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. 2024 Sep;55(3):2363-2370.
doi: 10.1007/s42770-024-01424-9. Epub 2024 Jul 11.

Existence of rare actinobacterial forms in the Indian sector of Southern Ocean: 16 S rRNA based metabarcoding study

Radhakrishnan Manikkam #  1 , Manigundan Kaari #  2   3 , Abirami Baskaran  2   4 , Meganathan P Ramakodi  5 , Gopikrishnan Venugopal  2 , Parli Venkateswaran Bhaskar  6
Affiliations

Existence of rare actinobacterial forms in the Indian sector of Southern Ocean: 16 S rRNA based metabarcoding study

Radhakrishnan Manikkam et al. Braz J Microbiol. 2024 Sep.

Abstract

The significance of the Southern Ocean (SO) as a sink of atmospheric CO2 and other greenhouse gases is well established. Earlier studies have highlighted the role of microbes in various SO ecosystem processes. However, the diversity and role of actinobacteria in the Indian sector of SO (ISO) water and sediments are unknown. This study aimed to analyze the diversity of actinobacteria in water and sediment samples of SO based on amplicon microbiome analyses. The taxonomic analysis identified a total number of 27 phyla of which Proteobacteria (40.2%), Actinobacteria (13.6%), and Firmicutes (8.7%) were found to be dominant. The comparative study of water and sediment samples revealed the dominance of different actinobacteria in water and sediments. While the order Streptomycetales was dominant in the water samples, Micrococcales was found to be dominant in the sediment samples. The genus level analysis found the presence of eight and seventeen genera in the sediment and water samples, respectively. The genus Streptomyces, Saccharopolyspora, Nocardioides, Sva0996 marine group, and Mycobacterium were seen both in sediment and water samples. Marmoricola, Ilumatobacter, and Glaciihabitans were observed only in sediment samples whereas Rhodococcus, Corynebacterium, Micrococcus, Turicella, Pseudonocardia, Bifidobacterium, Nesterenkonia, Collinsella, Knoellia, Cadidatus, Actinomarina, Libanicoccus and Cutibacterium were noticed exclusively in water samples. Our study also emphasizes the need for further detailed study to understand the links between actinobacterial diversity and their ecological functions in the ISO. The available metabarcoding data paves the way for future research in cultivable forms of novel and rare Actinobacteria for their bioprospecting applications.

Keywords: Actinobacteria specific primer; Amplicon sequencing; Diversity; Southern Ocean.

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Conflict of interest statement

The authors report no conflict of interest.

Figures

Fig. 1
Fig. 1
Location site for the sample collection (water samples- red dot and sediment samples- yellow dots)
Fig. 2
Fig. 2
Beta diversity analyses: Principal Coordinates Analysis (PCoA) plots based on Bray-Curtis distance. (a) PCoA plot based on the entire dataset; (b) PCoA plot based on the ASVs specific to the phylum actinobacteria
Fig. 3
Fig. 3
Composition of microbiome: (a) Phylum level diversity of microbiome in the water and sediment samples; (b) proportions of actinobacteria, proteobacteria and unclassified ASVs in the dataset
Fig. 4
Fig. 4
Diversity of actinobacteria in the water and sediment samples collected from the Southern Ocean: (a) composition of actinobacteria (genus-level) in the water and sediment samples (b) Comparison of actinobacterial diversity (order-level) in water and sediment samples; (c) Comparison of actinobacterial diversity (genus-level) in water and sediment samples
See this image and copyright information in PMC

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