Abstract
Metagenomics refers to the analysis of DNA from a whole community. Metagenomic sequencing of environmental DNA has greatly improved our knowledge of the identity and function of microorganisms in aquatic, terrestrial, and human biomes. Although open oceans have been the primary focus of studies on aquatic microbes, coastal and brackish ecosystems are now being surveyed. Here, we review so far published studies on microbes in the Baltic Sea, one of the world’s largest brackish water bodies, using high throughput sequencing of environmental DNA and RNA. Collectively the data illustrate that Baltic Sea microbes are unique and highly diverse, and well adapted to this brackish-water ecosystem, findings that represent a novel base-line knowledge necessary for monitoring purposes and a sustainable management. More specifically, the data relate to environmental drivers for microbial community composition and function, assessments of the microbial biodiversity, adaptations and role of microbes in the nitrogen cycle, and microbial genome assembly from metagenomic sequences. With these discoveries as background, prospects of using metagenomics for Baltic Sea environmental monitoring are discussed.
Highlights
Abundant and ubiquitous environmental microorganisms are important drivers of global biogeochemical cycles, and understanding factors controlling their abundance, activities, and diversity is a major area of research
Important findings from high throughput sequencing (HTS) of environmental DNA (eDNA) or RNA include the discovery of novel genes, proteins, and microbial species (Yooseph et al 2007; Gilbert et al 2008), and findings related to the role of microbes in global biogeochemical cycles of carbon and nitrogen (Frias-Lopez et al 2008)
The Baltic Sea picocyanobacteria may have evolved a set of phycobiliproteins with a potentially unique absorption spectrum, to match light conditions offered by the Baltic Sea
Summary
Abundant and ubiquitous environmental microorganisms are important drivers of global biogeochemical cycles, and understanding factors controlling their abundance, activities, and diversity is a major area of research. A preHTS-era metagenomic analysis (using a cloning approach) of Baltic Sea sediment microbial communities was published in 2007 (Hardeman and Sjoling 2007), while the first HTS-signature-gene-based (pyro-sequencing) study appeared in 2010 (Andersson et al 2010).
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