Phylogenetic and functional metagenomic profiling for assessing microbial biodiversity in environmental monitoring

• Published in: PloS one Vol. 7; no. 8; p. e43630
• Main Authors: Kisand, Veljo, Valente, Angelica, Lahm, Armin, Tanet, Gerard, Lettieri, Teresa
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 27.08.2012; Public Library of Science (PLoS)
• Subjects: Anthropogenic factors; Aquatic ecosystems; Bacteria; Bacteria - classification; Bacteria - genetics; Biodiversity; Biogeochemical cycles; Bioinformatics; Biology; Coastal zone; Deoxyribonucleic acid; DNA; DNA sequencing; Earth Sciences; Ecological effects; Ecological monitoring; Ecosystem assessment; Ecosystems; Environmental changes; Environmental conditions; Environmental management; Environmental Monitoring; Gene sequencing; Genetic testing; Genomics; Human influences; Metagenomics; Microbial activity; Microbiology; Microorganisms; Molecular Sequence Annotation; Oceans and Seas; Open Reading Frames - genetics; Phylogeny; Ports; Protected areas; Sequence Analysis, DNA; Stress, Physiological; Studies; Sustainability; Systematic review; Water analysis; Water quality; Water sampling; United States > US; Italy; Mediterranean Sea
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0043630

Decisions guiding environmental management need to be based on a broad and comprehensive understanding of the biodiversity and functional capability within ecosystems. Microbes are of particular importance since they drive biogeochemical cycles, being both producers and decomposers. Their quick and direct responses to changes in environmental conditions modulate the ecosystem accordingly, thus providing a sensitive readout. Here we have used direct sequencing of total DNA from water samples to compare the microbial communities of two distinct coastal regions exposed to different anthropogenic pressures: the highly polluted Port of Genoa and the protected area of Montecristo Island in the Mediterranean Sea. Analysis of the metagenomes revealed significant differences in both microbial diversity and abundance between the two areas, reflecting their distinct ecological habitats and anthropogenic stress conditions. Our results indicate that the combination of next generation sequencing (NGS) technologies and bioinformatics tools presents a new approach to monitor the diversity and the ecological status of aquatic ecosystems. Integration of metagenomics into environmental monitoring campaigns should enable the impact of the anthropogenic pressure on microbial biodiversity in various ecosystems to be better assessed and also predicted.