The ocean harbors vast biodiversity, ranging from microorganisms to megafauna. However, global environmental changes, pollution, and human activities are exerting immense pressure on marine ecosystems. In this context, biotechnology offers promising opportunities to support the conservation and sustainable use of marine resources.

Marine biodiversity plays a crucial role in maintaining the balance of the global ecosystem. Indonesia, as an archipelagic nation with extensive marine territory, possesses exceptionally high marine biodiversity. Unfortunately, overexploitation, pollution, and climate change have jeopardized the survival of marine species in various regions.

Molecular Biology Technology is a branch of biological science that focuses on the molecular basis of various biological processes within and between cells. This includes activities such as synthesis, modification, mechanisms, and molecular interactions. The rapid advancements in this field owe much to contributions from other disciplines, such as biochemistry, which studies proteins, their structures, and their synthesis, and genetics, which explores Mendel’s laws, chromosomes, and genes.

Genetic engineering, also known as recombinant DNA technology, is a method for manipulating the genetic traits of organisms by recognizing or deleting specific genes (Micklos et al., 1990). Generally, this technique involves modifying living organisms by transferring genes from one species to another. The process of genetic engineering typically includes gene isolation, modification, and transfer to a new organism to enhance its biological function, resulting in transgenic organisms. The products of this technique are referred to as Genetically Modified Organisms (GMOs).

One of the molecular biology technologies widely used today is the CRISPR method. Originally developed as a microbial defense system against viruses, CRISPR has evolved into a powerful biotechnology tool that enables genetic manipulation with exceptional efficiency and accuracy. CRISPR, which stands for “clustered regularly interspaced short palindromic repeats,” holds immense potential in marine biotechnology. This technology facilitates precise genome editing, which can be harnessed to enhance species adaptation to environmental stresses, improve population genetics, and even develop new, more resilient marine organisms.

CRISPR is one of the most promising genetic engineering technologies for the exploration and conservation of marine biodiversity. It enables precise genetic modifications for various purposes, such as increasing an organism’s resistance to environmental changes or pathogens, as well as managing genetic resources within marine ecosystems.

CRISPRloci workflow (Photo Credit : O. S. Alkhnbashi et al, 2021)

The workflow supports 4 different input types. If DNA is selected as input, the CRISPRlociwill identify the CRISPR array, predict its orientation and Leadersequence and then extract the repeat sequence and spacer. The repeated sequence is then analyzed for its structural stability while spacers are used to identify potential regions of self-targeting. If a protein sequence is delivered as input, CRISPRloci will classify and report the type and role of the protein. Users can optionally enter a series of repetition sequences. In this scenario, CRISPRlociwill perform a lookup for similar repeating sequences in an existing database. Users will be given hits as well as their region, similarity, and electronic value. Finally, users can provide viral DNA as input. In this scenario, CRISPRlociwill perform a protospacer search using the spacer database. The user will be provided with the protospacer coordinates as well as a description of the host CRISPR array (O. S. Alkhnbashi et al., 2021).

In marine ecosystems, CRISPR can be utilized for the following purposes:

1. Species Conservation

   CRISPR technology aids in conserving threatened species by enhancing their genetic resilience. It is used in conservation studies to map and protect vulnerable species. For example, this method can help identify species at risk of environmental changes through population genetic analysis. However, regulatory and ethical challenges in applying this technology require careful consideration.

2. Habitat Restoration

   CRISPR can modify the genes of organisms to increase their resistance to pollution or environmental changes, aiding in the restoration of degraded habitats.

3. Biotechnology Production

   CRISPR facilitates the development of marine organisms with superior traits, such as faster growth rates or enhanced resistance to diseases, promoting sustainable biotechnological production.

Evaluation of Genetic Technology Methods in Marine Species Conservation

1. Methods and Successes of Genetic Technology
   

   The table presents the successes of each method based on a literature review.

   Genetic technologies applied to marine species conservation encompass a range of methods, including environmental DNA monitoring (eDNA), CRISPR-based genetic engineering techniques, and population genetic analysis.

2. Case study of IMPLEMENTATION of genetic technology
   

   The table presents case studies of genetic technology implementation.

   Several case studies highlight the application of genetic technology in marine species conservation. For instance, in Raja Ampat, environmental DNA (eDNA) monitoring has been employed to identify and protect endangered species such as Napoleon fish (Cheilinus undulatus) and green turtles (Chelonia mydas). This innovative approach allows researchers to detect the presence of these species in the ecosystem without direct observation, aiding in their conservation and the management of their habitats.

Application of The CRISPR Method to Marine Microbes

The complexity of ocean dynamics drives microbes to adapt in unique and diverse ways, including establishing symbiotic relationships with marine invertebrates such as ascidia, forming a community known as the microbiome. A microbiome is a collection of microorganisms inhabiting a specific environment, including body parts of macroorganisms. Ascidia, or sea squirts, are marine invertebrates belonging to the class Ascidiacea within the subphylum Tunicata. The ascidia microbiome refers to the community of microorganisms living in association with ascidia.

One such microorganism, Prochloron diem, as reported by Rumengan et al. (2021), possesses a patE gene cluster that encodes cyclic peptides with potential as anticancer agents. Other microbes associated with marine ascidia in Manado Bay include Synechococcus sp. and Leptolyngbya sp.

The molecular potential of marine microbes, as recorded in their genomes, includes not only the production of bioactive compounds but also the ability to resist foreign nucleic acid infections, such as those from viruses and plasmids. These microbes, which are primarily bacteria and archaea, have distinctive genome sequences containing a specific nucleotide arrangement known as CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats). CRISPR sequences are regions in microbial genomes consisting of repeated palindromic nucleotide sequences (repeats) flanked by sequences (spacers) derived from foreign nucleic acids that previously infected the microbes. CRISPR systems are often paired with cas (CRISPR-associated) genes, which encode nuclease proteins responsible for cleaving nucleotides. This system, referred to as CRISPR-Cas, varies across different microbial species.

The study of CRISPR units in marine microbes from tropical waters, including those associated with ascidia, remains limited. However, in silico detection of CRISPR sequences presents opportunities for leveraging CRISPR-Cas systems in gene editing, with potential applications in developing superior marine biota, enhancing disease resistance, and promoting marine resource conservation. Research on microbes associated with ascidia in Manado Bay, North Sulawesi, has identified cyclic peptide-encoding genes and conducted in silico analyses of patellamide and ulithiacyclamide molecules. These findings pave the way for further investigation into CRISPR nucleotide sequences that could be harnessed for genome editing.

This research provides new insights into the genomic potential of microbes, particularly those with CRISPR systems, for applications in marine biotechnology. CRISPR technology allows for precise gene editing by targeting specific DNA sequences, enabling modifications or repairs. In the context of marine life, CRISPR has been applied to microorganisms such as Synechococcus sp. and Leptolyngbya sp., which are associated with ascidia. The detection of CRISPR in these microbes offers significant opportunities for designing gene-editing tools for both conservation and biotechnological applications.

Advantages and Challenges of CRISPR in Marine Biotechnology

Advantages of CRISPR Technology in Marine Conservation

• High Efficiency: Enables fast, precise, and efficient gene manipulation.
• Enhanced Adaptation: Facilitates the development of species that are more resilient to climate change, pollution, or pathogens.
• Reduced Mortality: For instance, in green turtles, CRISPR can increase genetic resistance to diseases previously considered untreatable.

The main advantage of CRISPR is its ability to perform efficient gene editing, allowing for the creation of more adaptive marine organisms.

Challenges of CRISPR Technology in Marine Biotechnology

1. Ethics and Regulation: The use of CRISPR requires strict regulatory frameworks to prevent unintended ecological consequences.
2. Limited Genetic Data: The lack of comprehensive genetic information for many marine organisms hinders genetic research.
3. Resource Constraints: Developing countries often face limitations in facilities, funding, and expertise for biotechnology research.

Additionally, clear ethical guidelines are essential to ensure the responsible use of CRISPR technology. Further research and broader field trials are necessary to address these challenges and unlock the full potential of CRISPR in conserving marine biodiversity.

-YN

References

2019. B. S. Haryani and A. Fauzi, "Bioeconomic analysis on coral fish in Raja Ampat Regency, West Papua Province," in IOP Conference Series: Earth and Environmental Science, Institute of Physics Publishing, May 2019. doi: 10.1088/1755-1315/278/1/012032

Betzy Victor Telaumbanua, Destriman Laoli, Ratna Dewi Zebua, Okniel Zebua, January Dawolo, and Asokhiwa Zega, "Implementation of Genetic Technology for the Conservation of Endangered Marine Species: A Literature Review on Methods and Successes," Manfish: Scientific Journal of Fisheries and Animal Husbandry, vol. 2, no. 2, pp. 58–68, Aug. 2024, doi: 10.62951/manfish.v2i2.46.

Purwanto et al., "The Bird's Head Seascape Marine Protected Area network—Preventing biodiversity and ecosystem service loss amidst rapid change in Papua, Indonesia," Conserv Sci Pract, vol. 3, no. 6, Jun. 2021, doi: 10.1111/csp2.393.

2015. Untu, I. F. M Rumengan, E. L. Ginting, P. Marine Science Studies, F. Fisheries and Marine Sciences, and U. Sam Ratulangi, "IDENTIFICATION OF THE CO-EXIST MICROBES WITH ASCIDIAN Lissoclinum patella BY USING 16S rRNA gene sequences," 2015.