To test for significant differences in alpha diversity between groups of samples, a non-parametric two sample t-test with Monte Carlo permutations was done using Observed OTUs, Shannon diversity index, and Simpson’s diversity index (diversity values represented in Fig. 2). Within leaves, the p-values were less than 0.05 between sites P2 and P3, P2 and P4, as well as P2 and P1 using Observed OTUs and the Shannon diversity index. Within roots, the p-values were less than 0.05 between sites P1 and P4, and P2 and P1 when using Shannon; the p-values were less than 0.05 between sites P2 and P3, and P2 and P1 using Simpson’s diversity index. Root communities also had a p-value less than 0.05 between Potamogeton perfoliatus and Vallisneria using all three diversity measures.
Microbes from the genera Methylotenera, Planctomyces, Rhodobacter, and Providencia are the most common amongst all the sites and SAV species (Fig. 1). Site P1 specifically had a higher relative abundance of the genus Prosthecobacter and family Verucomicrobiaceae than the other sites. In addition, site P2 had a high relative abundance of Cylindrospermopsis in the leaves of M. spicatum and Vallisneria. The genera Sulfuricurvum and Sulfurimonas, which are sulfur oxidizing bacteria, were present in the roots at site P2 and were particularly high in relative abundance in P. perfoliatus. Rhodocyclaceae was also commonly present in root samples from sites P2 and P3.
Fig. 3 shows a PCoA using unweighted UniFrac. Panel A represents the whole dataset. Leaves and roots tend to cluster separately within each site (p-value = 0.001). In addition, the sites cluster into two groups: P1, P3, P4 make up one group and P2 makes up another group (p-value = 0.001). Panel B shows data for only site P2 in order to examine patterns between samples within only one site. Site P2 was chosen since it was the most distinct in microbial community compared to P1, P3, and P4. Samples are differentiated by whether they are leaves or roots and by the host species (p-value = 0.001). Leaves and roots are most differentiated in P. perfoliatus and Vallisneria. At the same time, the leaves (regardless of host) tend to cluster more tightly with each other than the roots with themselves. Still, there are distinct clusters differentiated by the host species within site P2.
Unfortunately, since salinity readings were taken at varying tide heights, the salinity gradient was not apparent in this dataset. In addition, plants were collected from only four sites, all far from the mounth of the river. However, the water and sediment chemistry did vary significantly from site to site.