A Beginner’s Guide on Integrating *Omics Approaches to Study Marine Microbial Communities: Details and Discussions From Sample Collection to Bioinformatics Analysis

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.

Marine Microeukaryote Metatranscriptomics: Sample Processing and Bioinformatic Workflow Recommendations for Ecological Applications

“…Here we present a compiled resource highlighting the latest practices and procedures, from sample collection to computational analysis. This effort complements other valuable environmental metatranscriptomic reviews that have been recently published (e.g., Shakya et al, 2019;Mukherjee and Reddy, 2020;Zhang et al, 2021;Wilms, 2021;Kolody et al, 2022). We anticipate these recommendations will continue to evolve in the coming years, and encourage researchers to explore current sequencing platform options and bioinformatic workflows, and to consult updated versions of tool documentation before beginning new analyses.…”

“…In particular, focused community efforts on transcriptome sequencing of phylogenetically diverse protists will improve metatranscriptomic databases and strengthen our ability to track natural populations in the field. Single-cell transcriptomics (sc-RNA-Seq) performed on uncultured organisms isolated from the field will be especially valuable in expanding taxonomic and functional sequence coverage of microeukaryotes from complex communities (Wilms, 2021;Kolody et al, 2022).…”

“…Intriguingly, half of the gene functions are not annotated, and targeted efforts into protein characterization will drastically improve our understanding of protistan ecology and their biogeochemical roles (Carradec et al, 2018). There is furthermore value in combining marine metatranscriptomics with traditional physiological and chemical approaches (Marchetti, 2019;Wilms, 2021;Kolody et al, 2022), which can strengthen and guide biogeochemical interpretations, for example in relating metatranscriptomic community composition to microscope-derived cell counts or gene expression to empirically measured enzymatic rates. Integration of metatranscriptomic information with metaproteomics enables a broader view of protistan cell metabolism (Cohen et al, 2022), with recent modeling efforts offering a mechanistic understanding of the relationships between environmentally responsive transcripts and proteins in marine microbes (Walworth et al, 2022).…”

“…Early marine meta-omic studies relied upon high-throughput Sanger and second generation sequencing (454 pyrosequencing and SOLiD) platforms (Venter et al, 2004;Rusch et al, 2007;Gilbert et al, 2008;McCarren et al, 2010;Stewart et al, 2010), with the first metatranscriptomic study focusing on marine microeukaryotes released in 2012 (Marchetti et al, 2012). Pyrosequencing and SOLiD platforms were later replaced by Illumina bridge amplification-based sequencing as a result of unparalleled throughput, low error rates, and mid-range read lengths (~2 x 150 bp, paired-end) that were longer than SOLiD (~85 bp), but shorter than pyrosequencing and Sanger sequencing (>400 bp) (Liu et al, 2012;Ambardar et al, 2016;Wilms, 2021). The price of sequencing has continued to decrease, while the degree of throughput has increased (Muir et al, 2016).…”

Science and Dissemination for the UN Ocean Decade Outcomes: Current Trends and Future Perspectives

“…The bioinformatics field offers specialized analytical technology tools for both laboratory and networking technology fields to achieve the goal of finding natural bioactive compounds from marine organisms as potential drugs, antifouling compounds, biomaterials etc. It has the highest implication in marine based ecology, biology, biotechnology and molecular biology, which are integrated for the gene-based discovery and development of marine drugs (Liguori et al, 2020;Wilms, 2021). The marine bioinformatics includes marine genomics and marine proteomics.…”