed using MaxBin2 v2.2.4 (11), with refinement using anvi-refine in Anvi’o (12). Genome annotation was completed using PGAP with default settings (13). Initial bin taxonomy was determined using GTDB-tk in the PhyloSanity wrapper (14).

Clear-D4 consisted of 560 contigs, 5,029,933 bp, a GC content of 37%, and an N50 value of 52,616 bp. A total of 4,813 coding genes were identified (12). CheckM v1.0.18 (15) (with default settings) estimated this initial MAG to be 91.85% complete with 6.47% contamination. The refined genome was phylogenetically confirmed as Dolichospermum circinale using GTDB-tk v1.1.1 db_r95 using “classify_wf.” The predicted metabolism of Clear-D4 was analyzed using the FuncSanity module of MetaSanity (14) with default settings, which projected that this organism is a diazotrophic, oxygenic photoautotroph that can reduce arsenate and produce sulfolipids. Screening for secondary metabolites with antiSMASH revealed the predicted presence of geosmins; however, no cyanobacterial toxins were detected by this analysis (16).

Data availability.This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JACVZX000000000. The version described in this paper is the first version, JACVZX010000000. The BioProject number is PRJNA657201, and the reads are available at the SRA under accession number SRX8961729.

ACKNOWLEDGMENTS

This work was funded by the University of Southern California and was part of the laboratory component of BISC419, Environmental Microbiology.

K.M.F., J.C.T., and E.A.W. wrote the paper, and K.M.F. and E.A.W. are the sources of the cultures.

We thank Elaina Graham, Ben Tully, and John F. Heidelberg for assistance with the data analysis.

FOOTNOTES

    • Received 24 September 2020.
    • Accepted 12 November 2020.
    • Published 3 December 2020.
  • Copyright © 2020 Florea 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. Sivonen K,
    2. Namikoshi M,
    3. Evans WR,
    4. Carmichael WW,
    5. Sun F,
    6. Rouhiainen L,
    7. Luukkainen R,
    8. Rinehart KL
    . 1992. Isolation and characterization of a variety of microcystins from seven strains of the cyanobacterial genus Anabaena. Appl Environ Microbiol 58:2495–2500. doi:10.1128/AEM.58.8.2495-2500.1992.
    OpenUrlAbstract/FREE Full Text
  2. 2.↵
    1. Rantala-Ylinen A,
    2. Känä S,
    3. Wang H,
    4. Rouhiainen L,
    5. Wahlsten M,
    6. Rizzi E,
    7. Berg K,
    8. Gugger M,
    9. Sivonen K
    . 2011. Anatoxin—a synthetase gene cluster of the cyanobacterium Anabaena sp. strain 37 and molecular methods to detect potential producers. Appl Environ Microbiol 77:7271–7278. doi:10.1128/AEM.06022-11.
    OpenUrlAbstract/FREE Full Text
  3. 3.↵
    1. Pereyra JPA,
    2. D'Agostino PM,
    3. Mazmouz R,
    4. Woodhouse JN,
    5. Pickford R,
    6. Jameson I,
    7. Neilan BA
    . 2017. Molecular and morphological survey of saxitoxin-producing cyanobacterium Dolichospermum circinale (Anabaena circinalis) isolated from geographically distinct regions of Australia. Toxicon 138:68–77. doi:10.1016/j.toxicon.2017.08.006.
    OpenUrlCrossRef
  4. 4.↵
    1. Li X,
    2. Dreher TW,
    3. Li R
    . 2016. An overview of diversity, occurrence, genetics and toxin production of bloom-forming Dolichospermum (Anabaena) species. Harmful Algae 54:54–68. doi:10.1016/j.hal.2015.10.015.
    OpenUrlCrossRef
  5. 5.↵
    State Water Resources Control Board. 2011. Final 2014/2016 California Integrated Report [Clean Water Act Section 303(d) List/305(b) Report].
  6. 6.↵
    1. Komárek J,
    2. Zapomìlová E
    . 2008. Planktic morphospecies of the cyanobacterial genus Anabaena = subg. Dolichospermum—2. Part: straight types. Fottea 8:1–14. doi:10.5507/fot.2008.001.
    OpenUrlCrossRef
  7. 7.↵
    1. Arkin AP,
    2. Cottingham RW,
    3. Henry CS,
    4. Harris NL,
    5. Stevens RL,
    6. Maslov S,
    7. Dehal P,
    8. Ware D,
    9. Perez F,
    10. Canon S,
    11. Sneddon MW,
    12. Henderson ML,
    13. Riehl WJ,
    14. Murphy-Olson D,
    15. Chan SY,
    16. Kamimura RT,
    17. Kumari S,
    18. Drake MM,
    19. Brettin TS,
    20. Glass EM,
    21. Chivian D,
    22. Gunter D,
    23. Weston DJ,
    24. Allen BH,
    25. Baumohl J,
    26. Best AA,
    27. Bowen B,
    28. Brenner SE,
    29. Bun CC,
    30. Chandonia J-M,
    31. Chia J-M,
    32. Colasanti R,
    33. Conrad N,
    34. Davis JJ,
    35. Davison BH,
    36. DeJongh M,
    37. Devoid S,
    38. Dietrich E,
    39. Dubchak I,
    40. Edirisinghe JN,
    41. Fang G,
    42. Faria JP,
    43. Frybarger PM,
    44. Gerlach W,
    45. Gerstein M,
    46. Greiner A,
    47. Gurtowski J,
    48. Haun HL,
    49. He F,
    50. Jain R,
    51. Joachimiak MP,
    52. Keegan KP,
    53. Kondo S,
    54. Kumar V,
    55. Land ML,
    56. Meyer F,
    57. Mills M,
    58. Novichkov PS,
    59. Oh T,
    60. Olsen GJ,
    61. Olson R,
    62. Parrello B,
    63. Pasternak S,
    64. Pearson E,
    65. Poon SS,
    66. Price GA,
    67. Ramakrishnan S,
    68. Ranjan P,
    69. Ronald PC,
    70. Schatz MC,
    71. Seaver SMD,
    72. Shukla M,
    73. Sutormin RA,
    74. Syed MH,
    75. Thomason J,
    76. Tintle NL,
    77. Wang D,
    78. Xia F,
    79. Yoo H,
    80. Yoo S,
    81. Yu D
    . 2018. KBase: the United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol 36:566–569. doi:10.1038/nbt.4163.
    OpenUrlCrossRef
  8. 8.↵
    1. Andrews S
    . 2010. FastQC: a quality control tool for high throughput sequence data. Babraham Bioinformatics, Cambridge, United Kingdom.
  9. 9.↵
    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
  10. 10.↵
    1. Nurk S,
    2. Meleshko D,
    3. Korobeynikov A,
    4. Pevzner PA
    . 2017. MetaSPAdes: a new versatile metagenomic assembler. Genome Res 27:824–834. doi:10.1101/gr.213959.116.
    OpenUrlAbstract/FREE Full Text
  11. 11.↵
    1. Wu Y-W,
    2. Simmons BA,
    3. Singer SW
    . 2016. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32:605–607. doi:10.1093/bioinformatics/btv638.
    OpenUrlCrossRefPubMed
  12. 12.↵
    1. Eren AM,
    2. Esen OC,
    3. Quince C,
    4. Vineis JH,
    5. Morrison HG,
    6. Sogin ML,
    7. Delmont TO
    . 2015. Anvi’o: an advanced analysis and visualization platform for ’omics data. PeerJ 3:e1319. doi:10.7717/peerj.1319.
    OpenUrlCrossRefPubMed
  13. 13.↵
    1. Tatusova T,
    2. DiCuccio M,
    3. Badretdin A,
    4. Chetvernin V,
    5. Nawrocki EP,
    6. Zaslavsky L,
    7. Lomsadze A,
    8. Pruitt KD,
    9. Borodovsky M,
    10. Ostell J
    . 2016. NCBI Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 44:6614–6624. doi:10.1093/nar/gkw569.
    OpenUrlCrossRefPubMed
  14. 14.↵
    1. Neely CJ,
    2. Graham ED,
    3. Tully BJ
    . 2020. MetaSanity: an integrated microbial genome evaluation and annotation pipeline. Bioinformatics 36:4341–4344. doi:10.1093/bioinformatics/btaa512.
    OpenUrlCrossRef
  15. 15.↵
    1. Parks DH,
    2. Imelfort M,
    3. Skennerton CT,
    4. Hugenholtz P,
    5. Tyson GW
    . 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. doi:10.1101/gr.186072.114.
    OpenUrlAbstract/FREE Full Text
  16. 16.↵
    1. Blin K,
    2. Shaw S,
    3. Steinke K,
    4. Villebro R,
    5. Ziemert N,
    6. Lee SY,
    7. Medema MH,
    8. Weber T
    . 2019. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 47:W81–W87. doi:10.1093/nar/gkz310.
    OpenUrlCrossRefPubMed
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Metagenome-Assembled Genome Sequence of Dolichospermum circinale Strain Clear-D4, Assembled from a Harmful Cyanobacterial Bloom Enrichment Culture
Kyra M. Florea, J. Cameron Thrash, Eric A. Webb
Microbiology Resource Announcements Dec 2020, 9 (49) e01123-20; DOI: 10.1128/MRA.01123-20

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Metagenome-Assembled Genome Sequence of Dolichospermum circinale Strain Clear-D4, Assembled from a Harmful Cyanobacterial Bloom Enrichment Culture
Kyra M. Florea, J. Cameron Thrash, Eric A. Webb
Microbiology Resource Announcements Dec 2020, 9 (49) e01123-20; DOI: 10.1128/MRA.01123-20
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