Additional file 1 of Ecology of aerobic anoxygenic phototrophs on a fine-scale taxonomic resolution in Adriatic Sea unravelled by unsupervised neural network
Creators: name: Stojan, Iva
name: Šantić, Danijela
name: Villena-Alemany, Cristian
name: Trumbić, Željka
name: Matić, Frano
name: Vrdoljak Tomaš, Ana
name: Lepen Pleić, Ivana
name: Piwosz, Kasia
name: Kušpilić, Grozdan
name: Ninčević Gladan, Živana
name: Šestanović, Stefanija
name: Šolić, Mladen
Publisher: name: figshare
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Additional file 1. Table S1. Description of samples analysed in this study ordered by month (date of collection, W-Winter, Sp-Spring, S-Summer, A-Autumn).; Table S2. Number of reads per sample that passed through dada2 pipeline; input: number of raw reads, filtered: filtered out low quality sequences and tails, denoisedF and denoisedR: denoised sequences after the core sample inference algorithm of forward and reverse reads respectively, merged: merged sequenceswhich are output if the forward and reverse reads overlap by at least 12 bases and are identical to each other in the overlap region, nonchim: sequences after chimera removal [1]. Samples with an unacceptably low final number of reads per sample (N&lt;2000) were excluded from further analysis.; Figure S1. Rarefaction curve exhibiting sufficient sequencing depth (Sample Size) for AAP diversity metrics estimates. Rarefying to the smallest library size was performed multiple times (function rarefy_even_depth from phyloseq v1.32.0 R package [2], rarefying threshold =2000, N(times) =100)., Figure S2. Draftsman plots used to estimate correlation of abiotic environmental variables, made in PRIMER7 [3]. Variables are: temperature-Temp, salinity-Sal, nitrates-NO3-, nitrites-NO2-, ammonium ion-NH4, dissolved inorganic nitrogen-DIN, total nitrogen-NTOT, soluble reactive phosphorus-SRP, total phosphorus-PTOT, silicate-SiO4., Table S3. Permutational multivariate analysis of variance (PERMANOVA) on Euclidean distance of square-root transformed AAPs’ absolute (A) and relative (B) abundance dataset. Factors: Se-Season (fixed), Re-Region (fixed), La- Layer (nested in Region, L1 (0-30m), L2 (30-50m), L3 (50-75m), L4 (75-100m)). Pairwise comparisons for significant seasonality (W-Winter, Sp-Spring, S-Summer, A-Autumn) are given in the right part of the table. PERMANOVA was performed in PRIMER7 with 9999 permutations, unrestricted permutation of raw data, sums of squares type: Type II (conditional) [3]., Table S4. Permutational multivariate analysis of variance (PERMANOVA) on Aitchison distance of centered-log ratio transformed pufM sequencing dataset agglomerated on genus-level. Factors: Se- Season (fixed), Re-Region (fixed), La- Layer (nested in Region, L1 (0-30m), L2 (30-50m), L3 (50-75m), L4 (75-100m)). Pairwise comparisons for significant seasonality (W-Winter, Sp-Spring, S-Summer, AAutumn) are given in the right part of the table. PERMANOVA was performed in PRIMER7 with 9999 permutations, unrestricted permutation of raw data, sums of squares type: Type II (conditional) [3], Figure S3. AAP community composition obtained via pufM metabarcoding in the study area shown at the class level per station (ST101, CJ007, CJ009), month and depth., Table S5. Alpha diversity metrics based on rarefied pufM dataset (Observed number of ASVs, Shannon and Pielou’s index) given as average values with standard deviations (SD) calculated per season (vegan v2.5.7 R package [4]).