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Balasubramanian VK, Joseph Maran MI, Ramteke D, Vijaykumar DS, Kottarathail Rajendran A, Ramachandran P, Ramachandran R. Environmental DNA reveals aquatic biodiversity of an urban backwater area, southeast coast of India. MARINE POLLUTION BULLETIN 2021; 171:112786. [PMID: 34371435 DOI: 10.1016/j.marpolbul.2021.112786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 07/07/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
Strong conservation management needs comprehensive data on biodiversity. Rapid methods that document aquatic biodiversity or assess the health condition of an ecosystem remain scarce. Herein, we have performed a metagenomics study on environmental DNA (eDNA) collected from an urban backwater area - Muttukadu, located in the southeast coast of India. Shotgun metagenomics approach using Illumina®NextSeq500 sequencing yielded 88.4 million raw reads. The processed data was assigned as 80% prokaryotes, 0.4% eukaryotes, ~2% viruses, and ~17% remain unknown. This approach has the potential to identify small micro-eukaryote, unseen species from both estuarine and marine environments. We have identified 156 eukaryote organisms represented from 21 phyla and 112 families, including those that are of conservational significance and ecological importance. Furthermore, our data also demonstrated the presence of pathogenic microorganisms due to sewage mixing with the backwaters. Given its sensitivity, we suggest this approach for an initial assessment of biodiversity structure in an ecosystem for the biomonitoring program.
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Affiliation(s)
- Vignesh Kumar Balasubramanian
- Conservation of Coastal and Marine Resources Division (CMR), National Centre for Sustainable Coastal Management (NCSCM), India
| | - Midhuna Immaculate Joseph Maran
- Conservation of Coastal and Marine Resources Division (CMR), National Centre for Sustainable Coastal Management (NCSCM), India
| | - Darwin Ramteke
- Conservation of Coastal and Marine Resources Division (CMR), National Centre for Sustainable Coastal Management (NCSCM), India
| | - Deepak Samuel Vijaykumar
- Conservation of Coastal and Marine Resources Division (CMR), National Centre for Sustainable Coastal Management (NCSCM), India.
| | - Abhilash Kottarathail Rajendran
- Conservation of Coastal and Marine Resources Division (CMR), National Centre for Sustainable Coastal Management (NCSCM), India
| | - Purvaja Ramachandran
- Conservation of Coastal and Marine Resources Division (CMR), National Centre for Sustainable Coastal Management (NCSCM), India
| | - Ramesh Ramachandran
- Conservation of Coastal and Marine Resources Division (CMR), National Centre for Sustainable Coastal Management (NCSCM), India
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Tiknaik A, Khedkar C, Khedkar G, Prakash B, Mamatha DM, Sangale D, Kalyankar A. Microsatellite Genotyping Corroborated Loss of Genetic Diversity in Clarias batrachus as a Result of Lack of Regulatory Reforms in Aquaculture. Biochem Genet 2020; 58:595-616. [PMID: 32285324 DOI: 10.1007/s10528-020-09963-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 04/04/2020] [Indexed: 10/24/2022]
Abstract
In India, over the past 50 years, aquaculture practices of species such as those used for Clarias batrachus were developed without adequate regulatory oversight. In these situations, it is important to consider the influence that genetic factors can have on such vulnerable aquaculture species. Population genetic structure can be evaluated through the use of neutral molecular markers, and this can aid in predicting the risk of the demise of populations and for framing management strategies to conserve remaining populations. The study presented here reports on the genetic status of C. batrachus populations through the analysis of data collected using 22 microsatellite markers from seven natural and one hatchery population. The mean values for observed heterozygosity across loci within populations ranged from 0.242 to 0.485. Measures of genetic differentiation were low overall, with mean values for FST of 0.270, FIS of 0.113 and FIT of 0.353. An AMOVA analysis revealed that percentages of variation among and within populations were 27.16 and 6.86, respectively, and Bayesian clustering analyses showed a population subdivision consisting of five clusters with admixture of haplotypes from other populations leading to genetic bottleneck. We also examined how hatchery management factors leading to excessive exchanges of fish between river systems through could impact the structure of the C. batrachus populations. Overall, this study shows how the systematic use of molecular markers can facilitate the development of management policies for these populations and for the development of a comprehensive set of rules for hatcheries and aquaculture practices, including avoidance of excessive homozygosity by avoiding repeated use of feral broodstock and their interrogation.
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Affiliation(s)
- Anita Tiknaik
- Paul Hebert Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, Maharashtra, 431004, India
| | - Chandraprakash Khedkar
- Department of Dairy Microbiology, College of Dairy Technology, Maharashtra Animal Science and Fisheries University, Seminari Hill, Nagpur, Maharashtra, 440001, India
| | - Gulab Khedkar
- Paul Hebert Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, Maharashtra, 431004, India.
| | - Bharathi Prakash
- Department of Microbiology, University College, Hampenkatte, Mangalore, Karnataka, 575001, India
| | - Dadala Mary Mamatha
- Department of Seri Biotechnology, Sri Padmavati Mahila University, Tirupati, Andhra Pradesh, 517502, India
| | - Deepali Sangale
- Paul Hebert Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, Maharashtra, 431004, India
| | - Amol Kalyankar
- Paul Hebert Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, Maharashtra, 431004, India
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