MOESM1 of Microbial effects of part-stream low-frequency ultrasonic pretreatment on sludge anaerobic digestion as revealed by high-throughput sequencing-based metagenomics and metatranscriptomics
Creators: name: Xia, Yu
name: Yang, Chao
name: Zhang, Tong
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Plant Biology

description: Additional file 1: Table S1. The parameters measured and the corresponding references of analytical methods. Table S2. Statistics of metagenomes and metatranscriptomes used in this study. Table S3. Performance anaerobic digesters treating different percentage of ultrasound pretreatment TSAS. Table S4. Number of genes recovered from the metagenomic data sets (first column) and got transcriptional activities detected (second column). The corresponding annotation efficiency by different databases were listed in the last two columns. Table S5. Number of genes of Orders that could be functionally annotated and their transcriptional activities. Orders are sorted descendingly based on their relative abundance within the community. Only orders taking more than 0.1% of the community are shown in the table. Table S6. Transcription of the PULs identified in the LFUS-treated sludge digestion system. Figure S1. Setup of the for laboratory-scale digesters used in this study. Figure S2. 3-month reactor performance in term of pH variation (top figure), volatile solid reduction (VSR) (bottom figure). Sampling points for metagenomic and metatranscriptomic sequencing were indicated by red arrow. Figure S3. Rarefaction analysis based on 16S rRNA sequences (bottom figure) and assembled genes (upper figure) of the metagenome data sets. Figure S4. Reproducibility based on RPKM-RNA (top figure) and RPKM-DNA (bottom figure) between biological replicates. Regression line between replicates is shown as blue dashed line, while the diagonal line (no variation between replicates) and boundary for 4 times change between replicates are shown as red dash line. Dots are colored according to their RPKM values in corresponding data sets. And the Spearman correlation coefficient R2is shown on each subfigure. Figure S5. Phylogenetic tree of the available genomes (including metagenome-assembled genomes and complete genome) within Cloacimonetes phylum. Maximum-likelihood tree was built based on concatenated alignment of four essential single-copy genes (ESCGs) conserved in single-copy manner among 11 metagenome-assembled genomes (including our bin11) and one finished genome of Cloacamonas acidaminovorans Evry. Default protein model of PhyML3.1 was used to construct the tree with 100 bootstraps based on MUSCLE alignment. Boot strap values greater than 50% are indicated at branch points. Figure S6. Functions of major orders within the CEPT community(the most prevalent sixteen orders, showing relative abundance &gt; 0.6%). Stacked bar chart shows the transcriptional activities of genes whose functions could be assigned to SEED level 1 functional categories (primary y axis on the left).Only the top 10 most active SEED 1 functions were shown in the figure. The blue line showed the relative abundance of these orders based on RPKM-DNA (secondary y axis on the right). These Orders are sorted descendingly according to their relative abundance. The overall transcriptional activities in term of RPKM-RNA (secondary y axis on the left) were indicated as red diamond. Figure S7. Transcriptional activities (top figure) and relative abundance (bottom figure) of key genes involved in the SEED subsystem of â Protein degradationâ by different major orders of the LFUS-treated sludge digestion community.