Bacterial diversity associated with the tunic of the model chordate Ciona intestinalis

The sea squirt Ciona intestinalis is a well-studied model organism in developmental biology, yet little is known about its associated bacterial community. In this study, a combination of 454 pyrosequencing of 16S ribosomal RNA genes, catalyzed reporter deposition-fluorescence in situ hybridization and bacterial culture were used to characterize the bacteria living inside and on the exterior coating, or tunic, of C. intestinalis adults. The 454 sequencing data set demonstrated that the tunic bacterial community structure is different from that of the surrounding seawater. The observed tunic bacterial consortium contained a shared community of <10 abundant bacterial phylotypes across three individuals. Culture experiments yielded four bacterial strains that were also dominant groups in the 454 sequencing data set, including novel representatives of the classes Alphaproteobacteria and Flavobacteria. The relatively simple bacterial community and availability of dominant community members in culture make C. intestinalis a promising system in which to investigate functional interactions between host-associated microbiota and the development of host innate immunity.