Skip to main content
SpringerLink
Log in

Is the trophosome of Ridgeia piscesae monoclonal?

  • Published:
Symbiosis Aims and scope Submit manuscript

Abstract

The hydrothermal vent tubeworm Ridgeia piscesae relies on intracellular chemolithoautotrophic symbionts for its nutrition. Yet, little is known about symbiont diversity within and between individual worms. We report several lines of molecular evidence for multiple genotypes of very closely related symbionts within the trophosome of the R. piscesae. We examined the distribution of genotypic variants (insertions, deletions, and substitutions) in whole genome shotgun sequences of symbionts from the trophosome of a unique individual R. piscesae and the pooled sequences of five other tubeworms of the same species. Observed heterogeneity is unlikely to be the result of recent point or structural mutations of a monoclonal symbiont lineage. To assess inter-host diversity we examined single nucleotide polymorphisms (SNPs) in pyrosequences of the highly variable regions V1 to V3 of the symbiont 16S rRNA gene across 53 individual hosts from two vent sites. Most of the identified SNPs were found in more than one individual, and one seemed to be region specific. Two of the identified SNPs were also present in metagenomic data generated from high-throughput sequencing of trophosome material from an individual R. piscesae. Finally, we observed compositional and structural variations of CRISPR spacers within a CRISPR array.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Barnett D, Garrison E, Quinlan A, et al (2011) BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics btr174. doi:10.1093/bioinformatics/btr174

  • Barrick JE, Lenski RE (2009) Genome-wide mutational diversity in an evolving population of Escherichia coli. Cold spring Harb Symp quant Biol sqb.2009.74.018. doi:10.1101/sqb.2009.74.018

  • Bright M, Lallier FH (2010) The biology of vestimentiferan tubeworms. Oceanogr Mar Biol Annu Rev 48:213–266

  • Carney SL, Peoples JR, Fisher CR, Schaeffer SW (2002) AFLP analyses of genomic DNA reveal no differentiation between two phenotypes of the vestimentiferan tubeworm, Ridgeia piscesae. Cah Biol Mar 43:363–366

  • Chao LS, Davis RE, Moyer CL (2007) Characterization of bacterial community structure in vestimentiferan tubeworm Ridgeia piscesae trophosomes. Mar Ecol 28:72–85

    Article  CAS  Google Scholar 

  • Cheng AY, Teo Y-Y, Ong RT-H (2014) Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals. Bioinformatics 30:1707–1713. doi:10.1093/bioinformatics/btu067

    Article  CAS  PubMed  Google Scholar 

  • Cingolani P, Platts A, Wang LL et al (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly (Austin) 6:80–92. doi:10.4161/fly.19695

    Article  CAS  Google Scholar 

  • Cui Y, Li Y, Gorgé O et al (2008) Insight into microevolution of Yersinia Pestis by clustered regularly interspaced short palindromic repeats. PLoS One 3:e2652. doi:10.1371/journal.pone.0002652

    Article  PubMed  PubMed Central  Google Scholar 

  • Di Meo CA, Wilbur AE, Holben WE et al (2000) Genetic variation among endosymbionts of widely distributed vestimentiferan tubeworms. Appl Environ Microbiol 66:651–658

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dohm JC, Lottaz C, Borodina T, Himmelbauer H (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 36:e105–e105. doi:10.1093/nar/gkn425

    Article  PubMed  PubMed Central  Google Scholar 

  • Duperron S, Nadalig T, Caprais J-C et al (2005) Dual symbiosis in a Bathymodiolus sp. mussel from a methane seep on the Gabon continental margin (Southeast Atlantic): 16S rRNA phylogeny and distribution of the symbionts in gills. Appl Environ Microbiol 71:1694–1700

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Duperron S, Bergin C, Zielinski F et al (2006) A dual symbiosis shared by two mussel species, Bathymodiolus azoricus and Bathymodiolus puteoserpentis (Bivalvia: Mytilidae), from hydrothermal vents along the northern mid-Atlantic Ridge. Environ Microbiol 8:1441–1447

    Article  CAS  PubMed  Google Scholar 

  • Duperron S, Halary S, Lorion J et al (2008) Unexpected co-occurrence of six bacterial symbionts in the gills of the cold seep mussel Idas sp.(Bivalvia: Mytilidae). Environ Microbiol 10:433–445

    Article  CAS  PubMed  Google Scholar 

  • Duperron S, De Beer D, Zbinden M et al (2009) Molecular characterization of bacteria associated with the trophosome and the tube of Lamellibrachia sp., a siboglinid annelid from cold seeps in the eastern Mediterranean. FEMS Microbiol Ecol 69:395–409

    Article  CAS  PubMed  Google Scholar 

  • Consortium T 1000 GP (2010) A map of human genome variation from population-scale sequencing. Nature 467:1061–1073. doi:10.1038/nature09534

  • Forget NL, Perez M, Juniper SK (2014) Molecular study of bacterial diversity within the trophosome of the vestimentiferan tubeworm Ridgeia piscesae. Mar Ecol 36:35–44. doi:10.1111/maec.12169

    Article  Google Scholar 

  • Fujiwara Y, Kato C, Masui N et al (2001) Dual symbiosis in the cold-seep thyasirid clam Maorithyas hadalis from the hadal zone in the Japan trench, western Pacific. Mar Ecol Prog Ser 214:151–159

    Article  Google Scholar 

  • Grzymski JJ, Murray AE, Campbell BJ et al (2008) Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility. Proc Natl Acad Sci 105:17516–17521

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Held NL, Herrera A, Cadillo-Quiroz H, Whitaker RJ (2010) CRISPR associated diversity within a population of Sulfolobus islandicus. PLoS One 5:e12988. doi:10.1371/journal.pone.0012988

    Article  PubMed  PubMed Central  Google Scholar 

  • Huang HW, Mullikin JC, Hansen NF (2015) Evaluation of variant detection software for pooled next-generation sequence data. BMC Bioinformatics 16:235. doi:10.1186/s12859-015-0624-y

    Article  PubMed  PubMed Central  Google Scholar 

  • Kimura H, Higashide Y, Naganuma T (2003) Endosymbiotic microflora of the vestimentiferan tubeworm (Lamellibrachia sp.) from a bathyal cold seep. Mar Biotechnol 5:593–603

    Article  CAS  PubMed  Google Scholar 

  • Kleiner M, Wentrup C, Lott C et al (2012) Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use. Proc Natl Acad Sci 109:E1173–E1182

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Klose J, Polz MF, Wagner M et al (2015) Endosymbionts escape dead hydrothermal vent tubeworms to enrich the free-living population. Proc Natl Acad Sci 112:11300–11305. doi:10.1073/pnas.1501160112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Koboldt DC, Chen K, Wylie T et al (2009) VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25:2283–2285. doi:10.1093/bioinformatics/btp373

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kuno S, Sako Y, Yoshida T (2014) Diversification of CRISPR within coexisting genotypes in a natural population of the bloom-forming cyanobacterium Microcystis aeruginosa. Microbiology 160:903–916. doi:10.1099/mic.0.073494-0

    Article  CAS  Google Scholar 

  • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with bowtie 2. Nat Methods 9:357–359. doi:10.1038/nmeth.1923

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li H, Durbin R (2010) Fast and accurate long-read alignment with burrows-wheeler transform. Bioinforma Oxf Engl 26:589–595. doi:10.1093/bioinformatics/btp698

    Article  Google Scholar 

  • Li H, Homer N (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform 11:473–483. doi:10.1093/bib/bbq015

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079. doi:10.1093/bioinformatics/btp352

    Article  PubMed  PubMed Central  Google Scholar 

  • Loman NJ, Misra RV, Dallman TJ et al (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 30:434–439. doi:10.1038/nbt.2198

    Article  CAS  PubMed  Google Scholar 

  • Lopez-Sanchez M-J, Sauvage E, Da Cunha V et al (2012) The highly dynamic CRISPR1 system of Streptococcus agalactiae controls the diversity of its mobilome. Mol Microbiol 85:1057–1071. doi:10.1111/j.1365-2958.2012.08172.x

    Article  CAS  PubMed  Google Scholar 

  • Marinier E, Brown DG, McConkey BJ (2015) Pollux: platform independent error correction of single and mixed genomes. BMC Bioinformatics 16:10. doi:10.1186/s12859-014-0435-6

    Article  PubMed  PubMed Central  Google Scholar 

  • Meacham F, Boffelli D, Dhahbi J et al (2011) Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics 12:451. doi:10.1186/1471-2105-12-451

    Article  PubMed  PubMed Central  Google Scholar 

  • Mielczarek M, Szyda J (2015) Review of alignment and SNP calling algorithms for next-generation sequencing data. J Appl Genet:1–9. doi:10.1007/s13353-015-0292-7

  • Nussbaumer AD, Fisher CR, Bright M (2006) Horizontal endosymbiont transmission in hydrothermal vent tubeworms. Nature 441:345–348. doi:10.1038/nature04793

    Article  CAS  PubMed  Google Scholar 

  • Pabinger S, Dander A, Fischer M et al (2014) A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform 15:256–278. doi:10.1093/bib/bbs086

    Article  PubMed  Google Scholar 

  • Perez M (2016) Intra- and inter-population diversity of the Gammaproteobacteria Endorifita persephone in vestimentiferan tubeworms from the eastern Pacific. Thesis

  • Perez M, Juniper SK (2016) Insights into symbiont population structure among three Vestimentiferan tubeworm host species at eastern Pacific spreading centers. Appl Environ Microbiol 82:5197–5205. doi:10.1128/AEM.00953-16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Petersen JM, Ramette A, Lott C et al (2010) Dual symbiosis of the vent shrimp Rimicaris exoculata with filamentous gamma-and epsilonproteobacteria at four mid-Atlantic Ridge hydrothermal vent fields. Environ Microbiol 12:2204–2218

    CAS  PubMed  Google Scholar 

  • Pourcel C, Salvignol G, Vergnaud G (2005) CRISPR elements in Yersinia Pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 151:653–663

    Article  CAS  PubMed  Google Scholar 

  • Quail MA, Smith M, Coupland P et al (2012) A tale of three next generation sequencing platforms: comparison of ion torrent, Pacific biosciences and Illumina MiSeq sequencers. BMC Genomics 13:341. doi:10.1186/1471-2164-13-341

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Robidart JC (2006) Metagenomics of the Riftia pachyptila symbiont. University of California, San Diego

    Google Scholar 

  • Robidart JC, Bench SR, Feldman RA et al (2008) Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics. Environ Microbiol 10:727–737

    Article  CAS  PubMed  Google Scholar 

  • Schloss PD, Westcott SL, Ryabin T et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541. doi:10.1128/AEM.01541-09

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schmieder R, Edwards R (2011a) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27:863–864. doi:10.1093/bioinformatics/btr026

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schmieder R, Edwards R (2011b) Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One 6:e17288. doi:10.1371/journal.pone.0017288

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Skennerton CT, Imelfort M, Tyson GW (2013) Crass: identification and reconstruction of CRISPR from unassembled metagenomic data. Nucleic Acids Res 41:e105–e105. doi:10.1093/nar/gkt183

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stewart FJ, Young CR, Cavanaugh CM (2009) Evidence for homologous recombination in intracellular chemosynthetic clam symbionts. Mol Biol Evol 26:1391–1404. doi:10.1093/molbev/msp049

    Article  CAS  PubMed  Google Scholar 

  • Tyson GW, Banfield JF (2008) Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ Microbiol 10:200–207. doi:10.1111/j.1462-2920.2007.01444.x

    CAS  PubMed  Google Scholar 

  • Van der Auwera GA, Carneiro MO, Hartl C et al (2002) From FastQ data to high-confidence variant calls: the genome analysis toolkit best practices pipeline. Current Protocols in Bioinformatics. John Wiley & Sons, Inc., In

    Google Scholar 

  • Wang W, Xu F, Wang J (2013) Assessment of mapping and SNP-detection algorithms for next-generation sequencing data in cancer genomics. In: Choudhry H (ed) Wu W. Next Generation Sequencing in Cancer Research, Springer New York, pp 301–317

    Google Scholar 

  • Weinberger AD, Sun CL, Pluciński MM et al (2012) Persisting viral sequences shape microbial CRISPR-based immunity. PLoS Comput Biol 8:e1002475. doi:10.1371/journal.pcbi.1002475

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wielgoss S, Barrick JE, Tenaillon O et al (2011) Mutation rate inferred from synonymous substitutions in a long-term evolution experiment with Escherichia coli. G3 genes genomes genet:1, 183–186. doi:10.1534/g3.111.000406

  • Woyke T, Teeling H, Ivanova NN et al (2006) Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443:950–955

    Article  CAS  PubMed  Google Scholar 

  • Yi M, Zhao Y, Jia L, et al (2014) Performance comparison of SNP detection tools with illumina exome sequencing data—an assessment using both family pedigree information and sample-matched SNP array data. Nucleic acids res gku392. doi:10.1093/nar/gku392

  • Young C, Fujio S, Vrijenhoek R (2008) Directional dispersal between mid-ocean ridges: deep-ocean circulation and gene flow in Ridgeia piscesae. Mol Ecol 17:1718–1731

    Article  CAS  PubMed  Google Scholar 

  • Yu X, Sun S (2013) Comparing a few SNP calling algorithms using low-coverage sequencing data. BMC Bioinformatics 14:274. doi:10.1186/1471-2105-14-274

    Article  PubMed  PubMed Central  Google Scholar 

  • Yu F, Lu J, Liu X et al (2015) Population genomic analysis of 962 whole genome sequences of humans reveals natural selection in non-coding regions. PLoS One 10:e0121644. doi:10.1371/journal.pone.0121644

    Article  PubMed  PubMed Central  Google Scholar 

  • Zimmermann J, Lott C, Weber M, et al (2014) Dual symbiosis with co-occurring sulfur-oxidizing symbionts in vestimentiferan tubeworms from a Mediterranean hydrothermal vent. Environ Microbiol 16:3638–3656. doi: 10.1111/1462-2920.12427 

Download references

Acknowledgments

We thank Nathalie Forget for sharing her pyrosequences libraries. We also thank the crews of the R/V Atlantis and R/V Thomas G. Thompson, the pilots of the submersibles Alvin and the ROVs ROPOS and Millenium Plus, Carol Doya, and Steven Hallam for their assistance during sample collections and sequencing of the metagenomes. This research was enabled by computing assistance provided by Belaid Moa, WestGrid (westgrid.ca) and Compute Canada/Calcul Canada (computecanada.ca). We also thank the members of Verena Tunnicliffe’s lab, and all of the contributors to seqanswers.com and biostars.org.

This research was supported by a Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant and a Canadian Healthy Oceans Network (NSERC Canada) to S.K.J.

Author information

Authors and Affiliations

  1. School of Earth and Ocean Sciences, University of Victoria, Victoria, B.C., Canada

    Maëva Perez & S. Kim Juniper

  2. Department of Biology, University of Victoria, Victoria, B.C., Canada

    S. Kim Juniper

Authors
  1. Maëva Perez
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. S. Kim Juniper
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Maëva Perez.

Ethics declarations

Conflict of interest

The authors declare no conflict of interest.

Electronic supplementary material

Fig. S.1

Variant calling pipelines for whole genome shotgun sequences and pyrosequences. See supplemental material and methods for details and references. (JPEG 141 kb)

High Resolution Image (EPS 875 kb)

Fig. S.2

Frequency spectrum of variants detected by VarScan and GATK with multiple ploidy parameters. (JPEG 41 kb)

High Resolution Image (TIFF 1486 kb)

Fig. S.3

Comparisons of variants detected by VarScan only or both VarScan and GATK; a) variant positions in the genome (inside or outside coding regions), b) types of substitution (transition vs transversion), c) substitution effects on amino acid sequence. (JPEG 50 kb)

High Resolution Image (TIFF 111 kb)

Fig. S.4

Unassembled read pairs from the Symb_1 metagenome mapped onto the reference contig Ga0074115_104 (Ridgeia 1 symbiont). Only the portion of the contig containing the CRISPR array is visible. Read pairs with abnormally large insert sizes (1% percentile) are coloured in red. To help interpretation, a schematic representation of a deletion is presented in Box 1. (JPEG 107 kb)

High Resolution Image (TIFF 3719 kb)

Fig. S.5

Neighbor-joining tree based on the CRISPR sequences found in the symbiont metagenomes from 6 individual worms. The labels of the tree represent the names of the read sequence and are color coded by sample for clarity. Red: Ind11 (Symb_1); Grey: Ind10; Pink: Ind12; Green: Ind13; Blue: Ind14; Orange: Ind15. The symbiont metagenomes from Ind10, Ind12, Ind13 Ind14, and Ind15 were pooled together into Symb_pool. Spacers (SP) found in both Symb_1 and Symb_pool are represented outside the clades. See Table S. 3 for list of spacers. (JPEG 165 kb)

High Resolution Image (EPS 988 kb)

Table S 1

(DOCX 19 kb)

Table S. 2

(DOCX 19 kb)

Table S. 3

(DOCX 22 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Perez, M., Juniper, S. Is the trophosome of Ridgeia piscesae monoclonal?. Symbiosis 74, 55–65 (2018). https://doi.org/10.1007/s13199-017-0490-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13199-017-0490-7

Keywords

Search

Navigation