Community Research and Development Information Service - CORDIS

FP5

CODTRACE Report Summary

Project ID: Q5RS-2001-01697
Funded under: FP5-LIFE QUALITY
Country: Ireland

Deliverable: bacterial community classification of harvest location of cod

Composition and diversity within the bacterial assemblage
Phylogenetic analysis revealed that there was substantial diversity among sequences and when compared with database sequences, they were most similar to isolates and clones retrieved from marine samples. Sequences corresponding to the ?-proteobacteria dominated the clonal libraries for each sampling site and had high similarity (97-100%) to 16S rDNA sequences of Photobacterium sp., Psychrobacter sp., Acinetobacter sp. and Alteromonas sp. In contrast, ?-proteobacteria dominate free-living water marine bacteroplankton communities. Indeed, only a single member of the ?-proteobacterial group, with a 100% 16S rRNA gene identity to Loktanella salsilacus, was identified in our study and it comprised 4% of the Icelandic Sea clone library only. ?-Proteobacteria dominate libraries of bacteria isolated from marine systems. Clones clustering with 16S rDNA sequences from the CFB group showed the lowest level of similarity to published 16S rDNA sequence data, with two clones showing only a 92% similarity to the nearest relative (Bacteroides sp. ASF519) and it is possible that these clonal sequences (Accession Numbers DQ263705 and DQ263706) might represent novel genera.
Discriminant analyses clustered T-RFLPs by sample location, suggesting that the biogeography of bacterial communities differs significantly with water mass location. In this study, members of ?-proteobacteria consistently dominated cod epidermal communities throughout the North-East Atlantic, in correspondence with previous studies of the bacterial flora of fish indigenous to this area. However, within the ?-proteobacterial group, there were site-specific differences in the numbers of cod colonised by either Photobacterium sp. or Psychrobacter sp.. These results are in agreement with previous studies based upon culturable bacteria which showed that samples from spatially distinct sites were frequently dominated by different species. This study confirms the ubiquity of the CFB previously reported for marine samples.
If we assume no PCR (or other) bias, the dominant phylotypes detected in this study using T-RFLP are found to be existing in significant abundance, and must be assumed highly active. The oligotrophic nature of sea water and scarcity of nutrients mean that bacterial association with attached surfaces (such as marine aggregates and organisms) represents a good growth strategy and explains the composition of communities within fish epidermal mucous. Organisms related to the ?-proteobacteria (similar to those identified in this study) have been found to make up a significant proportion of particle-attached communities and to dominate these communities at depths greater than 50 m, similar to the depths at which the dermersal cod exist. Bacteria related to Psychrobacter sp., Acinetobacter sp. and Photobacterium sp. have all been previously isolated from fish; Photobacterium sp. (and closely related Vibrio sp.) have received much attention due to their luminous symbioses with marine organisms and chemotactic response to fish mucous.
In this study, relatively high levels of CFB bacteria on all fish sampled were found. This correlates well with their affinity for nutrient-rich environments and the phenotypic property of the group for the degradation of HMW compounds and biopolymers. Since mucous consists primarily of hydrated long chain polysaccharides, it is very likely that CFB bacteria are well adapted to metabolise this abundant source of dissolved organic matter (DOM). In a review of the group, Kirchman states that the levels of DOM in oceans is too low to support the high abundance of CFB bacteria that are found in a free-living state and suggests that it is the release of these bacteria from associated communities which contributes to these unusually high numbers. The CFB bacteria were found to be a dominant group in the mucous of almost all cod sampled in this study. It is therefore likely that these fish-associated communities serve as a significant reservoir for the group in aquatic systems.

The work in this study confirmed that a relative few phylogenetic clusters dominated the assemblages in the epidermal mucous of Atlantic Cod and that these comprised both resident and transient organisms. The data obtained in this study suggest that there may be a stable periodicity to bacterial community structure but the degree to which temporal and spatial scales affect this composition cannot be elucidated without analysing additional data over an extended sampling period.

Ultimately, the classification success varied from season to season, but this data when analysed across seasons and sites simultaneously (see Chapter 3G- classification by combined analysis) classification was at 78.3% overall. This is a very high success rate for classification, and indicates that this method is worth continued development as a tool for the traceability of cod.

Contact

Bret DANILOWICZ, (Associate Researcher)
Tel.: +353-1-7162347
Fax: +353-1-7161152
E-mail
Record Number: 44583 / Last updated on: 2008-01-15
Information source: e-TIP
Collaboration sought: Other