Microbial ecology of aquaculture sediments

Sediment bacterial communities were studied at two Tasmanian salmon farm sites and adjacent unimpacted reference sites. Microbial biomass and total diversity were investigated as well the diversity and population density of the Cytophaga-Flavobacteria-Bacteroides group (CFB) and beta-proteobacterial ammonia oxidizers (AOB). The study aimed to develop a conceptual understanding of microbial community dynamics in response to disturbance and to assess the efficacy of farm fallowing practices in allowing sediment bacterial communities to recover from organic loading. Sediments from two salmon farms were studied over two full farm production cycles of 12 months each. Each cycle consisted of a nine-month stocking period, during which organic loading occurred, followed by a three month fallow period, during which no loading occurred. To represent the range of sediment conditions prevalent at Tasmanian salmon farms, farms with differing sediment conditions were chosen. Sediment at farm 1 was coarse grained, while at that at farm 2, sediment was fine grained. Sampling was conducted at the beginning of each cycle and at the end of each period within a cycle. Bacterial numbers increased as farming and organic loading progressed through the farm cycle and declined during the fallowing period, although not to pre-stocking levels. Bacterial numbers ranged between approximately 2 x 108 and 3 x 109 cells/g sediment and were generally higher at cage sites than reference sites. Six, 16S rRNA gene clone libraries were constructed, comprising more than 600 clones sequences, from both cage and reference sites. These revealed that both cage and reference site sediments at both farms showed a very high level of diversity. Reference sites were dominated by delta and gamma-proteobacteria and CFB group bacteria. Cage site sediments also showed large numbers of these phylotypes, as well as members of the alpha and epsilon-proteobacteria. Diversity and coverage indices indicated that the diversity of all sediments studied was much greater than that detected in this study, despite a large sampling effort. All clone libraries were shown to be statistically different from one another, further supporting the idea that coverage was low. Many phylotypes did not group with cultured bacteria, but grouped with other environmental clones from a wide array of marine benthic environments. Clone libraries indicated the presence of a large number of bacterial types, including the Myxobacteria. Although thought to be unable to grow under marine conditions, the large number of Myxobacteria clones found in this study further supports the idea that this may not be the case. Denaturing gradient gel electrophoresis (DGGE) showed that bacterial communities shifted both in response to farm loading and the cessation of this loading. Communities also shifted frequently at reference site communities, indicating the highly dynamic nature of sediment bacterial communities and the possibility of a seasonal effect. Although bacterial communities did shift again during the fallowing period this shift was not necessarily evidence of a return to pre-loading communities. The complexity of community shifts and their interpretation could be attributed to the vast functional redundancy of bacterial groups. Respiration studies indicated that cage site sediments were as resilient and as diverse as reference site sediments. CFB and AOB communities too showed shifts and counter shifts with organic loading and fallowing. Again the exact nature of the shifts was difficult to elucidate: communities did not show a simple shift/counter-shift response to farm loading and fallowing. Real-time PCR showed that CFB numbers increased with farming and decreased with fallowing. The response of the CFB group to organic loading was typical of that expected of an opportunistic group. Real-time PCR analysis of the AOB showed that farm loading had little effect on their numbers. The AOB were absent from clone libraries, but analysis of DGGE band sequences showed that a diverse AOB community was present at both farms at all times during the study, thus maintaining at least the potential for the coupled nitrification/denitrification process. Bacterial community shifts and response to perturbation are difficult to interpret, as a result of the massive functional redundancy exhibited by bacteria. The sediment bacterial community though, appeared to be determined by sediment environmental parameters. This is in contrast to sediment infaunal communities, which tend to respond according to the equilibrium theory. Bacterial biomass and diversity responded to farm fallowing practices, thus these practices appeared efficacious in maintaining diverse, resilient sediment bacterial communities.