Distinct microbiome and nutrient status of a saline hydromorphic soil under rice cultivation in comparison with laterite soil

Abstract

Microbiomes present in soil influences the quantity of nutrients available to plants. A metagenomic approach was undertaken to study the microbial communities from an unexplored natural rice farming saline hydromorphic soil on comparison with commonly occurring laterite soil present in the state of Kerala, India. There was high species richness and OTU abundance of bacteria and fungi in saline hydromorphic soil in comparison with laterite soil. Among bacterial communities, the highest percentage of abundance was noticed for Proteobacteria followed by Chlorobi in saline hydromorphic soil. Both Epsilon and Zetaproteobacteria were characteristically present in saline hydromorphic soil, while their population was very less in laterite soils. There was high abundance of iron and sulphur metabolisers along with carbon fixing bacteria in saline hydromorphic soil. Although Wallemia was present as most abundant fungal genus in both saline hydromorphic and laterite soil, there was six-fold higher population of Olpidium in saline hydromorphic than laterite soils. Higher differential population of fungi involved in decomposition were also observed in saline hydromorphic soil over laterite. There was very high content of soil available nutrients especially, organic carbon, nitrogen, potassium, iron and sulphur in saline hydromorphic soil. Clay minerals such as smectite, mica and gibbsite were uniquely present in saline hydromorphic on comparison with laterite. Abundance of nutrients in association with specific clay minerals was found to harbour diverse and rich microbial population in saline hydromorphic soil.