An in situ method for cultivating microorganisms using a double encapsulation technique

FEMS Microbiol Ecol. 2009 Jun;68(3):363-71. doi: 10.1111/j.1574-6941.2009.00682.x. Epub 2009 Apr 21.


The lack of cultured microorganisms represents a bottleneck for advancement in microbiology. The development of novel culturing techniques is, therefore, a crucial step in our understanding of microbial diversity in general, and the role of such diversity in the environment, in particular. This study presents an innovative method for cultivating microorganisms by encapsulating them within agar spheres, which are then encased in a polysulfonic polymeric membrane and incubated in a simulated or natural environment. This method stimulates growth of the entrapped microorganisms by allowing them access to essential nutrients and cues from the environment. It allows for the discovery of microorganisms from dilutions that are 10-100-fold greater than possible with conventional plating techniques. Analysis of microorganisms grown in such spheres incubated in and on a number of different substrates yielded numerous novel ribotypes. For example, spheres incubated on the mucus surface of a Fungiid coral yielded numerous ribotypes, with only 50% sharing similarity (85-96%) to previously identified microorganisms. This suggests that many of the species represent novel ribotypes. Hence, the technique reported here advances our ability to retrieve and successfully culture microorganisms and provides an innovative tool to access unknown microbial diversity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Anthozoa / microbiology
  • Bacteria / classification
  • Bacteria / genetics
  • Bacteria / isolation & purification*
  • Bacteriological Techniques / methods*
  • Culture Media*
  • DNA, Bacterial / genetics
  • Phylogeny
  • Polymers
  • RNA, Ribosomal, 16S / genetics
  • Ribotyping
  • Seawater / microbiology
  • Sequence Analysis, DNA
  • Sulfones
  • Water Microbiology


  • Culture Media
  • DNA, Bacterial
  • Polymers
  • RNA, Ribosomal, 16S
  • Sulfones
  • polysulfone P 1700