Ecogenomic profiling of spatial variations in sediment microbial communities of a freshwater lake
"Freshwater lake sediments integrate physicochemical conditions and provide sensitive indicators of spatial variation in microbial community structure. This study investigated sediment bacterial communities from four sites in Singanallur Lake, Coimbatore, using 16S rRNA V3–V4 amplicon sequencing to characterize spatial heterogeneity in sediment microbial communities under uniform seasonal conditions. Across all samples, a total of 44 phyla, 114 classes, 257 orders, 466 families, and 1107 genera were detected, reflecting high taxonomic richness and spatial variability within the lake sediments. The community was dominated by Pseudomonadota, which ranged from 80.9 % in S1–51.8 % in S4, followed by Bacillota, Bacteroidota, and Cyanobacteriota. At the genus level, Caulobacter decreased from 30.6 % in S1–12.5 % in S4, along with notable genera such as Bosea and Phreatobacter. Alpha diversity increased steadily from S1 to S4, with observed OTUs ranging from 1722 to 13,796 and Shannon index values increasing from 5.14 to 8.44. Sequencing coverage ranged from 0.34 to 0.74, indicating incomplete sampling depth and representing a methodological limitation, while Gini coefficients (0.64–0.83) reflected uneven community structures, particularly in S1. Several low-abundance and site-enriched genera, including Akkermansia, Helicobacter, and Candidatus Saccharimonas, showed localized enrichment, indicating site-specific environmental conditions within the lake. Venn diagram analysis showed a core of five shared genera representing 31.3 % of total abundance, while rare and unique taxa exhibited minimal overlap (4.0 % and 3.8 %), highlighting strong spatial differentiation among sampling sites. Heatmap-based multivariate analysis integrating microbial OTU abundance with measured physicochemical water quality parameters and sediment heavy metal concentrations revealed clear associations between microbial assemblages and localized environmental gradients. These patterns indicate that sediment microbial communities respond sensitively to present-day physicochemical heterogeneity within the lake. This study provides a baseline spatial ecogenomic framework for Singanallur Lake and highlights the value of integrating microbial community profiling with water quality and metal measurements for future monitoring and comparative assessments."
