Abstract
The variety of Earth’s organisms is manifold. However, it is the small-scale marine community that makes the world goes round. Microbial organisms of pro- and eukaryotic origin drive the carbon supply and nutrient cycling, thus are mediating the primary productivity within the world largest ecosystem called ocean. But due to the ocean’s great size and large number of biogeographically habitats, the total of microbial species can hardly be grabbed and therefore their functional roles not fully described. However, recent advances in high-throughput sequencing technologies are revolutionizing our understanding of the marine microbial diversity, ecology and evolution. Nowadays, research questions on species differentiation can be solved with genomic approaches such as metabarcoding, while transcriptomics offers the possibility to assign gene functions even to a single cell, e.g., single-cell transcriptomics. On the other hand, due to the diversified amount of sequencing data, the certainty of a data crisis is currently evolving. Scientists are forced to broaden their view on bioinformatics resources for analysis and data storage in from of, e.g., cloud services, to ensure the data’s exchangeability. Which is why time resources are now shifting toward solving data problems rather than answering the eco-evolutionary questions stated in the first place. This review is intended to provide exchange on *omics approaches and key points for discussions on data handling used to decipher the relevant diversity and functions of microbial organisms in the marine ecosystem.
Highlights
The ocean is essential to all aspects of well-being and livelihood on earth as it thrives fundamental processes like global climate regulation, carbon and nutrient cycles (Salazar and Sunagawa, 2017; IPCC, 2019)
Transcriptomic ribonucleic acid (RNA) corresponds to total RNA extracted from a single individual or from a collection of individuals belonging to the same species
Assembly will become less challenging in the future as the length of reads increases and algorithms are continuously improved (Auer and Doerge, 2010). (A) Whole transcriptome sequencing (WTS) is the sequencing approach toward transcriptomic RNA extracted from a single individual or from a collection of individuals belonging to the same species (Richardson, 2008)
Summary
The ocean is essential to all aspects of well-being and livelihood on earth as it thrives fundamental processes like global climate regulation, carbon and nutrient cycles (Salazar and Sunagawa, 2017; IPCC, 2019). In addition to established methods, such as microscopy and Sanger sequencing (Hoffecker et al, 2019), nextgenerations of sequencing technologies with high-throughput have become an almost everyday research tool for revealing the intracellular-flow of genetic information ranging from single-cells to whole communities (Chui et al, 2020) These sequencing results improve the overall ability to understand biological processes across above mentioned disciplines and answer fundamental questions about microbial diversity and activity; hereby ranging from microbiome studies (Sunagawa et al, 2015), biomonitoring surveys (Pawlowski et al, 2016) to concepts of species and evolution (Strassert et al, 2018; Keeling, 2019). The information given here should lower the hurdle for many scientists in the field who lack practical expertise, wish to apply such methods to their research by considering details from sampling itself to downstream analysis
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