3.5 Extracellular eDNA can resolve broad-scale spatiotemporal changes in biodiversity across the tree of life 

As particle-bound extracellular eDNA can persist in the environment for a considerable amount of time depending on the abiotic conditions of the ecosystem, we examined whether extracellular eDNA can resolve broad-scale spatiotemporal changes in biodiversity across the tree of life. The sampling locations across the seasons and different sectors of the lagoon had a wide variation in abiotic conditions (Supplementary Fig. 8). The temperature of water ranged from 23 to 33.3 degrees Celsius and the salinity varied from 0.83 to 15.18 ppt. To check the variation in biodiversity at these locations, a read count matrix of the 1001 families detected across the tree of life in all the samples was generated. We then measured the spatial and temporal beta diversity with the richness-based Jaccard similarity index and the relative abundance-based Bray-Curtis dissimilarity. The Jaccard index indicated a very high degree of shared families across the tree of life among the spatiotemporal samples with a median similarity of 0.98 (SD 0.01). In contrast, the Bray-Curtis dissimilarity indicated a high variation of relative abundance of families across the tree of life among the spatial and temporal samples with median values of 0.37 (SD 0.09) and 0.46 (SD 0.10), respectively. Further, we inspected if the degree of spatiotemporal variation in relative abundances differed among the taxonomic domains. The Bray-Curtis dissimilarity was higher among Bacteria and Viruses, compared to Archaea and Eukaryotes (Fig. 5). There was a significant difference in both the spatial and temporal beta diversity across the domains of life (Kruskal-Wallis test p<0.01). Ordination of relative abundance-based beta diversity across the tree of life by NMDS resulted in the clustering of samples primarily by season (PERMANOVA: R2=0.37, p=0.003) and to a lesser extent by location (PERMANOVA: R2=0.4, p=0.9) (Fig. 6). This suggests that extracellular eDNA can resolve the broad-scale spatiotemporal changes in the composition of biodiversity across the tree of life in large ecosystems.