A Beginner’s Guide on Integrating *Omics Approaches to Study Marine Microbial Communities: Details and Discussions From Sample Collection to Bioinformatics Analysis
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 ecosyste...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-12-01
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| Series: | Frontiers in Marine Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmars.2021.692538/full |
| _version_ | 1818459204282744832 |
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| author | Sabrina Natalie Wilms Sabrina Natalie Wilms |
| author_facet | Sabrina Natalie Wilms Sabrina Natalie Wilms |
| author_sort | Sabrina Natalie Wilms |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-14T23:10:38Z |
| format | Article |
| id | doaj.art-9f99cf799fe14e929b9fdf06ae391cd8 |
| institution | Directory Open Access Journal |
| issn | 2296-7745 |
| language | English |
| last_indexed | 2024-12-14T23:10:38Z |
| publishDate | 2021-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Marine Science |
| spelling | doaj.art-9f99cf799fe14e929b9fdf06ae391cd82022-12-21T22:44:13ZengFrontiers Media S.A.Frontiers in Marine Science2296-77452021-12-01810.3389/fmars.2021.692538692538A Beginner’s Guide on Integrating *Omics Approaches to Study Marine Microbial Communities: Details and Discussions From Sample Collection to Bioinformatics AnalysisSabrina Natalie Wilms0Sabrina Natalie Wilms1Department of Ecological Chemistry, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), Bremerhaven, GermanyFaculty of Biology/Chemistry, University of Bremen, Bremen, GermanyThe 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.https://www.frontiersin.org/articles/10.3389/fmars.2021.692538/fullmicrobial organismsmolecular ecologyhigh-throughput sequencingdiversity estimatesfunctional traitsdata science |
| spellingShingle | Sabrina Natalie Wilms Sabrina Natalie Wilms A Beginner’s Guide on Integrating *Omics Approaches to Study Marine Microbial Communities: Details and Discussions From Sample Collection to Bioinformatics Analysis Frontiers in Marine Science microbial organisms molecular ecology high-throughput sequencing diversity estimates functional traits data science |
| title | A Beginner’s Guide on Integrating *Omics Approaches to Study Marine Microbial Communities: Details and Discussions From Sample Collection to Bioinformatics Analysis |
| title_full | A Beginner’s Guide on Integrating *Omics Approaches to Study Marine Microbial Communities: Details and Discussions From Sample Collection to Bioinformatics Analysis |
| title_fullStr | A Beginner’s Guide on Integrating *Omics Approaches to Study Marine Microbial Communities: Details and Discussions From Sample Collection to Bioinformatics Analysis |
| title_full_unstemmed | A Beginner’s Guide on Integrating *Omics Approaches to Study Marine Microbial Communities: Details and Discussions From Sample Collection to Bioinformatics Analysis |
| title_short | A Beginner’s Guide on Integrating *Omics Approaches to Study Marine Microbial Communities: Details and Discussions From Sample Collection to Bioinformatics Analysis |
| title_sort | beginner s guide on integrating omics approaches to study marine microbial communities details and discussions from sample collection to bioinformatics analysis |
| topic | microbial organisms molecular ecology high-throughput sequencing diversity estimates functional traits data science |
| url | https://www.frontiersin.org/articles/10.3389/fmars.2021.692538/full |
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