Correlation of acid-tolerance with pH adaptability of arbuscular mycorrhizal fungal phylotypes.

<p>Standard deviations (SDs) of soil sample pH (range of soil pH) were plotted against the lowest soil pH (acid-tolerance) for each phylotype that occurred in three or more samples in the trap culture surveys. Correlation coefficient (<i>r</i>) = −0.800, <i>P</i> < 0.001 (<i>n</i> = 33).</p

Scatter plot of soil sample pH at which arbuscular mycorrhizal fungal phylotypes were detected in the trap culture surveys.

<p>Rhizosphere soils of <i>M</i>. <i>sinensis</i> were collected from Rankoshi (red), Hazu (yellow), Nago (green), Atsuma (blue), Ishikari (purple), and Mukawa (black) sites and subjected to soil trap culture with <i>M</i>. <i>sinensis</i> seedlings for community analysis. pH was measured using subsamples of the soils. The phylotypes were sorted by the lowest pH values at which they occurred. The names of phylotypes were defined based on the genus to which they were assigned (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165035#pone.0165035.s002" target="_blank">S2 Fig</a>).</p

Responses of AM fungal communities originated from acidic and neutral soils to pH manipulation.

<p>Responses of AM fungal communities originated from acidic and neutral soils to pH manipulation.</p

Geographic/climatic data of the study sites and chemical properties of rhizosphere soils of <i>Miscanthus sinensis</i>.

<p>Geographic/climatic data of the study sites and chemical properties of rhizosphere soils of <i>Miscanthus sinensis</i>.</p

Nestedness in arbuscular mycorrhizal fungal communities as structured by pH manipulation.

<p>Rhizosphere soils of <i>M</i>. <i>sinensis</i> were collected from Ishikari (neutral soil) and Rankoshi (acidic soil) sites and subjected to trap culture at pH 3.4, 4.0, and 5.5 with <i>M</i>. <i>sinensis</i> seedlings for community analysis (<i>n</i> = 5). The names of phylotypes were defined based on the genus to which they were assigned (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165035#pone.0165035.s002" target="_blank">S2 Fig</a>) and indicated on the left of matrix. A combined matrix of the neutral- and acidic-soil communities was constructed according to the hypothesis; the columns of the neutral- and acidic-soil communities were placed to the left and right, respectively, and sorted by pH, and the rows were sorted by occurrence (number of sample in which they occurred was indicated on the right of the matrix). Darkness of the cells indicates the frequency of the phylotypes (numbers of sample in which they occurred). Significant nestedness was observed among the columns (NODF_column = 70.83, <i>Z</i> = 2.71, <i>P</i> < 0.001), but an anti-nestedness pattern was also observed among the rows (WNODF_row = 39.03, <i>Z</i> = −4.35, <i>P</i> < 0.001).</p

Nestedness in arbuscular mycorrhizal fungal communities along the soil pH gradient in the trap culture surveys.

<p>Rhizosphere soils of <i>M</i>. <i>sinensis</i> were collected from Rankoshi, Hazu, Nago, Atsuma, Ishikari, Mukawa sites and subjected to trap culture with <i>M</i>. <i>sinensis</i> seedlings for community analysis. The names of phylotypes were defined based on the genus to which they were assigned (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165035#pone.0165035.s002" target="_blank">S2 Fig</a>) and indicated on the left of matrix. The columns (sites) and rows (phylotypes) were sorted by the mean-pH value of the soil samples (mean ± SD was indicated above the matrix) and by occurrence (number of site at which they occurred was indicated on the right of the matrix), respectively. Darkness of the cells indicates percentage relative abundance of the phylotypes. Significant nestedness was observed among the columns (NODF_column = 55.95, <i>Z</i> = 1.79, <i>P</i> = 0.037), but an anti-nestedness pattern was also observed among the rows (WNODF_row = 18.97, <i>Z</i> = −16.03, <i>P</i> < 0.001).</p

Additional file 4 of The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi

: Table S3. KEGG pathways affected by genes missing in R. clarus and R. irregularis but present in other fungi. (XLSX 34 kb

Additional file 2 of The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi

: Table S1. Homology search results for FAS genes. (XLSX 51 kb

Additional file 3 of The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi

: Table S2. MGCGs in R. clarus compared with other AM fungi. (XLSX 36 kb

Additional file 1 of The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi

: Figure S1. The k-mer (k = 31) content of R. clarus (left panel) and R. irregularis (right panel) obtained from HiSeq short-reads analyzed with Jellyfish [65]. Figure S2. Common missing pathways in two Rhizophagus species. Figure S3. Pathways in vitamin B6 metabolism. Figure S4. Fermentation pathways converting pyrvate into lactate, formate and acetate, which causes cytosolic acidification. (DOCX 1385 kb