Appendix S5.
Phylogenetic trait conservatism was evaluated using a second approach in which traits
were assigned to Operational Taxonomic Units (OTUs) based on their taxonomic
affiliation. Prior to calculating all phylogenetic signals, we collapsed into single clades
those OTUs whose trait assignment originated from the same reference organism
(Appendix S2). Phylogeny reconstruction was performed using RAxML as explained in
the Phylogenetic community structure section in Materials and Methods. Phylogenetic
trees are given in Appendix S6. Phylogenetic signals were calculated by means of the
D statistic (Fritz & Purvis 2010; see the Phylogenetic trait conservatism section in
Materials and Methods). Phylogenetic signals were calculated using this second
approach both with the complete dataset including 3290 OTUs and with the subset of
1387 OTUs classified with confidence thresholds equal or over 80 % at the finest
taxonomic level (see Appendix S3). Regardless of the dataset used, we found a high
and significant correlation in the D values calculated based on reference organisms or
on the assignment of traits to environmental sequences (R ranging from 0.80 to 0.87; P
< 0.01; Table S5.1).
Table S5.1. Phylogenetic signals (D values) calculated based on traits assigned to
reference organisms or to environmental sequences
Traits
Formation of endospores
Formation of other spores
Formation of cysts
Tolerance to desiccation
Tolerance to salts
Organic C consumption
N fixation
Nitrate Reduction
Denitrification
Phototrophic C fixation
Formation of prosthecae
Formation of PHA inclusions
Ammonia oxidation
Formation of exospores
Formation of akinetes
Reference
Organisms *
-0.748
-0.565
0.678
0.608
0.521
-0.239
0.507
0.807
0.597
0.342
-0.160
0.438
NA
NA
NA
Taxonomic affiliation
All OTUs † OTUs CT ≥ 80 % ‡
-1.235
-1.165
-0.318
-0.350
0.778
1.256
0.794
0.993
0.738
0.733
-0.282
-0.458
0.864
0.851
0.755
0.516
0.876
0.401
0.476
0.444
1.185
0.310
0.499
0.140
NA
NA
NA
NA
NA
NA
* D values calculated using 385 reference organisms contained in the Silva database
(Quast et al. 2003), with the phylogenetic tree exported from ARB (Ludwig et al. 2002)
and the trait matrix provided in Appendix S4
† D values calculated using 3290 OTUs using a phylogenetic tree reconstructed using
RAxML (first tree in Appendix S6) and the trait matrix provided in Appendix S2
‡ D values calculated as in †, but exclusively using the subset of 1387 OTUs classified
with a confidence threshold equal or over 80 % according to Wang et al. (2007)