Decoding the ocean's microbiological secrets for marine enzyme biodiscovery

Abstract

A global census of marine microbial life has been underway over the past several decades. During this period, there have been scientific breakthroughs in estimating microbial diversity and understanding microbial functioning and ecology. It is estimated that the ocean, covering 71% of the earth's surface with its estimated volume of about 2 × 1018 m3 and an average depth of 3800 m, hosts the largest population of microbes on Earth. More than 2 million eukaryotic and prokaryotic species are thought to thrive both in the ocean and on its surface. Prokaryotic cell abundances can reach densities of up to 1012 cells per millilitre, exceeding eukaryotic densities of around 106 cells per millilitre of seawater. Besides their large numbers and abundance, marine microbial assemblages and their organic catalysts (enzymes) have a largely underestimated value for their use in the development of industrial products and processes. In this perspective article, we identified critical gaps in knowledge and technology to fast-track this development. We provided a general overview of the presumptive microbial assemblages in oceans, and an estimation of what is known and the enzymes that have been currently retrieved. We also discussed recent advances made in this area by the collaborative European Horizon 2020 project 'INMARE'.

Figure 1.

Phylogenetic tree representing the diversity of marine species spanning across the three domains of life. The figure represents the all-species living tree, release 132 (Yarza et al.; Munoz et al.2011), including all sequenced type strains belonging to the Archaea and Bacteria. The microorganisms of marine origin are shown in the outermost ring with grey lines. The tree comprises 13 903 leaves, from which 469 belong to microbial species isolated from marine environments. Major taxonomic clusters are highlighted by colours (see the legend). The scale bar represents the number of changes per site. The indications in the outer circle point the species from which full genome sequence, draft genome and/or with reviewed proteins in Swiss-Prot are available.

Figure 2.

Phylogenetic tree representing the diversity of studied enzymes spanning the three domains of life. The database used for the reconstruction corresponds to the release number 132 from the non-redundant SILVA database for the small sub-unit of the ribosomal RNA (September 2018). Phyla (or corresponding rank for the Eukaryotes) containing the characterised enzymes are depicted in colour (yellow for Eukaryotes, blue for Archaea and red for Bacteria). The graphs represent the families for which enzymes have been characterised (coloured cells) and the total number of families within the phylum according to the SILVA taxonomy (level D4 for taxonomic family). Bigger squares contain 10 × 10 units to allow easier visualisation. The number of genera with INMARE enzymes indicated for each coloured clade. Scale bar represents substitutions per site. Abbreviations in figure: OPU, Operational Phylogenetic Unit.