Unveiling the role of emerging metagenomics for the examination of hypersaline environments

ABSTRACT

Hypersaline ecosystems are distributed all over the globe. They are subjected to poly-extreme stresses and are inhabited by halophilic microorganisms possessing multiple adaptations. The halophiles have many biotechnological applications such as nutrient supplements, antioxidant synthesis, salt tolerant enzyme production, osmolyte synthesis, biofuel production, electricity generation etc. However, halophiles are still underexplored in terms of complex ecological interactions and functions as compared to other niches. The advent of metagenomics and the recent advancement of next-generation sequencing tools have made it feasible to investigate the microflora of an ecosystem, its interactions and functions. Both target gene and shotgun metagenomic approaches are commonly employed for the taxonomic, phylogenetic, and functional analyses of the hypersaline microbial communities. This review discusses different types of hypersaline niches, their residential microflora, and an overview of the metagenomic approaches used to investigate them. Various applications, hurdles and the recent advancements in metagenomic approaches have also been focused on here for their better understanding and utilization in the study of hypersaline microbiome.

KEYWORDS:

• Hypersaline ecosystems
• halophiles
• target gene sequencing
• shotgun metagenomics

Authors’ contributions

Kiran Dindhoria: Conceptualization, literature survey, image creation, and manuscript writing. Vivek Manyapu: Assistance literature survey, image creation, and manuscript writing. Ashif Ali: Assistance literature survey and manuscript writing. Rakshak Kumar: Conceptualized the idea, overall supervision and finalized the manuscript

Disclosure statement

No potential conflict of interest was reported by the author(s).

Ethics approval and consent to participate

No ethics approvals or consents were required.

Additional information

Funding

KD is thankful to CSIR, Govt. of India for the ‘Research Fellowship’ Grant CSIR-NET JRF award no: 31/054(0139)/2019-EMR-I/CSIR-NET JRF JUNE 2017. RK acknowledges financial support from CSIR in-house project no. MLP-0182, NMHS project of MoEF&CC no. NMHS2022-23/MG11/01, and DST-TDT project no. DST/TDT/WM/2019/43. This manuscript represents CSIR-IHBT communication no. 5206.

Notes on contributors

Kiran Dindhoria

Kiran Dindhoria is undergoing her doctoral studies at the Department of Biotechnology, CSIR Institute of Himalayan Bioresource Technology (CSIR-IHBT), Himachal Pradesh, India. Her research interests are metagenomics, genomics, microbial biotechnology, molecular biology, plant-microbe interactions, agricultural and environmental sustainability. Her present research focuses on the culture-dependent and culture-independent approaches to understand the microbiome of the hypersaline ecosystems in India.

Vivek Manyapu

Vivek Manyapu worked as a researcher and project coordinator at the CSIR-IHBT. He is interested in the research domains of environmental science and biotechnology, with specific interest in organic waste management, bioremediation, soil-microbe interactions, carbon sequestration, and environmental sustainability.

Ashif Ali

Ashif Ali holds a PhD in Microbiology from the University of Hyderabad [Institution of Eminence (IoE)], Hyderabad, India. He is working as a project associate at CSIR-IHBT. His work focuses on projects employing multidisciplinary approaches to understand the functional genomics and physiology of bacteria for important trait and their applications.

Rakshak Kumar

Rakshak Kumar is working as a senior scientist at the Department of Biotechnology, CSIR-IHBT. His research focuses on environmental microbiology with a specific interest in exploring the microbiome of extreme regions, organic waste management, and bioprospection of extremozymes and biomolecules from extreme regions. Currently, he is handling research projects for both fundamental and translational aspects (https://ham.ihbt.res.in/).