Supplement of Biogeosciences, 15, 1815–1826, 2018 https://doi.org/10.5194/bg-15-1815-2018-supplement © Author(s) 2018. This work is distributed under the Creative Commons Attribution 3.0 License.

Supplement of Plant n-alkane production from litterfall altered the diversity and com- munity structure of alkane degrading in litter layer in lowland subtropical rainforest in Taiwan

Tung-Yi Huang et al.

Correspondence to: Cheng-Wei Fan ([email protected])

The copyright of individual parts of the supplement might differ from the CC BY 3.0 License. Table S1. The prediction of alkB lineage-like OTUs and the reference genes. Informatics prediction by UTAX algorithm gives the prediction up to genus level. An estimated probability that correct prediction was higher than 90% is showed on this table. Relative Abundance (%) Phylum OTU Taxonomy Prediction Reference of bacteria with alkB gene Sequence ID Identities ravine windward leeward litter14 g: Rhizobium ( 97%) 4.5 1.0 0.2 Agrobacterium fabrum NR074266.1 377/382(99%) litter44 f: Rhizobiaceae (91%) 2.2 0.2 0.1 Rhizobium etli U28916.1 376/381(99%) litter50 o: Rhizobiales (98%) 2.1 0.9 0.6 Ensifer adhaerens CP007236.1 375/382(98%) litter117 o: Rhizobiales (97%) 1.6 <0.1 <0.1 Mesorhizobium amorphae NR024879.1 371/384(97%) litter6 f: Bradyrhizobiaceae (93%) 0.7 1.6 1.2 Bradyrhizobium diazoefficiens AB909430.1 380/382(99%) litter159 f: Pseudomonadaceae (91%) 0.6 <0.1 Stenotrophomonas maltophilia AM743169.1 390/406(96%) litter464 o: Rhizobiales (96%) 0.4 <0.1 <0.1 Sinorhizobium meliloti CP003933.2 377/384(98%) litter189 c: Gammaproteobacteria (99%) 0.4 <0.1 Stenotrophomonas maltophilia AM743169.1 394/408(97%) litter291 g: Pseudorhodoferax (97%) 0.3 Delftia acidovorans CP000884.1 387/408(95%) litter199 g: Caulobacter (95%) 0.3 0.1 <0.1 Caulobacter crescentus AE005673.1 384/384(100%) litter256 o: Rhizobiales (98%) 0.3 <0.1 0.1 Bradyrhizobium diazoefficiens AB909430.1 376/387(97%) litter506 f: (93%) 0.2 <0.1 Mesorhizobium ciceri CP002447.1 375/382(98%) litter152 f: Caulobacteraceae (96%) 0.1 0.1 <0.1 Caulobacter crescentus AE005673.1 370/384(96%) litter109 o: Rhizobiales (95%) 0.1 <0.1 0.7 Ochrobactrum anthropi CP000758.1 374/382(98%) litter9 c: (99%) 0.1 1.6 0.4 Ochrobactrum anthropi CP000758.1 369/382(97%) litter21 f: Enterobacteriaceae (98%) 0.1 0.7 <0.1 Enterobacter lignolyticus CP002272.1 398/407(98%) litter505 g: Pseudomonas (95%) <0.1 <0.1 <0.1 Pseudomonas putida LT799039.1 396/408(97%) litter487 f: Burkholderiaceae (94%) <0.1 0.2 0.2 Burkholderia pseudomallei CP009163.1 401/413(97%) litter75 f: Burkholderiaceae (95%) <0.1 0.2 1.4 Burkholderia phenoliruptrix CP003863.1 402/409(98%) litter11 f: Burkholderiaceae (95%) <0.1 1.2 0.4 Burkholderia phenoliruptrix CP003863.1 399/409(98%) litter384 f: Oxalobacteraceae (96%) <0.1 <0.1 Herbaspirillum seropedicae CP002039.1 384/406(95%) litter209 f: Burkholderiaceae (96%) <0.1 0.2 0.5 Burkholderia phenoliruptrix CP003863.1 399/410(97%) litter208 g: Ralstonia (91%) <0.1 Ralstonia solanacearum AL646052.1 394/406(97%) litter220 f: Burkholderiaceae (95%) 0.1 0.2 Burkholderia pseudomallei CP009163.1 389/407(96%) litter32 f: Pseudonocardiaceae (97%) 4.0 <0.1 Amycolatopsis orientalis NR 042104.1 375/389(96%) litter69 g: Pseudonocardia (98%) 1.6 <0.1 Amycolatopsis orientalis NR 042104.1 373/391(95%) litter426 g: Streptomyces (91%) 0.5 <0.1 <0.1 Streptomyces virginiae NR 115622.1 382/386(99%) litter147 g: Pseudonocardia (91%) 0.4 <0.1 <0.1 Amycolatopsis orientalis NR 042104.1 366/387(95%) Actinobacteria litter319 f: Micromonosporaceae (95%) 0.3 Amycolatopsis vancoresmycina NR 025565.1 370/390(95%) litter89 g: Mycobacterium (97%) 0.1 0.2 0.3 Mycobacterium smegmatis X52922.1 382/387(99%) litter228 g: Mycobacterium (91%) 0.1 0.1 0.1 Mycobacterium kansasii FR822390.1 378/399(95%) litter352 f: Mycobacteriaceae (91%) <0.1 <0.1 <0.1 Mycobacterium abscessus LC149865.1 370/388(95%) litter465 g: Mycobacterium (97%) <0.1 <0.1 Mycobacterium kansasii FR822390.1 391/403(97%) Table S2. Biodiversity index of plant vegetation, bacteria, and AlkB-lineage like OTUs. Biodiversity Index Sample type Habitat Shannon-Weiner effective numbers of species Evenness Ravine 3.26 26 0.69 Plant Windward 3.64 38 0.78 vegetation Leeward 3.78 44 0.78 Ravine 4.43 84 0.76 Bacteria Windward 4.22 68 0.70 Leeward 4.12 62 0.72 OTUs of Ravine 2.51 12 0.74 AlkB- Windward 2.39 11 0.70 lineage Leeward 2.46 12 0.76 Figure S1. Location of the sampling site (from Chao et al, 2010). (a) Map of

Taiwan. (b) Map of the Nanjenshan Reserve. (c) Stands set of windward habitat ( ) and Leewind habitat ( ) in Lanjenchi plot. (d) Stands set of ravine habitat ( ) in Nanjenshan plot I. (e) Stands set of ravine habitat ( ) in

Nanjenshan plot II.

This figure was produced with permission of original author Wei-Chun Chao who is the co-author of this study.

Ravine Windward Leeward 300 300 300 C31 C31 250 250 250 C31

200 200 200 C C29 29 150 150 150 C29

100 100 100 C C C C C C 27 28 27 28 C33 27 28 Detector Response (µV) Response Detector 50 C 50 5α C 50 5α C C33 IS 5α C30 32 C33 IS 30 C32 IS 30 C32 0 0 0 48 50 52 54 56 58 60 62 48 50 52 54 56 58 60 62 48 50 52 54 56 58 60 62 Time (min) Figure S2. Representative GC-FID chromatograms of aliphatic hydrocarbons of Iles rotunda in each habitat.

Figure 1 45 litter303 34 litter447

75 litter357 litter215 28 42 litter95 15 litter398 litter52 litter311 27 36 litter13 1 47 litter508

92 litter187 31 litter514 litter181

28 litter127 8 litter157

14 litter256 0 98 Bradyrhizobium diazoefficiens AB909430.1 95 litter6

68 litter137 60 litter31 74 litter171 67 litter409 litter306

28 litter143 16 litter112 litter403 1 93 100 litter199 52 Caulobacter crescentus AE005673.1 4011 litter152 litter268 litter104 15 57 litter125

3 6 litter18

20 litter105 74 litter91 litter67 24 litter236

94 litter110 litter60

18 litter365

80 litter144 8 88 litter238

99 Sinorhizobium meliloti AL591688.1 68 Sinorhizobium meliloti CP003933.2

78 litter464 litter506 53 72 Mesorhizobium ciceri CP002447.1 36 Mesorhizobium amorphae NR024879.1 litter117

99 litter44 58 Rhizobium etli U28916.1 21 99 Brucella abortus strain CP022876.1 56 Ochrobactrum anthropi CP000758.1 50 54 litter109 litter9 litter50 4070 Ensifer adhaerens CP007236.1 57 litter14 96 Agrobacterium fabrum NR074266.1

100 litter458 76 litter282 litter146 26 litter477 10 96 litter342 89 litter308

29 litter449 43 litter53

47 litter167 litter97

11 litter160 5 49 litter27

62 litter265 litter359

8 litter241

11 litter163 44 litter210 98 56 litter296

11 litter493 6 litter351 37 litter107

51 litter2 34 6 litter242 48 litter425 litter37

16 litter353 13 litter80 litter217 8 14 litter304 5 litter1

4 litter48 0 21 litter193 30 litter19 litter436 litter483 34 litter227 57 97 litter90 55 litter131 litter98

28 litter15

43 litter111 litter490 25 35 litter81 21 litter64 2 litter183

41 60 litter326 92 litter509 litter129

35 litter405 4 55 litter443 litter206 0 litter120 litter266 43 83 78 litter331

96 litter429

56 litter340 76 litter33 58 36 litter63 litter29 litter118 70 49 litter295 20 litter42 8 litter66

0 56 litter4 15 litter500 8 28 litter8 litter414 litter43 529 litter375 4 litter211 31 litter55 litter491

32 litter292 8 litter274 litter248

85 litter286 0 15 litter421 litter329

3 litter262 0 litter378

2 59 litter154 36 litter233 6 litter175

77 litter272 7 litter99

100 litter332 22 litter489 26 litter135 98 litter456

100 litter441 16 56 litter287 31 litter376 litter245

99 litter222 19 83 litter322 litter229

65 litter330 51 16 litter270

29 litter338

100 litter254 55 litter411 litter448

56 litter320 57 litter279 litter225

77 litter189 48 Stenotrophomonas maltophilia AM743169.1 82 litter159 99 litter35

35 Xylella fastidiosa AE003849.1 litter391

19 litter440 90 56 99 litter223 61 60 litter224 litter240 litter302

64 litter11 54 Burkholderia phenoliruptrix CP003863.1 62 litter75

47 litter209 litter220 litter487 3045 76 Burkholderia pseudomallei CP009163.1 litter126 Ralstonia eutropha AM260479.1 88 16 38 litter208 99 Ralstonia solanacearum AL646052.1 42 33 litter384 35 Herbaspirillum seropedicae CP002039.1 34 litter249 litter423 Achromobacter xylosoxidans CP002287.1 92 54 100 Bordetella parapertussis HE965803.1 99 Bordetella pertussis CP022362.1 litter275 litter484 39 Comamonas testosteroni CP001220.2 99 97 litter291 60 Delftia acidovorans CP000884.1 20 99 litter273 100 litter346 litter412

100 Acinetobacter radioresistens KX977571.1 91 Acinetobacter schindleri CP015615.1 Moraxella catarrhalis CP002005.1 Pseudomonas syringae CP000075.1 66 90 39 Pseudomonas syringae NR074597.1 46 Pseudomonas protegens strain AJ417072.1 48 Pseudomonas putida LT799039.1 41 litter505 73 44 Pseudomonas fluorescens CP003150.1 Pseudomonas fluorescens AM181176.4 100 54 Pseudomonas stutzeri CP000304.1 Pseudomonas stutzeri CP003677.1 21 Pseudomonas mendocina CP000680.1 42 Pseudomonas aeruginosa CP022526.1 27 litter145

99 Vibrio vulnificus BA000037.2 64 Vibrio parahaemolyticus BA000031.2 83 Vibrio cholerae CP006947.1 39 67 Photobacterium leiognathi AY292917.1 Pseudoalteromonas haloplanktis CR954246.1

97 Yersinia enterocolitica CP009846.1 86 89 Serratia plymuthica CP015613.1 Serratia marcescens HG326223.1 Klebsiella pneumoniae CP003200.1 91 Enterobacter sacchari CP007215.3 87 71 Salmonella enterica CP022069.1 68 64 Salmonella enterica LT906560.1 Enterobacter cloacae NR102794.1 36 Erwinia amylovora FN434113.1

46 litter21 50 Enterobacter lignolyticus CP002272.1 litter364

48 litter381 18 litter451

92 litter400 litter170 93 93 litter288 14 litter343 58 97 litter25

37 litter461 100 litter156 litter30

61 litter318 25 90 litter482 litter174

99 litter485 litter290 36 99 litter368 42 litter283

98 litter100 litter192 97 litter94 63 litter497 80 50 litter207 63 litter40

31 litter361 12 litter345 litter284

100 litter392

46 litter470 12 litter315 100 litter431

100 litter469 43 litter289

40 litter402 64 litter369 86 99 litter78 litter444 litter285 91 100 litter413

73 litter420

96 litter416 99 litter298

0.050 Mycobacterium tuberculosis (KY084565.1) Mycobacterium intracellulare (X52927.1)

99 Mycobacterium leprae (X53999.1) Mycobacterium avium (CP022105.1) 70 Mycobacterium bovis (AB292583.1) Mycobacterium kansasii (FR822390.1) 62 litter465 litter228 8 96 Mycobacterium smegmatis (X52922.1) litter89

19 Mycobacterium sp. (U46146.1) 68 Mycobacterium fortuitum (GU142933.1) 38 96 Mycobacterium chelonae (JX266694.1) 30 91 Mycobacterium abscessus (LC149865.1) litter352 Corynebacterium sp. (KP267833.1) 7 96 Corynebacterium jeikeium (NR 037035.1) 82 Corynebacterium simulans (NR 025309.1) Rhodococcus pyridinivorans (NR 025033.1) 14 60 Rhodococcus ruber (NR 026185.1) 100 Rhodococcus aetherivorans (KR920051.1) 52 Gordonia terrae (CP016594.1) 27 Nocardia mikamii (EU484389.1) Rhodococcus fascians (X53204.1) 35 52 Rhodococcus jostii (NR 024765.1) 71 Rhodococcus erythropolis (AF512836.1) litter325 litter513 99 51 litter196 68 litter446 23 74 litter264 56 litter313

94 litter260 12 litter319 litter32

81 litter147 37 87 litter172

11 litter69 Amycolatopsis orientalis (NR 042104.1) 45 99 Amycolatopsis japonica (NR 025561.1) 98 Amycolatopsis vancoresmycina (NR 025565.1) 99 Amycolatopsis mediterranei (NR 115160.1)

78 litter106 57 litter213 litter84 5 79 Rothia dentocariosa (AY594189.1) 56 Paenarthrobacter aurescens (KU977112.1)

63 Clavibacter michiganensis (NR 115038.1) 79 litter258 92 litter476 38 45 litter65 litter255

25 litter128 34 litter149 litter73 litter323 58 54 litter259 93 38 litter5

97 Streptomyces xanthophaeus (EU285474.1) 95 Streptomyces virginiae (NR 115622.1) 54 litter426 90 Streptomyces rimosus (FJ799189.1) Streptomyces griseorubens (KX156364.1) 43 Streptomyces hygroscopicus (FJ799176.1)

86 litter23 37 96 litter261 litter246

73 litter455

54 litter20 68 litter86 99 litter263 67 litter36

56 litter205 91 litter226 100 litter164 litter93

53 litter237 99 litter350

58 litter252 litter460 74 litter488

91 litter203

95 litter124 93 litter148 22 litter92 litter141 51 85 litter221 58 litter182 56 litter410

0.020 (a) (b) (c) 100% 100% 100% Alphaproteobacteria Actinomycetales Micromonosporaceae Sphingomonadaceae Rhizobiales Actinobacteria Rhizobiaceae unknown Sphingomonadales Hyphomicrobiaceae Pseudonocardiaceae 90% 90% 90% Sphingobacteriia unknown Kineosporiaceae Chitinophagaceae Sphingobacteriales unknown Phyllobacteriaceae Bdellovibrionaceae Bdellovibrionales Xanthomonadaceae Polyangiaceae 80% Deltaproteobacteria 80% Myxococcales 80% Methylocystaceae Sphingobacteriaceae Bacteroidetes_incertae_sedis Xanthomonadales Bradyrhizobiaceae Planctomycetaceae Rhodospirillales Xanthobacteraceae Methylobacteriaceae Gammaproteobacteria 70% 70% Planctomycetales 70% Rhodospirillaceae Caulobacteraceae Acidobacteria_Gp4 Acidimicrobiales Pseudomonadaceae Cryptosporangiaceae Caulobacterales Rhodobacteraceae Acidimicrobiaceae Planctomycetia Pseudomonadales Nocardioidaceae Streptomycetaceae 60% 60% 60% Flavobacteriia Flavobacteriales Microbacteriaceae Flavobacteriaceae Rhodobacterales Aurantimonadaceae Comamonadaceae Betaproteobacteria Burkholderiales Rhodocyclaceae Acetobacteraceae 50% 50% Acidobacteria_Gp3 Rhodocyclales 50% Iamiaceae Cryomorphaceae Alphaproteobacteria_incertae_sedis Opitutae Brucellaceae Mycobacteriaceae Opitutales Opitutaceae Kofleriaceae 40% Acidobacteria_Gp16 40% Syntrophobacterales 40% Syntrophaceae Acidimicrobineae_incertae_sedis Chloroplast Enterobacteriales Beijerinckiaceae Enterobacteriaceae Chloroflexales Chloroplast Chloroflexaceae Chloroflexia 30% 30% Gemmatimonadales 30% Gemmatimonadaceae Thermoanaerobacteraceae Gemmatimonadetes Methylophilales Thermomonosporaceae Burkholderiaceae Thermoanaerobacterales Hyphomonadaceae Marinilabiliaceae Clostridia Bacteroidales Micrococcaceae Rickettsiaceae 20% 20% 20% Acidobacteria_Gp1 Rickettsiales Cystobacteraceae Rhizobiales_incertae_sedis Solirubrobacterales Solirubrobacteraceae Oxalobacteraceae Bacteroidia Bacillales Labilitrichaceae Conexibacteraceae 10% 10% 10% Spartobacteria Chromatiales Cytophagaceae Desulfobacteraceae Ectothiorhodospiraceae Fimbriimonadaceae Fimbriimonadia Clostridiales Cytophagales Geodermatophilaceae Ktedonobacteraceae 0% Cytophagia 0% Desulfobacterales 0% Peptococcaceae_2 Rhodobiaceae Ktedonobacteria Fimbriimonadales Ruminococcaceae Sinobacteraceae Ktedonobacterales Syntrophomonadaceae Thermoactinomycetaceae_1 Bacilli Thiotrichales Thiotrichaceae Figure S5. Microbial community structure in the three habitats of Nanjenshan Reserve. Bacterial lineages were indicated in (a) class, (b) order, and (c) family. Figure S6. The distribution of OTUs and their relative abundance of microbial Actinobacteria. Size index of diameter vs relative abundance was showed at up-right panel.

Figure S7. The distribution of OTUs and their relative abundance of microbial Proteobacteria. Star symbol (★) indicates the location with multiple OTUs. Size index of diameter vs relative abundance was showed at up-right panel.