Vietnam’s First Discovery of Halophilic Archaea – A Promising Enzyme Source for Biotechnology
Cellulose, xylan, chitin, and hyaluronic acid are important natural polysaccharides, playing essential roles in the global carbon cycle and holding various biomedical and industrial applications. However, effective exploitation of these compounds requires specialized enzymes that can function in harsh environments. Among these, enzymes from halophilic Archaea (Haloarchaea) are gaining research interest due to their superior characteristics: salt tolerance, heat stability, and resilience across a wide pH range. Currently, there is a rapidly increasing demand for low-molecular-weight hyaluronic acid, a form with high bioactivity and better absorption, especially in medicine, healthcare, and cosmetics. This necessitates an urgent search for enzymes capable of efficiently degrading this compound. Thanks to their exceptional adaptability, Haloarchaea strains are expected to become a valuable enzyme source for modern biotechnological applications.
Vietnam has a vast network of natural salt fields stretching from north to south, offering ideal environments for the growth of Haloarchaea. However, research on this group of ancient microorganisms remains limited. In response to this need, an international collaboration project titled “HALOPHARM: Halophilic Archaea – A New Enzyme Source for Medicinal Applications” (code: QTIT01.01/23-24) was launched between the Nha Trang Institute of Research and Technology Applications (now the Institute of Oceanography) – Vietnam Academy of Science and Technology, and the Institute of Polar Sciences (ISP) – National Research Council of Italy (CNR). The Vietnamese side was led by Associate Professor Dr. Pham Duc Thinh, with the objective of identifying, isolating, and exploiting enzymes from indigenous Haloarchaea strains – extremophilic microorganisms thriving in high-salinity environments with potential applications in medicinal and high-tech bioproduct manufacturing.
Assoc. Prof. Dr. Pham Duc Thinh (third from left) and the Institute of Oceanography welcoming the ISP - CNR delegation (Italy), June 2023
As part of the project, scientists conducted sample collection at typical salt fields across all three regions of Vietnam, notably Hon Khoi (Khanh Hoa) and Hai Ly (Nam Dinh) – locations with extremely high salinity where most life forms struggle to survive.
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| Sampling at Hon Khoi, Ninh Diem, Ninh Hoa (June 15, 2023) | Sampling at Ninh Thuan salt fields (June 2024) |
As a result, the research team successfully isolated 27 highly salt-tolerant microbial strains from samples collected in Hon Khoi – Khanh Hoa. These strains showed impressive adaptability to salinity levels ranging from 165 to 375 g/L and temperatures between 36.5°C and 60.2°C—conditions classified as extreme for life. Notably, five of these strains were identified as halophilic Archaea (Haloarchaea), based on specific sensitivity to anisomycin. The ability of these strains not only to survive but also to thrive under artificial cultivation conditions has opened a gateway to exploring the microbial "dark matter" of ancient life.
From these five archaeal strains, the team screened for polysaccharide-hydrolyzing enzymatic functions. The results showed that strain VS7M5.3 had strong activity on all three substrates: cellulose, hyaluronic acid (HA), and chitin. Other strains such as VS7M5.1, VS7M5.7, and VS7M5.11 also demonstrated significant enzymatic activity on individual substrates, suggesting potential applications for cellulases/xylanases, chitinases, and hyaluronidases in biotechnology, medicine, environmental remediation, and biofuel production from biomass.
Microbial strains on isolation media after three weeks of culture, with some colonies already purified
A highlight of this research was the use of modern metagenomic technology to analyze microbial community structures. The team sequenced the V3–V4 region of the 16S rRNA gene from brine, sediment, and crystallized salt samples. Results showed high biodiversity levels, especially in sediment sample VS9sed. The Halobacterota group dominated most samples with high salt content, while the lesser-known DPANN Archaea group accounted for approximately 78.5% in sample VS7. Additionally, the team discovered deep evolutionary branches never previously recorded in international databases, such as DBCVW#1, DBCVN#2, and DBCVP#2. Notably, the DBCVW#1 cluster from sample VS7 is considered a potential evolutionary branch representing a new species.
Phylogenetic tree of halophilic Archaea (Haloarchaea) and related groups based on 16S rRNA gene sequences
Discussing the challenges of the research, Assoc. Prof. Dr. Pham Duc Thinh noted: One of the greatest obstacles was working with archaeal strains, which require extremely stringent environmental conditions, such as precise salinity, pH, and temperature. Even a slight deviation during culturing could prevent growth or result in loss of enzymatic activity, which is crucial for subsequent analyses. Furthermore, processing metagenomic data involving hundreds of thousands of short sequences required powerful computational systems and specialized bioinformatics expertise—something not all local institutions are fully equipped to provide.
Nevertheless, through this international collaboration with ISP - CNR (Italy), the team gained access to next-generation sequencing (NGS) technologies and successfully performed whole genome sequencing (WGS) on several carefully selected archaeal strains. While detailed analysis results cannot yet be published due to time constraints, these initial findings have already paved the way for significant advances—not only in technology but also in enhancing the expertise and research capacity of Vietnam’s scientific personnel.
Assoc. Prof. Dr. Pham Duc Thinh visiting ISP - CNR (Italy), November 2024
The research results have been published in one international SCIE-indexed journal and one national scientific journal, and also supported the training of one graduate student in experimental biology. This affirms the role of the research in enhancing scientific training and education quality.
Assoc. Prof. Dr. Pham Duc Thinh added: The enzymes isolated from halophilic Archaea strains initially showed activity on several polysaccharide substrates, indicating their potential in biotechnology. Although these strains have not yet been developed into commercial products, they serve as valuable genetic material, offering a foundation for studying salt- and heat-tolerant enzymes—critical properties for use in biotechnology, environmental treatment, and pharmaceutical production. These initial results lay the groundwork for further screening, optimization, and application assessment in subsequent specialized research.
Beyond practical applications, this study also contributes to the existing collection of nearly 2,000 marine microbial strains currently preserved at the institute, with the aim of establishing a National Marine Microorganism Bank. This will form a foundation for future research on biodiversity, development of specialized enzymes, and exploitation of bioactive compounds from marine microorganisms. At the same time, studying how microorganisms survive in extreme conditions expands our understanding of life’s adaptability—an essential scientific pursuit in the context of global climate change, where biotechnological solutions are increasingly needed.
Translated by Phuong Ha
Link to Vietnamese version
