Abstract
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.
Highlights
Natural microbial diversity encompasses a broad spectrum of microorganisms that exert a strong influence on global processes such as the carbon, nitrogen and sulphur biogeochemical cycles
The same trend was observed for the total number of bacteria (TNB), which was significantly higher at PolS than PriS
The Chlorophyll a (Chla) and TNB values indicate a global shift in biodiversity towards planktonic organisms such as bacteria and algae consistent with a higher level of nutrients at the polluted site
Summary
Natural microbial diversity encompasses a broad spectrum of microorganisms (bacteria, fungi, viruses) that exert a strong influence on global processes such as the carbon, nitrogen and sulphur biogeochemical cycles. Indices of microbial diversity are considered a sensitive measure of the state of the environment and the health of a given habitat or ecosystem. Assessment of biodiversity, represents a keystone in understanding the complex processes within ecosystems and needs to be taken into account in decisions concerning environmental resource management and conservation priorities [1], [2]. Relatively little attention has been given to a broad systematic assessment of microbial biodiversity, most likely because of the vast diversity of uncultured microbes [6] and the lack of appropriate methods that would allow studies to be performed in reasonable timescales and sampling resolutions
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