Biplot diagram calculated by redundancy analysis (RDA) on total bacteria, <i>Luteolibacter</i> and <i>Candidatus</i> genus <i>Rhizospheria</i> and of subdivisions 1, 3, 4 and 6 acidobacteria and holophaga as species, and location in soil, plant species, sampling time and soil pH as environmental variables.

<p>Environmental factors marked with * have significant effects on species variables at a significance level of <i>P</i> = 0.002.</p

Dynamics of total bacteria, <i>Luteolibacter</i> and <i>Candidatus</i> genus <i>Rhizospheria</i> and of subdivisions 1, 3, 4, 6 acidobacteria and holophaga in fallow field soil over time measured by qPCR.

<p>Bact, total bacteria; Lut, <i>Luteolibacter</i>; Rhiz, <b><i>Candidatus</i></b> genus <i>Rhizospheria</i>; AS1, AS3, AS4, AS6, respectively, subdivision 1, 3, 4, 6 acidobacteria; Holo, holophaga. Bars on top of columns represent standard errors of means; *, significant decrease and **, significant increase in comparison with respective samples drawn in May.</p

Luteolibacter, <i>Candidatus</i> genus <i>Rhizospheria</i>, subdivisions 1, 3, 4, 6 acidobacteria and holophaga as percentage of total bacteria in grass, potato and leek rhizospheres and bulk soil.

<div><p>Bars marked with ‘A’ indicate significant higher fraction than in corresponding bulk soil.</p> <p>Lut, <i>Luteolibacter</i>; Rhiz, <i>Candidatus</i> genus <i>Rhizospheria</i>; AS1, AS3, AS4, AS6, respectively, subdivision 1, 3, 4, 6 acidobacteria; Holo, holophaga. Bars on top of columns represent standard errors of means.</p></div

Effects of grass, potato and leek rhizospheres on abundances of total bacteria, <i>Luteolibacter</i> and <i>Candidatus</i> genus <i>Rhizospheria</i> and of subdivisions 1, 3, 4, 6 acidobacteria and holophaga (expressed as Δ Ceq _{rs, b} values, i.e. log cell equivalent numbers from bulk soil subtracted from those from corresponding rhizospheres).

<div><p>G, P, L: Respectively, grass, potato, leek; 0: Δ Ceq rs, b value is zero.</p> <p>Bact, total bacteria; Lut, <i>Luteolibacter</i>; Rhiz, <i>Candidatus</i> genus <i>Rhizospheria</i>; AS1, AS3, AS4, AS6, respectively, subdivision 1, 3, 4, 6 acidobacteria; Holo, holophaga.</p></div

Additional file 1 of Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome

Additional file 1: Figure S1. Phylogenomic analysis of the Ca. Thioglobaceae family using SpeciesTreeBuilder v.01.0. Figure S2. COG functions (N=76) significantly enriched (q-value < 0.05) in the octocoral-derived Ca. Gorgonimonas (Endozoicomonadaceae) MAGs (N= 11, green), compared with all other MAGs (N=55) of this dataset. Figure S3. KEGG metabolic pathway map of the Ca. Gorgonimonas (Endozoicomonadaceae) MAGs of this study. Figure S4. Phylogeny of 101 full-length, bacterial endo-chitinase (EC 3.2.1.14) encoding genes, including the 11 endo-chitinase (GH18-family) genes from Endozoicomonadaceae MAGs (grey shadings) of this study. Figure S5. COG functions (N=34) significantly enriched (p-value < 0.05) in the Ca. Thioglobaceae MAGs (N= 6, dark green), compared with all other MAGs (N=60) of this dataset. An one-sided Welch’s t-test for unequal variances was performed in STAMP v.2.1.3. Multiple test correction was performed using the Benjamini-Hochberg correction (FDR). To further limit the displayed number of significant entries, an effect size filter was also applied, setting the “ratio of proportions” to 5.00. Figure S6. KEGG metabolic pathway map of the Ca. Thioglobaceae MAGs of this study. The metabolic map features glycolysis, pyruvate, nitrogen, sulfur, and taurine metabolism. EC numbers of enzymes catalyzing the reactions are given in rectangular boxes. EC numbers highlighted in green represent enzymes encoded on Ca. Thioglobaceae MAGs. Beige boxes indicate connections to other metabolic pathways active in these MAGs. Figure S7. KEGG carbon fixation map of Ca. Thiocorallibacter gorgonii MAG EG15H_Bin1 (Ca. Thioglobaceae). EC numbers of enzymes catalyzing the reactions are given in rectangular boxes. EC numbers highlighted in green represent enzymes encoded on this MAG. Beige boxes indicate connections to other metabolic pathways active in these MAGs. Orange dots highlight the substrates (Ribulose-1,5-bisphosphate, CO2, and H2O) and product (2 Glycerate-3-phosphate, 2 H+) of Rubisco (EC 4.1.1.39)

Additional file 2 of Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome

Additional file 2: Table S1. General genomic features, taxonomic classification and genome assembly accession numbers of each of the 66 metagenome-assembled genomes (MAGs) obtained from octocoral- and seawater-derived microbial metagenomes. Table S2. Overview of the number and quality of MAGs obtained from octocoral- and seawater-derived microbial metagenome samples. Table S3. Clusters of Orthologous Groups of proteins (COGs) annotation of the 66 MAGs analysed in this study. Table S4. Results of the SIMPER test performed on COG profiles (Hellinger-transformed abundances; Euclidean distances) of the 66 MAGs grouped at order level. Table S5A. Absolute abundances (counts) of COG functions shown in Figure 4 that distinguished the 66 MAGs the most (based on SIMPER and Welch's tests). Table S5B. Relative abundances of COG functions shown in Figure 4 that distinguished the 66 MAGs the most (based on SIMPER and Welch's tests). Table S6A. Features of the endo-chitinase (EC 3.2.1.14) genes found on the 11 Endozoicomonadaceae MAGs of this study. Table S6B. Genes involved in chitin degradation present on the 11 Endozoicomonadaceae MAGs of this study and other, publicly available Endozoicomonadaceae genomes. Table S7. Amino acid (n= 20) and B vitamin (n = 8) biosynthesis capacities (based on genomic evidence) of the 11 bacterial species recovered from the microbiomes of healthy octocoral tissue. Table S8. Secondary metabolite biosynthetic gene clusters (SM-BGCs) present on the 66 MAGs, annotated using antiSMASH bacterial version 5.0. Table S9. List of SM-BGCs with some level of homology to MIBiG database entries