Exploration of uncultivable actinobacteria from pristine mangrove sediments of Palk Strait, India – A metagenomic approach

Abstract

Marine actinobacteria are ubiquitous and polyextremophilic microbes vastly studied from terrestrial and coastal ecosystems, leaving mangroves unexplored due to their uncultivable nature and complex media requirements. This study aims to explore the microbial diversity from the pristine mangrove ecosystems – Pathanendal (PN), Muthukuda (MK), and Karankadu (KK) from the coast of Tamil Nadu, India. The sediment geochemical analysis of these sites revealed moderate to high salinity with overall neutral pH, and lower to higher fluctuating levels of soil macro and micro-nutrients, which defines extreme environment conditions. The α-diversity analysis of the Shannon, Simpsons, Fischer, and Chao1 index revealed higher species richness, evenness, and diversity observed from the MK sampling site, followed by the KK and PN samples. The β-diversity analysis showcased the presence of 26 phyla and 108 families in MK, 21 phyla and 179 families from KK, and 19 phyla and 128 families in PN mangroves. In addition, the diversity analysis showed the dominance of Proteobacteria, Firmicutes, Bacteroidetes, Cyanobacteria, and Spirochaetes among all the sampling sites. Several rare microbes, such as Ignavibacteriae (0.005 %) and Calditrichaeota (0.006 %) from KK, Verrucomicrobia (0.0009 %) and Gemmatimonadetes (0.0006 %) from MK, and finally Deinococcus-Thermus and Elusimicrobia phyla were identified from PN mangroves. In addition, the Actinobacteria phyla were dominant in MK (MK1 – 2.09 % and MK_M − 0.02 %), followed by KK (KK_MR – 1.21 % and KK_M − 1.25 %) and PN (PAN_MR – 0.8 % and PAN_M − 0.49 %), with the presence of Microbacteriaceae, Micrococcaceae, Actinomycetaceae, and Bifidobacteriaceae as dominant families. These data could aid in deciphering the growth of media development and identifying natural products.