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The application of next-generation sequencing technology in microbial community analysis increased our knowledge and understanding of the complexity and diversity of a variety of ecosystems. In contrast to Bacteria, the archaeal domain was often not particularly addressed in the analysis of microbial communities. Consequently, established primers specifically amplifying the archaeal 16S ribosomal gene region are scarce compared to the variety of primers targeting bacterial sequences. In this study, we aimed to validate archaeal primers suitable for high throughput next generation sequencing. Three archaeal 16S primer pairs as well as two bacterial and one general microbial 16S primer pairs were comprehensively tested by in-silico evaluation and performing an experimental analysis of a complex microbial community of a biogas reactor. The results obtained clearly demonstrate that comparability of community profiles established using different primer pairs is difficult. 16S rRNA gene data derived from a shotgun metagenome of the same reactor sample added an additional perspective on the community structure. Furthermore, in-silico evaluation of primers, especially those for amplification of archaeal 16S rRNA gene regions, does not necessarily reflect the results obtained in experimental approaches. In the latter, archaeal primer pair ArchV34 showed the highest similarity to the archaeal community structure compared to observed by the metagenomic approach and thus appears to be the appropriate for analyzing archaeal communities in biogas reactors. However, a disadvantage of this primer pair was its low specificity for the archaeal domain in the experimental application leading to high amounts of bacterial sequences within the dataset. Overall our results indicate a rather limited comparability between community structures investigated and determined using different primer pairs as well as between metagenome and 16S rRNA gene amplicon based community structure analysis. This finding, previously shown for Bacteria, was as well observed for the archaeal domain. [ABSTRACT FROM AUTHOR]

The article discusses study on the evolution of bacteria because of the change in the habitat with bacterial community of seaweeds including Asparagopsis taxiformis and Asparagopsis armata, that were characterized using 16S rRNA barcoding through sequencing and metagenomics.

The scyphozoan Aurelia aurita is recognized as a key player in marine ecosystems and a driver of ecosystem change. It is thus intensely studied to address ecological questions, although its associations with microorganisms remain so far undescribed. In the present study, the microbiota associated with A. aurita was visualized with fluorescence in situ hybridization (FISH) analysis, and community structure was analyzed with respect to different life stages, compartments, and populations of A. aurita by 16S rRNA gene amplicon sequencing. We demonstrate that the composition of the A. aurita microbiota is generally highly distinct from the composition of communities present in ambient water. Comparison of microbial communities from different developmental stages reveals evidence for life stage-specific community patterns. Significant restructuring of the microbiota during strobilation from benthic polyp to planktonic life stages is present, arguing for a restructuring during the course of metamorphosis. Furthermore, the microbiota present in different compartments of the adult medusa (exumbrella mucus and gastric cavity) display significant differences, indicating body part-specific colonization. A novel Mycoplasma strain was identified in both compartment-specific microbiota and is most likely present inside the epithelium as indicated by FISH analysis of polyps, indicating potential endosymbiosis. Finally, comparison of polyps of different populations kept under the same controlled laboratory conditions in the same ambient water showed population-specific community patterns, most likely due the genetic background of the host. In conclusion, the presented data indicate that the associated microbiota of A. aurita may play important functional roles, e.g., during the life cycle. [ABSTRACT FROM AUTHOR]

Epibiotic biofilms have the potential to control major aspects of the biology and ecology of their hosts. Their composition and function may thus be essential for the health of the host. We tested the influence of salinity on the composition of epibacterial communities associated with the brown macroalga Fucus vesiculosus. Algal individuals were incubated at three salinities (5, 19, and 25) for 14 days and nonliving reference substrata (stones) were included in the experiment. Subsequently, the composition of their surface-associated bacterial communities was analyzed by 454 pyrosequencing of 16S rRNA gene sequences. Redundancy analysis revealed that the composition of epiphytic and epilithic communities significantly differed and were both affected by salinity. We found that 5% of 2494 epiphytic operational taxonomic units at 97% sequence similarity were responsible for the observed shifts. Epibacterial α-diversity was significantly lower at salinity 5 but did not differ between substrata. Our results indicate that salinity is an important factor in structuring alga-associated epibacterial communities with respect to composition and/or diversity. Whether direct or indirect mechanisms (via altered biotic interactions) may have been responsible for the observed shifts is discussed. [ABSTRACT FROM AUTHOR]