Statistics
Rarefaction curves of sequence counts versus the taxonomic classifications were conducted in the R package vegan (Oksanen et al., 2018) using the rrarefy function with default settings. Species richness (Chao1) and alpha diversity (Shannon’s H) were calculated in the software Explicet for each taxonomic group (Nematoda ,Foraminifera , and Ciliophora ). Before calculating Shannon’s H index the data was sub-sampled to the lowest sample size and bootstrapped × 100 (Nematoda 79,815 counts, Foraminifera2473 counts, Ciliophora 299,504 counts). Non-metric multidimensional scaling (NMDS) plots showing beta diversity were based on the presence/absence (Sørensen index) using the software past 3.26 (Hammer, Harper, & Ryan, 2001). The difference in read abundance between the high and low OC stations for Nematoda feeding type data was normalized and statistically tested using the R package DESeq2 1.26 with default settings (Love, Huber, & Anders, 2014). The DESeq2 output was plotted using the ggplot2 package in R (Wickham, 2016). Differences between groups on alpha diversity metrics (Chao1, Shannon’s H), relative abundance of taxonomic groups, and maturity index for nematodes were tested with univariate statistics conducted in the software IBM SPSS Statistics 26. First, Shapiro-Wilk tests were used to check if the data was normally distributed. Differences between groups in normally distributed data were tested with One-Way ANOVA tests, while non-parametric data were tested with Mann-Whitney U tests. PERMANOVA tests (9999 permutations) were used to identify differences in beta diversity between groups and stations in the software past 3.26. To investigate if the abiotic variables (% OC, % N, PO43-, NH4+, and water depth) were associated with the community composition canonical correspondence analysis (CCA) was conducted in the R package vegan (Oksanen et al., 2018) with thecca function and plotted using the ggplot2 package. The input data for the CCAs were the measured abiotic variables and relative abundances of the different taxa. Significant associations between abiotic variables and community compositions were tested for CCA axis 1 and axis 2 with PERMANOVA tests (9999 permutations) using the functionenvfit included in the vegan package.