Fig. A1 Scatter plots depicting the relationship between bacterial abundance and environmental parameters. Scatter plots of bacterial abundance versus oxygen (a, c).
Scatter plots of bacterial abundance versus total organic carbon (TOC) (b, d). Solid lines represent the best fit of the quadratic model to the data. Dashed lines represent best fit of a linear model to the data.
166
Fig. A2 Scatter plots depicting the relationship between sediment bacterial diversity and environmental parameters. Scatter plots of bacterial diversity indices versus temperature versus (a–c, j–l). Scatter plots of bacterial diversity indices versus salinity (d–f, m–o).
Scatter plots of bacterial diversity indices versus TOC (g–i, p–r). Solid lines represent the best fit of the quadratic model to the data. Dashed lines represent the best fit of a linear model to the data.
167
Fig. A3 Pictures of undisturbed sediment cores that were retrieved from the study site at the oxic condition (Dissolved oxygen concentration (DO); 118 µM, May 2017) and (A) and the dysoxic condition (DO; 27 µM, August 2017) (B). Sediment samples were collected with a G.S. type core sampler, Ashura. (Rigosha, Japan), equipped with three polycarbonate tubes (57 cm long with 82 mm inner diameter).
168
Fig. A4 Mean rank abundance plots of the dsrA-terminal restriction fragment for the top 10 operational taxonomic units (OTUs). The y axis shows the means of relative abundance of each OTU within same oxygen groups, whereas the x axis is the ordinal rank of OTUs from most abundant to least abundant. Error bars represent standard errors.
169
Table A1 Correlation coefficients of bottom-water dissolved oxygen (DO) with the relative abundance of OTUs (continued)
NA: not applicable
OTUs Uppermost Subsurface Combined
Correlation coefficient
(r)
P value
Correlation coefficient
(r)
P value
Correlation coefficient
(r)
P value
191 0.140 0.566 -0.158 0.519 -0.048 0.775
197 -0.052 0.832 -0.518 0.023 -0.316 0.053
211 0.106 0.665 0.180 0.461 0.090 0.593
215 0.027 0.914 NA NA 0.019 0.912
225 -0.096 0.696 0.098 0.689 -0.007 0.966
231 0.227 0.349 0.227 0.349 0.221 0.183
234 0.176 0.471 0.122 0.618 0.151 0.366
241 -0.413 0.079 -0.477 0.039 -0.442 0.005
247 -0.352 0.140 -0.243 0.316 -0.282 0.087
251 0.190 0.437 -0.281 0.243 -0.034 0.842
254 0.060 0.807 0.079 0.749 0.070 0.678
255 NA NA -0.318 0.184 -0.182 0.275
258 0.059 0.810 -0.612 0.005 -0.253 0.126
263 NA NA -0.484 0.036 -0.321 0.049
267 0.140 0.568 -0.330 0.168 -0.172 0.301
270 -0.380 0.108 -0.087 0.724 -0.262 0.112
272 -0.025 0.918 0.311 0.196 0.092 0.585
279 0.330 0.168 -0.202 0.406 0.011 0.948
280 0.257 0.289 -0.292 0.224 -0.050 0.764
283 0.214 0.380 -0.036 0.884 0.032 0.848
291 0.492 0.032 -0.193 0.429 0.118 0.480
293 NA NA 0.227 0.349 0.159 0.342
297 0.027 0.914 -0.765 0.000 -0.446 0.005
307 0.343 0.151 -0.018 0.941 0.194 0.243
312 0.196 0.422 0.180 0.461 0.171 0.304
314 0.155 0.526 -0.617 0.005 -0.337 0.039
317 -0.289 0.230 -0.481 0.037 -0.387 0.016
322 NA NA -0.052 0.833 -0.035 0.834
326 0.120 0.624 -0.182 0.455 -0.049 0.772
332 0.201 0.409 0.207 0.396 0.201 0.226
170 Table A1 (continued)
NA: not applicable
OTUs Uppermost Subsurface Combined
Correlation coefficient
(r)
P value
Correlation coefficient
(r)
P value
Correlatio n coefficient
(r)
P value
335 -0.362 0.12
8
-0.336 0.160 -0.311 0.05
337 0.233 0.33 8
7
0.180 0.461 0.187 0.26
340 0.238 0.32 2
7
-0.582 0.009 -0.248 0.13
355 0.280 0.24 3
6
0.354 0.137 0.274 0.09
366 NA NA NA NA NA 6 NA
372 0.227 0.34
9
0.289 0.231 0.242 0.14
374 0.136 0.57 4
9
0.298 0.216 0.171 0.30
375 0.227 0.34 4
9
0.227 0.349 0.227 0.17
377 -0.277 0.25 0
1
-0.298 0.216 -0.237 0.15
383 NA NA 0.022 0.927 0.015 3 0.92
394 -0.348 0.14 8
5
0.180 0.461 -0.008 0.96
396 0.089 0.71 1
6
0.118 0.631 0.085 0.61
400 -0.226 0.35 2
2
0.170 0.486 -0.026 0.87
412 0.017 0.94 9
4
0.358 0.133 0.167 0.31
420 -0.361 0.12 6
9
-0.332 0.165 -0.318 0.05
426 0.322 0.17 2
9
0.125 0.610 0.240 0.14
427 0.475 0.04 7
0
-0.251 0.300 0.138 0.40
430 -0.136 0.57 8
9
0.339 0.155 -0.035 0.83
435 -0.024 0.92 4
2
0.280 0.245 0.138 0.41
440 -0.629 0.00 0
4
-0.092 0.709 -0.388 0.01
444 0.009 0.97 6
2
-0.260 0.283 -0.157 0.34
447 -0.565 0.01 7
2
-0.522 0.022 -0.536 0.00
450 NA NA 0.199 0.413 0.136 1 0.41
454 -0.203 0.40 6
5
0.288 0.232 0.093 0.57
457 0.168 0.49 7
3
0.317 0.185 0.195 0.24
459 0.276 0.25 2
3
0.298 0.215 0.232 0.16
460 -0.399 0.09 2
0
0.313 0.193 -0.001 0.99
462 0.190 0.43 4
5
0.198 0.417 0.193 0.24
463 -0.258 0.28 5
6
-0.575 0.010 -0.401 0.01
467 0.016 0.94 3
9
0.366 0.124 0.156 0.35
1
171 Table A1 (continued)
NA: not applicable
OTUs Uppermost Subsurface Combined
Correlation coefficient
(r)
P value
Correlation coefficient
(r)
P value
Correlation coefficient
(r)
P value
469 -0.172 0.481 0.316 0.187 0.045 0.791
470 0.207 0.395 0.117 0.633 0.167 0.316
472 -0.252 0.298 -0.562 0.012 -0.410 0.011
479 -0.310 0.197 0.341 0.154 -0.009 0.956
483 -0.530 0.020 0.191 0.434 -0.043 0.800
487 0.079 0.748 0.061 0.803 0.067 0.688
490 -0.058 0.814 0.264 0.274 0.011 0.950
501 -0.533 0.019 -0.315 0.189 -0.427 0.008
502 0.217 0.372 -0.639 0.003 -0.231 0.163
503 -0.145 0.554 NA NA -0.098 0.560
506 0.027 0.914 -0.430 0.066 -0.042 0.800
507 0.027 0.914 NA NA 0.019 0.912
510 -0.392 0.097 0.234 0.336 -0.060 0.721
511 0.205 0.399 -0.599 0.007 -0.355 0.029
515 0.291 0.227 0.382 0.107 0.316 0.053
519 -0.493 0.032 0.162 0.508 -0.181 0.276
523 0.461 0.047 0.376 0.113 0.417 0.009
526 -0.108 0.660 0.463 0.046 0.127 0.447
530 0.313 0.192 0.358 0.133 0.325 0.046
542 0.227 0.349 0.051 0.836 0.162 0.331
548 -0.337 0.158 0.252 0.297 -0.051 0.762
554 0.183 0.452 0.244 0.313 0.214 0.198
555 0.205 0.399 0.028 0.909 0.112 0.505
565 -0.219 0.368 0.204 0.401 -0.026 0.875
567 0.198 0.417 -0.763 0.000 -0.305 0.063
570 -0.010 0.967 0.427 0.069 0.208 0.211
579 -0.460 0.047 0.301 0.210 -0.135 0.420
582 0.210 0.388 0.257 0.289 0.221 0.182
583 0.183 0.452 0.264 0.275 0.212 0.201
586 -0.429 0.067 -0.436 0.062 -0.429 0.007
172 Table A1 (continued)
NA: not applicable
OTUs Uppermost Subsurface Combined
Correlation coefficient
(r)
P value
Correlation coefficient
(r)
P value
Correlatio n coefficient
(r)
P value
589 0.108 0.65
9
0.263 0.276 0.185 0.26
590 -0.471 0.04 6
2
0.180 0.461 -0.105 0.53
592 -0.055 0.82 2
4
-0.426 0.069 -0.230 0.16
596 -0.071 0.77 4
4
-0.481 0.037 -0.249 0.13
598 0.264 0.27 1
4
0.265 0.273 0.264 0.10
602 0.355 0.13 9
5
0.281 0.244 0.317 0.05
606 0.390 0.09 3
9
0.197 0.419 0.294 0.07
614 0.481 0.03 3
7
0.207 0.395 0.341 0.03
617 -0.381 0.10 6
8
0.215 0.376 -0.027 0.87
619 0.501 0.02 4
9
-0.099 0.686 0.196 0.23
621 0.255 0.29 8
1
-0.616 0.005 -0.185 0.26
625 0.109 0.65 7
8
0.256 0.291 0.137 0.41
629 0.438 0.06 3
0
0.321 0.180 0.380 0.01
630 NA NA 0.281 0.244 0.190 9 0.25
631 0.183 0.45 4
2
0.090 0.715 0.102 0.54
634 -0.096 0.69 2
6
0.235 0.333 0.061 0.715
637 -0.357 0.13
4
0.254 0.293 -0.206 0.214
639 NA NA 0.180 0.461 0.126 0.452
643 0.398 0.09
1
-0.290 0.229 0.086 0.607
647 -0.364 0.12
6
0.222 0.360 -0.003 0.986
648 -0.277 0.25
1
0.163 0.506 -0.004 0.979
651 -0.277 0.25
1
0.288 0.231 0.073 0.662
654 -0.099 0.68
6
-0.456 0.050 -0.269 0.103
657 -0.337 0.15
9
-0.282 0.243 -0.310 0.058
662 -0.449 0.05
4
0.274 0.257 -0.078 0.644
664 0.198 0.41
7
0.221 0.363 0.188 0.260
670 0.415 0.07
7
NA NA 0.278 0.091
672 -0.425 0.06
9
0.114 0.643 -0.130 0.435
673 -0.285 0.23
6
0.302 0.209 -0.035 0.834
676 -0.517 0.02
3
0.094 0.703 -0.183 0.27
2
173 Table A1 (continued)
NA: not applicable
OTUs Uppermost Subsurface Combined
Correlation coefficient
(r)
P value
Correlation coefficient
(r)
P value
Correlation coefficient
(r)
P value
679 NA NA -0.075 0.761 -0.051 0.759
681 0.121 0.621 -0.519 0.023 -0.188 0.259
686 -0.367 0.122 0.254 0.293 -0.120 0.473
689 0.223 0.360 0.308 0.200 0.223 0.179
692 -0.156 0.524 -0.356 0.135 -0.222 0.180
698 -0.266 0.271 -0.479 0.038 -0.329 0.043
702 0.038 0.876 -0.630 0.004 -0.256 0.121
712 -0.238 0.326 -0.331 0.166 -0.274 0.096
721 -0.123 0.615 0.217 0.373 0.055 0.743
733 -0.508 0.026 0.168 0.492 -0.202 0.225
735 0.361 0.128 0.257 0.289 0.295 0.072
741 -0.023 0.927 0.434 0.064 0.128 0.443
745 0.289 0.231 0.180 0.461 0.239 0.149
746 0.217 0.373 NA NA 0.147 0.377
754 0.111 0.652 0.363 0.126 0.231 0.163
758 0.349 0.144 -0.305 0.204 0.139 0.406
764 0.466 0.045 -0.044 0.858 0.260 0.115
775 -0.236 0.330 0.119 0.627 -0.081 0.630
780 -0.212 0.383 0.247 0.308 0.042 0.801
782 -0.306 0.203 0.312 0.193 -0.020 0.906
789 0.166 0.498 0.183 0.452 0.166 0.319
791 0.168 0.491 0.051 0.835 0.105 0.531
792 0.256 0.291 -0.801 0.000 -0.326 0.046
800 0.210 0.389 -0.425 0.070 -0.039 0.814
811 0.029 0.906 0.475 0.040 0.247 0.134
820 0.091 0.710 0.306 0.202 0.201 0.227
827 0.150 0.540 0.158 0.519 0.152 0.363
843 0.228 0.348 0.507 0.027 0.358 0.027
845 0.435 0.063 -0.401 0.089 0.236 0.154
852 0.180 0.461 NA NA 0.126 0.452
174 Table A1 (continued)
NA: not applicable
OTUs Uppermost Subsurface Combined
Correlation coefficient
(r)
P value
Correlatio n coefficient
(r)
P value
Correlatio n coefficient
(r)
P value
867 0.096 0.696 0.255 0.292 0.159 0.34
889 0.061 0.804 0.161 0.511 0.107 0 0.52
895 0.526 0.021 -0.289 0.230 0.126 4 0.45
904 0.085 0.729 0.195 0.423 0.124 0 0.45
906 0.145 0.552 -0.832 0.000 -0.360 8 0.02
927 -0.041 0.867 0.282 0.243 0.105 7 0.53
928 0.325 0.175 NA NA 0.218 2 0.18
934 -0.529 0.020 0.453 0.051 -0.101 8 0.54
947 -0.301 0.210 -0.386 0.102 -0.330 6 0.04
959 0.079 0.748 -0.497 0.031 -0.277 3 0.09
962 0.227 0.349 0.227 0.349 0.201 2 0.22
986 -0.604 0.006 0.300 0.213 -0.201 7 0.22
987 -0.121 0.621 -0.277 0.251 -0.160 5 0.33
995 0.147 0.547 0.274 0.257 0.218 8 0.18
9
175
Table A2 Phylogenetic affiliation and putative automated ribosomal intergenic spacer analysis (ARISA) fragment length of 16S rRNA sequences of clone libraries retrieved from Omura Bay sediment (continued)
a: Underline indicates overlapping ARISA fragments length with different taxonomy.
b: The putative oxygen sensitivity and function were determined by the reported physiology of closely related species.
c: Strict anaerobes are represented in bold.
1 657 -0.34 LC145654 90 Strictly anaerobic Sulfate reduction
2 657 -0.34 LC145644 96 Strictly aerobic
3 657 -0.34 LC145681 93 Aerobic
Facultatively Anaerobic
4 444 0.01 LC145669 93 Strictly anaerobic Sulfate reduction
5 444 0.01 LC145670 93 Strictly anaerobic
Sulfate reduction Mn reduction Ferm entation
6 548 -0.34 LC145652 91 Strictly anaerobic Ferm entation
7 501 -0.53 LC145695 92 Strictly anaerobic
Fe reduction Mn reduction Ferm entation
8 662 -0.45 LC145677 90 Strictly anaerobic disproportionation
of elem ental sulfur
9 662 -0.45 LC145680 94 Strictly anaerobic Sulfate reduction
10 460 -0.40 LC145685 97 Strictly anaerobic Sulfate reduction
Toluen oxy dation
11 420 -0.36 LC145651 90 Strictly anaerobic Fe reduction
12 906 0.15 LC145690 98 Strictly aerobic facultative
photoheterotroph
13 510 -0.39 LC145671 89 Strictly anaerobic Sulfate reduction
Sulfite reduction
14 510 -0.39 LC145672 89 Strictly anaerobic
Fe reduction Mn reduction Ferm entation
15 490 -0.06 LC145657 95 Strictly anaerobic Sulfate reduction
Toluen oxy dation
16 579 -0.46 LC145675 97 Strictly anaerobic
Ferm entation Sulfate reduction
Fe reduction, Nitrate reduction
17 686 -0.37 LC145647 88 Strictly anaerobic Sulfate reduction
18 686 -0.37 LC145682 87 Strictly anaerobic Sulfate reduction
19 506 0.03 LC145696 87 Strictly anaerobic
Fe reduction Mn reduction Ferm entation
20 374 0.14 LC145662 88 Strictly aerobic
21 721 -0.12 LC145684 92 Strictly aerobic
22 469 -0.17 LC145694 94 Strictly anaerobic Sulfate reduction
Toluen oxy dation
23 758 0.35 LC145687 88 Strictly anaerobic Ferm entation
24 735 0.36 LC145686 92 Strictly aerobic
25 234 0.18 LC145664 86 Strictly anaerobic Fe reduction
Mn reduction
26 811 0.03 LC145649 95 m icroaerophilly anaerobic phototrphy
27 254 0.06 LC145665 90 Aerobic Metanotrophic
28 602 0.36 LC145643 94 Aerobic
29 764 0.47 LC145688 91 Aerobic
Facultatively Anaerobic
30 523 0.46 LC145656 90 Strictly anaerobic Ferm entation
31 606 0.39 LC145676 91 Aerobic
Facultatively Anaerobic
32 643 0.40 LC145678 93 Facultatively anaerobic Fe reduction
33 643 0.40 LC145679 93 Facultatively anaerobic Fe reduction
a: Underline indicates overlapping ARISA fragm ents length with different taxonom y .
b: The putative oxy gen sensitivity and function were determ ined by the reported phy siology of closely related species.
c: Strict anaerobes are represented in bold.
Putative oxy gen sensitivityb c Clone No. OTUa
(bp)
Correlation coefficient across
DO gradient
Accession num ber
Sequence Sim ilarity (%)
Putative functionb
176 Table A2 (continued)
a: Underline indicates overlapping ARISA fragments length with different taxonomy.
b: The putative oxygen sensitivity and function were determined by the reported physiology of closely related species.
c: Strict anaerobes are represented in bold.
1 657 Proteobacteria Deltaproteobacteria Sy ntrophobacterales Therm odesulforhabdus norvegica strain A8444 Beeder et al. (1995)
2 657 Proteobacteria Gam m aproteobacteria Cellvibrionales Pseudohaliea rubra strain CM41_15a Urios et al. (2009)
3 657 Proteobacteria Gam m aproteobacteria Aerom onadales Aerom onas salm onicida subsp.
m asoucida strain NBRC 13784 Hirvelä-Koski (2005)
4 444 Proteobacteria Deltaproteobacteria Desulfobacterales Desulfobacter hy drogenophilus strain DSM 3380 Schauder et al. 1987
5 444 Proteobacteria Deltaproteobacteria Desulfurom onadales Desulfurom onas acetoxidans strain DSM 684 Pfennig and Biebl (1976) ,Roden and Lovley (1993)
6 548 Chloroflexi Anaerolineae Anaerolineales Bellilinea caldifistulae strain GOMI-1 Yam ada et al. (2007)
7 501 Acidobacteria Acidobacteria subdivision 23 Therm oanaerobaculum Therm oanaerobaculum aquaticum strain MP-01 A. Losey (2013)
8 662 Proteobacteria Deltaproteobacteria Dissulfuribacter Dissulfuribacter therm ophilus strain S69 Slobodkin er al. (2013) 9 662 Proteobacteria Deltaproteobacteria Desulfobacterales Desulfatiglans parachlorophenolica strain DS Suzuki et al. (2014)
10 460 Proteobacteria Deltaproteobacteria Desulfobacterales Desulfobacula toluolica strain Tol2 Rabus et al. (1995)
11 420 Proteobacteria Deltaproteobacteria Desulfurom onadales Desulfurom usa ferrireducens strain 102 Vandieken et al. (2006) 12 906 Proteobacteria Gam m aproteobacteria Cellvibrionales Chrom atocurvus halotolerans strain EG19 Csotony i et al. (2010) 13 510 Proteobacteria Deltaproteobacteria Desulfurom onadales Desulfobulbus alkaliphilus strain APS1 Sorokin et al. (2012)
14 510 Acidobacteria Acidobacteria subdivision 23 Therm oanaerobaculum Therm oanaerobaculum aquaticum strain MP-01 A. Losey (2013)
15 490 Proteobacteria Deltaproteobacteria Desulfobacterales Desulfobacula toluolica strain Tol2 Rabus et al. (1995)
16 579 Proteobacteria Deltaproteobacteria Desulfurom onadales Pelobacter seleniigenes strain KM Narasingarao and Ha¨
ggblom (2007)
17 686 Proteobacteria Deltaproteobacteria Desulfurom onadales Desulfurom onas thiophila strain NZ27 Finster et al. (1997) 18 686 Proteobacteria Deltaproteobacteria Desulfobacterales Desulfatibacillum alkenivorans strain PF2803 Cravo-Laureau et al. (2004)
19 506 Acidobacteria Acidobacteria subdivision 23 Therm oanaerobaculum Therm oanaerobaculum aquaticum strain MP-01 A. Losey (2013)
20 374 Firm icutes. Bacilli Bacillales Calditerricola y am am urae strain YMO722 Moriy a et al. (2011)
21 721 Bacteroidetes Bacteroidetes-Cy tophagia Cy tophagales Marivirga tractuosa strain DSM 4126 Pagani et al. (2011)
22 469 Proteobacteria Deltaproteobacteria Desulfobacterales Desulfobacula toluolica strain Tol2 Rabus et al. (1995)
23 758 Chlorobi Chlorobi-Ignavibacteria Ignavibacteriales Ignavibacterium album strain JCM 16511 Lino et al. (2010)
24 735 Bacteroidetes Bacteroidetes-Cy tophagia Cy tophagales Marivirga tractuosa strain DSM 4126 Nedashkovskay a et al.(2010) 25 234 Proteobacteria Deltaproteobacteria Desulfurom onadales Geobacter bem idj iensis strain Bem Nevin et al. (2005)
26 811 Proteobacteria Gam m aproteobacteria Chrom atiales Marichrom atium gracile strain DSM 203 Thar and Kühl (2001)
27 254 Proteobacteria Gam m aproteobacteria Methy lococcales Methy lohalobius crim eensis strain 10Ki Hey er et al. (2005) 28 602 Proteobacteria Gam m aproteobacteria Oceanospirillales Neptuniibacter halophilus strain antisso-13 Chen et al. (2012) 29 764 Proteobacteria Gam m aproteobacteria Aerom onadales Aerom onas salm onicida subsp.
m asoucida strain NBRC 13784 Hirvelä-Koski (2005)
30 523 Chloroflexi Anaerolineae Anaerolineales Therm om arinilinea lacunifontana strain SW7 Nunoura et al. (2013)
31 606 Proteobacteria Gam m aproteobacteria Aerom onadales Aerom onas salm onicida subsp.
m asoucida strain NBRC 13784 Hirvelä-Koski (2005)
32 643 Proteobacteria Gam m aproteobacteria Alterom onadales Paraferrim onas sedim enticola strain NBRC 101628 Khan and Haray am a (2007) 33 643 Proteobacteria Gam m aproteobacteria Alterom onadales Paraferrim onas sedim enticola strain NBRC 101628 Khan and Haray am a (2007) a: Underline indicates overlapping ARISA fragm ents length with different taxonom y .
b: The putative oxy gen sensitivity and function were determ ined by the reported phy siology of closely related species.
c: Strict anaerobes are represented in bold.
Referenceb
Clone No. OTUa
(bp)
Phy lum Class Order Nearest neighbor (species) Strain
177 Reference for Table A2
1. Beeder, J., T. Torsvik, and T. Lien. 1995. Thermodesulforhabdus
norvegicus gen. nov., sp. nov., a novel thermophilic
sulfate-reducing bacterium from oil field water. Archives of Microbiology
164: 331–336. doi:10.1007/BF02529979
2. Chen, M. H., S. Y. Sheu, T. F. Chiu, and W. M. Chen. 2012.
Neptuniibacter halophilus sp. nov., isolated from a salt pan, and
emended description of the genus Neptuniibacter. International
Journal of Systematic and Evolutionary Microbiology 62: 1104–
1109. doi:10.1099/ijs.0.030379-0
3. Cravo-Laureau, C., R. Matheron, C. Joulian, J.-L. Cayol, and A.
Hirschler-Réa. 2004. Desulfatibacillum alkenivorans sp. nov., a
novel n-alkene-degrading, sulfate-reducing bacterium, and
emended description of the genus Desulfatibacillum.
International journal of systematic and evolutionary
microbiology 54: 1639–42. doi:10.1099/ijs.0.63104-0
4. Csotonyi, J. T., E. Stackebrandt, J. Swiderski, P. Schumann, and
V. Yurkov. 2011. Chromocurvus halotolerans gen. nov., sp. nov.,
178
a gammaproteobacterial obligately aerobic anoxygenic
phototroph, isolated from a Canadian hypersaline spring.
Archives of Microbiology 193: 573–582.
doi:10.1007/s00203-011-0698-5
5. Finster, K., J. D. Coates, W. Liesack, and N. Pfennig. 1997.
Desulfuromonas thiophila sp. nov., a new obligately
sulfur-reducing bacterium from anoxic freshwater sediment.
International journal of systematic bacteriology 47: 754–758.
doi:10.1099/00207713-47-3-754
6. Heyer, J., U. Berger, M. Hardt, and P. F. Dunfield. 2005.
Methylohalobius crimeensis gen. nov., sp. nov., a moderately
halophilic, methanotrophic bacterium isolated from hypersaline
lakes of Crimea. International Journal of Systematic and
Evolutionary Microbiology 55: 1817–1826.
doi:10.1099/ijs.0.63213-0
7. Hirvelä-koski, V. 2005. Fish Pathogens Aeromonas salmonicida
and Renibacterium salmoninarum: Diagnostic and
179
epidemiological aspects. Faculty of Veterinary Medicine;
University of Helsinki (Academic Dissertation).
8. Iino, T., K. Mori, Y. Uchino, T. Nakagawa, S. Harayama, and K.
-i. Suzuk-i. 2010. Ignavibacterium album gen. nov., sp. nov., a
moderately thermophilic anaerobic bacterium isolated from
microbial mats at a terrestrial hot spring and proposal of
Ignavibacteria classis nov., for a novel lineage at the periphery of
green sulfur bacteria. International journal of systematic and
evolutionary microbiology 60: 1376–1382.
doi:10.1099/ijs.0.012484-0
9. Khan, S. T., and S. Harayama. 2007. Paraferrimonas
sedimenticola gen. nov., sp. nov., a marine bacterium of the
family Ferrimonadaceae. International journal of systematic and
evolutionary microbiology 57: 1493–8. doi:10.1099/ijs.0.64529-0
10. Losey, N. A., B. S. Stevenson, H.-J. Busse, J. S. S. Damste, W. I.
C. Rijpstra, S. Rudd, and P. A. Lawson. 2013.
Thermoanaerobaculum aquaticum gen. nov., sp. nov., the first
cultivated member of Acidobacteria subdivision 23, isolated from
180
a hot spring. International journal of systematic and
evolutionary microbiology 63: 4149–4157.
doi:10.1099/ijs.0.051425-0
11. Moriya, T., T. Hikota, I. Yumoto, T. Ito, Y. Terui, A. Yamagishi,
and T. Oshima. 2011. Calditerricola satsumensis gen. nov., sp.
nov. and Calditerricola yamamurae sp. nov., extreme
thermophiles isolated from a high-temperature compost.
International journal of systematic and evolutionary
microbiology 61: 631–636. doi:10.1099/ijs.0.018416-0
12. Narasingarao, P., and M. M. Haggblom. 2007. Pelobacter
seleniigenes sp. nov., a selenate-respiring bacterium.
International journal of systematic and evolutionary
microbiology 57: 1937–1942. doi:10.1099/ijs.0.64980-0
13. Nedashkovskaya, O. I., M. Vancanneyt, S. B. Kim, and K. S. Bae.
2010. Reclassification of Flexibacter tractuosus (Lewin 1969)
Leadbetter 1974 and “Microscilla sericea” Lewin 1969 in the genus Marivirga gen. nov. as Marivirga tractuosa comb. nov. and
Marivirga sericea nom. rev., comb. nov. International journal of
181
systematic and evolutionary microbiology 60: 1858–1863.
doi:10.1099/ijs.0.016121-0
14. Nevin, K. P., D. E. Holmes, T. L. Woodard, E. S. Hinlein, D. W.
Ostendorf, and D. R. Lovley. 2005. Geobacter bemidjiensis sp.
nov. and Geobacter psychrophilus sp. nov., two novel
Fe(III)-reducing subsurface isolates. International Journal of
Systematic and Evolutionary Microbiology 55: 1667–1674.
doi:10.1099/ijs.0.63417-0
15. Nunoura, T., M. Hirai, M. Miyazaki, and others. 2013. Isolation
and characterization of a thermophilic, obligately anaerobic and
heterotrophic marine Chloroflexi bacterium from a
Chloroflexi-dominated microbial community associated with a Japanese
shallow hydrothermal system, and proposal for
Thermomarinilin. Microbes and environments 28: 228–35.
doi:10.1264/jsme2.ME12193
16. Pagani, I., O. Chertkov, A. Lapidus, and others. 2011. Complete
genome sequence of Marivirga tractuosa type strain (H-43).
182
Standards in genomic sciences 4: 154–62.
doi:10.4056/sigs.1623941
17. Pfennig, N., and H. Biebl. 1976. Desulfuromonas acetoxidans
gen. nov. and sp. nov., a new anaerobic, sulfur-reducing,
acetate-oxidizing bacterium. Archives of Microbiology 110: 3–12.
doi:10.1007/BF00416962
18. Rabus, R., and F. Widdel. 1995. Conversion studies with
substrate analogues of toluene in a sulfate-reducing bacterium,
strain Tol2. Archives of Microbiology 164: 448–451.
doi:10.1007/BF02529744
19. Roden, E. E., and D. R. Lovley. 1993. Dissimilatory Fe(III)
Reduction by the Marine Microorganism Desulfuromonas
acetoxidans. Applied and environmental microbiology 59: 734–
42.
20. Schauder, R., F. Widdel, and G. Fuchs. 1987. Carbon
assimilation pathways in sulfate-reducing bacteria II. Enzymes
of a reductive citric acid cycle in the autotrophic Desulfobacter
183
hydrogenophilus. Archives of Microbiology 148: 218–225.
doi:10.1007/BF00414815
21. Slobodkin, A. I., A.-L. Reysenbach, G. B. Slobodkina, T. V.
Kolganova, N. A. Kostrikina, and E. A. Bonch-Osmolovskaya.
2013. Dissulfuribacter thermophilus gen. nov., sp. nov., a
thermophilic, autotrophic, sulfur-disproportionating, deeply
branching deltaproteobacterium from a deep-sea hydrothermal
vent. International journal of systematic and evolutionary
microbiology 63: 1967–1971. doi:10.1099/ijs.0.046938-0
22. Sorokin, D. Y., T. P. Tourova, A. N. Panteleeva, and G. Muyzer.
2012. Desulfonatronobacter acidivorans gen. nov., sp. nov. and
desulfobulbus alkaliphilus sp. nov., haloalkaliphilic
heterotrophic sulfate-reducing bacteria from soda lakes.
International journal of systematic and evolutionary
microbiology 62: 2107–2113. doi:10.1099/ijs.0.029777-0
23. Suzuki, D., Z. Li, X. Cui, C. Zhang, and A. Katayama. 2014.
Reclassification of Desulfobacterium anilini as Desulfatiglans
anilini comb. nov. within Desulfatiglans gen. nov., And
184
description of a 4-chlorophenol-degrading sulfate-reducing
bacterium, Desulfatiglans parachlorophenolica sp. nov.
International Journal of Systematic and Evolutionary
Microbiology 64: 3081–3086. doi:10.1099/ijs.0.064360-0
24. Thar, R., and M. Kühl. 2001. Motility of Marichromatium gracile
in response to light, oxygen, and sulfide. Applied and
environmental microbiology 67: 5410–9.
doi:10.1128/AEM.67.12.5410-5419.2001
25. Urios, L., L. Intertaglia, F. Lesongeur, and P. Lebaron. 2009.
Haliea rubra sp. nov., a member of the Gammaproteobacteria
from the Mediterranean Sea. International journal of systematic
and evolutionary microbiology 59: 1188–1192.
doi:10.1099/ijs.0.002220-0
26. Vandieken, V., M. Mußmann, H. Niemann, and B. B. Jørgensen.
2006. Desulfuromonas svalbardensis sp. nov. and Desulfuromusa
ferrireducens sp. nov., psychrophilic, Fe(III)-reducing bacteria
isolated from Arctic sediments, Svalbard. International Journal
185
of Systematic and Evolutionary Microbiology 56: 1133–1139.
doi:10.1099/ijs.0.63639-0
27. Yamada, T., H. Imachi, A. Ohashi, H. Harada, S. Hanada, Y.
Kamagata, and Y. Sekiguchi. 2007. Bellilinea caldifistulae gen.
nov., sp. nov and Longilinea arvoryzae gen. nov., sp. nov., strictly
anaerobic, filamentous bacteria of the phylum Chloroflexi
isolated from methanogenic propionate-degrading consortia.
International Journal of Systematic and Evolutionary
Microbiology 57: 2299–2306. doi:10.1099/ijs.0.65098-0
186
Table A3 Mean rank abundance of the dsrA-terminal restriction fragment (OTUs) within same oxygen groups.
(Continued)
Rank (All sample)
Uppermost
OTU
Oxic Dysoxic Suboxic All samples
Relative abundance
SD
Relative abundance
SD
Relative abundance
SD
Relative abundance
SD
1 217 25.91 8.03 25.16 2.76 25.80 5.41 25.70 5.69 2 375 11.07 5.13 18.64 2.61 14.95 4.17 14.35 4.94 3 128 6.34 1.46 6.50 1.21 6.15 1.40 6.30 1.28 4 111 7.19 5.29 4.96 1.42 5.44 1.85 5.96 3.34 5 219 4.06 2.10 7.55 2.08 6.23 1.89 5.74 2.31 6 264 5.36 1.72 6.24 1.50 5.69 1.36 5.69 1.44
7 80 5.32 3.18 5.72 0.75 5.69 0.69 5.56 1.85
8 78 3.87 0.70 2.92 2.53 3.88 0.81 3.67 1.25
9 365 2.24 0.85 3.31 0.84 3.03 1.28 2.81 1.08 10 105 3.07 2.37 1.54 1.35 2.82 1.33 2.64 1.75 11 56 3.85 3.66 1.77 0.04 1.99 0.65 2.61 2.28 12 222 2.22 1.43 1.49 1.61 2.04 0.58 1.99 1.11 13 131 2.08 0.36 1.50 1.31 2.12 0.28 1.97 0.63 14 153 1.73 0.33 1.44 1.25 1.73 0.54 1.67 0.63 15 619 0.92 0.26 2.48 2.71 1.06 0.50 1.32 1.29 16 372 1.17 1.61 0.70 0.62 1.58 0.73 1.25 1.09 17 93 1.05 0.61 1.31 0.27 0.99 0.51 1.08 0.49 18 83 1.10 0.56 0.87 0.76 1.13 0.46 1.06 0.53 19 108 1.06 0.09 0.78 0.68 1.13 0.13 1.03 0.32 20 267 0.90 0.53 0.87 0.75 1.21 0.22 1.03 0.47 21 383 1.17 2.61 0.00 0.00 0.53 1.00 0.64 1.64 22 272 0.82 0.54 0.93 0.93 0.32 0.51 0.63 0.63 23 269 0.79 1.59 0.10 0.18 0.76 0.17 0.63 0.94 24 352 0.64 0.59 0.85 0.74 0.44 0.57 0.60 0.59 25 380 0.89 0.53 0.43 0.74 0.36 0.56 0.56 0.60 26 379 0.20 0.46 0.87 0.81 0.66 0.73 0.54 0.67 27 79 1.15 2.58 0.00 0.00 0.00 0.00 0.41 1.54 28 75 0.53 0.37 0.52 0.47 0.25 0.39 0.41 0.39
Bold indicates more abundant OTUs in suboxic condition as compared to that in oxic condition.
187 Table A3 (Continued)
Rank (All sample)
Uppermost
OTU
Oxic Dysoxic Suboxic All samples
Relative abundance
SD
Relative abundance
SD
Relative abundance
SD
Relative abundance
SD
29 161 0.38 0.36 0.10 0.18 0.37 0.40 0.32 0.35 30 614 0.26 0.39 0.10 0.18 0.34 0.31 0.26 0.31 31 148 0.31 0.70 0.00 0.00 0.25 0.34 0.22 0.46 32 54 0.13 0.18 0.10 0.18 0.32 0.54 0.21 0.37 33 336 0.00 0.00 0.25 0.43 0.32 0.35 0.19 0.31 34 635 0.32 0.44 0.00 0.00 0.15 0.38 0.18 0.36 35 67 0.45 0.48 0.00 0.00 0.00 0.00 0.16 0.35 36 60 0.37 0.51 0.00 0.00 0.00 0.00 0.13 0.34 37 134 0.36 0.51 0.00 0.00 0.00 0.00 0.13 0.33 38 147 0.24 0.55 0.00 0.00 0.00 0.00 0.09 0.33 39 141 0.09 0.19 0.00 0.00 0.12 0.30 0.08 0.22 40 150 0.08 0.17 0.00 0.00 0.11 0.27 0.07 0.20 41 151 0.16 0.35 0.00 0.00 0.00 0.00 0.06 0.21 42 122 0.15 0.33 0.00 0.00 0.00 0.00 0.05 0.20
Bold indicates more abundant OTUs in suboxic condition as compared to that in oxic condition.
188
Table A3 (Continued)
Bold indicates more abundant OTUs in suboxic condition as compared to that in oxic condition.
Rank (All sample)
Subsurface
OTU
Oxic Dysoxic Suboxic All samples
Relative abundance
SD
Relative abundance
SD
Relative abundance
SD
Relative abundance
SD
1 217 21.38 6.29 21.86 3.00 23.95 4.30 22.58 4.71 2 375 14.48 3.77 18.80 2.64 17.81 1.35 16.83 3.10 3 215 10.48 6.52 12.69 1.98 6.51 7.17 9.25 6.34 4 219 4.99 1.19 5.85 0.89 6.58 1.87 5.85 1.56
5 79 5.60 1.77 4.18 0.44 5.13 0.51 5.09 1.17
6 128 5.46 0.53 4.72 1.17 4.97 0.59 5.09 0.72 7 111 5.69 2.75 3.35 0.51 4.37 0.63 4.62 1.83 8 264 4.58 1.10 4.09 1.13 4.76 0.63 4.55 0.89
9 78 3.59 1.30 3.17 0.77 4.06 1.22 3.70 1.15
10 365 2.08 0.58 2.06 0.17 2.34 0.35 2.18 0.42 11 105 2.68 1.93 1.22 0.15 1.79 0.47 1.99 1.26 12 267 1.51 0.40 2.37 0.32 1.89 0.26 1.86 0.45 13 131 1.66 0.86 1.28 0.30 2.13 0.66 1.78 0.73 14 153 1.52 0.32 2.04 0.36 1.70 0.32 1.71 0.36 15 619 1.59 0.21 1.48 0.42 1.53 0.24 1.54 0.26 16 56 1.26 0.94 1.69 0.97 1.56 0.37 1.48 0.71 17 372 1.31 0.51 1.80 0.45 1.33 0.29 1.42 0.43 18 222 1.61 1.09 0.85 0.23 1.34 0.52 1.33 0.75 19 108 1.42 0.58 1.20 0.27 1.21 0.28 1.28 0.39 20 93 1.06 0.63 1.17 0.18 1.39 0.30 1.22 0.43 21 269 1.13 0.48 0.79 0.27 0.89 0.13 0.95 0.33 22 379 0.76 0.49 1.06 0.14 0.99 0.11 0.92 0.31 23 54 0.99 2.21 0.67 0.64 0.39 0.38 0.66 1.31 24 83 0.38 0.41 0.69 0.35 0.44 0.40 0.47 0.38 25 74 0.27 0.37 0.61 0.61 0.55 0.44 0.46 0.44 26 383 0.91 2.03 0.00 0.00 0.00 0.00 0.32 1.21 27 746 0.12 0.27 0.11 0.18 0.17 0.30 0.14 0.25 28 272 0.17 0.38 0.20 0.17 0.05 0.13 0.13 0.25