Activity and abundance in varying bacterial communities.

Campbell and Kirchman (2013) attempt to determine growth properties of the bacterial community in the Delaware bay to help gage the contribution of bacteria to bio-chemical cycling. Using 16S ribosomal RNA as an indication of , and the presence of rRNA genes (rDNA) as an indication of abundance. The ratio between the rRNA and the rDNA can then be used as an indication of relative contribution of bacterial communities to biochemical processes. Campbell and Kirchman (2013) examine the potential growth rates and activity of individual bacterial taxa, and how certain environmental factors may impact this.

Campbell and Kirchman (2013) took samples along a transect spanning Delaware Bay and at a nearby coastal ocean observatory. Samples were either collected directly onto 0.22mm membranes, the whole water community, or filtered through a 0.8mm filter before collection on a 0.22mm membrane, the free living community. DNA and RNA was isolated, quantified and sequenced. After “cleaning” sequences were clustered using the average neighbour algorithm at 0.03 distance which resulted in 2446 operational taxonomic units (OTU), and phylogenetic distances were calculated.

It was found that there were distinct differences in richness and diversity between different salinities. Richness was observed to be highest in the whole water communities between 1.2 PSU and 6.4 PSU, with a steep drop to less than half the number of OTUs present by 10 PSU. There was no significant difference in richness observed (Chao1 index) between the low and high salinities in the free-living communities. The diversity (inverse Simpson) of the samples on the other hand, showed a distinct U curve in both the whole and free living communities with both the lowest and highest salinities having a significantly higher overall diversity than the mid salinity samples. 

Community structure changed drastically over the salinity gradient. In low salinities and fresh water the community was dominated by Actinobacteria, Verrucomicrobiota and Betaproteobacteria, and shifted to a community dominated by the SAR11 taxa, Rhodobacterales, Gammaproteobacteria and Bacteroidetes. 

Ratios or rRNA to rDNA were also examined. Using rRNA as a model for activity and rDNA as a model for abundance, relationships between abundance and activity can be determined. This relationship was examined for each OTU. It was found that overall the contribution to activity did not follow the relative abundance of phylotypes. Though when the whole-water and free-living communities were examined separately, it was found that for the whole water communities the ratios did differ whereas the ratios between phylotypes in the free-living communities did not. Also noted was the difference in ratio at different salinities. Results suggest that the ratios of some taxa were higher at certain salinity ranges compared to others. Though other factors may also be involved, as nitrate levels and light attenuation are mentioned to be correlated with the rRNA : rDNA ratio.

This study attempts to help understand how constantly fluctuating environmental conditions may impact bacterial communities and how these communities respond. Campbell and Kirchman (2013) suggest that rRNA:rDNA ratios may be more informative than abundance alone, to understand how environmental factors can influence bacterial communities. Especially if these ratios can be converted into estimates of individual bacterial growth. 

Campbell, B., A.; Kirchman, D., L,. (2013). Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient. International Society for Microbial Ecology. 7 (1), 210-220.