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Genome Sequences

Two Metagenome-Assembled Genome Sequences of Magnetotactic Bacteria in the Order Magnetococcales

Wensi Zhang, Runjia Ji, Jia Liu, Yongxin Pan, Long-Fei Wu, Wei Lin
J. Cameron Thrash, Editor
Wensi Zhang
aKey Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
bInnovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China
cFrance-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China
dCollege of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
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Runjia Ji
aKey Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
bInnovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China
cFrance-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China
dCollege of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
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Jia Liu
aKey Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
bInnovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China
cFrance-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China
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Yongxin Pan
aKey Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
bInnovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China
cFrance-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China
dCollege of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
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Long-Fei Wu
cFrance-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China
eAix Marseille University, CNRS, LCB, Marseille, France
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Wei Lin
aKey Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
bInnovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China
cFrance-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, China
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J. Cameron Thrash
University of Southern California
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DOI: 10.1128/MRA.00363-20
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ABSTRACT

Magnetotactic bacteria represent a valuable model system for the study of microbial biomineralization and magnetotaxis. Here, we report two metagenome-assembled genome sequences of uncultivated magnetotactic bacteria belonging to the order Magnetococcales. These genomes contain nearly complete magnetosome gene clusters responsible for magnetosome biomineralization.

ANNOUNCEMENT

Magnetotactic bacteria (MTB) are a diverse group of microorganisms that swim along the geomagnetic field lines, a behavior known as magnetotaxis or microbial magnetoreception (1). MTB affiliated within the order Magnetococcales are often the dominant MTB group in nature (2, 3). This group was previously thought to be an order (4) or a subclass (5) near the base of Alphaproteobacteria but was recently reclassified as a novel candidate class (“Candidatus Etaproteobacteria” [6, 7] or Magnetococcia [8]) within the Proteobacteria phylum. Genomes of Magnetococcales are required to better understand the phylogenetic position, genomic diversity, and evolutionary history of this MTB lineage.

Here, we report two metagenome-assembled Magnetococcales genome sequences isolated from freshwater sediments. Surface sediments were collected from East Lake in Hubei Province, China (30.56°N, 114.41°E). MTB cells were magnetically enriched from 300 ml of sediments using a double-ended open magnetic separation apparatus known as the “MTB trap” (9) through 4 h of collection. DNA was directly amplified from magnetically enriched cells using the Genomiphi V2 DNA amplification kit (GE Healthcare, USA) according to the manufacturer’s protocol and purified with the AxyPrep Mag PCR clean-up kit (Axygen, USA). Libraries were prepared with the Nextera XT DNA library preparation kit (Illumina, USA), following the manufacturer’s instructions. DNA sequencing was performed with an Illumina HiSeq 2500 instrument using the paired-end 125-bp by 125-bp library with a 200-bp insert size (BGI-Wuhan, Wuhan, China). Paired-end reads were filtered and trimmed using SOAPnuke (10) and were assembled using metaSPAdes (11) with the following parameters: --only-assembler -k 31, 41, 51, 61, 71, 81, 91, 101, 111. Assembled scaffolds of ≥2,500 bp were binned separately using MetaBAT v0.26.1 (12) and MyCC (13), and the high-scoring, nonredundant set of bins were dereplicated and selected using DASTool (14). QUAST v4.1 (15) was used to assess the quality of acquired genome sequences, and their completeness and contamination were estimated using CheckM (16) (taxonomy_wf domain Bacteria). Coverage information was determined using Bowtie 2 v2.3.4.3 (17) and SAMtools v1.6 (18). Genome sequences were annotated using the Prokaryotic Genome Annotation Pipeline (PGAP) (19). Putative magnetosome genes were checked using NCBI PSI-BLAST (20). Average amino acid identity (AAI) values were calculated using enveomics (21). Unless otherwise specified, default parameters were used for all software.

Two distinct (54% of AAI score) genome sequences, designated DH2bin6 and DH2bin20, have been reconstructed here, both of which contain partial 16S rRNA genes (>900 bp). An analysis of the 16S rRNA gene sequence of DH2bin6 using the online NCBI BLASTn nucleotide collection (nonredunant [nr]/nucleotide) database (https://blast.ncbi.nlm.nih.gov) shows the best hit to an uncultured magnetotactic coccus, MDA-1 (GenBank accession number AB537162; 99.89% identity) (22), while DH2bin20 has a 95.84% BLASTn identity to uncultivated Magnetic coccus CS92 (X81182) (23). Genomes of DH2bin6 and DH2bin20 consist of 80 and 525 scaffolds with average GC contents of 56.76% and 52.96%, respectively (Table 1). Nearly complete magnetosome gene clusters, a group of genes responsible for magnetosome biogenesis and arrangement, have been identified in both genomes, which contain genes homologous to magnetosome genes of mamD, mamH, mamI, mamE, mamK, mamF, mamL, mamM, mamN, mamO, mamP, mamA, mamQ, mamB, mamS, mamT and mmsF. These two genomes will provide insights into the genome biology and magnetosome biomineralization of MTB within the order Magnetococcales.

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TABLE 1

Genome statistics of Magnetococcales isolates DH2bin6 and DH2bin20

Data availability.These two genome sequences have been deposited in GenBank under the accession numbers JAANAU000000000 and JAANAV000000000 (BioProject number PRJNA400260). The raw metagenomic read data have been deposited in the NCBI Sequence Read Archive under the accession number SRR11267947.

ACKNOWLEDGMENTS

We thank Emmanuel Talla for his helpful comments and Jingqi Sun, Fuxian Wang, and Courtney L. Wagner for their help in sampling.

This work was funded by National Natural Science Foundation of China (NSFC) grants 41621004 and 41822704.

FOOTNOTES

    • Received 7 April 2020.
    • Accepted 10 August 2020.
    • Published 27 August 2020.
  • Copyright © 2020 Zhang 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. Blakemore RJS
    . 1975. Magnetotactic bacteria. Science 190:377–379. doi:10.1126/science.170679.
    OpenUrlAbstract/FREE Full Text
  2. 2.↵
    1. Flies CB,
    2. Peplies J,
    3. SchüLer Dirk
    . 2005. Combined approach for characterization of uncultivated magnetotactic bacteria from various aquatic environments. Appl Environ Microbiol 71:2723–2731. doi:10.1128/AEM.71.5.2723-2731.2005.
    OpenUrlAbstract/FREE Full Text
  3. 3.↵
    1. Lin W,
    2. Wang Y,
    3. Gorby Y,
    4. Nealson K,
    5. Pan Y
    . 2013. Integrating niche-based process and spatial process in biogeography of magnetotactic bacteria. Sci Rep 3:1643. doi:10.1038/srep01643.
    OpenUrlCrossRefPubMed
  4. 4.↵
    1. Bazylinski DA,
    2. Williams TJ,
    3. Lefèvre CT,
    4. Berg RJ,
    5. Zhang CL,
    6. Bowser SS,
    7. Dean AJ,
    8. Beveridge TJ
    . 2013. Magnetococcus marinus gen. nov., sp. nov., a marine, magnetotactic bacterium that represents a novel lineage (Magnetococcaceae fam. nov., Magnetococcales ord. nov.) at the base of the Alphaproteobacteria. Int J Syst Evol Microbiol 63:801–808. doi:10.1099/ijs.0.038927-0.
    OpenUrlCrossRefPubMedWeb of Science
  5. 5.↵
    1. Ferla MP,
    2. Thrash JC,
    3. Giovannoni SJ,
    4. Patrick WM
    . 2013. New rRNA gene-based phylogenies of the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and phylogenetic instability. PLoS One 8:e83383. doi:10.1371/journal.pone.0083383.
    OpenUrlCrossRefPubMed
  6. 6.↵
    1. Ji B,
    2. Zhang S-D,
    3. Zhang W-J,
    4. Rouy Z,
    5. Alberto F,
    6. Santini C-L,
    7. Mangenot S,
    8. Gagnot S,
    9. Philippe N,
    10. Pradel N,
    11. Zhang L,
    12. Tempel S,
    13. Li Y,
    14. Médigue C,
    15. Henrissat B,
    16. Coutinho PM,
    17. Barbe V,
    18. Talla E,
    19. Wu L-F
    . 2017. The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria. Environ Microbiol 19:1103–1119. doi:10.1111/1462-2920.13637.
    OpenUrlCrossRef
  7. 7.↵
    1. Lin W,
    2. Zhang W,
    3. Zhao X,
    4. Roberts AP,
    5. Paterson GA,
    6. Bazylinski DA,
    7. Pan Y
    . 2018. Genomic expansion of magnetotactic bacteria reveals an early common origin of magnetotaxis with lineage-specific evolution. ISME J 12:1508–1519. doi:10.1038/s41396-018-0098-9.
    OpenUrlCrossRef
  8. 8.↵
    1. Parks DH,
    2. Chuvochina M,
    3. Waite DW,
    4. Rinke C,
    5. Skarshewski A,
    6. Chaumeil P-A,
    7. Hugenholtz P
    . 2018. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36:996–1004. doi:10.1038/nbt.4229.
    OpenUrlCrossRef
  9. 9.↵
    1. Jogler C,
    2. Lin W,
    3. Meyerdierks A,
    4. Kube M,
    5. Katzmann E,
    6. Flies C,
    7. Pan Y,
    8. Amann R,
    9. Reinhardt R,
    10. Schüler D
    . 2009. Toward cloning of the magnetotactic metagenome: identification of magnetosome island gene clusters in uncultivated magnetotactic bacteria from different aquatic sediments. Appl Environ Microbiol 75:3972–3979. doi:10.1128/AEM.02701-08.
    OpenUrlCrossRefPubMed
  10. 10.↵
    1. Chen Y,
    2. Chen Y,
    3. Shi C,
    4. Huang Z,
    5. Zhang Y,
    6. Li S,
    7. Li Y,
    8. Ye J,
    9. Yu C,
    10. Li Z,
    11. Zhang X,
    12. Wang J,
    13. Yang H,
    14. Fang L,
    15. Chen Q
    . 2018. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. GigaScience 7:gix120. doi:10.1093/gigascience/gix120.
    OpenUrlCrossRef
  11. 11.↵
    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
  12. 12.↵
    1. Kang DD,
    2. Froula J,
    3. Egan R,
    4. Wang Z
    . 2015. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3:e1165. doi:10.7717/peerj.1165.
    OpenUrlCrossRefPubMed
  13. 13.↵
    1. Lin H-H,
    2. Liao Y-C
    . 2016. Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes. Sci Rep 6:24175. doi:10.1038/srep24175.
    OpenUrlCrossRef
  14. 14.↵
    1. Sieber CMK,
    2. Probst AJ,
    3. Sharrar A,
    4. Thomas BC,
    5. Hess M,
    6. Tringe SG,
    7. Banfield JF
    . 2018. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat Microbiol 3:836–843. doi:10.1038/s41564-018-0171-1.
    OpenUrlCrossRef
  15. 15.↵
    1. Gurevich A,
    2. Saveliev V,
    3. Vyahhi N,
    4. Tesler G
    . 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. doi:10.1093/bioinformatics/btt086.
    OpenUrlCrossRefPubMedWeb of Science
  16. 16.↵
    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
  17. 17.↵
    1. Langmead B,
    2. Salzberg SL
    . 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. doi:10.1038/nmeth.1923.
    OpenUrlCrossRefPubMedWeb of Science
  18. 18.↵
    1. Li H,
    2. Handsaker B,
    3. Wysoker A,
    4. Fennell T,
    5. Ruan J,
    6. Homer N,
    7. Marth G,
    8. Abecasis G,
    9. Durbin R, 1000 Genome Project Data Processing Subgroup
    . 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079. doi:10.1093/bioinformatics/btp352.
    OpenUrlCrossRefPubMedWeb of Science
  19. 19.↵
    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
  20. 20.↵
    1. Altschul SF,
    2. Madden TL,
    3. Schäffer AA,
    4. Zhang J,
    5. Zhang Z,
    6. Miller W,
    7. Lipman DJ
    . 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402. doi:10.1093/nar/25.17.3389.
    OpenUrlCrossRefPubMedWeb of Science
  21. 21.↵
    1. Rodriguez-R LM,
    2. Konstantinidis KT
    . 2016. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Prepr 4:e1900v1. doi:10.7287/peerj.preprints.1900v1.
    OpenUrlCrossRef
  22. 22.↵
    1. Arakaki A,
    2. Shibusawa M,
    3. Hosokawa M,
    4. Matsunaga T
    . 2010. Preparation of genomic DNA from a single species of uncultured magnetotactic bacterium by multiple-displacement amplification. Appl Environ Microbiol 76:1480–1485. doi:10.1128/AEM.02124-09.
    OpenUrlAbstract/FREE Full Text
  23. 23.↵
    1. Spring S,
    2. Amann R,
    3. Ludwig W,
    4. Schleifer KH,
    5. Schüler D,
    6. Poralla K,
    7. Petersen N
    . 1995. Phylogenetic analysis of uncultured magnetotactic bacteria from the alpha-subclass of Proteobacteria. Syst Appl Microbiol 17:501–508. doi:10.1016/S0723-2020(11)80068-8.
    OpenUrlCrossRef
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Two Metagenome-Assembled Genome Sequences of Magnetotactic Bacteria in the Order Magnetococcales
Wensi Zhang, Runjia Ji, Jia Liu, Yongxin Pan, Long-Fei Wu, Wei Lin
Microbiology Resource Announcements Aug 2020, 9 (35) e00363-20; DOI: 10.1128/MRA.00363-20

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Two Metagenome-Assembled Genome Sequences of Magnetotactic Bacteria in the Order Magnetococcales
Wensi Zhang, Runjia Ji, Jia Liu, Yongxin Pan, Long-Fei Wu, Wei Lin
Microbiology Resource Announcements Aug 2020, 9 (35) e00363-20; DOI: 10.1128/MRA.00363-20
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