Supplementary files
Bacterial community structure and function shift across a northern boreal forest fire chronosequence
Hui Sun1,2, *, Minna Santalahti2, Jukka Pumpanen3, Kajar Köster4,5, Frank Berninger4, Tommaso Raffaello4, Fred O. Asiegbu4, Jussi Heinonsalo2
1Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
2Department of Food and Environmental Sciences, University of Helsinki, Helsinki, 00790, Finland
3Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, 70210, Finland
4Department of Forest Sciences, University of Helsinki, Helsinki, 00790, Finland
5Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, 51014, Estonia
*Correspondence:
Hui Sun.
E-mail:
Tel: +86-85427370
(a)
(b)
Figure S1. Principle Coordinate Analysis (PCoA) plot showing differences in bacterial community structure based on the relative abundance of rare OTUs (< 0.1%) (a), and based on the relative abundance of abundant OTUs (> 0.1%) (b) with time since fire.
Figure S2. The relative abundance of bacterial phylum in each site after fire
Figure S3. Bacterial gene diversity index (Shannon, H’) across the three sites differing in fire histories. The bar representing the standard deviations, and different letters in each panel represent Tukey’s significance at a P value of 0.05.
Table S1. Twelve genera showing significant difference in abundance between sitesGenus / Relative abundance (%)a / Significant P value
2y / 60y / 152y
Aciditerrimonas / 1,53b / 1,70bc / 2,12c / 0.034c
Acidocella / 0,37b / 0,54bc / 0,61c / 0.032c
Methylobacterium / 0,21b / 0,03c / 0.03c
Rudaea / 0,10bc / 0,21b / 0,03c / 0.046d
Sphingomonas / 0,18b / 0,09bc / 0,02c / 0.029c
Amnibacterium / 0,07
Rhizobium / 0,07
Spirosoma / 0,09
Subtercola / 0,07
Humicoccus / 0,05
Kaistia / 0,05
Marmoricola / 0,05
a The abundance of each genus were calculated as mean of the three replicates from each site.
b c Different letters in each row represent Tukey’s significant difference at a P value of 0.05 between sites.
Table S2. The environmental factors that significantly correlated with bacterial communities and gene structures
Variable / Taxonomic structure / Gene structure
Sum of square (trace) / Pseudo-F / P / Proportion / Sum of square (trace) / Pseudo-F / P / Proportion
Temperature / 1331,2 / 18,825 / 0,011 / 0,21193 / 39,561 / 24,955 / 0,031 / 0,26281
water content / 1257,3 / 17,519 / 0,015 / 0,20017 / 41,172 / 26,354 / 0,022 / 0,27351
Soi pH / 1286,1 / 18,024 / 0,017 / 0,20476 / 40,43 / 25,705 / 0,026 / 0,26858
SoilC / 1119,7 / 15,185 / 0,055 / 0,17826 / 34,204 / 20,583 / 0,052 / 0,22723
SoilN / 1094,8 / 14,777 / 0,062 / 0,1743 / 42,69 / 2,771 / 0,005 / 0,28359
TRootBiom / 827,33 / 10,619 / 0,355 / 0,13172 / 18,408 / 0,97525 / 0,416 / 0,12228
Ergosterol / 1082,6 / 14,577 / 0,055 / 0,17235 / 36,4 / 22,325 / 0,055 / 0,24181
The significant level (P) were determined by Distance Based Linear Models with Pearson Correlation in PRIMER 6.
4
Table S4. The average signal intensity of detected gene probes in each gene category from the sites with different fire historiesGene category / Average signal intensity of detected gene probes (mean ± SD)a / No. of gene probe in each category
2-year after fire / 60-year after frie / 152-year after fire
Carbon Cycling / 0,84584 / ± / 0,00476b / 0,76637 / ± / 0,03942c / 0,81382 / ± / 0,01124bc / 9443
Electron transfer / 0,77963 / ± / 0,02239b / 0,66198 / ± / 0,06417c / 0,72063 / ± / 0,03297bc / 382
Metal Homeostasis / 0,81477 / ± / 0,01161b / 0,74740 / ± / 0,03779c / 0,77906 / ± / 0,00449bc / 17208
Nitrogen / 0,80843 / ± / 0,01019b / 0,72570 / ± / 0,04606c / 0,76069 / ± / 0,00647bc / 2592
Organic Remediation / 0,85456 / ± / 0,01106b / 0,80354 / ± / 0,02833c / 0,82384 / ± / 0,00127bc / 5571
Phosphorus / 0,88353 / ± / 0,02090b / 0,81603 / ± / 0,03757c / 0,85744 / ± / 0,00951bc / 1430
Secondary metabolism / 0,88140 / ± / 0,01334b / 0,81643 / ± / 0,04825c / 0,85835 / ± / 0,01776bc / 1479
Stress / 0,79707 / ± / 0,00848b / 0,71693 / ± / 0,04168c / 0,76422 / ± / 0,00695bc / 10439
Sulfur / 0,79782 / ± / 0,02156b / 0,72009 / ± / 0,05083c / 0,75468 / ± / 0,00813bc / 1748
virulence / 0,87113 / ± / 0,00673b / 0,81513 / ± / 0,02911c / 0,84196 / ± / 0,01025bc / 9415
Other / 0,77781 / ± / 0,01339b / 0,71443 / ± / 0,03920c / 0,74088 / ± / 0,02877bc / 3153
aThe signal intensities per gene category were calculated as the sum of intensities of the gene probes, divided by the total number of the gene probes detected in each category, and averaged across the three replicates per sample.
Different letters in each gene category represent Tukey’s significant difference at a P value of 0.05 between the sites after fire.
Table S3. The number of gene detected in each site
No. / Gene / 2y_1 / 2y_2 / 2y_3 / 60y_1 / 60y_2 / 60y_3 / 150y_1 / 150y_2 / 150y_3 / Total probe count / Gene_category / Subcategory1 / Subcategory2
1 / accD / 2 / 2 / 2 / 2 / 2 / 1 / 2 / 2 / 1 / 2 / Carbon Cycling / Carbon fixation / 3-hydroxypropionate bicycle
2 / AceA / 178 / 169 / 175 / 155 / 173 / 157 / 177 / 184 / 172 / 216 / Carbon Cycling / Carbon degradation / Glyoxylate cycle
3 / AceB / 282 / 286 / 284 / 278 / 287 / 260 / 272 / 280 / 263 / 336 / Carbon Cycling / Carbon degradation / Glyoxylate cycle
4 / acetylglucosaminidase / 323 / 318 / 324 / 280 / 298 / 270 / 294 / 313 / 315 / 392 / Carbon Cycling / Carbon degradation / Chitin
5 / aclb / 20 / 21 / 23 / 23 / 22 / 20 / 22 / 21 / 22 / 31 / Carbon Cycling / Carbon fixation / Reductive tricarboxylic acid cycle
6 / AcnA / 17 / 16 / 15 / 15 / 14 / 14 / 14 / 17 / 16 / 19 / Carbon Cycling / Carbon fixation / Reductive tricarboxylic acid cycle
7 / amyA / 1740 / 1725 / 1768 / 1600 / 1651 / 1496 / 1666 / 1709 / 1686 / 2141 / Carbon Cycling / Carbon degradation / Starch
8 / amyx / 1 / 2 / 2 / 2 / 2 / 2 / 2 / 1 / 2 / 2 / Carbon Cycling / Carbon degradation / Starch
9 / ara / 214 / 211 / 211 / 199 / 208 / 179 / 203 / 211 / 204 / 257 / Carbon Cycling / Carbon degradation / Hemicellulose
10 / camdcab / 6 / 6 / 6 / 7 / 6 / 6 / 6 / 6 / 7 / 8 / Carbon Cycling / Carbon degradation / Camphor
11 / ccl / 2 / 2 / 2 / 2 / 2 / 1 / 1 / 1 / 1 / 2 / Carbon Cycling / Carbon fixation / Reductive tricarboxylic acid cycle
12 / ccmL / 110 / 107 / 106 / 96 / 100 / 92 / 98 / 99 / 102 / 131 / Carbon Cycling / Carbon fixation / Bacterial Microcompartments
13 / ccmM / 5 / 5 / 4 / 4 / 4 / 2 / 5 / 5 / 4 / 5 / Carbon Cycling / Carbon fixation / Bacterial Microcompartments
14 / ccmN / 3 / 3 / 3 / 3 / 3 / 3 / 3 / 3 / 3 / 3 / Carbon Cycling / Carbon fixation / Bacterial Microcompartments
15 / cda / 112 / 117 / 120 / 101 / 101 / 91 / 108 / 114 / 113 / 148 / Carbon Cycling / Carbon degradation / Starch
16 / cdh / 42 / 43 / 40 / 40 / 42 / 39 / 39 / 40 / 39 / 48 / Carbon Cycling / Carbon degradation / Terpenes
17 / cellobiase / 159 / 170 / 171 / 147 / 162 / 149 / 165 / 158 / 170 / 209 / Carbon Cycling / Carbon degradation / Cellulose
18 / chitinase / 554 / 538 / 551 / 488 / 530 / 486 / 521 / 546 / 548 / 706 / Carbon Cycling / Carbon degradation / Chitin
19 / codh / 120 / 119 / 120 / 109 / 111 / 105 / 114 / 113 / 115 / 137 / Carbon Cycling / Carbon fixation / Reductive acetyl¨CCoA pathway
20 / CsoS1_CcmK / 173 / 168 / 165 / 144 / 153 / 131 / 140 / 154 / 154 / 204 / Carbon Cycling / Carbon fixation / Bacterial Microcompartments
21 / CsoS2 / 22 / 22 / 22 / 23 / 21 / 22 / 20 / 21 / 21 / 27 / Carbon Cycling / Carbon fixation / Bacterial Microcompartments
22 / CsoSCA / 16 / 17 / 15 / 15 / 15 / 13 / 18 / 17 / 15 / 21 / Carbon Cycling / Carbon fixation / Bacterial Microcompartments
23 / cutinase / 110 / 109 / 111 / 101 / 105 / 95 / 106 / 106 / 109 / 120 / Carbon Cycling / Carbon degradation / Cutin
24 / endoglucanase / 114 / 109 / 113 / 103 / 104 / 94 / 106 / 106 / 102 / 132 / Carbon Cycling / Carbon degradation / Cellulose
25 / exoglucanase / 13 / 13 / 10 / 6 / 7 / 6 / 10 / 8 / 10 / 17 / Carbon Cycling / Carbon degradation / Cellulose
26 / FBP_aldolase / 84 / 80 / 80 / 70 / 77 / 72 / 83 / 85 / 78 / 105 / Carbon Cycling / Carbon fixation / Calvin cycle
27 / FBPase / 182 / 179 / 181 / 162 / 166 / 159 / 167 / 173 / 168 / 215 / Carbon Cycling / Carbon fixation / Calvin cycle
28 / frdA_rTCA / 24 / 25 / 25 / 25 / 22 / 20 / 21 / 20 / 20 / 31 / Carbon Cycling / Carbon fixation / Reductive tricarboxylic acid cycle
29 / fthfs / 278 / 281 / 283 / 244 / 256 / 230 / 269 / 267 / 265 / 350 / Carbon Cycling / Carbon fixation / Reductive acetyl¨CCoA pathway
30 / fumarase_3HP4HB / 2 / 2 / 2 / 2 / 2 / 2 / 2 / 2 / 2 / 2 / Carbon Cycling / Carbon fixation / 3-hydroxypropionate/4-hydroxybutyrate cycle
31 / GAPDH_Calvin / 162 / 157 / 157 / 147 / 149 / 126 / 157 / 157 / 160 / 210 / Carbon Cycling / Carbon fixation / Calvin cycle
32 / glucoamylase / 53 / 54 / 54 / 48 / 55 / 49 / 48 / 50 / 50 / 62 / Carbon Cycling / Carbon degradation / Starch
33 / glx / 14 / 14 / 13 / 13 / 13 / 12 / 14 / 15 / 15 / 16 / Carbon Cycling / Carbon degradation / Lignin
34 / hdrB / 53 / 52 / 52 / 44 / 49 / 44 / 43 / 48 / 48 / 65 / Carbon Cycling / Methane / Methanogenesis
35 / icd / 0 / 1 / 1 / 0 / 1 / 1 / 0 / 2 / 2 / 2 / Carbon Cycling / Carbon fixation / Reductive tricarboxylic acid cycle
36 / IcfA / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / Carbon Cycling / Carbon fixation / Bacterial Microcompartments
37 / inulinase / 7 / 8 / 8 / 7 / 8 / 4 / 7 / 6 / 7 / 8 / Carbon Cycling / Carbon degradation / Inulin
38 / isopullulanase / 2 / 2 / 2 / 1 / 1 / 1 / 2 / 2 / 1 / 2 / Carbon Cycling / Carbon degradation / Starch
39 / limeh / 55 / 53 / 58 / 50 / 53 / 45 / 52 / 48 / 52 / 67 / Carbon Cycling / Carbon degradation / Terpenes
40 / lmo / 5 / 7 / 7 / 6 / 7 / 7 / 8 / 9 / 8 / 10 / Carbon Cycling / Carbon degradation / Terpenes
41 / mannanase / 100 / 97 / 96 / 88 / 87 / 77 / 90 / 89 / 87 / 113 / Carbon Cycling / Carbon degradation / Hemicellulose
42 / mch / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / Carbon Cycling / Carbon fixation / 3-hydroxypropionate bicycle
43 / mcl / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / Carbon Cycling / Carbon fixation / 3-hydroxypropionate bicycle
44 / MCM / 4 / 4 / 3 / 4 / 5 / 4 / 3 / 3 / 3 / 5 / Carbon Cycling / Carbon fixation / 3-hydroxypropionate bicycle
45 / mcr / 2 / 2 / 2 / 2 / 2 / 1 / 1 / 1 / 1 / 2 / Carbon Cycling / Carbon fixation / 3-hydroxypropionate bicycle
46 / mcra / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / Carbon Cycling / Methane / Methanogenesis
47 / mct / 1 / 2 / 2 / 2 / 1 / 2 / 2 / 1 / 2 / 2 / Carbon Cycling / Carbon fixation / 3-hydroxypropionate bicycle
48 / mdh / 11 / 12 / 11 / 10 / 11 / 9 / 12 / 12 / 11 / 14 / Carbon Cycling / Carbon fixation / Reductive tricarboxylic acid cycle
49 / MMCE / 2 / 2 / 2 / 1 / 1 / 1 / 1 / 2 / 2 / 2 / Carbon Cycling / Carbon fixation / 3-hydroxypropionate bicycle
50 / mmox / 12 / 12 / 12 / 10 / 11 / 10 / 9 / 13 / 12 / 17 / Carbon Cycling / Methane / Methane oxidation
51 / mrtH / 2 / 3 / 3 / 2 / 2 / 2 / 2 / 2 / 2 / 3 / Carbon Cycling / Methane / Methanogenesis
52 / mtaB / 1 / 1 / 1 / 1 / 1 / 1 / 2 / 2 / 2 / 2 / Carbon Cycling / Methane / Methanogenesis
53 / nplT / 32 / 30 / 30 / 22 / 23 / 23 / 23 / 29 / 27 / 36 / Carbon Cycling / Carbon degradation / Starch
54 / oorA / 5 / 4 / 5 / 5 / 5 / 3 / 5 / 6 / 5 / 8 / Carbon Cycling / Carbon fixation / Reductive tricarboxylic acid cycle
55 / pcc / 264 / 262 / 259 / 249 / 244 / 228 / 256 / 261 / 257 / 311 / Carbon Cycling / Carbon fixation / multiple systems
56 / pcs / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 0 / 1 / Carbon Cycling / Carbon fixation / 3-hydroxypropionate bicycle
57 / pectinase (pectate_lyase) / 87 / 90 / 85 / 82 / 90 / 79 / 79 / 84 / 85 / 114 / Carbon Cycling / Carbon degradation / Pectin
58 / pgk / 112 / 108 / 111 / 99 / 105 / 99 / 109 / 110 / 108 / 136 / Carbon Cycling / Carbon fixation / Calvin cycle
59 / phenol_oxidase / 75 / 80 / 78 / 77 / 76 / 66 / 81 / 80 / 74 / 100 / Carbon Cycling / Carbon degradation / Lignin
60 / pme / 88 / 85 / 87 / 79 / 79 / 73 / 80 / 81 / 83 / 110 / Carbon Cycling / Carbon degradation / Pectin
61 / pmoa / 28 / 26 / 29 / 23 / 25 / 23 / 26 / 27 / 21 / 35 / Carbon Cycling / Methane / Methane oxidation
62 / PRI / 122 / 122 / 123 / 104 / 115 / 101 / 121 / 122 / 124 / 149 / Carbon Cycling / Carbon fixation / Calvin cycle
63 / PRK / 55 / 54 / 55 / 55 / 55 / 50 / 51 / 59 / 58 / 67 / Carbon Cycling / Carbon fixation / Calvin cycle
64 / pula / 102 / 102 / 103 / 93 / 100 / 91 / 100 / 105 / 98 / 134 / Carbon Cycling / Carbon degradation / Starch
65 / RgaE / 102 / 99 / 101 / 92 / 96 / 91 / 98 / 99 / 101 / 123 / Carbon Cycling / Carbon degradation / Pectin
66 / rgh / 9 / 8 / 8 / 6 / 8 / 8 / 8 / 8 / 6 / 9 / Carbon Cycling / Carbon degradation / Pectin
67 / rgl / 62 / 61 / 64 / 54 / 60 / 54 / 62 / 64 / 64 / 73 / Carbon Cycling / Carbon degradation / Pectin