Microbial diversity in selected Indonesian marine organisms
Metagenomics, the study of genetic material taken directly from the environment, generally includes the analysis of a whole microbial community, from both a taxonomic and functional perspective. In contrast to traditional microbiological techniques, this approach makes the isolation and cultivation of single organisms unnecessary. This allows the investigation of non-cultivable microorganisms, which represent the majority of microorganisms. While most metagenomic studies have focused on human and model organisms, the metagenome of marine species is relatively unknown. One area in particular that could be of major interest for aquaculture, but which has not been sufficiently investigated, is the influence of the environment on the composition of the bacterial community. This work deals with the effects that highly polluted and non-polluted environmental conditions have on bacterial communities. To do this, the microbial communities of three fish species (Atule mate, Epinephelus sexfasciatus and Epinephelus fuscoguttatus) and one shrimp species (Penaeus monodon) were investigated. Two different metagenomic techniques were applied. The results of a 16S amplicon-based approach did not reveal any differences between the investigated environments at a high taxonomic level. However, differences between the sampling locations could be found. A subsequent whole metagenome sequencing approach revealed, that predominant members of the microbiome living within a controlled environment of a mariculture facility are more stably distributed than those within free-living host species. Furthermore, the interactions between endoparasites and potential pathogenic bacteria were investigated. An analysis of the microbiome of shrimp shows only minor differences in the microbial community composition between free-living and aquacultured Penaeus monodon. In contrast, the microbial communities of the polluted environment showed significant differences.