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Supplementary Table S1 Single cell genome sequencing results.
Smithella single cell amplified Number of Reads
genome number
Smithella 1
27,285,040
Smithella 2
22,941,674
Smithella 3
11,040,252
Smithella 4
41,347,156
Smithella 5
54,143,206
Smithella 6
18,027,584
Sequencing output (Gb)
1.96
1.65
0.79
2.40
3.14
1.05
Supplementary Table S2 COG Analysis of the Smithella draft genome based on known COGs in from S.
aciditrophicus. Expected percentages were determined by dividing the number of Smithella genes falling
into a particular COG by the number of S. aciditrophicus genes falling into the same COG.
COG Group
Gene Count (% of expected COGs)
A - RNA Processing and modification
3 (300%)
B - Chromatin structure and dynamics
4 (100%)
C - Energy production and conversion
186 (90.3%)
D - Cell cycle control, cell division, chromosome partitioning
28 (121.7%)
E - Amino acid transport and metabolism
138 (89.6%)
F - Nucleotide transport and metabolism
52 (78.8%)
G - Carbohydrate transport and metabolism
81 (78.6%)
H - Coenzyme transport and metabolism
104 (87.4%)
I - Lipid transport and metabolism
146 (208.5%)
J - Translation, ribosomal structure and biogenesis
141 (87.6%)
K - Transcription
107 (110.3%)
L - Replication, recombination and repair
82 (52.9%)
M - Cell wall/membrane/envelope biogenesis
222 (112.7%)
N - Cell motility
45 (55.6%)
O - Posttranslational modification, protein turnover,
chaperones
76 (75.2%)
P - Inorganic ion transport and metabolism
53 (54%)
Q - Secondary metabolites biosynthesis, transport and
catabolism
51 (137.8%)
R - General function prediction only
330 (121.8%)
S - Function unknown
71 (38.6%)
T - Signal transduction mechanisms
133 (95%)
U - Intracellular trafficking, secretion, and vesicular transport
79 (79.8%)
V - Defense mechanisms
21 (51.2%)
Genes not in COGs
713 (67.1%)
Supplementary Table S3
Smithella vs. S. aciditrophicus comparison based on functional ModelSEED subsystems (see separate
excel spreadsheet).
Supplementary Table S4 Mapping statistics of metatransciptomic datasets aligned to reference genome
sequences of the indicated organisms.
Organism
Hexadecane
Butyric Acid
Caprylic Acid
Smithella
2,180,800 (436Mb)
2,383,310 (146Mb)
796,546 (50Mb)
Methanosaeta concilii
2,685,244 (536Mb)
1,021,523 (62Mb)
3,433,948 (212Mb)
Methanosaeta harundinacea
14,093 (2.8Mb)
1,886,871 (116Mb)
1,019,371 (62Mb)
Methanoculleus marisnigri
11,762 (2.4Mb)
6,365,706 (394Mb)
3,653,437 (226Mb)
Methanocorpusculum labreanum
7,988 (1.6Mb)
3,391 (0.2Mb)
22,476 (1.4Mb)
2,828,478 (564Mb)
2,044,143 (126Mb)
4,999,458 (310Mb)
667 (1.2Mb)
7,744,785 (480Mb)
2,834,881 (176Mb)
Methanogens1
Deltaproteobacteria1
53,168,342(10.6 Gb) 74,720,236 (4.6 Gb)
98,916,818 (6.2 Gb)
Total reads sequenced
1
See Supplementary Table S9 for a complete list of organisms included in these categories.
Supplementary Table S5 Gene expression data (Smithella) (see separate excel spreadsheet).
Supplementary Table S6 Gene expression data (Methanogens) (see separate excel
spreadsheet).
Supplementary Table S7 Potential hexadecane–related genes based on gene expression data. Gene
expression values were taken from the hexadecane vs. caprylic acid DESeq expression profile.
Gene ID
smith_1305
Gene Expression
321.1
Gene Product
Radical Activating enzyme
Similarities to
Syntrophus aciditrophicus,
Desulfococcus oleovorans HDX3
smith_1206
551.0
Radical SAM domain protein
Sorangium cellulosum,
Desulfatibacillum alkenivorans
smith_2601
475.5
Radical SAM domain protein
Desulfatibacillum alkenivorans,
Desulfococcus oleovorans HDX3
smith_1539
405.2
Radical SAM domain protein
Desulfatibacillum alkenivorans,
Desulfococcus oleovorans HDX3
smith_255
409.7
Radical SAM domain protein
Geobacter uraniireducens,
Desulfococcus oleovorans HDX3
smith_427
248.6
COG1180: Radical SAM2C Pyruvateformate lyase-activating enzyme like
Syntrophobacter fumaridoxins,
Geobacter uraniireducens,
Desulfatibacillum alkenivorans
Supplementary Table S8 Potential hypothetical proteins involved in hexadecane degradation based on
gene expression data. Hypothetical proteins falling into the highest 10% of all expressed genes were
further investigated for homologies to sequenced organisms. Expression values were obtained from the
hexadecane vs. caprylic acid gene expression profile. Homology was determined using the Seed Viewer
region comparison and Psi-Blast (alignment score >=200).
Gene ID
smith_7
smith_57
smith_71
smith_234
smith_259
smith_260
smith_284
smith_313
smith_319
smith_394
smith_431
smith_583
Expression
310.6
432.5
470.6
499.4
309.5
826.9
466.9
817.9
420.2
477.7
440.7
908.0
smith_588
smith_620
smith_916
smith_923
smith_932
smith_1116
smith_1188
392.1
595.1
485.2
616.1
454.6
310.6
314.8
smith_1223
smith_1243
818.7
557.4
smith_1372
smith_1367
smith_1368
smith_1374
smith_1423
smith_1474
smith_1495
smith_1542
442.2
474.7
318.9
838.8
870.6
422.8
409.0
313.3
smith_1574
smith_1581
smith_1613
smith_1705
382.8
323.0
395.1
357.7
smith_1709
smith_1712
smith_1866
smith_1960
smith_1967
smith_2050
smith_2051
smith_2144
598.1
329.0
422.4
309.9
646.0
474.7
565.2
373.8
Homology to genes in sequenced organism
No known homology
No known homology
Desulfatibacillum alkenivorans
No known homology
Desulfatibacillum alkenivorans
Synechococcus
No known homology
No known homology
No known homology
No known homology
Desulfococcus oleovorans HDX3
Desulfococcus oleovorans HDX3,
Desulfatibacillum alkenivorans
No known homology
No known homology
No known homology
No known homology
No known homology
No known homology
Desulfococcus oleovorans HDX3,
Desulfatibacillum alkenivorans
Desulfatibacillum alkenivorans
Desulfococcus oleovorans HDX3,
Desulfatibacillum alkenivorans,
Dehalococcoides
No known homology
No known homology
No known homology
Desulfatibacillum alkenivorans
Desulfatibacillum alkenivorans
No known homology
No known homology
Desulfococcus oleovorans HDX3,
Pseudomonas
No known homology
Desulfatibacillum alkenivorans
No known homology
Desulfococcus oleovorans HDX3,
Desulfatibacillum alkenivorans
Desulfococcus oleovorans HDX3
No known homology
No known homology
Desulfococcus oleovorans HDX3
No known homology
No known homology
No known homology
No known homology
smith_2179
smith_2189
309.5
565.2
smith_2193
smith_2200
smith_2268
smith_2346
smith_2429
smith_2437
smith_2478
smith_2532
smith_2583
smith_2630
smith_2677
smith_2678
smith_2760
smith_2788
smith_2846
401.9
407.5
373.1
859.8
404.8
400.7
328.2
325.6
852.3
638.9
441.9
457.2
356.6
449.7
383.9
Candidate Div OP9
Desulfococcus oleovorans HDX3,
Desulfatibacillum alkenivorans
No known homology
No known homology
No known homology
No known homology
No known homology
No known homology
No known homology
No known homology
No known homology
No known homology
Desulfococcus oleovorans HDX3
Desulfococcus oleovorans HDX3
No known homology
No known homology
No known homology
Supplementary Table S9 Number of metatranscriptomic reads mapping to energy conserving
hydrogenases and formate dehydrogenases identified in de novo assembled metatranscriptome
(hexadecane-degrading condition).
Gene Product
Energy conserving hydrogenase Eha large subunit homolog (protein O)
Energy conserving hydrogenase Eha proton-sodium antiporter homolog
protein H
Energy conserving hydrogenase Eha small subunit homolog (protein N)
Energy conserving hydrogenase Eha transmembrane protein B
Energy conserving hydrogenase Eha transmembrane protein C
Energy conserving hydrogenase Eha transmembrane protein D
Energy conserving hydrogenase Eha transmembrane protein F
Energy conserving hydrogenase Eha transmembrane protein G
Energy conserving hydrogenase Eha transmembrane protein J
Energy conserving hydrogenase Ehb protein Q
Hexadecane
133
8
Butyric Acid
4
0
Caprylic Acid
149
0
22
0
48
33
45
49
129
112
0
0
0
0
0
0
2
0
0
0
0
54
0
0
165
0
Formate dehydrogenase -O2C gamma subunit (EC 1.2.1.2)
Formate dehydrogenase O alpha subunit (EC 1.2.1.2) @ selenocysteinecontaining
Formate dehydrogenase O beta subunit (EC 1.2.1.2)
Formate dehydrogenase O gamma subunit (EC 1.2.1.2)
Formate dehydrogenase alpha subunit (EC 1.2.1.2)
Formate dehydrogenase beta subunit (EC 1.2.1.2)
Formate dehydrogenase chain D (EC 1.2.1.2)
Formate dehydrogenase-O2C major subunit (EC 1.2.1.2)
NAD-dependent formate dehydrogenase alpha subunit
NAD-dependent formate dehydrogenase alpha subunit @
selenocysteine-containing
formate dehydrogenase alpha subunit
formate dehydrogenase alpha subunit( EC:1.2.1.2 )
formate dehydrogenase formation protein FdhE
formate dehydrogenase2C alpha subunit
0
42
0
0
0
0
22
66
985
419
633
49
700
153
0
0
1
0
19
0
0
4
0
0
3
1
43
0
0
0
2
71
28
899
0
18
0
0
0
0
0
0