Samra has a BS in biotechnology from the Capital University of Science, and Technology in Islamabad. She enjoys writing about biotechnology.
Marine biotechnology utilizes biotechnological applications by exploiting the world's marine resources to manufacture new products and processes using biotechnological tools. It has made significant progress in food, energy, and human health. Pharmaceutical firms’ interest in marine biotechnology has also evolved as they get a better grasp of the efficacy of natural therapies.
Despite the fact that marine biotechnology is still in its early stages, it has made significant contributions to the identification, characterization, and application of bio-diversified marine ecosystems through the use of cutting-edge omics technologies.
A General Introduction to Omics
Omics is the cluster of various fields of biology that end in omics, like metabolomics, proteomics, transcriptomics, and genomics. It deals with the tools and techniques applied in investigating the functions, interactions, and behaviors of the different sorts of components that constitute an individual's cells. These investigations are routinely carried out using cutting-edge technologies, resulting in enormous databases on cell structural and functional alterations.
"These omic disciplines are creating the appropriate platform for the growth of biological disciplines, which will focus on identifying the complicated connections that exist inside live organisms," (Veenstra, 2021).
Omics for Marine Biotechnology
Omics, which include genomes, transcriptomics, proteomics, metabolomics, and nutrigenomics, are revolutionizing biotechnology and medicinal research. It has shifted the focus away from a single nucleotide and toward the entire living organism.
These omics-driven methodologies aim to quantify and identify all biologic components that architecturally, physiologically, and periodically transition into living forms. On a macro scale, omics focus on grasping the complicated life contained within confined "omes." This comprehensive approach offers a wide range of important applications in marine biotechnology, including drug discovery, biofuel production, and aquaculture.
“Metabolic Synthesis of E. coli and Yeast using omics to produce biofuels and bioproducts based on primary and secondary Metabolism” (Amer & Baidoo, 2021)
"Omics" plays a significant role in enhancing quality, uniformity, and production and combating global food shortages through improved nutritive value.
“Many genome-based studies are developing new concepts for selective breeding, expansion, modifications, for various fish species.” (Wong et al., 2022)
With the introduction of genomics, marine biotechnology has grown dramatically. Biotechnologically manufactured items derived from marine creatures add to marine biotechnology's uniqueness.
Marine species may now be easily identified owing to mitochondrial and genomic research. In addition to shedding light on the development of marine life, it also aids in decoding the living species' whole genome. However, metagenomics for marine ecology is still in its early stages and has not yet been widely used. These genetic technologies and recent breakthroughs in marine life have increased our understanding of marine life biodiversity and its influence on the blue ecosystem. Genomics shows the DNA sequence and structure, assisting in resolving challenges such as ecosystem function, biodiversity loss, and climate change.
The advancement of omics technologies has also piqued the interest of researchers since they are becoming increasingly important in determining the genetic capacities of marine species. Since the completion of the sequences of numerous microbial genomes, more proteins per genome have been found than were previously known. This suggests that a large pool of bioactive chemicals cannot be expressed under standard laboratory settings.
Daniotti & Re, in their review, documented that bioactive compounds like terragins, violacein, and turbomycins were discovered by metagenomic techniques as a result of their antibiotic activity, demonstrating their potential use for discovering drugs from non-cultivable microorganisms. The meta-genomic approach can be used to discover novel bioactive chemicals produced by marine microbes.
In a recent study, Leão et al studied natural product genes and their expressed products in Benthic tropical cyanobacteria. They identified several biosynthetic gene clusters that could be used for genome mining.
The advancement of high-throughput screening and sequencing technology has resulted in the study of meta-transcriptomics, which quantifies the link between changing environmental circumstances and microbial activity.
Scientists used meta-transcriptomics in natural settings to disclose both known and undiscovered transcripts to investigate the influence of changing circumstances on the metabolism of marine species.
“Geoghegan and his fellow researchers characterized the viromes of nineteen wild-caught species of marine fish using total RNA sequencing (meta-transcriptomics) and concluded that fish harbor particularly large and complex viromes.”
Metatranscriptomics provides estimates of species composition and richness that are quite close to those derived from morphological data.
“Previously in the study of zooplanktons, Lopez and his colleagues utilized metatranscriptomics to monitor the diversity and composition of zooplankton.”
In biotechnology, proteomics is a highly complex and commonly utilized "omics." It can recognize and measure all proteins excreted by an organism at a given period. The data gathered from such a large number of samples enables us to obtain a better knowledge of the biological behavior of the organism in various settings.
Reindado and group in his study have discovered the anticancer protein UCA01 by utilizing proteomics data collected from Nannochloropsis gaditana, which is thereby translated into high-value information in the biomedical and agro-food industries. It allows for a better understanding of complex biochemical processes that genomes and transcriptomics cannot provide at the molecular level.
In a study, Zhou with his colleagues explored the molecular basis of overwintering metabolic alterations in Scylla paramamosain belonging to varying salinities at the protein level.
Metabolomics is another "Omics" technology that has evolved over the last two decades to better understand the many metabolites generated by diverse marine species. Metabolomics is a cutting-edge approach in marine chemical ecology that provides information about chemically induced interactions between marine animals.
Furthermore, this approach has proven to be effective in advancing the characterization of the structure and function of new metabolites.
In a study, Zhang et al have discovered a cluster of alkaloids, namely, phallusalides A-E from marine bacteria Micromonospora sp. With the help of the metabolomics tool. However, the ecology heavily influences the characterization of these metabolites. The metabolomics technique also aids in clarifying the influence of the ecosystem on metabolite synthesis.
In their investigation via LC-MS, Molina and colleagues described the distinct terpenoids produced from Erythropodium caribeorum found in three distinct areas.
Multi-Omics in Marine Biotechnology
Despite discovering the genomes of various marine creatures and their products, it is still critical to understand their interactions with metabolites encoded by them.
When all of the cutting-edge omics technologies (genomics, transcriptomics, and metabolomics) are combined, it provides us with a channel to connect metabolite production with the molecular events that regulate it. Integrating these omic approaches can provide in-depth knowledge about gene clusters, their expression, ultimate product, molecular mechanisms controlling them, and enzymes engaged in these processes for bioactive molecule production.
For instance, Wang et al in their research, used an integrated approach of multi-omics o identify genes related to the biosynthesis of eicosanoid in the sea urchin Strongylocentrotus intermedius.
Due to recent improvements in high-throughput sequencing technologies, we now have a better understanding of marine microbial diversity, ecology, and evolution.
Transcriptomics approaches such as metabarcoding suggest that identifying the function of genes in a single cell may be achievable. Despite the numerous advantages of metabolomics and its massive potential for finding new in vivo physiologically active chemicals, the lack of marine natural product coverage in public databases remains the fundamental disadvantage.
Furthermore, a data crisis looks to be on the horizon due to the massive number of sequencing data. To assure data sharing, scientists are taking a broader perspective of bioinformatics resources such as cloud services that may be utilized for research and data storage. This can be addressed, for instance, by adding identified and emergent marine natural products (from macro- and microorganisms found using both traditional and omics techniques) into existing databases such as GNPS.
- Amer, B., & Baidoo, E. (2021). Omics-Driven Biotechnology for Industrial Applications. Frontiers In Bioengineering And Biotechnology, 9. https://doi.org/10.3389/fbioe.2021.613307
- Barbosa, A., & Roque, A. (2019). Free Marine Natural Products Databases for Biotechnology and Bioengineering. Biotechnology Journal, 14(11), 1800607. https://doi.org/10.1002/biot.201800607
- Carrasco-Reinado, R., Escobar-Niño, A., Fajardo, C., Morano, I., Amil-Ruiz, F., & Martinez-Rodríguez, G. et al. (2020). Development of New Antiproliferative Compound against Human Tumor Cells from the Marine Microalgae Nannochloropsis gaditana by Applied Proteomics. International Journal Of Molecular Sciences, 22(1), 96. https://doi.org/10.3390/ijms22010096
- Daniotti, S., & Re, I. (2021). Marine Biotechnology: Challenges and Development Market Trends for the Enhancement of Biotic Resources in Industrial Pharmaceutical and Food Applications. A Statistical Analysis of Scientific Literature and Business Models. Marine Drugs, 19(2), 61. https://doi.org/10.3390/md19020061
- Geoghegan, J., Di Giallonardo, F., Wille, M., Ortiz-Baez, A., Costa, V., & Ghaly, T. et al. (2021). Virome composition in marine fish revealed by meta-transcriptomics. Virus Evolution, 7(1). https://doi.org/10.1093/ve/veab005
- Leão, T., Wang, M., Moss, N., da Silva, R., Sanders, J., & Nurk, S. et al. (2021). A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria. Marine Drugs, 19(1), 20. https://doi.org/10.3390/md19010020
- Lopez, M., Lin, Y., Sato, M., Hsieh, C., Shiah, F., & Machida, R. (2021). Using metatranscriptomics to estimate the diversity and composition of zooplankton communities. Molecular Ecology Resources, 22(2), 638-652. https://doi.org/10.1111/1755-0998.13506
- Molina, S., Forero, A., Ayala, F., Puyana, M., Zea, S., & Castellanos, L. et al. (2019). Metabolic Profiling of the Soft Coral Erythropodium caribaeorum (Alcyonacea: Anthothelidae) from the Colombian Caribbean Reveals Different Chemotypes. Marine Drugs, 18(1), 4. https://doi.org/10.3390/md18010004
- van der Hooft, J., Mohimani, H., Bauermeister, A., Dorrestein, P., Duncan, K., & Medema, M. (2020). Linking genomics and metabolomics to chart specialized metabolic diversity. Chemical Society Reviews, 49(11), 3297-3314. https://doi.org/10.1039/d0cs00162g
- Veenstra, T. (2021). Omics in Systems Biology: Current Progress and Future Outlook. PROTEOMICS, 21(3-4), 2000235. https://doi.org/10.1002/pmic.202000235
- Wang, H., Ding, J., Ding, S., & Chang, Y. (2020). Integrated metabolomic and transcriptomic analyses identify critical genes in eicosapentaenoic acid biosynthesis and metabolism in the sea urchin Strongylocentrotus intermedius. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-58643-x
- Wong, L., Razali, S., Deris, Z., Danish-Daniel, M., Tan, M., & Nor, S. et al. (2022). Application of second-generation sequencing (SGS) and third generation sequencing (TGS) in aquaculture breeding program. Aquaculture, 548, 737633. https://doi.org/10.1016/j.aquaculture.2021.737633
- Zhang, F., Braun, D., Chanana, S., Rajski, S., & Bugni, T. (2019). Phallusialides A–E, Pyrrole-Derived Alkaloids Discovered from a Marine-Derived <i>Micromonospora</i> sp. Bacterium Using MS-Based Metabolomics Approaches. Journal Of Natural Products, 82(12), 3432-3439. https://doi.org/10.1021/acs.jnatprod.9b00808
- Zhou, J., Li, N., Wang, H., Wang, C., & Mu, C. (2021). iTRAQ‐based quantitative proteomic analysis reveals metabolic changes in overwintering <i>Scylla paramamosain</i> at two different salinities. Aquaculture Research, 52(8), 3757-3770. https://doi.org/10.1111/are.15221
© 2022 Samra Hayat Khan