Microbial Ecology

, Volume 73, Issue 3, pp 668–676

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

  • Sigmund Jensen
  • Sofia A. V. Fortunato
  • Friederike Hoffmann
  • Solveig Hoem
  • Hans Tore Rapp
  • Lise Øvreås
  • Vigdis L. Torsvik
Invertebrate Microbiology

DOI: 10.1007/s00248-016-0836-3

Cite this article as:
Jensen, S., Fortunato, S.A.V., Hoffmann, F. et al. Microb Ecol (2017) 73: 668. doi:10.1007/s00248-016-0836-3

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.

Keywords

Microbiome Marine sponge Geodia barretti Sulfur cycling 16S rRNA aprA Genes Transcripts 

Supplementary material

248_2016_836_MOESM1_ESM.pdf (998 kb)
ESM 1Fig. 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)
248_2016_836_MOESM2_ESM.pdf (311 kb)
ESM 2Fig. 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)
248_2016_836_MOESM3_ESM.zip (1.2 mb)
ESM 3Fig. 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)

Funding information

Funder NameGrant NumberFunding Note
Norwegian Research Council
  • 179560
VISTA
  • 6146

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Sigmund Jensen
    • 1
  • Sofia A. V. Fortunato
    • 2
  • Friederike Hoffmann
    • 3
  • Solveig Hoem
    • 3
  • Hans Tore Rapp
    • 3
  • Lise Øvreås
    • 1
  • Vigdis L. Torsvik
    • 3
  1. 1.Department of BiologyUniversity of BergenBergenNorway
  2. 2.ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleAustralia
  3. 3.Department of Biology, Centre for GeobiologyUniversity of BergenBergenNorway

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