Coupling of the chemical niche and microbiome in the rhizosphere: implications from watermelon grafting

doi:10.15302/J-FASE-2016105

Front. Agr. Sci. Eng.

2016, Vol. 3

Issue (3) : 249-262 https://doi.org/10.15302/J-FASE-2016105

RESEARCH ARTICLE

Coupling of the chemical niche and microbiome in the rhizosphere: implications from watermelon grafting

Yang SONG¹,Chen ZHU¹,Waseem RAZA¹,Dongsheng WANG²,Qiwei HUANG¹,Shiwei GUO¹,Ning LING¹(

),Qirong SHEN¹

¹. Jiangsu Provincial Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
². Nanjing Institute of Vegetable Science, Nanjing 210042, China

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Abstract

Grafting is commonly used to overcome soil-borne diseases. However, its effects on the rhizodeposits as well as the linkages between the rhizosphere chemical niche and microbiome remained unknown. In this paper, significant negative correlations between the bacterial alpha diversity and both the disease incidence (r = −0.832, P = 0.005) and pathogen population (r = −0.786, P = 0.012) were detected. Moreover, our results showed that the chemical diversity not only predicts bacterial alpha diversity but also can impact on overall microbial community structure (beta diversity) in the rhizosphere. Furthermore, some anti-fungal compounds including heptadecane and hexadecane were identified in the rhizosphere of grafted watermelon. We concluded that grafted watermelon can form a distinct rhizosphere chemical niche and thus recruit microbial communities with high diversity. Furthermore, the diverse bacteria and the antifungal compounds in the rhizosphere can potentially serve as biological and chemical barriers, respectively, to hinder pathogen invasion. These results not only lead us toward broadening the view of disease resistance mechanism of grafting, but also provide clues to control the microbial composition by manipulating the rhizosphere chemical niche.

Keywords rhizodeposits rhizosphere microbiome diversity MiSeq sequencing watermelon grafting

Corresponding Author(s): Ning LING

Just Accepted Date: 23 June 2016 Online First Date: 04 July 2016 Issue Date: 21 September 2016

Cite this article:

Yang SONG,Chen ZHU,Waseem RAZA, et al. Coupling of the chemical niche and microbiome in the rhizosphere: implications from watermelon grafting[J]. Front. Agr. Sci. Eng. , 2016, 3(3): 249-262.

URL:

https://academic.hep.com.cn/fase/EN/10.15302/J-FASE-2016105
https://academic.hep.com.cn/fase/EN/Y2016/V3/I3/249

	No.	RT	Name	Area%
	No.	RT	Name	W	WB	WP	B	P
Alkane	GC11	12.17	2,6,10-Trimethyldecane	0 (0) b	0.19 (0.12) a	0.18 (0.12) a	0.18 (0.09) a	0 (0) b
	GC22	17.34	Heptadecane	0 (0) b	0.46 (0.13) a	0.54 (0.13) a	0.56 (0.28) a	0.50 (0.20) a
	GC28	19.18	10-methyl nonadecane	0 (0) b	0 (0) b	0.19 (0.14) a	0 (0) b	0 (0) b
	GC37	23.22	2,6,10-Trimethyl tetradecane	1.19 (0.60) b	2.23 (0.96) a	2.66 (0.88) a	2.62 (0.74) a	2.27 (0.85) a
	GC38	23.42	Heptacosane	0 (0) c	0 (0) c	0.79 (0.10) a	0 (0) c	0.40 (0.18) b
	GC47	25.08	Octadecane,3-ethyl-5-(2-ethylbutyl)-	0 (0) b	0.76 (0.45) a	0.73 (0.17) a	0 (0) b	0 (0) b
	GC50	25.71	9-Hexyl heptadecane	0 (0) b	0.51 (0.36) a	0 (0) b	0 (0) b	0 (0) b
	GC64	36.18	Pentacosane	0 (0) b	0.39 (0.24) ab	0.57 (0.10) a	0.65 (0.57) a	0 (0) b
	GC67	40.61	Tetratetracontane	0 (0) b	0.74 (0.38) a	0 (0) b	0.25 (0.08) b	0.32 (0.09) b
Arene	GC9	11.50	3,5-Dimethyl cumene	0 (0) b	0.29 (0.10) b	0.36 (0.16) b	1.07 (0.77) a	0 (0) b
	GC10	11.87	Pentamethyl benzene	0 (0) b	0.27 (0.21) ab	0.26 (0.12) ab	0.7 (0.55) a	0 (0) b
	GC21	17.14	1,8-Dimethylnaphthalene	0 (0) b	0.74 (0.49) a	0.62 (0.18) ab	0.71 (0.33) a	0.75 (0.53) a
Alcohol	GC3	8.45	2-Methyloctanol	0 (0) b	0.29 (0.23) a	0 (0) b	0 (0) b	0 (0) b
Phenol	GC18	14.58	3-tert-Butylphenol	0 (0) b	2.41 (1.69) a	3.78 (1.94) a	2.65 (2.30) a	0 (0) b
Phenol	GC68	42.25	2,2'-Methylenebis(6-tert-butyl-4-methylphenol)	5.73 (1.82) a	1.19 (0.78) b	0.34 (0.31) b	0 (0) b	0.54 (0.34) b
Ester	GC26	18.65	Dimethyl phthalate	0 (0) b	0.75 (0.44) a	0.59 (0.07) a	1.88 (1.64) a	0.65 (0.16) a
	GC54	28.17	1,2-Benzenedicarboxylic acid, dihexyl ester	0 (0) b	6.72 (5.23) ab	10.24 (6.09) a	4.96 (4.11) ab	6.68 (6.72) ab
	GC58	30.05	Methyl 3-(3,5-di-tert-butyl-4-hydroxyphenyl)propionate	0 (0) b	0.37 (0.24) a	0.53 (0.16) a	0 (0) b	0.35 (0.25) a
	GC65	38.31	3-Methoxy-4-(methoxycarbonyl)-5-methylphenyl 4-[(2,4- dimethoxy-6-methylbenzoyl)oxy]-2-methoxy-6-methylbenzoate	0 (0) b	0.35 (0.02) a	0.35 (0.06) a	0.2 (0.16) ab	0.22 (0.18) ab
	GC69	45.61	1,2-Benzenedicarboxylicacid, 1,2-bis(2-propylhexyl) ester	28.74 (23.76) a	2.55 (1.83) b	2.40 (1.77) b	0.43 (0.10) b	2.50 (1.06) b
Acid	GC56	29.38	2-Propenoic acid,3-[3,5-bis(1,1-dimethylethyl)-4-hydroxyphenyl]-	0 (0) b	0 (0) b	0 (0) b	0.32 (0.21) a	0.50 (0.15) a
Others	GC2	7.00	Hydroxylamine, O-decyl-	0 (0) b	0.20 (0.12) a	0 (0) b	0 (0) b	0.20 (0.09) a

Tab.1 Identified chemicals with significant difference in relative abundance between treatments

Fig.1 Shannon diversities for the chemical composition (a), bacteria (b) and fungi (c) in the rhizosphere of all the treatments. Each column represents the mean value of three replicates. Bars represent the SEs of the mean. The means in a column with the same letter are not significantly different at P<0.05. Different colors represent different treatments. W, un-grafted watermelon; WB, watermelon grafted onto bottle gourd; WP, watermelon grafted onto pumpkin; B, bottle gourd rootstock; P, pumpkin rootstock.

Fig.2 First two non-metric multidimensional scaling (NMDS) axes of community structures of chemical composition (a), bacteria (b) and fungi (c). The points represent the means (both axes) of three replicates and are colored by treatments. The bars show the SE along each NMDS axis. W, un-grafted watermelon; WB, watermelon grafted onto bottle gourd; WP, watermelon grafted onto pumpkin; B, bottle gourd rootstock, P, pumpkin rootstock.

Fig.3 Relationships between the chemical Shannon diversity and Shannon diversities for bacteria (a) and fungi (b) in the rhizosphere of all treatments. The relationship between the Shannon diversities for chemical composition with bacteria (r = 0.910, P<0.001) was stronger than with fungi (r = 0.506, P = 0.054). Different colors represent the different treatments, and each treatment includes three replicates. W, un-grafted watermelon; WB, watermelon grafted onto bottle gourd; WP, watermelon grafted onto pumpkin; B, bottle gourd rootstock; P, pumpkin rootstock.

Fig.4 Relationships between the beta diversity for the chemical composition and bacteria (a) (r = 0.684, P = 0.005) and fungi (b) (r = 0.780, P = 0.001). Each point represents the dissimilarity in the taxonomic composition between a pair of treatments, calculated as the average of the Bray-Curtis dissimilarities for all the comparisons (typically 9) between the replicates from those two treatments. The different colors represent the comparisons between two different treatments or within a treatment. W, un-grafted watermelon, WB, watermelon grafted onto bottle gourd; WP, watermelon grafted onto pumpkin; B, bottle gourd rootstock; P, pumpkin rootstock.

Fig.5 Relationships between the bacterial Shannon diversity and the disease incidence (a), the bacterial Shannon diversity and the number of FON (b), the fungal Shannon diversity and the disease incidence (c), the fungal Shannon diversity and the number of FON (d). Different colors represent the different treatments, and each treatment includes three replicates. W, un-grafted watermelon; WB, watermelon grafted onto bottle gourd; WP, watermelon grafted onto pumpkin.

Fig.6 Network analysis revealing the co-occurrence patterns among the bacterial genera and chemicals in the rhizosphere. A connection stands for a strong (Spearman’s r>0.6) and significant (P<0.01) correlation. The nodes were colored according to modularity class. The size of each node is proportional to the number of connections (the degree). A red label represents an identified chemical and a black label represents a bacterial genus.

Fig.7 Network analysis revealing the co-occurrence patterns among the fungal genera and chemicals in the rhizosphere. A connection stands for a strong (Spearman’s r>0.6) and significant (P<0.01) correlation. The nodes were colored according to modularity class. The size of each node is proportional to the number of connections (the degree). A red label represents an identified chemical and a black label represents a fungal genus.

Fig.8 Schematic representation of the disease resistance mechanism achieved through grafting. Before the pathogen successfully invades the roots, it must break through two barriers in the rhizosphere: one is the biological barrier (the blue arc) comprising diverse bacteria, and the other barrier is the chemical barrier (the red arc) consisting of some anti-fungal compounds in rhizodeposits.

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