Microbial Richness of Marine Biofilms Revealed by Sequencing Full-Length 16S rRNA Genes

Marine biofilms are a collective of microbes that can grow on many different surfaces immersed in marine environments. Estimating the microbial richness and specificity of a marine biofilm community is a challenging task due to the high complexity in comparison with seawater. Here, we compared the resolution of full-length 16S rRNA gene sequencing technique of a PacBio platform for microbe identification in marine biofilms with the results of partial 16S rRNA gene sequencing of traditional Illumina PE250 platform. At the same time, the microbial richness, diversity, and composition of adjacent seawater communities in the same batch of samples were analyzed. Both techniques revealed higher species richness, as reflected by the Chao1 index, in the biofilms than that in the seawater communities. Moreover, compared with Illumina sequencing, PacBio sequencing detected more specific species for biofilms and less specific species for seawater. Members of Vibrio, Arcobacter, Photobacterium, Pseudoalteromonas, and Thalassomonas were significantly enriched in the biofilms, which is consistent with the previous understanding of species adapted to a surface-associated lifestyle and validates the taxonomic analyses in the current study. To conclude, the full-length sequencing of 16S rRNA genes has probably a stronger ability to analyze more complex microbial communities, such as marine biofilms, the species richness of which has probably been under-estimated in previous studies.

Automated summary

This study compared the ability of full-length 16S rRNA gene sequencing technique on the PacBio platform and partial 16S rRNA gene sequencing on the traditional Illumina platform to identify microbes in marine biofilms. The results showed that marine biofilms had higher microbial species richness compared to seawater communities, and PacBio sequencing detected more specific species unique to biofilms. The enrichment of specific species in biofilms, such as Vibrio, Arcobacter, Photobacterium, Pseudoalteromonas, and Thalassomonas, confirms previous understanding of species adapted to a surface-associated lifestyle.