Supplemental Information
Phylogenetic community composition changes under global change
manipulation
For both fungi and bacteria, the phylogenetic composition of communities
subjected to drought stress differed significantly from undisturbed communities
(Table S3). Nitrogen fertilization was also a significant determinant of fungal
phylogenetic composition, although the effect was not significant when
phylogenetic distinction was “weighted” by sequence abundance. Nitrogen
fertilization did not significantly impact bacterial phylogenetic composition.
Drought manipulations significantly decreased the diversity of microbes in
leaf litter (Table S3). Fungal and Bacterial taxon diversity estimates (the number
of taxa) as well as phylogenetic diversity (cumulative branch length of community
members) estimates were significantly lower in drought treated plots compared to
controls (phylogenetic diversity of bacteria only marginally so). Nitrogen
fertilization significantly impacted fungal taxon diversity, but not bacterial taxon or
phylogenetic diversity of either group.
Phylogenetic clustering of the microbial responses
Phylogenetic clustering of microbial communities has been extensively
documented (e.g. 4, 5), and may be the result of normal community assembly
rather than a response to disturbance per se. Indeed, even the communities of
fungi and bacteria in the control plots were both significantly clustered according
1
to the nearest taxon (NTI) index, and there was no evidence that communities in
the perturbed communities were more clustered than those of the controls.
The depth of response traits may explain the discrepancy we found
between phylogenetic community measures of microbial composition using the
NTI and NRI metrics. Because NTI only measures the relatedness between
sister taxa, it is more sensitive to phylogenetic clustering towards terminal nodes
(tips) of a tree, whereas NRI is more sensitive to phylogenetic clustering at
deeper nodes (6). So a difference between the two indexes is expected if
clustering is relatively shallow. Likewise, NRI, a measure of how all taxa are
related within a community, will approach zero if a community contains multiple
distinct lineages of clustering and those clusters are separated by substantial
distance on a phylogenetic tree such as occurs here.
Differences between the consenTRAIT and Mantel metrics of phylogenetic
cluster depth.
To look specifically at the depth of the microbial response, we used two
independent analyses that compared the relative abundance of each taxon in the
treatment plots to that in the control plots. Although both consenTRAIT and
Mantel tests measure depths of phylogenetic clustering, there are important
differences in how they are calculated and interpreted. ConsenTRAIT, which
focuses on high levels of consensus for binary characters will likely emphasize
clades with responses that are farthest from neutral. Because the relative
abundance of the majority of taxa in our study were not significantly impacted by
2
global change, most taxa display only slight increases or decreases resulting in
phylogenetically shallow consensus clusters. The Mantel tests, in contrast,
measure the correlation of the magnitude of change in relative abundance, so
taxa with slight increases, slight decreases or no changes in relative abundance
will be more similar to each other than to those more strongly impacted. Thus,
consenTRAIT may be a better metric for identifying clades most strongly
impacted by global change, whereas the Mantel metric is better for inferring the
phylogenetic patterns of changes in community composition.
1.
Nemergut DR et al. (2013) Patterns and Processes of Microbial Community
Assembly. Microbiology and Molecular Biology Reviews 77:342–356.
2.
Hanson CA, Fuhrman JA, Horner-Devine MC, Martiny JB (2012) Beyond
biogeographic patterns: processes shaping the microbial landscape. Nat
Rev Microbiol 10:497–506.
3.
Kembel SW et al. (2010) Picante: R tools for integrating phylogenies and
ecology. Bioinformatics 26:1463–1464.
4.
Horner-Devine MC, Bohannan BJM (2006) Phylogenetic clustering and
overdispersion in bacterial communities. Ecology 87:S100–8.
5.
DeAngelis KM, Firestone MK (2012) Phylogenetic Clustering of Soil
Microbial Communities by 16S rRNA but Not 16S rRNA Genes. Appl Environ
Microbiol 78:2459–2461.
6.
Kraft NJB, Cornwell WK, Webb CO, Ackerly DD (2007) Trait Evolution,
Community Assembly, and the Phylogenetic Structure of Ecological
Communities. Am Nat 170:271–283.
3
Table S1. Precipitation in ambient and drought plots
since 2006. Seasonal year runs from September 1August 31.
Ambient
Drought
Seasonal Precipitation Rain Precipitation Rain
Year
(mm)
Days
(mm)
Days
2006-07
72.39
7
53.34
5
2007-08
223.266
16
133.35
11
2008-09
212.344
17
115.57
9
2009-10
369.316
23
193.548
12
2010-11
540.004
36
212.598
24
2011-12
233.124
24
144.516
14
2012-13
166.116
20
109.728
15
4
Table S2. Main treatment effects on fungal and bacterial diversity.
Multivariate ANOSIM and ANOVA analyses were calculated in a mixed model
accounting for variance contributed by sampling date and sampling block.
Because the interaction between treatments was not measured, treatments were
calculated in separate statistical models. Where a statistical difference was
found, the diversity in the treatment was lower.
weighted
unweighted
UniFrac
UniFrac
Chao
PDiv
pvalue
pvalue
pvalue
F1,31
F1,31
F1,31 pvalue F1,31
Fungi
Drought 19.2
0.001 3.6
0.001 5.4
0.03 10.6 0.005
N+
1.6
0.4
1.8
0.011 5.4
0.02 0.43 0.51
Bacteria
Drought 2.8
N+
1.6
0.023
0.155
2.5
1
0.008
0.45
5.4
0.8
0.03
0.38
3.84
0.5
0.06
0.48
5
Table S3. Results of phylogenetic clustering analysis demonstrate that
nearly all replicates were significantly clustered according to the nearest taxon
index (NTI), whereas only a smaller subset of fungal communities were clustered
according to the net relatedness index (NRI). Proportion significant is the
proportion of replicates that significantly differed from null expectations at p<0.05.
Standardized effect size scores (Z; the difference between observed and
expected values, divided by the SD of the expected values) are reported as
means of all replicates per factor. The Z values are equivalent to -NTI or -NRI.
SD of Z scores across replicates are reported. Taxon based analyses measure
the relationships among taxa, abundance based analyses measure the
relationships among individuals.
Taxon Based
Fungi
Bacteria
Proportion
NTI
Controll
Nitrogen Fertilization
Drought
NRI
Controll
Nitrogen Fertilization
Drought
Abundance Based
NTI
Controll
Nitrogen Fertilization
Drought
NRI
Controll
Nitrogen Fertilization
Drought
Significant
Proportion
Z
SD
Significant
Z
SD
100%
100%
100%
-5.71
-5.77
-5.91
0.99
1.09
1.45
100%
100%
100%
-6.23 1.23
-6.23 1.15
-5.74 1.63
28%
19%
21%
-0.07
0.08
-1.02
2.06
1.80
2.07
0%
0%
0%
1.94 0.92
2.08 1.11
1.55 0.88
96%
96%
96%
-1.76
-1.96
-1.89
0.26
0.31
0.23
100%
96%
100%
-2.74 0.67
-2.83 0.66
-2.72 0.65
34%
29%
34%
-1.33
-1.32
-1.69
0.50
0.46
0.35
0%
0%
0%
4.04 1.14
4.11 1.09
3.51 1.27
6
Table S4. Results of a linear model analysis comparing Log2fold
ratios of the treatment effect size with glycoside hydrolase gene
copies, binned by predicted function. Phylogenetic non-independence was
accounted for using a Brownian motion trait evolutionary model as an error
term.
GH
Standard
Coefficient
T value
P value
Treatment
Function
Error
Nitrogen
Addition
Intercept
Cellulose
Oligos
Xylan
Starch
Chitin
Dextran
Sucrose
Animal Carb.
Other Plant
Carb.
-1.199
0.789
0.116
-1.624
-0.166
-0.156
0.494
0.845
0.016
1.286
0.299
0.131
0.390
0.049
0.179
0.366
0.317
0.177
-0.932
2.634
0.886
-4.160
-3.377
-0.871
1.349
2.660
0.090
0.356
0.011
0.380
0.001
0.001
0.388
0.184
0.010
0.927
0.067
0.161
0.419
0.676
Intercept
0.566
2.028
0.279
Xylan
0.141
0.615
0.230
Cellulose
-0.522
0.472
-1.105
Oligos
-0.117
0.207
-0.563
Starch
0.130
0.077
1.680
Chitin
0.155
0.282
0.548
Dextran
0.256
0.577
0.444
Sucrose
-0.106
0.501
-0.211
Animal Carb.
0.001
0.280
0.002
Other Plant
Carb.
-0.533
0.254
-2.096
Abbreviations: GH=Glycoside hydrolase; Carb.=Carbohydrate
Drought
0.781
0.818
0.275
0.576
0.100
0.586
0.659
0.833
0.998
0.042
7