Molecular methods reveal responses of bacterial communities, including indicator species, to ballast water management

Ballast water (BW) is an important vector for the global translocation of bacterial taxa, including pathogens. Legal frameworks establishing limits on the discharge of live organisms into recipient environments have been designed to reduce risks of microbial invasions, and understanding the impacts of BW management on bacterial communities is critical for assessing the effectiveness of these practices. Here we evaluate changes in bacterial communities associated with both BW treatment (BWT) and a combined management approach of BWT plus BW exchange (BWT+E). Samples were collected on two experimental voyages designed specifically to compare BW-associated biota before and after management. Microbial community structure and inferred function were assessed based on high throughput sequencing of 16S rRNA amplicons, and bacterial indicator taxa E. coli and enterococci were analyzed using targeted qPCR. As expected, both BWT alone and BWT+E dramatically changed bacterial communities, with the latter resulting in the largest overall decreases in bacterial diversity. Increases in Gammaproteobacteria, especially in the genus Pseudomonas, were particularly notable, with concomitant decreases in Alphaproteobacteria and Bacteroidia. Shifts in predicted bacterial function associated with BWT were similar for both voyages, despite significant differences in community structure, and may represent selection for r-strategists capable of active regrowth after BWT. qPCR estimates of indicator taxa were similar to those obtained through standard culture methods but may offer increased sensitivity for detecting changes associated with management. Our results indicate that BW management is effective at reducing bacterial communities but suggest that further research is needed to understand risks associated with taxa that may survive BWT.