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.