Figure 3
Microbiome diversity, composition and distribution in four metagenomic groups of the anaerobic digestate samples. (A-B) Box plots showing significant differences in observed species richness in AD associated microbiome. Alpha diversity, as measured by PathoScope (PS) analysis using the Shannon and Simpson diversity indices, revealed distinct microbiome diversity across four metagenome samples (p = 0.03541, Kruskal–Wallis test). (C) The experimental groups were clearly separated by principal coordinate analysis (PCoA), which was measured using non-metric multidimensional scaling (NMDS) ordination plots. The different shapes represent the assigned populations in four metagenomes. As the day progresses, the group color becomes lighter. Values in parentheses represent the fraction of the total variance explained by each PCoA axis. (D) Venn diagram showing unique and shared bacterial strains, (E) Venn diagram showing unique and shared archaeal strains. (F) Stacked bar plots showing the relative abundance and distribution of the total microbial community (phyla level), The archaeal phylum, Euryacaeota showed an increasing trend from initial stage to the final stage (Group-IV) of digestion. (G) Dominant microbial community (≥ 1% reads at least one sample) at species level were visualized in heatmap. Forty-three dominant species were found in this study. Red, blue, and white colors represent different mapped reads to specific taxa from higher to lower respectively. FunRich (http://funrich.org/) tool was used to draw Venn diagram. Data were processed through Phyloseq (https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html) R package, visualized by using ggplot2 (https://cran.r-project.org/web/packages/ggplot2/index.html). Heatmap was generated by using Pheatmap (https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf) R package.
