Skip to main content

Advertisement

SpringerLink
Log in

The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle

  • Invertebrate Microbiology
  • Published:
Microbial Ecology Aims and scope Submit manuscript

Abstract

During the last decades, our knowledge about the activity of sponge-associated microorganisms and their contribution to biogeochemical cycling has gradually increased. Functional groups involved in carbon and nitrogen metabolism are well documented, whereas knowledge about microorganisms involved in the sulfur cycle is still limited. Both sulfate reduction and sulfide oxidation has been detected in the cold water sponge Geodia barretti from Korsfjord in Norway, and with specimens from this site, the present study aims to identify extant versus active sponge-associated microbiota with focus on sulfur metabolism. Comparative analysis of small subunit ribosomal RNA (16S rRNA) gene (DNA) and transcript (complementary DNA (cDNA)) libraries revealed profound differences. The transcript library was predominated by Chloroflexi despite their low abundance in the gene library. An opposite result was found for Acidobacteria. Proteobacteria were detected in both libraries with representatives of the Alpha- and Gammaproteobacteria related to clades with presumably thiotrophic bacteria from sponges and other marine invertebrates. Sequences that clustered with sponge-associated Deltaproteobacteria were remotely related to cultivated sulfate-reducing bacteria. The microbes involved in sulfur cycling were identified by the functional gene aprA (adenosine-5′-phosphosulfate reductase) and its transcript. Of the aprA sequences (DNA and cDNA), 87 % affiliated with sulfur-oxidizing bacteria. They clustered with Alphaproteobacteria and with clades of deep-branching Gammaproteobacteria. The remaining sequences clustered with sulfate-reducing Archaea of the phylum Euryarchaeota. These results indicate an active role of yet uncharacterized Bacteria and Archaea in the sponge’s sulfur cycle.

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

Similar content being viewed by others

References

  1. Hoffmann F, Larsen O, Thiel V, Rapp HT, Pape T, Michaelis W (2005) An anaerobic world in sponges. Geomicrobiol J 22:1–10

    Article  Google Scholar 

  2. Taylor MW, Radax R, Steger D, Wagner M (2007) Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. Microbiol Mol Biol Rev 71:295–347

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Hoffmann F, Radax R, Woebken D, Holtappels M, Lavik G, Rapp HT, Schlãppy ML, Schleper C, Kuypers MMM (2009) Complex nitrogen cycling in the sponge Geodia barretti. Environ Microbiol 11:2228–2243

  4. Maldonado M, Ribes M, van Duyl FC (2012) Nutrient fluxes through sponges: biology, budgets, and ecological implications. Adv Mar Biol 62:113–182

    Article  PubMed  Google Scholar 

  5. Radax R, Hoffmann F, Rapp HT, Leininger S, Schleper C (2012) Ammonia-oxidizing Archaea as main drivers of nitrification in cold-water sponges. Environ Microbiol 14:909–923

    Article  CAS  PubMed  Google Scholar 

  6. Hentschel U, Fieseler L, Wehrl M, Gernert C, Steinert M, Hacker J, Horn M (2003) Microbial diversity of marine sponges. In: Müller, WEG (ed) Marine molecular biotechnology. Springer, Berlin, Germany, pp. 59–88

  7. Schöttner S, Hoffmann F, Cárdenas P, Rapp HT, Boetius A, Ramette A (2013) Relationships between host phylogeny, host type and bacterial community diversity in cold-water coral reef sponges. PLoS One 8:e55505

    Article  PubMed  PubMed Central  Google Scholar 

  8. Bayer K, Kamke J, Hentschel U (2014) Quantification of bacterial and archaeal symbionts in high and low microbial abundance sponges using real-time PCR. FEMS Microbiol Ecol 89:679–690

    Article  CAS  PubMed  Google Scholar 

  9. Hentschel U, Usher KM, Taylor MW (2006) Marine sponges as microbial fermenters. FEMS Microbiol Ecol 55:167–177

    Article  CAS  PubMed  Google Scholar 

  10. Weisz JB, Lindquist N, Martens CS (2008) Do associated microbial abundances impact marine demosponge pumping rates and tissue densities? Oecologia 155:367–376

    Article  PubMed  Google Scholar 

  11. Reveillaud J, Maignien L, Eren AM, Huber JA, Apprill A, Sogin ML, Vanreusel A (2014) Host-specificity among abundant and rare taxa in the sponge microbiome. ISME J 8:1198–1209

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Hentschel U, Hopke J, Horn M, Friedrich AB, Wagner M, Hacker J (2002) Molecular evidence for a uniform microbial community in sponges from different oceans. Appl Environ Microbiol 68:4431–4440

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Moitinho-Silva L, Bayer K, Cannistraci CV, Giles EC, Ryu T, Seridi L, Ravasi T, Hentschel U (2014) Specificity and transcriptional activity of microbiota associated with low and high microbial abundance sponges from the Red Sea. Mol Ecol 23:1348–1363

    Article  CAS  PubMed  Google Scholar 

  14. Gurgui C, Piel J (2010) Metagenomic approaches to identify and isolate bioactive natural products from microbiota of marine sponges. In: Streit WR, Daniel R (eds) Metagenomics: methods and protocols. Humana Press Inc, Totowa, pp 247–264

    Chapter  Google Scholar 

  15. Fan L, Reynolds D, Liu M, Stark M, Kjelleberg S, Webster NS, Thomas T (2012) Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts. Proc Natl Acad Sci U S A 109:E1878–E1887

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Fiore CL, Labrie M, Jarett JK, Lesser MP (2015) Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: molecular evidence for metabolic interchange. Front Microbiol 6:364

    Article  PubMed  PubMed Central  Google Scholar 

  17. Radax R, Rattei T, Lanzen A, Bayer C, Rapp HT, Urich T, Schleper C (2012) Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community. Environ Microbiol 14:1308–1324

    Article  CAS  PubMed  Google Scholar 

  18. Webster NS, Taylor MW (2012) Marine sponges and their microbial symbionts: love and other relationships. Environ Microbiol 14:335–346

    Article  CAS  PubMed  Google Scholar 

  19. Arellano S, Lee O, Lafi F, Yang J, Wang Y, Young C, Qian P-Y (2013) Deep sequencing of Myxilla (Ectyomyxilla) methanophila, an epibiotic sponge on cold-seep tubeworms, reveals methylotrophic, thiotrophic, and putative hydrocarbon-degrading microbial associations. Microb Ecol 65:450–461

    Article  CAS  PubMed  Google Scholar 

  20. Meyer B, Kuever J (2008) Phylogenetic diversity and spatial distribution of the microbial community associated with the Caribbean deep-water sponge Polymastia cf. corticata by 16S rRNA, aprA, and amoA gene analysis. Microb Ecol 56:306–321

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Nishijima M, Lindsay D, Hata J, Nakamura A, Kasai H, Ise Y, Fisher C, Fujiwara Y, Kawato M, Maruyama T (2010) Association of thioautotrophic bacteria with deep-sea sponges. Mar Biotechnol 12:253–260

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Kamke J, Taylor MW, Schmitt S (2010) Activity profiles for marine sponge-associated bacteria obtained by 16S rRNA vs 16S rRNA gene comparisons. ISME J 4:498–508

    Article  CAS  PubMed  Google Scholar 

  23. Blazewicz SJ, Barnard RL, Daly RA, Firestone MK (2013) Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses. ISME J 7:2061–2068

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Meyer B, Kuever J (2007) Phylogeny of the alpha and beta subunits of the dissimilatory adenosine-5′-phosphosulfate (APS) reductase from sulfate-reducing prokaryotes—origin and evolution of the dissimilatory sulfate-reduction pathway. Microbiology 153:2026–2044

    Article  CAS  PubMed  Google Scholar 

  25. Becker PT, Samadi S, Zbinden M, Hoyoux C, Compère P, De Ridder C (2009) First insights into the gut microflora associated with an echinoid from wood falls environments. Cah Biol Mar 50:343–352

    Google Scholar 

  26. Kleiner M, Petersen JM, Dubilier N (2012) Convergent and divergent evolution of metabolism in sulfur-oxidizing symbionts and the role of horizontal gene transfer. Curr Opin Microbiol 15:621–631

    Article  CAS  PubMed  Google Scholar 

  27. Stewart FJ, Dmytrenko O, DeLong EF, Cavanaugh CM (2011) Metatranscriptomic analysis of sulfur oxidation genes in the endosymbiont of Solemya velum. Front Microbiol 2:134

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Ahn Y-B, Kerkhof LJ, Häggblom MM (2009) Desulfoluna spongiiphila sp. nov., a dehalogenating bacterium in the Desulfobacteraceae from the marine sponge Aplysina aerophoba. Int J Syst Evol Microbiol 59:2133–2139

    Article  CAS  PubMed  Google Scholar 

  29. Øvreås L, Forney L, Daae FL, Torsvik V (1997) Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 63:3367–3373

    PubMed  PubMed Central  Google Scholar 

  30. Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC (1989) Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 17:7843–7853

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Muyzer G, Dewaal EC, Uitterlinden AG (1993) Profiling of complex microbial-populations by denaturing gradient gel-electrophoresis analysis of polymerase chain reaction amplified genes coding for 16S ribosomal-RNA. Appl Environ Microbiol 59:695–700

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Böer SI, Hedtkamp SIC, van Beusekom JEE, Fuhrman JA, Boetius A, Ramette A (2009) Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands. ISME J 3:780–791

    Article  PubMed  Google Scholar 

  33. Hammer Ø, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:9

    Google Scholar 

  34. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A 82:6955–6959

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Fieseler L, Horn M, Wagner M, Hentschel U (2004) Discovery of the novel candidate phylum “Poribacteria” in marine sponges. Appl Environ Microbiol 70:3724–3732

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Meyer B, Kuever J (2007) Molecular analysis of the diversity of sulfate-reducing and sulfur-oxidizing prokaryotes in the environment, using aprA as functional marker gene. Appl Environ Microbiol 73:7664–7679

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Hall T (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  38. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–D145

    Article  CAS  PubMed  Google Scholar 

  39. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188–7196

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing MOTHUR: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16:276–277

    Article  CAS  PubMed  Google Scholar 

  42. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar BA (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Felsenstein J (2013) PHYLIP-phylogeny inference package (version 3.69). Department of Genomic Sciences, University of Washington, Seattle

    Google Scholar 

  46. Kennedy J, Flemer B, Jackson SA, Morrissey JP, O’Gara F, Dobson ADW (2014) Evidence of a putative deep sea specific microbiome in marine sponges. PLoS One 9:e91092

    Article  PubMed  PubMed Central  Google Scholar 

  47. Schmitt S, Tsai P, Bell J, Fromont J, Ilan M, Lindquist N, Perez T, Rodrigo A, Schupp PJ, Vacelet J, Webster N, Hentschel U, Taylor MW (2012) Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges. ISME J 6:564–576

    Article  CAS  PubMed  Google Scholar 

  48. Li L, Kato C, Horikoshi K (1999) Microbial diversity in sediments collected from the deepest cold-seep area, the Japan Trench. Mar Biotechnol 1:391–400

    Article  CAS  PubMed  Google Scholar 

  49. Kaesler-Neumann I (2013) Investigation of sponge-associated bacteria from marine cold-water sponges. Dissertation, Technische Universität, Berlin

  50. Giovannoni SJ, Rappé MS, Vergin KL, Adair NL (1996) 16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the green non-sulfur bacteria. Proc Natl Acad Sci U S A 93:7979–7984

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Yousuf B, Kumar R, Mishra A, Jha B (2014) Unravelling the carbon and sulphur metabolism in coastal soil ecosystems using comparative cultivation-independent genome-level characterisation of microbial communities. PLoS One 9:e107025

    Article  PubMed  PubMed Central  Google Scholar 

  52. Blazejak A, Kuever J, Erséus C, Amann R, Dubilier N (2006) Phylogeny of 16S rRNA, ribulose 1,5-bisphosphate carboxylase/oxygenase, and adenosine 5-phosphosulfate reductase genes from Gamma-and Alphaproteobacterial symbionts in gutless marine worms (Oligochaeta) from Bermuda and the Bahamas. Appl Environ Microbiol 72:5527–5536

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Hoffmann F, Rapp HT, Reitner J (2006) Monitoring microbial community composition by fluorescence in situ hybridization during cultivation of the marine cold-water sponge Geodia barretti. Mar Biotechnol 8:373–379

    Article  CAS  PubMed  Google Scholar 

  54. Brück WM, Brück TB, Self WT, Reed JK, Nitecki SS, McCarthy PJ (2010) Comparison of the anaerobic microbiota of deep-water Geodia spp. and sandy sediments in the Straits of Florida. ISME J 4:686–699

    Article  PubMed  Google Scholar 

  55. Jensen S, Neufeld JD, Birkeland N-K, Hovland M, Murrell JC (2008) Insight into the microbial community structure of a Norwegian deep-water coral reef environment. Deep-Sea Res I Oceanogr Res Pap 55:1554–1563

    Article  Google Scholar 

  56. Simister RL, Deines P, Botté ES, Webster NS, Taylor MW (2012) Sponge-specific clusters revisited: a comprehensive phylogeny of sponge-associated microorganisms. Environ Microbiol 14:517–524

    Article  CAS  PubMed  Google Scholar 

  57. Schmitt S, Hentschel U, Taylor M (2012) Deep sequencing reveals diversity and community structure of complex microbiota in five Mediterranean sponges. Hydrobiologia 687:341–351

    Article  CAS  Google Scholar 

  58. Varela MM, Van Aken HM, Herndl GJ (2008) Abundance and activity of Chloroflexi-type SAR202 bacterioplankton in the meso- and bathypelagic waters of the (sub)tropical Atlantic. Environ Microbiol 10:1903–1911

    Article  PubMed  Google Scholar 

  59. Swan BK, Martinez-Garcia M, Preston CM, Sczyrba A, Woyke T, Lamy D, Reinthaler T, Poulton NJ, Masland EDP, Gomez ML, Sieracki ME, DeLong EF, Herndl GJ, Stepanauskas R (2011) Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333:1296–1300

    Article  CAS  PubMed  Google Scholar 

  60. Aoki M, Kakiuchi R, Yamaguchi T, Takai K, Inagaki F, Imachi H (2015) Phylogenetic diversity of aprA genes in subseafloor sediments on the Northwestern Pacific margin off Japan. Microbes Environ 30:276–280

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

We gratefully acknowledge Dagmar Woebken for providing the Poribacteria sequences, the crew on the research vessel “Hans Brattstrøm” for help with sampling, Elinor Bartle for correcting the manuscript, and Anders Lanzén for help with quality checks on the sequences. This work was supported by the Norwegian Research Council through the Centre for Geobiology (project 179560), and partly funded by the Norwegian Academy of Science and Statoil (VISTA project: 6146).

Author information

Authors and Affiliations

  1. Department of Biology, University of Bergen, Bergen, Norway

    Sigmund Jensen & Lise Øvreås

  2. ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia

    Sofia A. V. Fortunato

  3. Department of Biology, Centre for Geobiology, University of Bergen, PO Box 7803, Bergen, 5020, Norway

    Friederike Hoffmann, Solveig Hoem, Hans Tore Rapp & Vigdis L. Torsvik

Authors
  1. Sigmund Jensen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sofia A. V. Fortunato
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Friederike Hoffmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Solveig Hoem
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hans Tore Rapp
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Lise Øvreås
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Vigdis L. Torsvik
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Vigdis L. Torsvik.

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

ESM 1

Fig. S1 Comparison of bacterial community profiles by molecular fingerprinting using DGGE and ARISA. Bacterial community DNA from three different tissue parts (S close to the surface, M middle tissue, O close to osculum opening for water outflow) of three different specimens (1, 2, 3) of G. barretti were analyzed with PCR-amplified 16S rRNA genes. Four bands from surface tissue of specimen 1 were identified as indicated by asterisks. (PDF 997 kb)

ESM 2

Fig. S2 Rarefaction curves from cloned 16S rRNA and aprA gene and transcript sequences from microbial communities in the Geodia barretti sponge. The sequences were in MOTHUR [40] ascribed to operational taxonomic units (OTUs) at 97 % sequence identity. (PDF 310 kb)

ESM 3

Fig. S3 Maximum-likelihood phylogenetic trees based on 16S rRNA nucleotide sequences from Geodia barretti tissue DNA and cDNA clone libraries: Alphaproteobacteria (a), Gammaproteobacteria (b), Deltaproteobacteria (c), Chloroflexi (d), Acidobacteria (e), and Deferribacteres (f). The sequences are highlighted in bold and for cDNA also underlined. Dashed lines indicate short sequences (458 bp) that were added using the ARB parsimony interactive tool [43]. Silva 119 classification [39] of a minimum of 80 % bootstrap values and inferred physiology of sulfur-oxidizing bacteria (SOB), sulfur reducing bacteria/archaea (SRB/A), cultured strains, and single cell genome (stars) are indicated. Filled stars indicate species also represented by aprA. Reference sequences were retrieved from GenBank, and the trees were constructed in Phylip [45] from 1255 nucleotides aligned in MOTHUR [40] and filtered in ARB to cover the same positions excluding ambiguities and missing data. Bootstrap values above 50 % are indicated at the branch points with 90–100 % supported clades of exclusively sponge-derived sequences being shaded. One of the poribacterial sequences was used as an outgroup (clone Pori20). The scale bar indicates 0.1 substitutions per nucleotide position. (ZIP 1.17 mb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jensen, S., Fortunato, S.A.V., Hoffmann, F. et al. The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle. Microb Ecol 73, 668–676 (2017). https://doi.org/10.1007/s00248-016-0836-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-016-0836-3

Keywords

Search

Navigation