Bacterial diversity in continuous cultures supplied with varying sources of dissolved organic matter

Heterotrophic bacterial metabolism is tightly linked to the availability of dissolved organic matter (DOM), but the relationship between substrate supply and bacterial diversity remains an open question. The objective of the first study was to determine how an increase in the supply of bioavailable DOM affects bacterial metabolism and diversity. We addressed this issue by growing a natural bacterial community over 5 generations in continuous cultures either on seawater (dissolved organic carbon concentration equal to 74 µM) or on seawater amended with 13 µM of diatom-derived DOM. Bacteria markedly responded to the additional DOM supply, as revealed by 1.6-fold higher bacterial abundances and 10-fold higher cell-specific alpha and beta-glucosidase activities in the +DOM treatment than in the control throughout the experimental period. Analysis of diversity as determined by tag pyrosequencing of 16S rRNA genes after 3 and 5 bacterial generations showed that bacterial communities in the +DOM treatment were more similar to each other than to communities in the control. Diversity indices such as richness and phylogenetic distance were higher in the DOM-amended cultures than in the control. Gammaproteobacteria dominated the communities selected in our cultures, representing between 87 and 99% of the sequences. The addition of DOM led to a higher relative abundance of several bacterial groups, in particular Alphaproteobacteria, Bacteroidetes and Verrucomicrobia, that accounted for up to 14% of the sequences, compared to the control where they represented less than 5% of the sequences. Our results demonstrate that in this experimental context an increased supply of bioavailable DOM sustained a higher bacterial diversity. To investigate interactions between bacterial diversity and DOM composition, we performed a second experiment where we followed the response of natural bacterial communities to two sources of phytoplankton-derived DOM over six bacterial generation times in continuous cultures. Analyses of total hydrolyzable neutral sugars and amino acids and ultrahigh resolution mass spectrometry revealed large differences in the chemical composition of the two DOM sources. According to 454 pyrosequences of 16S rRNA genes, diatom-derived DOM sustained higher levels of bacterial richness, evenness and phylogenetic diversity than cyanobacteria-derived DOM. However, these distinct community structures were not associated with specific taxa. Grazing pressure affected bacterial community composition without changing the overall pattern of bacterial diversity levels set by DOM. Our results demonstrate that resource composition can shape several facets of bacterial diversity without influencing the phylogenetic composition of bacterial communities.