Bacterial community composition and potential controlling mechanisms along a trophic gradient in a barrier reef system

Abstract

Bacterial abundance and community composition were investigated along trophic gra- dients in the barrier reef lagoon of Noumea, New Caledonia. Bacterial abundance and the percent- age of high nucleic acid (%HNA) bacteria (a potential indicator for bacterial production) increased from offshore waters towards the head of the bays. 16S rRNA gene PCR and denaturing gradient gel electrophoresis (DGGE) were used as genetic fingerprints for assessing differences in bacterial com- munity composition. Sequences of DGGE bands were assigned to (1) the genera Rugeria and Roseobacter (Rhodobacteriaceae), (2) the SAR11 cluster, (3) other Alphaproteobacteria, and (4) the genus Alteromonas. Removal of the operationally defined attached bacteria by prefiltration did not affect community profiles in offshore waters but had a strong influence in the bays, probably due to the much higher particle load and thus, attached bacteria in the bays. For the free-living community, the number of bands decreased linearly with increasing water residence time, chlorophyll a concen- tration, and viral abundance. Specific bands were found for offshore waters and the 2 investigated semi-enclosed bays, whereas the lagoon showed no specific bands. A similarity analysis showed spe- cific clusters for offshore water, the lagoon, and the bays. A principle component analysis together with cluster and correlation analysis indicated that water residence time, viruses, and a complex top- down cascading effect of ciliate grazers on flagellates influenced community composition. Also, data from fingerprints of the total and free-living communities suggest that the free-living and the attached community are controlled by different mechanisms.