Spatiotemporal variation of microbial communities in surficial sediments of Cochin estuary, southwest coast of India

Microorganisms play a major role in the degradation of organic matter in sediments. However, the spatiotemporal variation and factors affecting these communities are not clearly understood. At the same time, conventional hydrographic and geochemical parameters do not offer an accurate assessment of transitional ecosystems. PLFA biomarkers which are specific to different taxonomic groups of microorganisms are able to provide a detailed assessment of the community composition in an environment and reflect a more direct assessment of the biological health of transitional ecosystems. We, therefore, conducted a comparison of PLFA biomarkers at four stations (Barmouth, B; Vaduthala, V; Munambam, M; and Arookutty, A) during three seasons (pre-monsoon, PRE; monsoon, MON; and post-monsoon, POST) in the Cochin estuary (CE). Each of the stations represented either a reference point (B), high pollution (V), high salinity (M), or low pollution (A). The communities determined using PLFA profiles could be categorized into six major groups with each group capable of reflecting the state of the ecosystem which correlated with the conventional parameters. The six groups were: G + ve Bacillota (formerly Firmicutes) and G-ve anaerobes (G-I), G-ve aerobic prokaryotes (G-II), ectomycorrhizal fungi (G-III), arbuscular mycorrhizae (G-IV), type-I methanotrophs (G-V), and microeukaryotes (G-VI). The prokaryotes were predominant in sediments amounting to over 78% of the total PLFAs detected, followed by the microeukaryotes. The freshwater-influenced stations were partially anaerobic in nature during PRE and MON and were mainly affected by both marine and terrestrial organic matter inputs, at times prominent in sewage matter. During POST season, CE behaves uniformly, especially in station M. Salinity and DO of BW and texture and organic matter of the sediment were the driving forces for microbial community structure. The reduced presence of cyclopropane fatty acids suggested that the CE was not under any stress during the study period. Our results using PLFA-based community profiling not only provide the fundamental information required to quickly access the impact of stress and other environmental inputs on the CE but also offer a more robust and realistic assessment of the nature of microbial communities in the ecosystem. A periodic and systemic assessment of PLFA profiles at these stations in CE throughout the year will enable the generation of enough metadata enabling a better understanding of this ecosystem and its efficient management in the long term.