Bepaling van de microbiële diversiteit op mariene sedimenten via DGGE profielen voor het bepalen van de mogelijke impact van antropogene activiteiten
Dobbelaere, C. (2015). Bepaling van de microbiële diversiteit op mariene sedimenten via DGGE profielen voor het bepalen van de mogelijke impact van antropogene activiteiten. BA Thesis. Howest (Hogeschool West-Vlaanderen): Brugge. 63 pp.
Sand extraction and the disposal of dredged material could have an effect on the microbial communities in the Belgian part of the North Sea (BPNS). The bacterial profiles are evaluated in sediments of sand extraction zones and dredged zones in BPNS. This thesis examines the method based on the clustering of denaturing gradient gel electrophoresis (DGGE) bacterial fingerprints, and is optimized for the use in monitoring.The Van Veen grab collected 55 sediment samples at different locations on the BPNS. Extracted DNA from the sediments was used for the amplification of the V3 region of the 16S rRNA. . The obtained PCR product was loaded on a DGGE gel, which resulted in a DGGE fingerprint with a lot of bands. The program Bionumerics, makes the clustering between different locations.An important observation is that the bacterial biodiversity is remarkably higher in the autumn compared with the spring. The genetic fingerprints from muddy sediments as well as from sandy sediments showed a high bacterial diversity. The results indicate that sediment characteristics, like grain size and presence of sludge, will influence the bacterial communities. The proposed method is certainly useful, but it should be further optimized in the future, for example to identify environment specific bacterial groups and indicator bacteria.. Bacterial species or families could also be identified by using NGS (next generation sequencing). The results of this thesis, recommend a PCR-DGGE method combined with metagenomics (using NGS, for the sequence of many bacteria) on all the sediments. In this way, it’s possible to collect all the necessary information for monitoring based on bacterial communities. Although a lot is known about the used methods, still there are unanswered questions. So it stays a challenge to gather more knowledge about the techniques by scientific investigation and practice-oriented experience.
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