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Title: Invariant community structure of soil bacteria in subtropical coniferous and
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broadleaved forests
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Authors: Xiaoli Wang1, 2, Xiaoling Wang1, Weixin Zhang1, Yuanhu Shao1, Xiaoming
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Zou1,3,Tao Liu1, 2, Lixia Zhou1, Songze Wan1, Xingquan Rao1, Zhian Li1, Shenglei Fu1,*
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Affiliations:
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1Key
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South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650,
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China;
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2 University
Laboratory of Vegetation Restoration and Management of Degraded Ecosystems,
of Chinese Academy of Sciences, Beijing 100049, China;
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San Juan, PR 00936-8377, USA.
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*Corresponding author: Prof. Dr. Shenglei Fu
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Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems,
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South China Botanical Garden, Chinese Academy of Sciences,
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No. 723, Xingke Road, Tianhe District, Guangzhou 510650, China
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E-mail address: sfu@scbg.ac.cn; Tel.: +86 20 37252722; Fax: +86 20 37252831.
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Type of contribution: Original Research;
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Date of resubmission: Nov 15, 2015
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Number of text pages: 29; Number of words: 6209
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Number of tables: 2
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Number of figures: 6
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Number of supplementary materials: 8
Department of Environmental Sciences, University of Puerto Rico, P.O. Box 70377,
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Running title: Invariant bacterial composition in contrasting forests
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Table S1 | the average distribution of partial sequences of bacterial 16S rRNA gene at genus level from the
broadleaved (n1=6) and coniferous forests (n2=6). Proportions were calculated based on the pooled sequences
classified with 80% confidence threshold. Genus accounting for <0.01% of all classified sequences were not shown in table.
Significant effects are shown in bold by independent-sample t-tests (n1=6; n2=6, df=10; P<0.05).
No.
Broadleaved Forests
Genus name
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
Acetobacteraceae;Other
Acidimicrobiales;Other
Acidisoma
Aciditerrimonas
Acidobacteria;Gp1
Acidobacteria;Gp13
Acidobacteria;Gp14
Acidobacteria;Gp2
Acidobacteria;Gp3
Acidobacteria;Gp4
Acidobacteria;Gp6
Acidobacteria;Gp7
Actinoallomurus
Actinobacteria;Other
Actinomadura
Actinomycetales;Other
Actinospica
Alicyclobacillus
Alphaproteobacteria;Other
Aminomonas
relative
abundance
0.53%
0.80%
0.23%
0.28%
16.67%
0.25%
0.02%
10.28%
5.87%
0.05%
0.17%
0.03%
3.27%
0.10%
0.25%
0.85%
6.57%
1.15%
0.60%
0.22%
Coniferous Forests
Genus name
Acetobacteraceae;Other
Acidimicrobiales;Other
Acidisoma
Aciditerrimonas
Acidobacteria;Gp1
Acidobacteria;Gp13
Acidobacteria;Gp14
Acidobacteria;Gp2
Acidobacteria;Gp3
Acidobacteria;Gp4
Acidobacteria;Gp6
Acidobacteria;Gp7
Actinoallomurus
Actinobacteria;Other
Actinomadura
Actinomycetales;Other
Actinospica
Alicyclobacillus
Alphaproteobacteria;Other
Aminomonas
T-test
relative
abundance
0.33%
0.97%
0.28%
0.33%
15.90%
0.12%
0.01%
6.85%
7.57%
0.08%
0.12%
0.12%
2.45%
0.43%
0.17%
1.02%
5.43%
0.03%
0.40%
0.05%
P
0.371
0.530
0.743
0.604
0.804
0.136
0.341
0.043
0.404
0.661
0.629
0.425
0.370
0.179
0.399
0.607
0.726
0.057
0.512
0.094
3
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
Anaeromyxobacter
Arthrobacter
Bacillus
Bacteria;Other
Betaproteobacteria;Other
Blastopirellula
Bradyrhizobiaceae;Other
Bradyrhizobium
Burkholderia
Burkholderiales_incertae_sedis;Other
Catenulispora
Chitinophagaceae;Other
Chloroflexi;Other
Chromatiales;Other
Chryseobacterium
Clostridia;Other
Conexibacter
Cystobacteraceae;Other
Deltaproteobacteria;Other
Dyella
Ferrimicrobium
Ferruginibacter
Firmicutes;Other
Flavitalea
Gammaproteobacteria;Other
Gemmata
Gemmatimonas
Haliangium
Ktedonobacter
Ktedonobacterales;Other
Ktedonobacteria;Other
0.08%
0.83%
0.45%
1.88%
0.20%
0.10%
0.28%
0.68%
0.88%
0.07%
0.62%
0.47%
1.42%
2.70%
0.01%
0.30%
0.48%
0.02%
0.72%
0.52%
0.17%
0.10%
6.07%
0.08%
1.03%
0.85%
0.52%
0.05%
2.87%
0.18%
0.07%
Anaeromyxobacter
Arthrobacter
Bacillus
Bacteria;Other
Betaproteobacteria;Other
Blastopirellula
Bradyrhizobiaceae;Other
Bradyrhizobium
Burkholderia
Burkholderiales_incertae_sedis;Other
Catenulispora
Chitinophagaceae;Other
Chloroflexi;Other
Chromatiales;Other
Chryseobacterium
Clostridia;Other
Conexibacter
Cystobacteraceae;Other
Deltaproteobacteria;Other
Dyella
Ferrimicrobium
Ferruginibacter
Firmicutes;Other
Flavitalea
Gammaproteobacteria;Other
Gemmata
Gemmatimonas
Haliangium
Ktedonobacter
Ktedonobacterales;Other
Ktedonobacteria;Other
0.08%
0.47%
0.05%
2.67%
0.27%
0.03%
0.18%
1.02%
1.80%
0.20%
1.58%
0.60%
0.97%
2.82%
0.27%
0.53%
1.02%
0.23%
0.32%
0.15%
0.22%
0.02%
4.30%
0.10%
1.00%
0.72%
0.57%
0.10%
2.60%
0.43%
0.25%
1.000
0.687
0.068
0.241
0.755
0.341
0.416
0.129
0.324
0.358
0.342
0.508
0.220
0.896
0.341
0.467
0.093
0.259
0.314
0.395
0.411
0.341
0.479
0.868
0.950
0.810
0.799
0.568
0.785
0.016
0.003
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53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
Leifsonia
Massilia
Methylocystaceae;Other
Mucilaginibacter
Mycobacterium
Myxococcales;Other
Nocardia
Others
Pedomicrobium
Perlucidibaca
Phenylobacterium
Planctomyces
Planctomycetaceae;Other
Planctomycetes;Other
Proteobacteria;Other
Ramlibacter
Rhizobiales;Other;Other
Rhizomicrobium
Rhodanobacter
Rhodospirillaceae;Other
Rhodospirillales;Other
Rugosimonospora
Selenomonadales;Other
Singulisphaera
Sinomonas
Skermanella
Solirubrobacterales;Other
Stenotrophomonas
Steroidobacter
Streptacidiphilus
Streptomyces
0.02%
0.43%
0.38%
0.17%
2.10%
0.35%
0.68%
1.28%
0.13%
0.08%
4.68%
0.15%
0.72%
0.20%
0.20%
0.02%
2.70%
0.68%
0.27%
1.50%
0.25%
0.02%
0.02%
0.18%
0.01%
0.07%
0.08%
0.01%
0.37%
5.92%
0.01%
Leifsonia
Massilia
Methylocystaceae;Other
Mucilaginibacter
Mycobacterium
Myxococcales;Other
Nocardia
Others
Pedomicrobium
Perlucidibaca
Phenylobacterium
Planctomyces
Planctomycetaceae;Other
Planctomycetes;Other
Proteobacteria;Other
Ramlibacter
Rhizobiales;Other;Other
Rhizomicrobium
Rhodanobacter
Rhodospirillaceae;Other
Rhodospirillales;Other
Rugosimonospora
Selenomonadales;Other
Singulisphaera
Sinomonas
Skermanella
Solirubrobacterales;Other
Stenotrophomonas
Steroidobacter
Streptacidiphilus
Streptomyces
0.10%
1.62%
0.23%
0.33%
1.50%
0.43%
0.70%
2.22%
0.05%
0.02%
3.13%
0.08%
0.98%
0.38%
0.30%
0.18%
2.20%
0.48%
0.01%
1.25%
0.13%
0.63%
0.15%
0.30%
0.35%
0.08%
0.27%
0.92%
0.28%
7.40%
0.03%
0.341
0.479
0.083
0.365
0.477
0.381
0.967
0.429
0.399
0.217
0.477
0.493
0.582
0.197
0.418
0.336
0.558
0.231
0.268
0.504
0.262
0.295
0.046
0.246
0.286
0.721
0.049
0.341
0.678
0.619
0.145
5
83
84
85
86
87
88
89
90
Synergistaceae;Other
Syntrophaceticus
Thermoanaerobacteraceae;Other
Thermogemmatispora
Thermoleophilum
Thermomonosporaceae;Other
Tumebacillus
Zavarzinella
0.12%
0.37%
0.42%
0.03%
0.02%
0.77%
1.13%
0.27%
Synergistaceae;Other
Syntrophaceticus
Thermoanaerobacteraceae;Other
Thermogemmatispora
Thermoleophilum
Thermomonosporaceae;Other
Tumebacillus
Zavarzinella
0.07%
0.62%
0.37%
0.17%
0.13%
2.28%
0.57%
0.18%
0.535
0.329
0.885
0.049
0.272
0.179
0.535
0.658
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Table S2 | Model summary and ANOVA of the regression for bacterial
biomass at the site scale (n=60) and the regional scale (n = 180). pHwater, STN,
LTN, SOC, LOC, and SMC stand for soil pH, soil total nitrogen, litter total nitrogen,
soil organic carbon, litter organic carbon and soil moisture content, respectively.
Sites
ALS
Dependent
variables
Bacteria
GramGram+
DMS
Gram+/GramBacteria
GramGram+
Gram+/GramDHS
Regional
Scale
Bacteria
GramGram+
Gram+/GramBacteria
GramGram+
Gram+/Gram-
Model
predictors
R2
F
P
1
2
3
1
1
2
1
1
2
3
1
2
1
2
1
2
1
SOC
SOC:STN
LOC
SMC
SMC
SOC
SMC
LTN
LOC: LTN
SOC
STN
LOC
STN
LOC
SOC:STN
LOC
pHwater
0.477
0.534
0.619
0.787
0.836
0.863
0.702
0.801
0.864
0.878
0.495
0.553
0.521
0.554
0.245
0.332
0.258
52.824
32.662
30.319
214.684
296.372
178.878
136.900
233.911
180.916
134.586
56.800
35.272
63.035
35.405
18.809
14.177
20.208
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
1
1
n.s.
1
2
3
4
5
1
2
1
2
1
2
STN
STN
n.s.
SOC
LOC
LTN
pH
SOC:STN
STN
SOC
SMC
LTN
SMC
pH
0.205
0.134
n.s.
0.215
0.271
0.316
0.369
0.407
0.524
0.540
0.775
0.796
0.450
0.605
14.997
8.939
n.s.
48.692
32.875
27.114
25.553
23.865
195.999
104.056
613.494
344.646
145.527
135.526
0.000
0.004
n.s.
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
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Table S3 | The general characteristics of the three pairs of forest ecosystems in the south subtropical region of China.
Sites
Temperature
(°C)
Precipitation
(mm)
Longitude & Latitude
Altitude (m)
ALS-BF
11.3
1931
24°32'N,102°01'E
2400–2600
ALS-CF
18.7
1103
24°16'N,100°48'E
1500-2000
DMS-BF
14.7
2746
23°24'N,108°31'E
355-365
DMS-CF
15.1
2630
23°24'N,108°31'E
175-365
DHS-BF
20.9
1927
23°10'N,112°31'E
250-300
DHS-CF
21.4
1927
23°10'N,112°31'E
90-115
Soil Types
Typically
yellow-brown
Mountain
yellow red
Yellow
podzolic
Mountain
yellow
Hydration
lateritic
Hydration
lateritic
Dominant
Tree species
Lithocarpus
xylocarpu
Pinus kesiya var.
langbianesnis
Quercus griffithii
Hook. f. et Thoms
ex Miq
Pinus massoniana
Cryptocarya
concinna Hance
Pinus massoniana
Dominant
understory species
Sinarundinaria nitida
Eupatorium
adenophora
Indocalamus
tessellatus
Dicranopteris
dichotoma
Psychotria rubra
Evodia
lepta(Spreng.)Merr.
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Figure S1| Rarefaction curves of high-throughput sequencing data of the
samples from the broadleaved forests and the coniferous forests.
1200
Coniferous Forests
Broadleaved Forests
Rarefaction measure: observed species
1000
800
600
400
200
0
0
1000
2000
3000
4000
Numbers of sequences per sample
5000
6000
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Figure S2| Principal coordinates analysis (PCoA) of bacterial community
based on high-throughput sequencing data in the subtropical coniferous
and broadleaved forests. The values for Axes 1 and 2 are percentages of
variation attributed to the corresponding axis. Solid circles represent samples of
the broadleaved forests, and solid triangle represent samples of the coniferous
forests. The blue color represents ALS site, the orange color represents DMS site,
and the red color represents DHS site.
PCoA_PC1 vs PC2
PC2-Percent variations explained 15.47%
0.4
0.3
0.2
0.1
0.0
-0.1
-0.2
-0.3
-0.4
-0.4
-0.3
-0.2
-0.1
0.0
0.1
0.2
0.3
PC1-Percent variations explained 44.52%
0.4
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Figure S3| Redundancy analysis (RDA) of PLFA profiles for soil samples
using 8 microbial group PLFAs and 9 environmental parameters at the site
scale. Blue line vectors represent microbial variables: bacterial PLFA biomarkers.
Red line vectors represent environmental variables: Soil moisture content (SMC),
soil organic carbon (SOC), soil total nitrogen (STN), the ratio of soil organic
carbon to soil total nitrogen (SOC: STN), pH water (pH), litter organic carbon
(LOC), litter total nitrogen (LTN), litter storage (LS) and the ratio of litter organic
carbon to litter total nitrogen (LOC: LTN). (A) The bacterial communities and the
environment factors at the ALS site, n = 60; (B) The bacterial communities and the
environment factors at the DMS site, n = 60; (C) The bacterial communities and
the environment factors at the DHS site, n = 60.
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Figure S4| Location of nine paired coniferous and broadleaved forests from three study sites in subtropical China. The
original map was from Data Sharing Infrastructure of National Administration of Surveying, Mapping and Geoinformation of
China. This figure was generated by using Adobe Illustrator CS6 software from Adobe Company (San Jose, California,
USA).
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Figure S5| the diagrammatic sketch of experimental design and sampling. The total number of samples for each of the nine
forest pairs was 180: namely, 3 sites * 2 forest types * 3 replicated plots * 5 subplots * 2 seasons. The 180 samples were used to
determinate the bacterial biomass by using PLFAs. We extracted 180 DNA samples and then mixed these 180 DNA samples into
12 composite samples, namely, 2 seasons * 3 sites * 2 forest types. The 12 composite samples were used to determinate the
bacterial composition by using 16S pyro-sequencing. The 12 composite samples were named Dry-ALS-CF, Dry-ALS-BF,
Dry-DMS-CF, Dry-DMS-BF, Dry-DHS-CF, Dry-DHS-BF, Wet-ALS-CF, Wet-ALS-BF, Wet-DMS-CF, Wet-DMS-BF, Wet-DHS-CF,
and Wet-DHS-BF, respectively. ALS, DMS, DHS, Dry, Wet, CF, and BF are the abbreviations of Ailaoshan, Damingshan,
Dinghushan, Dry season, Wet season, Coniferous forest, Broadleaved forest, respectively.
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