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Supplementary Information
Supplementary Figure 1-3
Supplementary Table 1-9

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(A) 16S rRNA genes (Bacteria)
(B) ITS (Fungi)
(C) nifH genes (N fixers)
Supplementary Fig. 1. Rarefaction analysis of OTUs at different taxonomic resolutions.
97%
99%
95%
97%
95%
97%

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Supplementary Fig. 2. Relationships between taxon richness and several other soil and climate
variables. Line represents least squares regression fit and shaded area represents 95% confidence. The
relationships of taxon richness with temperature, pH and moisture were seen in Fig. 1. The relationships of
microbial biodiversity (taxon richness, Shannon diversity and phylogenetic diversity) to all soil, climate and
plants were summarized in Table S5.

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Supplementary Fig. 3. Relationships between taxon richness of individual samples and temperature. The
sequences of individual samples in a site were used for estimating theoretical Chao1 value for a given sample at
the taxonomic resolution of 97%. The natural log of the estimated Chao1 values of individual samples were
calculated for examining the relationships between taxon richness and temperature, which was expressed as the
inverse of annual mean temperature in degree of Kelvin. Line represents least squares regression fit and the shaded
area represents their 95% confidence limits (A) Bacteria based on16S rRNA gene; (B) Fungi based on ITS; and
(C) N fixers based on nifH gene. The relationships between microbial taxon richness of individual sites and
temperature were seen in Fig. 3.

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Supplementary Table 1. Summary of soil and climate characteristics for the 6 sampling sites.
Sitesa
Latitude
Elevation
(m)
Mean
temperature
(°C)
Precipitation
(mm)
Soil
moistureb
(%)
Soil pH
Total
carbon
content
(mg/g)
Total
nitrogen
content
(mg/g)
Plant
species
numberc
BCI
9.16
157
25.71
2383.0
31.43±6.77
5.87±0.42
3.99±2.09
0.31±0.12
263
LUQ
18.32
386
23.62
3069.2
40.53±4.42
5.06±0.39
7.54±3.05
0.47±0.17
93
CWT
35.05
864
12.62
1853.8
30.28±6.05
4.72±0.37
6.68±4.07
0.25±0.08
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AND
44.23
860
8.94
1587.4
36.88±13.79
5.28±0.64
19.36±13.87
0.40±0.18
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HFR
42.54
356
8.27
1128.7
34.35±10.45
3.84±0.29
19.21±8.60
0.62±0.29
25
NWT
40.04
3,186
2.50
481.6
16.00±8.74
4.83±0.37
11.46±7.03
0.33±0.18
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aThe symbols for these sites are: BCI, Barro Colorado Island, Panama; LUQ: Luquillo, El Yunque National
Forest, Puerto Rico; CWT: Coweeta Hydrological Laboratory, North Carolina; AND: H.J. Andrews
Experimental Forest, Oregon; HFR: Harvard Forest, Massachusetts; NWT: Niwot Ridge, Colorado.
bAverage individual soil variables (moisture, pH, total C and N) over 21 samples.
cPlant species is the total of five 0.1 ha Gentry plots within the 25 ha plot at each site.

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Supplementary Table 2. Pairwise Pearson correlations (r values, n=6) between major soil and site
variables. For the soil variables, the site averages among 21 samples were used for calculating correlations.
Elevation
Mean
temperature
Precipitation
Soil
moisture
Soil
pH
Total
carbon
Total
nitrogen
Plant
richness
Latitude
0.447
-0.934**
-0.774
-0.252
-0.656
0.816*
0.252
-0.916**
Elevation
-0.706
-0.722
-0.876*
-0.106
0.088
-0.320
-0.511
Mean
temperature
0.929**
0.571
0.587
-0.673
-0.106
0.852*
Precipitation
0.740
0.482
-0.551
-0.044
0.608
Soil moisture
0.057
0.127
0.452
0.197
Soil pH
-0.550
-0.612
0.690
Total carbon
0.648
-0.688
Total nitrogen
-0.282
* p<0.05
** p<0.01
*** p<0.001

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Supplementary Table 3. Summary of sequence statistics
MiSeq sequencing
Targets
Total base pairs
(bp)
bp per sample
Total No. of reads
Average No. of
reads per sample
16S-rRNA gene
Soil bacteria +
archaea*
2.05 G
16.3 M
8.10 M
64±18 K
ITS (internal
transcribed spacer)
Soil fungi
1.39 G
11.0 M
4.94 M
39±11 K
nifH (nitrogenase
subunit H)
Nitrogen fixing
bacteria
1.17 G
9.3 M
3.75 M
30±9 K
*Very small percentages of sequences from Archaea were obtained.

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Supplementary Table 4. OTU classifications at different cutoffs.
Gene targets
Similarity thresholds
No of OTUs without resamplinga
No of OTUs with resamplingb
16S
0.97
257,867
188,620
0.99
789,214
524,047
ITS
0.95
13,762
12,942
0.97
18,442
17,239
nifH
0.95
102,941
87,938
0.97
160,082
133,192
aEstimated numbers of OTUs based on all sequences obtained, without resampling.
bEstimated numbers of OTUs after sampling the minimum numbers of sequences from each sample. The minimum numbers of
sequences resampled are 25,901 for 16S rRNA genes, 13,688 for ITS and 16,000 for nifH.

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Supplementary Table 5. Changes of microbial biodiversity with latitudes. The changes of taxon richness
and Shannon diversity with latitudes were fitted with the linear model: y=a + bx. The significance of the
relationships was evaluated based correlation (r) and probability (p) values.
Taxonomic groupsa
Taxon richness
Shannon diversity
r
p
r
p
Bacteria (16S rRNA)
-0.550
2.6x10-11
-0.389
6.9x10-6
Fungi (ITS)
-0.744
< 2.2x10-16
-0.454
9.3x10-8
Nitrogen fixers (nifH)
-0.808
< 2.2x10-16
-0.746
< 2.2x10-16
aThe taxonomic resolution used in this analysis is 97% for 16S rRNA gene and ITS, and 95% for nifH gene.

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Supplementary Table 6. Summary of determination coefficients (R2) from fitting a linear univariate
model(y=a + bx) for predicting microbial biodiversity (taxon richness, Shannon diversity, phylogenetic
diversity) as a function of various site and soil variables. Taxon richness, and Shannon diversity were calculated
based on the observed sequences after resampling. Since the relative roles of pH and temperature on controlling
microbial communities are controversial, their values were particularly bolded in the Tables.
(A) Taxon richness
Variables
16S (97%)
ITS (97%)
nifH (95%)
R2
AIC
R2
AIC
R2
AIC
Latitude
0.30
2161.9
0.55
1656.4
0.65
1986.5
Elevation
0.22
2175.3
0.14
1738.8
0.17
2096.7
Annual average Temperature
0.41
2141.8
0.48
1675.5
0.63
1994.8
Annual precipitation
0.39
2144.8
0.27
1718.5
0.49
2034.6
Soil moisture
0.20
2179.2
0.01
1756.4
0.13
2103.2
pH
0.35
2152.8
0.40
1693.7
0.34
2067.4
Total Carbon
0.12
2190.9
0.44
1685.6
0.28
2077.9
Total Nitrogen
0.04
2202.6
0.18
1733.6
0.00
2119.7
Plant richness
0.30
2162.0
0.65
1626.0
0.51
2030.6
(B) Shannon diversity
Variables
16S (97%)
ITS (97%)
nifH (95%)
R2
AIC
R2
AIC
R2
AIC
Latitude
0.15
89.4
0.21
270.3
0.56
303.6
Elevation
0.21
80.7
0.01
297.7
0.13
388.3
Annual average temperature
0.28
68.5
0.16
278.1
0.53
312.3
Annual precipitation
0.37
50.9
0.09
287.4
0.39
344.5
Soil moisture
0.29
66.5
0.00
299.3
0.11
391.5
pH
0.19
84.1
0.20
271.1
0.35
350.9
Total carbon
0.04
105.0
0.23
265.7
0.18
381.8
Total nitrogen
0.00
109.6
0.16
277.8
0.00
406.2
Plant richness
0.11
95.7
0.22
268.7
0.46
328.8

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(C) Inverse Simpson diversity
Variables
16S (97%)
ITS (97%)
nifH (95%)
R2
AIC
R2
AIC
R2
AIC
Latitude
0.00
1817.0
0.19
1129.5
0.56
1400.3
Elevation
0.07
1807.7
0.01
1155.0
0.14
1485.0
Annual average temperature
0.05
1811.2
0.14
1137.0
0.52
1411.6
Annual precipitation
0.18
1792.6
0.08
1145.5
0.37
1445.6
Soil moisture
0.24
1782.6
0.00
1156.5
0.08
1492.7
pH
0.00
1817.1
0.15
1136.5
0.28
1461.8
Total carbon
0.00
1817.3
0.20
1129.1
0.23
1470.2
Total nitrogen
0.04
1812.0
0.09
1144.3
0.00
1503.7
Plant richness
0.02
1815.0
0.19
1130.6
0.46
1426.1
(D) Faith’s phylogenetic diversity
Variables
16S (97%)
ITS (97%)
nifH (95%)*
R2
AIC
R2
AIC
R2
AIC
Latitude
0.36
1383.7
0.69
1280.7
0.04
1444.3
Elevation
0.23
1408.2
0.23
1394.7
0.00
1449.7
Annual average temperature
0.47
1361.9
0.65
1296.2
0.04
1444.3
Annual precipitation
0.44
1367.9
0.42
1360.1
0.04
1444.6
Soil moisture
0.20
1413.0
0.06
1420.4
0.02
1447.9
pH
0.43
1370.8
0.43
1356.4
0.14
1431.4
Total carbon
0.16
1418.9
0.48
1345.7
0.00
1449.6
Total nitrogen
0.05
1433.9
0.13
1410.4
0.00
1449.7
Plant richness
0.36
1384.9
0.74
1255.6
0.04
1445.4
*The phylogenetic diversity of nifH gene fits poorly with all variables. Most likely, this is due to the difficulty in
obtaining reliable sequence alignments for constructing phylogenetic tree to calculate phylogenetic diversity.

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(E) NRI phylogenetic diversity
Variables
16S
ITS
nifH
R2
AIC
R2
AIC
R2
AIC
Latitude
0.48
569.7
0.26
457.2
0.64
473.1
Elevation
0.19
625.8
0.14
477.2
0.18
574.7
Annual average temperature
0.53
556.7
0.28
453.7
0.60
485.9
Annual precipitation
0.47
572.4
0.24
460.6
0.44
526.9
Soil moisture
0.18
627.0
0.09
484.2
0.08
589.9
pH
0.45
577.1
0.01
494.7
0.16
578.1
Total carbon
0.17
627.6
0.14
477.2
0.40
535.5
Total nitrogen
0.02
649.7
0.02
493.7
0.01
599.4
Plant richness
0.41
585.9
0.16
474.6
0.48
518.2

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Supplementary Table 7. Summary of determination (R2) coefficients from fitting a non-linear univariate
model(y=a+bx+cx2) for predicting microbial biodiversity (taxon richness, diversity) as a function of pH and
temperature
(A) Taxon richness
Variables
16S (97%)
ITS (97%)
nifH (95%)
R2
AIC
R2
AIC
R2
AIC
Annual average
temperature
0.41
2142.7
0.51
1671.4
0.71
1966.2
Soil pH
0.36
2151.5
0.51
1669.3
0.40
2058.1
(B) Shannon index
Variables
16S (97%)
ITS (97%)
nifH (95%)
R2
AIC
R2
AIC
R2
AIC
Annual average
temperature
0.32
62.8
0.18
277.1
0.65
277.3
Soil pH
0.19
86.0
0.21
272.3
0.43
337.5
(C) Inverse Simpson index
Variables
16S (97%)
ITS (97%)
nifH (95%)
R2
AIC
R2
AIC
R2
AIC
Annual average
temperature
0.15
1798.41
0.17
1134.89
0.61
1388.30
Soil pH
0.08
1808.52
0.15
1137.48
0.36
1448.88
(D) ln(Faith’s phylogenetic diversity)
Variables
16S (97%)
ITS (97%)
nifH (95%)*
R2
AIC
R2
AIC
R2
AIC
Annual average
Temperature
0.47
1363.4
0.67
1291.9
0.08
1441.8
Soil pH
0.44
1369.2
0.56
1326.0
0.14
1433.4
*The phylogenetic diversity of nifH gene fits poorly with all variables. Most likely, this is due to the difficulty in
obtaining reliable sequence alignments for constructing phylogenetic tree to calculate phylogenetic diversity.
(E) ln(NRI phylogenetic diversity)
Variables
16S (97%)
ITS (97%)
nifH (95%)*
R2
AIC
R2
AIC
R2
AIC
Annual average
Temperature
0.55
552.7
0.29
455.4
0.63
477.0
Soil pH
0.47
572.8
0.05
491.7
0.23
569.0

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Supplementary Table 8. Summary of multiple linear regressions by including additional environmental or
plant variables beyond temperature based on observed OTU richness.
Model
16S
ITS
nifH
AIC
R2
AIC
R2
AIC
R2
richness ~ temperature
2141.84
0.41
1675.49
0.48
1994.82
0.63
richness ~ temperature+ precipitation
2142.06
0.41
1646.41
0.59
1993.64
0.64
richness ~ temperature+ pH
2127.36
0.48
1657.02
0.56
1989.34
0.65
richness ~ temperature+ pH + precipitation
2123.65
0.50
1633.54
0.64
1989.72
0.66
richness ~ temperature+ pH + precipitation +
plant richness
2121.70
0.52
1621.91
0.68
1961.63
0.73
richness ~ temperature+ pH + precipitation +
plant richness + total carbon + total nitrogen
2118.08
0.54
1614.83
0.70
1960.97
0.73

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Supplementary Table 9. Summary of the fitting results to different statistical models to evaluate the
relationships between temperature and taxa richness estimated with Chao1.
Model
16S
ITS
nifH
AIC
R2
AIC
R2
AIC
R2
Linear
-191.36
0.42
-212.99
0.42
-88.47
0.61
Quadratic polynomial
-190.17
0.42
-211.44
0.42
-100.20
0.65
Piecewise relationship
-*
-
-
-
-102.44
0.66
* There is no turnover point observed