Category: Lipopolysaccharide related (LPS), Cell envelope related (CE). 41. Cell envelope ..... Appl Environ Microbiol 69:2463â2483. 103. Bowman JP, Rea SM ...
Supplementary Information
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Genomic insights into members of the Candidate phylum Hyd24-12 common in mesophilic anaerobic digesters
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Authors: Rasmus Hansen Kirkegaard, Morten Simonsen Dueholm, Simon Jon McIlroy, Marta Nierychlo, Søren Michael Karst, Mads Albertsen, and Per Halkjær Nielsen
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Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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Content:
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Supplementary Figures
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Figure S1. Heat map of the ten most abundant bacterial OTUs in reactor 1 from Viborg during the period 2013 to 2015.
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Figure S2. Cell envelope classification.
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Figure S3: Geographic locations of the sample sites.
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Figure S4: Evaluation of the effect of bead beating.
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Supplementary Tables
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Table S1: Metadata for the anaerobic digester plants sampled in this study. Separate file.
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Table S2: Titles and pubmed IDs for 16S rRNA gene sequence surveys detecting Hyd24-12 within the SILVA database. Separate file.
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Table S3: Abundance estimates based on read mapping of TruSeq DNA PCR free metagenome data to the 16S rRNA genes of the MiDAS database (McIlroy et al., 2015)
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Supplementary Data:
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Supplementary Data 1: V1-V3 Primer sequences incl. Illumina adaptors and barcodes. Separate file.
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Supplementary Data 2: Curated annotations for the three Hyd24-12 genomes. Separate file.
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Supplementary References
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32 33 34
Figure S1. Heat map of the ten most abundant bacterial OTUs in reactor 1 from Viborg during the period 2013 to 2015. Hyd24-12 is stably present in the period and has a read abundance of up to 8.2 %.
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DL
DL
DL
Aquificae
Hyd24-12
0.92 0.98 0.98 0.98 0.98 0.99 1 0.99 0.99 0.08 0.98 0.23 0.98 0.98 0.98 0.97 0.95 0.8 0.72 0 0 0.01 0.07 0 0 0 0 0.02 0 0
DL
Acidobacteria
0.22 0.16 0.22 0.22 0.22 0.33 1 1 1 0.18 0.87 0.91 0.29 0.24 0.31 0.18 0.38 0.13 0.47 0 0.09 0 0.02 0 0 0 0 0.91 0 1
DL
Proteobacteria
0 0 0.17 0.25 0 0.75 1 1 1 1 0.83 0.92 0 0 0 0 0 0 0.08 0 0 1 0.92 0 0 0 0 1 1 1
DL
Planctomycetes
0 0 0 0 0 0 1 1 0.77 1 0.62 0.62 0 0 0 0.08 0.23 0 0 0 0 1 0.38 1 0.69 0 0 1 1 1
DL
Verrucomicrobia
0.67 0.67 0.67 0.67 0.33 1 0.67 0.67 0.67 1 0.67 1 0.67 0.67 0.67 0.33 0.33 0 0 0 0 0 1 0.67 0 0.33 0 0.67 1 1
DL
Chlamydiae
D(L) DL
Chlorobi
D
Bacteroidetes
DA
Spirochaetes
Fusobacteria
0 0 0.01 0 0.02 1 0 0 0.01 0 0.05 1 0 0 0.02 0 1 0.96 0 0 0.02 0 0.98 1 0 0 0.02 0 1 1 0 0 0.02 0 0.59 1 0 0 0.02 0 1 1 0 0 0.02 0 1 1 0 0 0.02 0 1 1 0 0 0.01 0 0.8 1 0 0 0.13 0 1 1 0 0 0.02 0 0.8 0.88 0.01 0 0.01 0 0.34 0.96 0 0 0.02 0 0.46 0.83 0 0 0.01 0 0.36 0.96 0.14 0 0.16 0 0.98 0.5 0 0 0.01 0 0.97 0.75 0 0 0 0 0.98 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.65 1 0.96 1 0 0.96 0.98 0.33 0.91 0.71 0 0 0.98 0 0.98 1 0 1 0.94 0 0.94 0.57 0 0.92 0.99 0 0.97 0.57 0.98 1 0.78 0.6 0.84 0 0 0 0.99 0.6 0.98 0 0.82 0.17 0.98 1 0.98 1 0 1 0.9 1 0.81 0.07 0.61 0.96
DA
Deinococcus-Thermus
DA
Thermotogae
DA
Cyanobacteria
PFAM description Glycos_transf_N - (kdotransferase) LpxK - Tetraacyldisaccharide-1-P 4'-kinase LpxB - Lipid-A-disaccharide synthetase LpxC - UDP-3-O-acyl N-acetylglycosamine deacetylase LpxD - UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD ExbD - Biopolymer transport protein ExbD/TolR Surf_Ag_VNR - Surface antigen variable number repeat YjgP_YjgQ - Predicted permease YjgP/YjgQ family Bac_surface_Ag - Surface antigen Secretin - Bacterial type II and III secretion system protein OEP - Outer membrane efflux protein OstA - OstA-like protein TonB_dep_Rec - TonB dependent receptor TonB - Gram-negative bacterial tonB protein Plug - TonB-dependent Receptor Plug Domain PdxA - Pyridoxal phosphate biosynthetic protein PdxA Lipopolysaccharide-assembly, LptC-related PdxJ - Pyridoxal phosphate biosynthesis protein PdxJ LolA - Outer membrane lipoprotein carrier protein LolA TolB_N - TolB amino-terminal domain OstA_C - Organic solvent tolerance protein DegV - Uncharacterised protein, DegV family COG1307 DivIVA - DivIVA protein HTH_WhiA - Sporulation Regulator WhiA C terminal domain WhiA_N - Sporulation Regulator WhiA N terminal DUF552 - Protein of unknown function (DUF552) Sortase - Sortase family LytR_cpsA_psr - Cell envelope-related transcriptional attenuator domain DUF1967 - Domain of unknown function (DUF1967) R3H - R3H domain
M
Tenericutes
PFAM PF04413 PF02614 PF02684 PF03331 PF04613 PF02472 PF07244 PF03739 PF01103 PF00263 PF02321 PF03968 PF00593 PF03544 PF07715 PF04166 PF06835 PF03740 PF03548 PF04052 PF04453 PF02645 PF05103 PF02650 PF10298 PF04472 PF04203 PF03816 PF09269 PF01424
M
Firmicutes
Category LPS LPS LPS LPS LPS CE CE CE CE CE CE CE CE CE CE CE CE CE CE CE CE CE CE CE CE CE CE CE Other Other
M
Synergistetes
36 37 38 39 40 41
Enriched in P P P P P P P P P P P P P P P P P P P P P A+F A+F A+F A+F A+F A+F A+F A+F A+F
M
Chloroflexi
Cell envelope characteristics
Actinobacteria
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1 0.97 0.88 1 0.93 1 1 1 1 1 1 0.94 1 1 1 1 1 1 0.93 1 1 1 1 1 1 0.93 1 0.92 1 1 1 1 0.91 1 0.5 1 1 1 1 0.96 1 1 1 1 1 1 1 1 1 1 1 1 1 0.95 1 1 1 1 1 1 1 1 1 0.42 1 0.88 1 0.85 1 1 1 0 1 1 0.98 1 1 0.25 0 0.75 0.11 0.95 0.6 1 1 0 1 0.33 0.87 1 1 1 0 0.88 0.33 0.89 1 1 1 0 1 0.33 0.88 1 1 1 0 1 1 0.88 0.4 1 1 0 0.38 0.11 0.81 0.4 0.75 1 0 1 1 0.9 0 1 0 0 0.25 0.22 0.97 1 1 0.83 0 0.13 0 0.92 1 0 0 0 0.5 0.33 0.93 1 0.5 0.08 0 0 0 0.06 0 0 0.08 0 0 0 0.05 0 0.17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.07 0.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.38 0 0.05 0.8 0
1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 1 0 1 0 1 0 0 0 0 0 0 0
Figure S2. Cell envelope classification. Protein families substantially enriched or depleted in archetypal monoderm lineages (Actinobacteria and Firmicutes, A+F) relative to an archetypal diderm lineage (Proteobacteria, P), most of which have known roles in cell envelope biosynthesis. Cell envelope classification: Monoderm (M), Diderm (D), Diderm-LPS (DL), Diderm-Atypical (DA). Category: Lipopolysaccharide related (LPS), Cell envelope related (CE).
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42 43 44 45 46
Figure S3: Geographic locations of the sample sites for the studies that make up the Hyd24-12 sequences in the SILVA database (v. 121, 1982 sequences from 48 studies in total).
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47 48 49
50 51 52 53
Figure S4: Evaluation of the effect of bead beating duration on DNA yield and DNA integrity for digester-sludge using the FastDNA Spin kit for soil (MP Biomedicals, Santa Ana, CA, USA).
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54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73
Supplementary Tables: Table S1: Metadata for the anaerobic digester plants sampled in this study. See separate file. Table S2: Titles and pubmed IDs for 16S rRNA gene sequence surveys detecting Hyd24-12 within the SILVA database. See separate file.
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74 75
Table S3: Abundance estimates based on read mapping of TruSeq DNA PCR free metagenome data to the 16S rRNA genes of the MiDAS database (McIlroy et al., 2015). Location
Damhusaaen
Damhusaaen
Viborg
Viborg
Viborg
Viborg
(Foam)
Randers
Randers
(Foam)
(Foam)
Sample date (yyyymmdd)
76 77 78 79 80 81 82 83 84
20110404
20111214
20111005
20111005
20111214
20111214
20111214
20111214
Archaea*
3.95
4.56
7.89
7.00
7.58
11.52
9.35
12.69
Bacteria*
95.8
95.2
91.6
89.2
89.5
86.6
87.6
87.2
Eukaryota*
0.30
0.22
0.56
3.85
2.93
1.84
3.03
0.16
p_Hyd24-12*
1.30
3.46
0.53
0.37
1.82
1.40
1.86
1.18
* % of total mapped reads
Supplementary Data: Supplementary Data 1: V1-V3 Primer sequences incl. Illumina adaptors and barcodes. See separate file. Supplementary Data 2: Curated annotations for the three Hyd24-12 genomes. See separate file.
85 86
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87 88 89 90 91 92 93
Supplementary references: All 16S rRNA gene sequences within the Hyd24-12 lineage of SILVA from surveys from 48 separate studies, with 10 studies of engineered systems and 38 studies of natural systems such as marine sediments, microbial mats in hydrogen, methane rich waters, and mud volcanoes:
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