Integrated multi-platform approaches to gain insights into ecosystems fundamental ecology and habitat specific alterations

The increasing availability of metagenome-assembled genomes and environmental metagenomes provides unprecedented access to the metabolic potential and functional differences within the habitats. The hot spring microbiome with its diverse habitats and relatively well-characterized microbial inhabitants offers an opportunity to investigate core and habitat specific community structures at an ecosystem scale. Here, we employed tailored genome-resolved metagenomics and a novel approach that offers metagenomic overlaps to investigate the core and habitat-specific microbial diversity and multifunctionality of microbial residents of three habitats: microbial mat, sediment and water. We recovered 6% of the Ecosystem core community (ECC) in the habitats suggesting the widespread acquisition of Proteobacteria involving in the diverging trajectories of the hot spring and 72% of the Habitat specific community (HSC) in microbial mat, sediment and water habitats offers insights into specific adaptations due to extreme conditions. Strain-level resolution of metagenome-assembled genomes defined the habitat specific genotypes (HSGs) and comparative metagenomic analysis exposed ecosystem-core genotypes (ECGs). Further, the functional attributes of ECGs revealed a complete metabolic potential of nitrate reduction, ammonia assimilation and sulfate reduction. The highest cycling entropy scores (H) of N cycle suggested the enrichment of nitrogen fixing microbes commonly present in all three habitats. While specifically HSGs possessed the amino acid transport and metabolism functions in microbial mat (9.5%) and water (13%) and 19% of translation, ribosomal structure and biogenesis in sediment. Our findings provide insights into population structure and multifunctionality in the different habitats of hot spring and form specific hypotheses about habitat adaptation. The results illustrated the supremacy of using genome-resolved metagenomics and ecosystem core metagenomics postulating the differential ecological functions rather than that of explaining the presence of functions within ecosystem.