Genetic and Physiological Diversity of Marine Actinobacteria from the Okha Coast, Gujarat, India

Abstract

Saline and alkaline habitats of the Okha coastline, Gujarat, India, were explored for the diversity of actinobacteria. Based on the phenotypic and genotypic heterogeneity, nine haloalkaliphilic actinobacterial strains were characterized and identified. The PCR amplification of 16S rDNA using universal and genus-specific primers corroborated the trends that emerged through cultural and physiological characterization. Streptomyces was the most abundant genus amplified with the Streptomyces-specific primers (StreptB/E, StreptB/F), whereas other actinobacterial strains were amplified by the universal primers U1 and U2. Further molecular diversity was investigated by the gradient PCR-DGGE as a fingerprinting tool that generated group-specific DGGE patterns. Based on the nucleotide homology and phylogenetic analysis, strains OK-1 and OK-2 were identified as Streptomyces somaliensis. At the same time, OK-3 and OK-7 were detected as Streptomyces sp., while OK-5, OK-6, OK-8, OK-9, and OK-10 belonged to Nocardiopsis alba. Further, the cluster analysis using the UPGMA method generated 3 clusters based on biochemical characterization, sugar utilization, and enzyme production. The dendrogram based on the DGGE band pattern created with Jaccard-distance revealed two major clades with 33.33% similarity. Further, the study of alpha diversity calculation using phenotypic characteristics discloses highly diverse sugar utilization abilities. Moreover, a stress value of 0.1236 was obtained based on the NMDS analysis of the plots using Bary-Curties dissimilarity. Overall, the distinct phenotypic, metabolic, and molecular profiling illustrated the diversity among marine actinobacteria.

Keywords:

• DGGE
• haloalkhaliphilic actinobacteria
• heterogeneity
• NMDS
• 16S rDNA
• Streptomyces specific primers

Acknowledgements

The authors are grateful to Saurashtra University for its infrastructural facilities.

Disclosure statement

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

Additional information

Funding

VRM acknowledges the SHODH Fellowship by the Government of Gujarat, India. Authors gratefully acknowledge the support under the UGC (University Grants Commission)-CAS (Center of Advanced Study) and DST-FIST Programs. Research funding to SDG under the UGC-BSR (Basic Science Research) Start-up Grant Program [Sanction No. F.30-101/2015(BSR)] and DST-SERB, New Delhi, India [Sanction order No. ECR/2016/000928) is duly acknowledged. Further, DBT-Multi-Institutional Project, MoES-Net Working Project, and UGC-BSR Faculty Fellowship to SPS are acknowledged. International Travel Grants to SPS from DBT, CSIR, UGC, and SERB are also acknowledged. The authors are grateful to Saurashtra University for its financial support.