Differences between the effects of plant species and compartments on microbiome composition in two halophyte Suaeda species

Figures & data

Figure 1. Alpha-diversity indices for the 16S rRNA gene sequence in different samples.

SS: Suaeda salsa, SC: S. corniculata; BL: bulk soil, RH: rhizosphere soil; BL(SS), RH(SS), RT(SS), ST(SS) and LF(SS) indicate bulk soil, rhizosphere soil, root, stem and leaf under S. salsa, respectively; BL(SC), RH(SC), RT(SC), ST(SC) and LF(SC) represent bulk soil, rhizosphere soil, root, stem and leaf under S. corniculata, respectively. Different letters indicate significant difference between means, lower case indicates P < 0.05.

Figure 2. Venn diagram analysis showing the number of unique and shared OTU in different samples. BL(SS), RH(SS), RT(SS), ST(SS) and LF(SS) indicate bulk soil, rhizosphere soil, root, stem and leaf under S. salsa, respectively; BL(SC), RH(SC), RT(SC), ST(SC) and LF(SC) represent bulk soil, rhizosphere soil, root, stem and leaf under S. corniculata, respectively. A: the number of shared and unique OTUs in the different plant compartments of S. salsa species; B: the number of shared and unique OTUs in the different plant compartments of S. corniculata species; C: the relative abundance of shared and unique OTUs.

Figure 3. The relative abundance of bacteria at the phylum level in the different samples.

BL(SS), RH(SS), RT(SS), ST(SS) and LF(SS) indicate bulk soil, rhizosphere soil, root, stem and leaf under S. salsa, respectively; BL(SC), RH(SC), RT(SC), ST(SC) and LF(SC) represent bulk soil, rhizosphere soil, root, stem and leaf under S. corniculata, respectively.

Table 1. Significance tests of the effects of on the bacterial community structure with three different statistical approaches

	Adonis		ANOSIM		MRPP
	F	P	R	P	δ	P
Total	4.436	0.001	0.727	0.001	0.559	0.001
Plant species	1.425	0.141	0.037	0.161	0.812	0.113
Bulk soil	3.546	0.1	0.926	0.1	0.550	0.1
Rhizosphere soil	2.49	0.1	0.667	0.1	0.700	0.1
Root	1.722	0.1	0.333	0.2	0.663	0.1
Stem	1.257	0.5	0.037	0.5	0.648	0.3
Leaf	0.891	0.6	−0.148	1	0.484	1
Above ground: under ground*	8.381	0.001	0.606	0.001	0.724	0.001
Soil: tissue	16.117	0.001	0.993	0.001	0.666	0.001
Bulk soil: Rhizosphere soil	1.355	0.121	0.096	0.141	0.625	0.123
Bulk soil: root	9.096	0.003	0.998	0.003	0.607	0.002
Rhizosphere soil: root	6.068	0.002	0.985	0.004	0.682	0.002
Rhizosphere soil: stem	7.148	0.002	1	0.001	0.674	0.001
Rhizosphere soil: leaf	9.809	0.002	1	0.003	0.592	0.003
Root: stem	1.489	0.084	0.109	0.127	0.656	0.068
Root: leaf	5.038	0.005	0.556	0.008	0.574	0.004
Stem: leaf	3.013	0.009	0.270	0.017	0.566	0.007

*Above ground: stem and leaf, under ground: root, rhizosphere soil and bulk soil. Bold values represent a signifcant difference (P < 0.05).

Figure 4. LEfSe analysis indicating the phylogenetic distribution of microbial lineages associated with the different samples. Differences are represented in the color of the most abundant class. Circles represent phylogenetic levels from domain to genus inside out. RE, root endosphere; RH, rhizosphere; BL, bulk control soil; LF: leaf; RT: root; ST: stem; SS, S. salsa; SC: S. corniculata Bunge.

Table 2. Topological properties of molecular ecological networks (MENs) of different Suaeda species and their associated random MENs

Network name	Topological properties	BL	RH	RT	ST	LF
Empirical networks	Similarity threshold	0.98	0.98	0.80	0.75	0.70
	Total nodes	705	510	109	86	49
	Total links	1465	756	395	262	254
	Average degree (avgK)	4.16	4.39	7.25	6.09	10.37
	Betweenness	0.16	0.16	0.13	0.24	0.13
	Degree Centrality	0.08	0.06	0.16	0.13	0.34
	Average path (GD)	9.32	7.12	3.36	3.31	2.05
	Average clustering coefficient (avgCC)	0.23	0.25	0.38	0.39	0.29
	Modularity	0.725	0.71	0.55	0.53	0.22
Random networks	Modularity	0.49 ± 0.01	0.63 ± 0.01	0.30 ± 0.01	0.26 ± 0.01	0.18 ± 0.01
	Average path (GD)	4.07 ± 0.04	4.76 ± 0.07	2.64 ± 0.03	2.34 ± 0.01	1.94 ± 0.02
	Average clustering coefficient (avgCC)	0.02 ± 0.00	0.01 ± 0.00	0.10 ± 0.01	0.014 ± 0.01	0.29 ± 0.02

BL: network based on bulk soil of different Suaeda species.

RH: network based on rhizosphere soil of different Suaeda species.

RT: network based on root endosphere of different Suaeda species.

ST: network based on stem endosphere of different Suaeda species.

LF: network based on leaf endosphere of different Suaeda species.

Figure 5. Phylogenetic molecular ecological networks based on different Suaeda species microbiomes and the topological roles of nodes. A node represents an OTU, and its color represents its module. The green and red lines indicate negative and positive interaction, respectively. pp: positive interaction; np: negative interaction.

Figure 6. Circos plots showing the distribution of links among interacting phyla in different networks.

The band between two segments represents the network connection among phylum, and the width of indicates the number of connection.

Data availability statement

All data included in this study are available upon request by contact with the corresponding author (https://dataview.ncbi.nlm.nih.gov/object/PRJNA593778).