The freshwater sponge Ephydatia fluviatilis harbours diverse Pseudomonas species (Gammaproteobacteria, Pseudomonadales) with broad-spectrum antimicrobial activity

PLoS One. 2014 Feb 12;9(2):e88429. doi: 10.1371/journal.pone.0088429. eCollection 2014.

Abstract

Bacteria are believed to play an important role in the fitness and biochemistry of sponges (Porifera). Pseudomonas species (Gammaproteobacteria, Pseudomonadales) are capable of colonizing a broad range of eukaryotic hosts, but knowledge of their diversity and function in freshwater invertebrates is rudimentary. We assessed the diversity, structure and antimicrobial activities of Pseudomonas spp. in the freshwater sponge Ephydatia fluviatilis. Polymerase Chain Reaction--Denaturing Gradient Gel Electrophoresis (PCR-DGGE) fingerprints of the global regulator gene gacA revealed distinct structures between sponge-associated and free-living Pseudomonas communities, unveiling previously unsuspected diversity of these assemblages in freshwater. Community structures varied across E. fluviatilis specimens, yet specific gacA phylotypes could be detected by PCR-DGGE in almost all sponge individuals sampled over two consecutive years. By means of whole-genome fingerprinting, 39 distinct genotypes were found within 90 fluorescent Pseudomonas isolates retrieved from E. fluviatilis. High frequency of in vitro antibacterial (49%), antiprotozoan (35%) and anti-oomycetal (32%) activities was found among these isolates, contrasting less-pronounced basidiomycetal (17%) and ascomycetal (8%) antagonism. Culture extracts of highly predation-resistant isolates rapidly caused complete immobility or lysis of cells of the protozoan Colpoda steinii. Isolates tentatively identified as P. jessenii, P. protegens and P. oryzihabitans showed conspicuous inhibitory traits and correspondence with dominant sponge-associated phylotypes registered by cultivation-independent analysis. Our findings suggest that E. fluviatilis hosts both transient and persistent Pseudomonas symbionts displaying antimicrobial activities of potential ecological and biotechnological value.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Antibiosis*
  • Biofilms
  • Gene Expression Regulation, Bacterial
  • Genome, Bacterial
  • Genotype
  • Likelihood Functions
  • Microbial Sensitivity Tests
  • Multivariate Analysis
  • Phylogeny
  • Polymerase Chain Reaction
  • Porifera / microbiology*
  • Principal Component Analysis
  • Pseudomonas / physiology*
  • RNA, Ribosomal, 16S / genetics
  • Species Specificity

Substances

  • RNA, Ribosomal, 16S

Grants and funding

This research was partially supported by the European Regional Development Fund (ERDF) through the COMPETE (Operational Competitiveness Programme) and national funds through FCT (Foundation for Science and Technology), under the project “PEst-C/MAR/LA0015/2011”. Further financial support was obtained from the FCT-funded project PTDC/BIA-MIC/3865/2012. Tina Keller-Costa received a mobility grant from the Federation of European Microbiological Societies (FEMS) to perform field and laboratory work in Groningen, The Netherlands. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.