Exploration of Mycobiota in Cypripedium japonicum, an Endangered Species

Figures & data

Figure 1. Relative abundance of top10 order and family. The two top 10 samples are selected based on the average of all samples in order (A) and in family (B).

Figure 2. Principal coordinates analysis in national habitat. The panels are emphasized by (A) habitat location, (B) sampling time, (C) shoot length, (D) area, (E) population. The place and sampling times are indicated by different colors and the same location samples in different times connect the lines. The characteristics of the measured habitats are indicated by a blue and black gradation.

Table 1. PERMANOVA of the PCoA results in natural habitats of Cypripedium japonicum.

Habitant location, PERMANOVA, p = 0.0000 (***)
Pairs	Sums of Sqs.	F. Model	R^2	padj	Significant
Mt. Cheonma vs Mt. Deokyu 1	0.3640	1.9241	0.1614	0.1334
Mt. Cheonma vs Mt. Deokyu 2	0.3738	1.9448	0.1628	0.1525	*
Mt. Cheonma vs Hwacheon	0.5872	2.9003	0.2248	0.0233	*
Mt. Cheonma vs Pocheon	0.4228	2.1609	0.1777	0.0413
Mt. Deokyu 1 vs Mt. Deokyu 2	0.2225	1.2862	0.1140	1.0000
Mt. Deokyu 1 vs Hwacheon	0.3318	1.8104	0.1533	0.2618
Mt. Deokyu 1 vs Pocheon	0.2525	1.4309	0.1252	1.0000
Mt. Deokyu 2 vs Hwacheon	0.4007	2.1510	0.1770	0.1122
Mt. Deokyu 2 vs Pocheon	0.3399	1.8933	0.1592	0.2661
Hwacheon vs Pocheon	0.3904	2.0573	0.1706	0.1786
Sampling time, PERMANOVA, p = 0.1054
Shoot length (cm), PERMANOVA, p = 0.0289 (*)
Pairs (cm)
20 vs 25	0.2407	1.1213	0.0485	0.8184
20 vs 35	0.3238	1.4986	0.0638	0.1481
25 vs 30	0.2225	1.2862	0.1140	0.5553
Population, PERMANOVA, p = 0.0155 (*)
Pairs (population)
18 vs 98	0.3640	1.9241	0.1614	0.1266
18 vs 8	0.3738	1.9448	0.1628	0.1379
18 vs 16	0.5872	2.9003	0.2248	0.0234	*
18 vs 196	0.4228	2.1609	0.1777	0.0468	*
98 vs 8	0.2225	1.2862	0.1140	1.0000
98 vs 16	0.3318	1.8104	0.1533	0.2543
98 vs 196	0.2525	1.4309	0.1252	1.0000
8 vs 16	0.4007	2.1510	0.1770	0.1107
8 vs 196	0.3399	1.8933	0.1592	0.2666
16 vs 196	0.3904	2.0573	0.1706	0.1699
Habitat area (m^2), PERMANOVA, p = 0.0155 (*)
Pairs (m^2)
0.8 vs 4	0.3640	1.9241	0.1614	0.1322
0.8 vs 1	0.3738	1.9448	0.1628	0.1438
0.8 vs 0.6	0.5872	2.9003	0.2248	0.0208	*
0.8 vs 10	0.4228	2.1609	0.1777	0.0439	*
4 vs 1	0.2225	1.2862	0.1140	1.0000
4 vs 0.6	0.3318	1.8104	0.1533	0.2629
4 vs 10	0.2525	1.4309	0.1252	1.0000
1 vs 0.6	0.4007	2.1510	0.1770	0.1081
1 vs 10	0.3399	1.8933	0.1592	0.2544
0.6 vs 10	0.3904	2.0573	0.1706	0.1723

PERMANOVA and paired-wise PERMANOVA are performed by the Bray–Curtis distance of the relative abundance in each rhizosphere sample.

Permutations is 99,999 in PERANOVA and paired-wised PERANOVA.

P_adj is calculated by Bonferroni correction.

*0.01 < p ≤ 0.05, or 0.01 < p_adj ≤ 0.05.

**0.001 < p ≤ 0.05, or 0.001 < p_adj ≤ 0.01.

***p ≤ 0.001, or p_adj ≤ 0.001.

Figure 3. Correlation between Lycoperdon nigrescens and Cypripedium japonicum Thunberg population. (A) real values. (B) Ranks. The blue line indicates a regression in ranks. Among 243 Spearman’s ranking correlations of taxonomy and habitat indicators, only L. nigrescens were positively correlated with population. Bonferroni corrected p-value is 0.033 and p-value meaning correlation is 0.634.

Figure 4. Difference abundance between the native habitats and the artificial garden. This analysis was run by DESeq2 package in R. The adjusted p-values were conducted by Bonferroni adjustment. (A) all of the analyzed is zoom in and separated to (B) more in nature, and (C) more in the garden. The criteria for the significant are p_adj < 0.001, and │log₂(fold change)│ > 2.

Figure 5. Correlation network among taxonomic groups in the natural habitats. When correlation p-value is under 0.05, top 30 of eigencentrality, Lycopedon and Rusulla are selectively described. Green and yellow lines mean positive and negative correlation and their thickness mean correlation magnitude. The size of the point represents the eigencentrality of a significant network, including all taxonomic groups not plotted in this figure. The top 30 is described by red edge at the point. The filled colors of the points represented the taxonomic levels of the groups.