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Metagenomic Sequencing of Marine Periphyton: Taxonomic and Functional Insights into Biofilm Communities

Journal article
Authors Kemal Sanli
Johan Bengtsson-Palme
R. Henrik Nilsson
Erik Kristiansson
Magnus Alm Rosenblad
Hans Blanck
Karl Martin Eriksson
Published in Frontiers in Microbiology
Volume 6
Issue 1192
ISSN 1664-302X
Publication year 2015
Published at Department of marine sciences
Department of Mathematical Sciences, Mathematical Statistics
Department of Biological and Environmental Sciences
Department of Chemistry and Molecular Biology
Institute of Biomedicine, Department of Infectious Medicine
Language en
Links dx.doi.org/10.3389/fmicb.2015.01192
Keywords Shotgun metagenomics, microbial ecology, Marine biofilms, Biofouling, next generation sequencing, Shotgun sequencing, Biodiversity, pathway analysis
Subject categories Databases, Data processing, Bioinformatics (Computational Biology), Environmental Sciences, Oceanography, Water in nature and society, Biochemistry and Molecular Biology, Cell Biology, Microbiology, Botany, Zoology, Bioinformatics and Systems Biology, Marine ecology, Biological Systematics, Functional genomics, Other Natural Sciences, Vehicle Engineering, Environmental Biotechnology, Fish and Aquacultural Science, Agricultural Biotechnology

Abstract

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.

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