Additional file 1 of Deep-sea Bacteroidetes from the Mariana Trench specialize in hemicellulose and pectin degradation typically associated with terrestrial systems
Creators: name: Zhu, Xiao-Yu
name: Li, Yang
name: Xue, Chun-Xu
name: Lidbury, Ian D. E. A.
name: Todd, Jonathan D.
name: Lea-Smith, David J.
name: Tian, Jiwei
name: Zhang, Xiao-Hua
name: Liu, Jiwen
Publisher: name: figshare
Year: 2023
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Ecology

description: Additional file 1: Fig. S1. The distribution of Bacteroidetes in the Mariana Trench water column based on 16S rRNA gene sequencing from Nunoura et al. [2]. Fig. S2. NMDS (Non-metric Multi-Dimensional Scaling) analysis of Bacteroidetes community across all samples. The shaded ellipses represent the 80% confidence interval. Fig. S3. NMDS analysis of Bacteroidetes GH and PL genes across all samples. The shaded ellipses represent the 80% confidence interval. Fig. S4. Relative abundance (percent of mapped reads) of Bacteroidetes MAGs in the Mariana Trench, southern North Sea (algae bloom) and surface Pacific Ocean. Fig. S5. Bray-Curtis dissimilarities of Bacteroidetes MAGs illustrated by NMDS analysis based on the composition of GH and PL genes in each MAG. The shaded ellipses represent the 80% confidence interval. Fig. S6. Phylogenetic tree of MTRN7 with closely related taxa based on 16S rRNA gene sequences using Olleya aquimaris DSM 24464 as an outgroup. Fig. S7. High-pressure endurance of strain MTRN7 at room temperature when supplied with nutrient-rich 2216E medium. Fig. S8. Relative abundance of MTRN7 arabinan PUL across the whole water column of the Mariana Trench. Fig. S9. Predicted pathway for the degradation of arabinans in strain MTRN7. Locus tags (APDGNPDO_#) are indicated by the numbers given in parentheses. Based on the results of SignalP [3], enzymes with signal peptides were considered as secretory enzymes associated with the periplasmic space and/or to the outer membrane while those without signal peptides were considered as cytoplasmic proteins. Arabinans are firstly degraded into arabino-oligosaccharides and then transferred into the periplasm through the SusC/D transport system. These oligo-arabinoses can be further degraded into lower-level oligo-arabinose or arabinose, which are transported into the cytoplasm by an MFS transporter. In the cytoplasm, all oligo-arabinoses are decomposed into arabinoses. Finally, arabinose isomerase converts arabinose into ribulose, which is then converted to ribulose-5-phosphate which enters the pentose phosphate pathway. XynD (Arabinoxylan arabinofuranohydrolase, APDGNPDO_02643) is not shown in this plot considering its function in cleaving arabinose units from O-2- or O-3-monosubstituted xylose residues from arabinoxylan. SSF (sodium/sugar cotransporter, APDGNPDO_02653) and SusB (alpha-glucosidase, APDGNPDO_02654) are also not included, both of which are likely involved in glucan degradation and absorption. Fig. S10. Maximum likelihood trees of CAZymes from GH43, GH51 and GH127 families located in the MTRN7 arabinan PUL, a GTPase (APDGNPDO_02636) located 30 genes upstream of the arabinan PUL and a GH43_28 enzyme (APDGNPDO_01973) outside the arabinan PUL. The tree of each enzyme was constructed with 100 homologues downloaded from NCBI. Enzymes from MTRN7 were marked in red font. These enzymes were grouped based on their isolated environments: Black, terrestrial or freshwater; blue, marine. Fig. S11. Growth of MTRN7 under different pressures at 2 °C using marine minimal medium (MMM) supplied with 2% arabinan as the carbon source.