Supporting Information
Colonization patterns of soil microbial communities in the
Atacama Desert
Alexander Crits-Christoph1, Courtney K. Robinson1, Tyler Barnum1, Jacques Ravel2, W.
Florian Fricke2, Alfonso F. Davila3, Bruno Jedynak4, Christopher P. McKay3, and
Jocelyne DiRuggiero1§
1. Supporting tables
Table S1 Relationships between geochemical properties of soil samples
Table S2 Geochemical elemental composition for sampling locations
Table S3 Observed richness and diversity indices for soil samples
Table S4 OTU0.03 distribution for soil samples
Table S5 Relationships between geochemical properties of soil samples and diversity
metrics; rarefaction to 200 sequence reads
Table S6 Relationships between geochemical properties of soil samples and diversity
metrics; rarefaction to 1000 sequence reads
Table S7 Relationships between climatic properties of locations and richness of
individual samples; rarefaction to 200 sequence reads
Table S8 Average pairwise comparisons of unweighted UniFrac distances
Table S9 Complete legend for Fig. 6
Table S10 Geochemical data for soil samples at each sampling locations
2. Supporting figures
Fig. S1 Rarefaction plot for soil samples for observed OTU0.03
Fig. S2 UPGMA tree of Brays-Curtis distances
Fig. S3 Weighted Unifrac PCoA of soil samples at the 200-rarefied level
Fig. S4 Unweighted Unifrac PCoA of soil samples at the 1000-rarefied level
1
Table S1 Least squares linear regression of relationships between geochemical properties
of soil samples. n=68, df=67
R2
P-value
F-statistic
Calcium - Sulfur
0.95
2.2*10 -16
1237
Calcium - Conductivity
0.57
6.8*10 -14
88.7
Sulfur - Conductivity
0.53
1.3*10 -12
75.6
Conductivity - pH
0.52
2.56*10 -12
72.9
Relationship
2
Table S2 Geochemical elemental composition for each of the sampling locations
mg/Kg
KEV
BEA
AND
AC
AL
CH
Al
11869.3
23284.6
10878.8
15241.7
25088
27139.1
P
449.804
454.763
305.8
351.636
187.38
410.638
S
24470.4
9015.24
25218.2
12822.1
3.2153
20.2606
Ti
825.703
776.127
564.827
620.543
1030.28
1336.7
Mn
302.707
233.749
226.204
206.567
285.457
740.471
Fe
11183.8
9033.78
7508.12
8053.37
11068.6
28160.9
Co
8.4956
7.0782
5.5602
5.9652
7.1411
11.6505
Ni
7.3453
4.9864
5.6167
3.2923
3.6797
8.8196
Cu
29.2693
16.5218
14.4056
10.356
19.466
29.0987
Mo
1.3011
0.606
1.9019
0
0
0
Pb
6.3392
0
8.5491
0
0
3.5397
Cd
0.3844
0
0.1684
0
0
0.4624
Na
1944.49
3233.12
2248.9
2908.57
3498.25
2928.54
Mg
3352.93
4348.49
1904.99
2430.13
4145.14
5945.87
K
8915.14
10165.6
11411.4
10916.9
10019.9
13826.7
As
19.2127
7.112
10.6275
7.1438
3.0507
11.7265
V
3.8391
3.3241
2.7425
2.6451
3.5957
6.6668
B
25.0691
20.531
23.1697
30.6514
27.3211
23.6669
Cr
9.9104
9.2551
6.4642
5.5455
6.9148
18.7349
Ca
34186.3
21308.2
33525.9
27244.9
9631.47
6013.74
Zn
39.9319
21.2633
30.7414
21.253
30.6441
63.8353
Sr
117.706
139.001
190.157
270.573
126.084
86.4081
Li
26.1064
18.8415
21.1482
16.5783
19.4658
34.5365
Be
0.3141
0.3571
0.4392
0.3728
0.0881
0.4759
Se
3.0983
3.2653
3.0666
3.0277
3.2768
2.701
Sb
16.7648
27.8552
15.1667
19.3896
29.5605
33.1499
Ba
465.471
364.441
548.939
375.768
254.439
320.091
3
Table S3 Observed richness and diversity indices for soil samples based on 16S rRNA
gene sequence assignments with a 97% sequence similarity threshold, rarefied to 200
sequence reads (n=68)
Samples
KEV
BEA
AND
AC
AL
CH
OTUs 0.03
Observed
Richness
28
43
35
71
115
114
Shannon
Index
Estimated
Diversity
2.5
3.9
3.6
5.3
6.4
6.4
Faith's
Phylogenetic
Diversity
Index
2.0
3.4
3.2
5.6
7.7
8.6
Chao1
Diversity
Estimate
Pielou's
Evenness
Index
52
81
57
129
270
256
0.53
0.71
0.70
0.87
0.94
0.93
Abbreviation: OTU, operational taxonomic units
Analysis using datasets of equal size subsampled at 200 sequence reads; average of 10 iterations
Table S4 OTU0.03 distribution for soil samples (n=48)
KEV
BEA
AND
AC
Total OTUs0.03
69
99
83
163
Doublet OTUs 0.03
10
15
11
27
Singleton OTUs 0.03
37
42
43
67
% Rare OTUs0.03
68.1
57.6
65.1
57.7
Analysis using dataset subsampled at 1000 reads; average of duplicates
AL
330
71
156
68.8
CH
282
61
131
68.1
Rare OTUs0.03: doublets contain 2 sequence reads; singletons contain one sequence read
Table S5 Least squares linear regression of relationships between geochemical properties
of soil samples and diversity metrics. n=68, df=66, rarefaction to 200 sequence reads
R2
P-value
F-statistic
Conductivity - OTUs0.03
0.72
2.2*10 -16
176.4
pH - OTUs0.03
0.61
3.7*10 -15
103.6
Conductivity - Shannon
0.68
2.2*10 -16
142.5
pH- Shannon
0.56
3.7*10 -15
85.4
Relationship
4
Table S6 Least squares linear regression of relationships between geochemical properties
of soil samples and diversity metrics. n=48, df=46, rarefaction to 1000 sequence reads
R2
P-value
F-statistic
Conductivity - OTUs0.03
0.60
5.4*10 -11
72.3
pH - OTUs0.03
0.51
6.0*10 -9
50.7
Conductivity - Shannon
0.58
2.5*10 -10
64.8
pH- Shannon
0.52
4.4*10 -9
52.0
Relationship
Table S7 Least squares linear regression of relationships between climatic properties of
locations and richness of individual samples within those locations. n=68, df=66,
rarefaction to 200 sequence reads
Relationship
F-statistic
R2
P-value
Mean Rainfall - OTUs 0.03
308
0.82
2.2*10 -16
Mean Temp. - OTUs0.03
326
0.83
2.2*10 -16
Mean air RH - OTUs0.03
311
0.82
2.2*10 -16
Table S8 Average pairwise comparisons of unweighted UniFrac distances between
samples from each location at the rarefied 200-sequence level (n=68). The distances of
each sample to itself were not included in the calculation
AC
AL
AND
BEA
CH
KEV
AC
0.632
0.669
0.702
0.692
0.673
0.749
AL
0.669
0.592
0.761
0.732
0.626
0.793
AND
0.702
0.761
0.675
0.694
0.755
0.721
BEA
0.692
0.732
0.694
0.671
0.727
0.694
CH
0.673
0.626
0.755
0.727
0.598
0.775
KEV
0.749
0.793
0.721
0.694
0.775
0.662
5
Table S9 Legend for Fig. 6; abundance goes from low (top) to high (bottom)
6
Table S10 Geochemical data for soil samples at each sampling locations
sample name
AND A0-0
AND A50-0
AND B0-0
AND B50-0
AND A0-5
AND B10-5
AND B30-5
AND B50-5
AND A50-10
AND B10-10
AND B50-10
BEA A0-0
BEA A10-0
BEA A50-0
BEA B0-0
BEA B30-0
BEA B50-0
BEA-A5
BEA-B5
BEA A0-5
BEA A10-5
BEA A50-5
BEA B20-5
BEA-B10
BEA A0-10
BEA A10-10
BEA A30-10
BEA A50-10
BEA B30-10
KEV A0-0
KEV A10-0
KEV A20-0
KEV A30-0
KEV A40-0
KEV A50-0
KEV B0-0
KEV B10-0
KEV B20-0
KEV B40-0
KEV B10-5
KEV B20-5
KEV B40-5
KEV A50-10
KEV B10-10
KEV B20-10
AL-A5
AL-B5
AL-C5
AL-A10
AL-B10
AL-C10
AL-A20
AL-B20
AL-C20
CH-A5
CH-B5
CH-C5
CH-A10
CH-B10
CH-C10
CH-A20
CH-B20
CH-C20
AC-A5
AC-B5
AC-C5
AC-A10
AC-B10
AC-C10
sampling depth
cm
0
0
0
0
5
5
5
5
10
10
10
0
0
0
0
0
0
0
0
5
5
5
5
5
10
10
10
10
10
0
0
0
0
0
0
0
0
0
0
5
5
5
10
10
10
0
0
0
5
5
5
10
10
10
0
0
0
5
5
5
10
10
10
0
0
0
5
5
5
pH
7.5
7.4
7.8
7.4
7.9
7.8
7.9
7.8
7.9
7.9
8.0
7.0
8.0
6.8
7.1
7.0
7.5
6.9
7.8
7.9
8.5
7.7
8.0
8.0
7.5
7.9
7.8
7.7
7.9
7.2
7.2
7.2
7.3
7.2
7.2
7.0
6.6
7.4
7.1
7.8
7.9
7.9
7.8
7.9
7.9
9.1
8.4
8.6
9.4
8.9
8.9
9.2
8.9
9.1
8.9
9.1
9.2
8.9
9.3
9.4
8.9
9.4
9.3
7.7
7.8
7.5
7.5
7.8
8.3
conductivity
mS.cm -1
2.45
2.32
0.65
2.21
2.03
2.06
2.14
2.14
2.06
2.04
2.15
2.10
0.18
2.88
2.31
1.75
3.05
1.54
1.56
0.93
0.20
2.15
1.59
2.36
2.09
1.42
1.18
2.19
1.39
3.04
2.28
2.62
2.52
2.49
2.71
2.55
1.74
2.38
2.48
2.00
2.24
2.09
2.11
1.62
2.15
0.12
0.03
0.04
0.04
0.02
0.02
0.03
0.02
0.02
0.07
0.06
0.06
0.03
0.04
0.09
0.04
0.19
0.19
1.56
0.06
0.28
2.21
0.90
0.15
In bold, samples from 2011; naming strategy different than from 2008
7
400
Rarefac on Mesaure: observed OTUs
CH
350
AL
AC
300
BEA
AND
250
KEV
200
150
100
50
0
0
100
200
300
400
500
600
700
800
900 1000
Sequences per Samples
Fig. S1 Rarefaction plot for soil samples for observed OTU0.03 rarefied to the 1000
sequence level (n=48).
8
AND.A0.0
AND.B0.0
AND.B50.0
AND.A50.0
BEA.A10.0
BEA.A0.0
BEA.B0.0
BEA.B30.0
BEA.B50.0
BEA.A50.0
KEV.A50.0
KEV.A40.0
KEV.B10.0
KEV.A20.0
KEV.B0.0
KEV.B40.0
KEV.A10.0
KEV.B20.0
KEV.A30.0
KEV.A0.0
BEA.A5
BEA.A0.5
KEV.A50.10
KEV.B20.10
KEV.B40.5
KEV.B20.5
AND.B50.5
BEA.A50.5
BEA.A10.5
AND.B10.5
AND.B30.5
AND.B10.10
AND.A50.10
BEA.A50.10
AND.B50.10
AND.A0.5
KEV.B10.5
AC.A10
AC.A5
AC.C5
AL.A5
BEA.B10
BEA.B5
KEV.B10.10
BEA.B30.10
BEA.B20.5
BEA.A30.10
BEA.A10.10
BEA.A0.10
AC.C10
AC.B10
CH.A5
CH.C5
CH.B5
CH.C20
CH.C10
CH.B20
CH.B10
AL.B5
AL.C5
AL.C10
AL.A10
CH.A20
CH.A10
AL.B10
AL.C20
AL.A20
AL.B20
North locations
Central location
*
North locations
Central location
South locations
0.05
Fig. S2 β-diversity analysis of soil microbial communities. UPGMA tree of Brays-Curtis
distances for rarefied 200-sequence reads (n=68) based on OTUs0.03 relative abundance
with geographic location of each samples, North (KEN, BEA, AND), Central (AC), and
South (AL, CH). Scale bar represents 0.05% sequence divergence. *sample from a south
location in a central location cluster.
9
a
c
b
d
Fig. S3 Weighted Unifrac Principal Coordinate Analyses (PCoA) of samples at the 200rarefied level (n=48) using QIIME. (a) PCoA color coded by conductivity values (low
conductivity: red, average: white, high: blue), and (b) the same plot detrended with
QIIME. (c) PCoA color coded by relative air humidity values (high humidity: blue,
average: white, low: red), and (c) the same plot detrended with QIIME.
10
a
c
b
d
Fig. S4 Unweighted Unifrac Principal Coordinate Analyses (PCoA) of samples at the
1000-rarefied level (n=48), calculating using QIIME. (a) PCoA color coded by
conductivity values (low conductivity: red, average: white, high: blue), and (b) the same
plot detrended with QIIME. (c) PCoA color coded by relative air humidity values (high
humidity: blue, average: white, low: red), and (c) the same plot detrended with QIIME.
11