Legends to Supporting Information
Table S1 Bacterial 16S rRNA gene pyrosequencing data set.
Table S2 Taxonomic classification and absolute abundance of bacterial OTUs found
exclusively in each sampling year.
Table S3 Archaeal 16S rRNA gene pyrosequencing data set.
Figure S1 PCR-DGGE fingerprinting of bacterial 16S rRNA (a), archaeal 16S rRNA (b) and
bacterial amoA (c) gene fragments amplified from the marine sponge Sarcotragus spinosulus
in three consecutive years. Ordination diagrams obtained via Redundancy Analysis (RDA) of
bacterial 16S rRNA gene (d), archaeal 16S rRNA gene (e) and bacterial amoA gene (f) PCRDGGE profiles are shown. Symbols: S. spinosulus specimens collected  in 2010,  in
2011, and  in 2012. Labels displayed on the diagram axes refer to the percentage variations
of PCR-DGGE ribotypes - environment correlation accounted for the respective axis. The
‘‘star’’ symbol represents the centroid positions of the independent variables (i.e. years of
sampling) in the diagram. Variables that significantly influence community composition
(p<0.05) are indicated by an asterisk. Arrows represent PCR-DGGE bands displaying
significant relative abundance variation according to the year of sampling, the direction of the
arrow revealing positive correlations with their closest samples/sampling years.
Figure S2 Phylum- (a, b) and class-level (c, d) bacterial community composition in
Sarcotragus spinosulus in three consecutive years using the normalized data set (3155 sequence
reads per sample). The compositions of each replicate sample (a, c) and of pooled replicate
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samples (b, d) are shown. Asterisks on bars denote dominant taxa displaying significant shifts
in relative abundance through time.
Figure S3 Observed and estimated (Chao1 index) richness and diversity indices of bacterial
(a,b) and archaeal (c,d) 454 pyrosequencing OTUs (97% cut-off) detected in the marine
sponge Sarcotragus spinosulus along three consecutive years. Results were obtained from
libraries normalized at 3155 bacterial and 4050 archaeal sequence reads per sample.
Figure S4 Bacterial OTU networking and maintenance in the marine sponge Sarcotragus
spinosulus across time using normalized library sizes (3155 sequence reads per sample). A
network made with all OTUs found in composite samples where replicates were pooled
according to the sampling year (a) and the respective Venn diagram (b) are shown. In the
network, red, green, and purple lines correspond to years 2010, 2011, and 2012, respectively.
Figure S5 The pan- (left) and essential core (right) bacteriome of Sarcotragus spinosulus.
Microbiomes are portrayed as the specimen-to-specimen cumulative and common number of
bacterial symbionts (OTUs), respectively, across 12 S. spinosulus specimens analysed by 454
pyrosequencing using the full data set.
Figure S6 Redundancy Analysis (RDA) of bacterial OTU profiles using the normalized data
set. Details are as provided in legend to Fig. 4.
Appendix S1 Detailed 454-pyrosequencing methodology.
Appendix S2 Detailed description of PCR-DGGE results.
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Appendix S3 Bacterial OTU table constructed from the full quality-filtered data set.
Appendix S4 Taxonomic assignment of bacterial OTUs.
Appendix S5 Archaeal OTU table constructed from the full quality-filtered data set.
Appendix S6 Taxonomic assignment of archaeal OTUs.
Appendix S7 Alignment of CO1 sequences used in sponge phylogenetic inference.
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