Metagenomic Sequencing of Marine Periphyton: Taxonomic and Functional Insights into Biofilm Communities
Journal article, 2015

Periphyton communities are complex phototrophic, multispecies biofilms that develop on surfaces in aquatic environments. These communities harbor a large diversity of organisms comprising viruses, bacteria, algae, fungi, protozoans and metazoans. However, thus far the total biodiversity of periphyton has not been described. In this study, we use metagenomics to characterize periphyton communities from the marine environment of the Swedish west coast. Although we found approximately ten times more eukaryotic rRNA marker gene sequences compared to prokaryotic, the whole metagenome-based similarity searches showed that bacteria constitute the most abundant phyla in these biofilms. We show that marine periphyton encompass a range of heterotrophic and phototrophic organisms. Heterotrophic bacteria, including the majority of proteobacterial clades and Bacteroidetes, and eukaryotic macro-invertebrates were found to dominate periphyton. The phototrophic groups comprise Cyanobacteria and the alpha-proteobacterial genus Roseobacter, followed by different micro- and macro-algae. We also assess the metabolic pathways that predispose these communities to an attached lifestyle. Functional indicators of the biofilm form of life in periphyton involve genes coding for enzymes that catalyze the production and degradation of extracellular polymeric substances, mainly in the form of complex sugars such as starch and glycogen-like meshes together with chitin. Genes for 278 different transporter proteins were detected in the metagenome, constituting the most abundant protein complexes. Finally, genes encoding enzymes that participate in anaerobic pathways, such as denitrification and methanogenesis, were detected suggesting the presence of anaerobic or low-oxygen micro-zones within the biofilms.

pathway analysis

Shotgun sequencing

Shotgun metagenomics

Biodiversity

Marine biofilms

next generation sequencing

Biofouling

microbial ecology

Author

Kemal Sanli

University of Gothenburg

Johan Bengtsson-Palme

University of Gothenburg

R. Henrik Nilsson

University of Gothenburg

Erik Kristiansson

University of Gothenburg

Chalmers, Mathematical Sciences, Mathematical Statistics

Magnus Alm Rosenblad

University of Gothenburg

Hans Blanck

University of Gothenburg

Martin Eriksson

Chalmers, Shipping and Marine Technology, Maritime Environmental Sciences

Frontiers in Microbiology

1664-302X (ISSN)

Vol. 6 1192

Subject Categories

Botany

Biological Systematics

Cell Biology

Biochemistry and Molecular Biology

Ecology

Other Biological Topics

Microbiology

Bioinformatics (Computational Biology)

Vehicle Engineering

Fish and Aquacultural Science

Bioinformatics and Systems Biology

Agricultural Biotechnology

Oceanography, Hydrology, Water Resources

Zoology

Environmental Sciences

Environmental Biotechnology

Computer Science

Other Natural Sciences

DOI

10.3389/fmicb.2015.01192

More information

Created

10/8/2017