Frequency of the most abundant bacterial genera, indicated in % of all classified sequences, within each treatment of bio-organic fertilizer (BIO), cattle manure compost (CM), Chinese medicine residue compost (CMR), general operation control (GCK) and pig manure compost (PM).

<p>Only the genera frequency higher than 1% was listed in the table. Values are the means followed by standard error of the mean. Different letters indicate statistically significant differences at the 0.05 probability level according to Fisher's least significant difference test (LSD) and the Duncan test.</p

Additional file 2 of High abundance of Ralstonia solanacearum changed tomato rhizosphere microbiome and metabolome

Additional file 2: Table S1. The characters of co-occurrence networks of two groups with different abundance of RS

Electron micrographs of chloroplasts in newly expanded leaves of Shanyou 63 (a, low-N supply; b, intermediate.-N supply; c, high-N supply) and Yangdao 6 (d, low-N supply; e, intermediate.-N supply; f, high-N supply).

<p>Bar = 1 µm. C, chloroplasts; M, mitochondrion; N, nucleus; SG, starch granules; CW, cell wall; arrows point to plasma membrane.</p

The relationships between the ratio of mesophyll conductance (g_m) to Rubisco content and (a) photosynthetic N-use efficiency (PNUE) and (b) the ratio of leaf photosynthetic rate (<i>A</i>) and Rubisco content on Shanyou 63 (solid cycles) and Yangdao 6 (open cycles).

<p>The lines represent the following regressions: (a) y = 32.89x+26.28 R² = 0.86 <i>P</i><0.01; (b) y = 0.096x−0.038 R² = 0.80 <i>P</i><0.05.</p

Redundancy analysis (RDA) of the abundant phyla and soil properties for soil samples from treatments with bio-organic fertilizer (BIO), cattle manure compost (CM), Chinese medicine residue compost (CMR), general operation control (GCK) and pig manure compost (PM).

<p>Redundancy analysis (RDA) of the abundant phyla and soil properties for soil samples from treatments with bio-organic fertilizer (BIO), cattle manure compost (CM), Chinese medicine residue compost (CMR), general operation control (GCK) and pig manure compost (PM).</p

Frequency of the most abundant bacterial genera, indicated in % of all classified sequences, within each treatment of bio-organic fertilizer (BIO), cattle manure compost (CM), Chinese medicine residue compost (CMR), general operation control (GCK) and pig manure compost (PM).

<p>Only the genera frequency higher than 1% was listed in the table. Values are the means followed by standard error of the mean. Different letters indicate statistically significant differences at the 0.05 probability level according to Fisher's least significant difference test (LSD) and the Duncan test.</p

Additional file 1 of High abundance of Ralstonia solanacearum changed tomato rhizosphere microbiome and metabolome

Additional file 1: Figure S1. Principal coordinates analysis (PCoA) with Bray-Curtis dissimilarity of the rhizosphere bacterial communities using the whole OTU table excluding the OTUs belonging to Ralstonia solanacearum

The relationship between Rubisco content and total chloroplast volume per leaf area.

<p>The line represents the regression equation: y = 0.79x+1.36, R² = 0.88, <i>P</i><<i>0.01</i>. Data sources: <i>Nicotiana tabacum</i> □ <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062036#pone.0062036-Evans3" target="_blank">[21]</a>; <i>Chenopodium album</i> ▴ <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062036#pone.0062036-Oguchi1" target="_blank">[48]</a>; <i>Aucuba japonica</i> Thunb. △ <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062036#pone.0062036-Muller1" target="_blank">[24]</a>. The two data points in dotted cycles are from transgenic tobacco with a reduced Rubisco content.</p

The relationships between chloroplast size and photosynthetic N-use efficiency (PNUE), and the ratio of leaf photosynthetic rate (<i>A</i>) to Rubisco.

<p>The lines represent the following regression equations: (a) y = 91.04x/(x–2.87), R² = 0.53, <i>P</i><0.01; (b) y = 121.76x/(x–0.96), R² = 0.75, <i>P</i><0.01; (c) y = 180.56x/(x–2.12), R² = 0.72, <i>P</i><0.01; (d) y = 0.21x/(x–2.86), R² = 0.53, <i>P</i><0.01; (e) y = 0.29x/(x–0.95), R² = 0.69, <i>P</i><0.01; (f) y = 0.42x/(x–2.06), R² = 0.63, <i>P</i><0.01. Data sources: data of solid squares were collected from Wuyujing 3 (<i>Oryza sativa</i> L. ssp. japonica) with different N supplies; data of open squares were from Shanyou 63 with different N forms and water supply <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062036#pone.0062036-Li2" target="_blank">[42]</a>; data of solid and open cycles were from Shanyou 63 and Yangdao 6 with different N supplies.</p

Effects of N supply level on leaf photosynthesis in rice seedlings.

<p>Rice plants (<i>cv.</i> Shanyou 63 and Yangdao 6) were supplied with N at three different levels (low: 20 mg L⁻¹ N, intermediate: 40 mg L⁻¹ N, and high: 100 mg L⁻¹ N). Data are means ± SD of more than 20 individual chloroplasts for their length and thickness, and 5 individual plants for other variables.</p><p>Notes: Significant differences (<i>P</i><5%) between N supplies or varieties were indicated by different lowercase letters or different uppercase letters, respectively. <i>A</i>, g_s, g_m, N, Rubisco and PNUE represent leaf photosynthetic rate, stomatal conductance to CO₂, mesophyll conductance to CO₂, leaf nitrogen content, leaf Rubisco content, photosynthetic N-use efficiency, respectively.</p