Supporting Information for
“Deciphering cyanide-degrading potential of a microbial community in a coking
wastewater treatment plant with a novel draft genome”
Zhiping Wang1,2, Lili Liu1,3, Feng Guo1, Tong Zhang1*
1
Environmental Biotechnology Laboratory, The University of Hong Kong, Hong
Kong; 2 School of Environmental Science and Engineering, Shanghai Jiao Tong
University, Shanghai; 3 State Environmental Protection Key Laboratory of
Environmental Risk Assessment and Control on Chemical Process, East China
University of Science and Technology, Shanghai, China
*Corresponding author: Tong Zhang, Environmental Biotechnology Laboratory, The
University of Hong Kong, Hong Kong. Tel. 852-2857-8551, E-mail: zhangt@hku.hk
Table S1. Summary of de novo assembly of metagenomic sequencing
Parameters
Length (bp)
N50/middle length
Total number
Reads used in assembly
Reads usage percentage (%)
Contigs
>500
>1000
>2000
3, 113/742
4, 543/1, 520
6, 774/3, 046
269,292
80,802
25,978
74,303,899
59,618,922
45,794,185
71.7
57.5
44.2
Table S2. Genes related with the cyanide resistance and decomposition.
Gene ID
Encoding proteins
Best hit
References taxa
Identity
Gene_1097
Bacterioferritin
WP028839153
Thermomonas fusca
85%
Gene_1098
bacterioferritin-associated
WP028839154
Thermomonas fusca
68%
ferredoxin
Gene_1159
high-affinity iron transporter
WP028838585
Thermomonas fusca
71%
Gene_1037
ferric uptake regulator
WP028839657
Thermomonas fusca
88%
Gene_923
iron complex outer membrane
WP028839452
Thermomonas fusca
72%
WP028838677
Thermomonas fusca
92%
WP027071947
Luteimonas sp.
66%
WP008267205
Stenotrophomonas sp.
61%
WP027080658
Luteimonas mephitis
70%
receptor protein
Gene_1711
iron complex outer membrane
receptor protein
Gene_1714
iron complex outer membrane
receptor protein
Gene_1761
iron complex outer membrane
receptor protein
Gene_2395
iron complex outer membrane
receptor protein
Gene_1699
cytochrome oxidase I
WP028840243
Thermomonas fusca
88%
Gene_2134
cytochrome oxidase II
WP024539814
Comamonas badia
55%
Gene_2135
cytochrome oxidase I
WP008438371
Rhodanobacter thiooxydans
61%
Gene_2307
cytochrome oxidase III
WP011260481
Xanthomonas translucens
69%
Gene_2310
cytochrome oxidase I
WP027069910
Lysobacter defluvii
85%
Gene_2267
cbb3-type cytochrome c
WP028838528
Thermomonas fusca
94%
WP028838527
Thermomonas fusca
90%
WP014160475
Pseudoxanthomonas spadix
61%
WP028838526
Thermomonas fusca
91%
WP028838526
Thermomonas fusca
98%
WP028838526
Thermomonas fusca
93%
WP014160475
Pseudoxanthomonas spadix
61%
WP028838527
Thermomonas fusca
98%
WP028838528
Thermomonas fusca
99%
oxidase subunit I
Gene_2268
cbb3-type cytochrome c
oxidase subunit II
Gene_2269
cbb3-type cytochrome c
oxidase subunit III
Gene_2270
cbb3-type cytochrome c
oxidase subunit IV
Gene_2432
cbb3-type cytochrome c
oxidase subunit III
Gene_2961
cbb3-type cytochrome c
oxidase subunit I
Gene_2962
cbb3-type cytochrome c
oxidase subunit II
Gene_2963
cbb3-type cytochrome c
oxidase subunit III
Gene_2964
cbb3-type cytochrome c
oxidase subunit IV
Gene_285
carbon-nitrogen hydrolase
WP028839917
Thermomonas fusca
76%
WP028838282
Thermomonas fusca
90%
WP028839730
Thermomonas fusca
76%
family protein
Gene_2670
N-carbamoylputrescine
amidase
Gene_845
thiosulfate/3-mercaptopyruvate
sulfurtransferase
Table S3. List of reference genomes/draft genomes for PCoA analysis of COGs
Number
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
Genome / draft genome
Hydrocarboniphaga effusa AP103
Lysobacter defluvii DSM 18482
Nevskia ramosa DSM 11499
Pseudoxanthomonas spadix BD-a59
Pseudoxanthomonas sp. j35
Pseudoxanthomonas suwonensis 11-1
Pseudoxanthomonas suwonensis j42
Silanimonas lenta DSM 16282
Singularimonas variicoloris DSM 15731
Sinobacter flavus DSM 18980
Stenotrophomonas maltophilia Ab55555
Stenotrophomonas maltophilia ATCC 19867
Stenotrophomonas maltophilia AU12-09
Stenotrophomonas maltophilia D457
Stenotrophomonas maltophilia EPM1
Stenotrophomonas maltophilia K279a
Stenotrophomonas maltophilia R551-3
Stenotrophomonas sp. SKA14
Thermomonas fusca DSM 15424
Xanthomonas albilineans GPE PC73
Xanthomonas axonopodis pv. citri 306
Xanthomonas axonopodis pv. citrumelo F1
Xanthomonas axonopodis pv. malvacearum GSPB1386
Xanthomonas axonopodis pv. malvacearum GSPB2388
Xanthomonas axonopodis pv. punicae LMG 859
Xanthomonas campestris pv. campestris 8004
Xanthomonas campestris pv. campestris ATCC 33913
Xanthomonas campestris pv. campestris B100
Xanthomonas campestris pv. musacearum NCPPB 4381
Xanthomonas campestris pv. raphani 756C
Xanthomonas campestris pv. vasculorum NCPPB 702
Xanthomonas campestris pv. vesicatoria 85-10
Xanthomonas fragariae LMG 25863
Xanthomonas fuscans aurantifolii ICPB 10535
Xanthomonas fuscans aurantifolii ICPB 11122
Xanthomonas gardneri PDDCC 1620 ATCC 19865
Xanthomonas oryzae ATCC 35933
Xanthomonas oryzae pv. oryzae KACC10331
Xanthomonas oryzae pv. oryzae MAFF 311018
Xanthomonas oryzae pv. oryzae PXO99a
Xanthomonas oryzae pv. oryzicola BLS256
Xanthomonas perforans 91-118
Xanthomonas translucens pv. graminis art XTG29
44
45
46
47
48
49
50
51
52
53
Xanthomonas translucens pv. translucens DSM 18974
Xanthomonas vesicatoria maraite ATCC 35937
Xylella fastidiosa Dixon
Xylella fastidiosa EB92-1
Xylella fastidiosa fastidiosa GB514
Xylella fastidiosa M12
Xylella fastidiosa M23
Xylella fastidiosa multiplex ATCC 35871
Xylella fastidiosa sandyi Ann-1
Xylella fastidiosa temecula1
A
Proteobacteria
80.99
Bacteroidetes
7.22
Actinobacteria
3.32
Chloroflexi
2.94
Firmicutes
1.81
Gemmatimonadetes 1.14
Chlorobi
0.72
Acidobacteria
0.59
OD1
0.41
Deinococcus
0.26
Others
0.58
B
Thermomonas
Thiobacillus
Comamonas
Gemmatimonas
Rhodobacter
Ferruginibacter
Steroidobacter
Methyloversatilis
Ignavibacterium
Rhodanobacter
Tissierella
Humicoccus
Novosphingobium
Brevundimonas
Wolinella
Bdellovibrio
Thauera
OD1_genera
Sulfurimonas
others
39.48
9.95
7.00
2.96
1.98
1.94
1.93
1.91
1.85
1.55
1.45
1.44
1.36
1.30
1.25
1.24
1.12
1.07
0.93
18.28
Fig. S1 The abundance (%) of taxonomic assignment of the activated sludge samples
from coking wastewater treatment using RDP classifier at a confidence threshold of
80%. (A) main phyla (top 10); (B) main genera (top 20)
Fig. S2 Phylogenetic tree of top 20 OTUs in the microbial communities based on
Neighbor Joining method. Bootstrap values were calculated as a percentage of 1000
analysis and only those values of > 50% was indicated. Data in parentheses following
taxonomy presented accession number of reference on web of NCBI, and those
following pyro-sequences presented the relative abundance (%) of OTUs in this
microbial community.
Fig. S3 Genome binning of the dominant populations was carried out with the
coverage and GC contents of contigs. Contigs clustered according to coverage and
GC contents might derive from the same population and was colored by taxonomy of
essential single copy genes (ESCGs). These enclosed with black line were selected to
construct the draft genome of the dominant population.
Fig. S4 Phylogenetic analysis of hydrolase/nitrilase and sulfurtransferase in this draft
genome. ORFs of the draft genome were annotated with PfamA and done BLASTp on
web of NCBI. The top 20 hit sequences were used to construct phylogenetic tree
together with the targeting sequences. Parentheses presented the access number in
NCBI.