Effects of crop rotation and microbial agent application on the rhizosphere soil microbial community of protected tomato

doi:10.3969/j.issn.1004-1524.20250263

Acta Agriculturae Zhejiangensis ›› 2026, Vol. 38 ›› Issue (5): 979-990.DOI: 10.3969/j.issn.1004-1524.20250263

• Environmental Science • Previous Articles Next Articles

Effects of crop rotation and microbial agent application on the rhizosphere soil microbial community of protected tomato

MAO Xiaomei¹(), JU Xinghui¹, ZHU Lijing², YANG Jian¹^,^*()

¹ Changxing County Agricultural Technology Extension Station, Changxing 313100, Zhejiang, China
² Changxing Lijing Family Farm, Changxing 313100, Zhejiang, China

Received:2025-04-03 Online:2026-05-25 Published:2026-06-02

Abstract

Abstract:

Changes in soil microbial communities are one of the main factors affecting continuous cropping obstacles. This study, focusing on the protected tomato (Solanum lycopersicum L.) cultivation area in Changxing County, used Illumina MiSeq technology to investigate the effects of different cropping systems—rice-tomato rotation (D treatment), continuous tomato cropping with microbial agent application (M treatment), and continuous tomato cropping (N treatment) on the rhizosphere soil microbial community. The results showed that compared with the N treatment, both D and M treatments altered the rhizosphere soil microbial community structure, but did not significantly affect microbial richness or diversity. The microbial community structures in the rhizosphere soil of tomatoes under D, M, and N treatments were similar, but significant differences existed in relative abundances at the phylum and genus levels. Differences in relative abundance at the phylum level mainly occurred between D and M treatments and between D and N treatments, whereas the bacterial community composition and abundance were relatively similar between M and N treatments. Differences in relative abundance at the genus level primarily appeared between D and M treatments, with some differences also observed between D and N treatments. Both D and M treatments significantly reduced soil organic matter, total nitrogen, and available phosphorus contents. The D treatment decreased exchangeable calcium content and increased exchangeable magnesium content, while the M treatment significantly reduced both exchangeable calcium and exchangeable magnesium contents. Soil nutrients had a greater influence on bacterial community structure than on fungal community structure. In conclusion, rice-tomato rotation is the primary factor influencing the rhizosphere soil microbial community structure in tomatoes, while microbial agent application has a certain effect on the fungal community structure. These measures contribute to alleviating soil salinization and continuous cropping obstacles in tomato cultivation.

Key words: facility vegetable, continuous cropping obstacle, crop rotation, rhizosphere soil, microbial inoculant, microbial community

CLC Number:

MAO Xiaomei, JU Xinghui, ZHU Lijing, YANG Jian. Effects of crop rotation and microbial agent application on the rhizosphere soil microbial community of protected tomato[J]. Acta Agriculturae Zhejiangensis, 2026, 38(5): 979-990.

Figures/Tables 9

References 17

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样本 Sample	序列数 Sequence number		平均长度/bp Average length/bp		最小长度/bp Minimum length/bp		最大长度/bp Maximum length/bp
样本 Sample	细菌Bacteria	真菌Fungi	细菌Bacteria	真菌Fungi	细菌Bacteria	真菌Fungi	细菌Bacteria	真菌Fungi
D	72 535±9 034	65 014±7 045	413	250	259	133	458	490
M	78 392±3 510	74 703±5 058	416	248	229	117	493	496
N	76 315±2 328	80 091±4 870	416	246	228	141	470	522

样本 Sample	序列数 Sequence number		平均长度/bp Average length/bp		最小长度/bp Minimum length/bp		最大长度/bp Maximum length/bp
样本 Sample	细菌Bacteria	真菌Fungi	细菌Bacteria	真菌Fungi	细菌Bacteria	真菌Fungi	细菌Bacteria	真菌Fungi
D	72 535±9 034	65 014±7 045	413	250	259	133	458	490
M	78 392±3 510	74 703±5 058	416	248	229	117	493	496
N	76 315±2 328	80 091±4 870	416	246	228	141	470	522

分类 Taxonomy	门 Phylum	相对丰度Relative abundance
分类 Taxonomy	门 Phylum	D	M	N
细菌Bacteria	放线菌门Actinobacteriota	33.420±5.496 a	16.600±2.028 b	21.380±4.258 b
	变形菌门Proteobacteria	20.570±0.908 a	23.630±2.958 a	25.550±3.005 a
	绿弯菌门Chloroflexi	20.090±1.929 a	17.900±0.812 ab	15.350±2.469 b
	厚壁菌门Firmicutes	7.929±1.372 b	17.540±3.100 a	14.840±3.331 a
	酸杆菌门Acidobacteriota	5.917±0.876 b	9.845±1.323 a	7.439±1.345 ab
	芽单胞菌门Gemmatimonadota	4.195±0.224 b	5.762±0.591 ab	6.434±0.964 a
	髌骨菌门Patescibacteria	0.366±0.091 b	1.062±0.054 a	1.020±0.131 a
	盐厌氧菌门Halanaerobiaeota	0.252±0.085 a	0.508±0.242 a	0.146±0.007 a
	脱铁杆菌门Deferrisomatota	0.021±0.008 a	0 b	0 b
	河床菌门Zixibacteria	0.011±0.001 a	0.001 a	0 a
	Methylomirabilota	0.090±0.034 a	0.012±0.021 b	0.023±0.024 ab
真菌Fungi	子囊菌门Ascomycota	88.470±0.801 a	74.110±18.300 a	85.820±2.091 a
	被孢霉门Mortierellomycota	3.554±0.762 a	19.45±14.890 a	9.470±1.529 a
	担子菌门Basidiomycota	3.727±0.139 a	3.727±3.253 a	1.631±0.360 a
	罗兹菌门Rozellomycota	0.068±0.019 a	0.007±0.012 b	0.014±0.024 b
	壶菌门Chytridiomycota	0.062±0.024 a	0.006±0.008 b	0.012±0.007 b

分类 Taxonomy	门 Phylum	相对丰度Relative abundance
分类 Taxonomy	门 Phylum	D	M	N
细菌Bacteria	放线菌门Actinobacteriota	33.420±5.496 a	16.600±2.028 b	21.380±4.258 b
	变形菌门Proteobacteria	20.570±0.908 a	23.630±2.958 a	25.550±3.005 a
	绿弯菌门Chloroflexi	20.090±1.929 a	17.900±0.812 ab	15.350±2.469 b
	厚壁菌门Firmicutes	7.929±1.372 b	17.540±3.100 a	14.840±3.331 a
	酸杆菌门Acidobacteriota	5.917±0.876 b	9.845±1.323 a	7.439±1.345 ab
	芽单胞菌门Gemmatimonadota	4.195±0.224 b	5.762±0.591 ab	6.434±0.964 a
	髌骨菌门Patescibacteria	0.366±0.091 b	1.062±0.054 a	1.020±0.131 a
	盐厌氧菌门Halanaerobiaeota	0.252±0.085 a	0.508±0.242 a	0.146±0.007 a
	脱铁杆菌门Deferrisomatota	0.021±0.008 a	0 b	0 b
	河床菌门Zixibacteria	0.011±0.001 a	0.001 a	0 a
	Methylomirabilota	0.090±0.034 a	0.012±0.021 b	0.023±0.024 ab
真菌Fungi	子囊菌门Ascomycota	88.470±0.801 a	74.110±18.300 a	85.820±2.091 a
	被孢霉门Mortierellomycota	3.554±0.762 a	19.45±14.890 a	9.470±1.529 a
	担子菌门Basidiomycota	3.727±0.139 a	3.727±3.253 a	1.631±0.360 a
	罗兹菌门Rozellomycota	0.068±0.019 a	0.007±0.012 b	0.014±0.024 b
	壶菌门Chytridiomycota	0.062±0.024 a	0.006±0.008 b	0.012±0.007 b

分类 Taxonomy	属 Genera			相对丰度Relative abundance
分类 Taxonomy	属 Genera			D		M		N
细菌Bacteria	芽孢杆菌属Bacillus			3.165±0.356 b		8.249±0.953 a		7.299±1.977 a
	链霉菌属Streptomyces			5.559±0.454 a		2.388±0.472 b		2.466±0.392 b
	东氏菌属Dongia			1.381±0.161 b		2.192±0.742 ab		2.709±0.100 a
	鞘氨醇单胞菌属Sphingomonas			1.206±0.098 a		2.305±0.561 a		2.526±1.209 a
	诺卡氏菌属Nocardioides			1.361±0.451 a		0.951±0.363 a		1.691±0.252 a
	Iamia			2.584±1.119 a		0.392±0.070 b		0.530±0.216 b
	Actinophytocola			1.536±0.211 a		0.280±0.078 b		0.490±0.231 b
	分枝杆菌属Mycobacterium			1.285±0.238 a		0.428±0.131 b		0.575±0.190 b
	德沃斯氏菌属Devosia			0.963±0.045 a		0.520±0.151 b		0.610±0.167 b
	海洋芽孢杆菌属Oceanobacillus			0.376±0.068 b		0.827±0.289 a		0.595±0.012 ab
	气氨微菌属Aeromicrobium			0.878±0.144 a		0.394±0.163 b		0.409±0.088 b
	类芽孢杆菌属Paenibacillus			0.131±0.080 b		0.894±0.276 a		0.608±0.169 ab
	嗜热碱性菌属Anoxybacillus			0.370±0.035 b		0.620±0.097 a		0.481±0.130 ab
	Kribbella			0.735±0.153 a		0.182±0.043 b		0.321±0.172 b
	Lysobacter			0.495±0.010 a		0.236±0.136 b		0.331±0.097 ab
	野村菌属Nonomuraea			0.717±0.096 a		0.145±0.069 b		0.125±0.012 b
	藤黄单胞菌属Luteimonas			0.495±0.077 a		0.224±0.106 b		0.255±0.104 ab
	诺卡氏菌属Nocardia			0.584±0.143 a		0.165±0.096 b		0.141±0.028 b
	Candidatus_Solibacter			0.433±0.102 a		0.210±0.069 b		0.245±0.058 ab
	Pseudolabrys			0.447±0.058 a		0.256±0.131 ab		0.178±0.035 b
	Nitrospira			0.238±0.043 b		0.254±0.034 ab		0.342±0.038 a
	中慢生根瘤菌属Mesorhizobium			0.413±0.030 a		0.260±0.096 ab		0.138±0.051 b
真菌Fungi	曲霉属Aspergillus			20.44±4.012 a		12.110±11.820 a		31.25±6.714 a
	被孢霉属Mortierella			3.411±0.738 a		19.180±14.720 a		9.332±1.488 a
	毛葡孢属Botryotrichum			16.15±6.427 a		5.210±1.755 a		10.45±7.969 a
	金孢属Chrysosporium			0.911±0.455 a		24.270±41.90 a		0.307±0.044 a
	无茎真菌属Acaulium			8.716±1.238 a		0.191±0.070 b		0.312±0.162 b
	Fungi_gen_Incertae_sedis			2.427±0.267 a		0.561±0.428 b		0.908±0.514 b
		头梗霉属Cephaliophora	2.537±1.031 a		0.008±0.014 b		0 b
		绿核菌属Ustilaginoidea	2.127±0.377 a		0.064±0.087 b		0.166±0.135 b
		Chaetomium	1.294±0.482 a		0.425±0.242 ab		0.353±0.350 b
		枝孢属Cladosporium	0.633±0.102 a		0.199±0.098 b		0.338±0.066 b
		Sarocladium	0.713±0.172 a		0 b		0 b
		节担菌属Wallemia	0.004±0.007 b		0.092±0.067 ab		0.226±0.068 a
		韦斯特壳属Westerdykella	0.276±0.054 a		0.002±0.004 b		0.007±0.006 b
		球腔菌属Phaeosphaeria	0.167±0.054 a		0 b		0 b
		假单胞菌属Pseudogymnoascus	0.097±0.035 a		0 b		0 b

Effects of crop rotation and microbial agent application on the rhizosphere soil microbial community of protected tomato

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处理 Treatment	OM/ (g·kg^-1)	pH值 pH value	TN/ (g·kg^-1)	AP/ (mg·kg^-1)	AK/ (mg·kg^-1)	EX-Ca/ (cmol·kg^-1)	EX-Mg/ (cmol·kg^-1)	TDS/ (g·kg^-1)	CEC/ (cmol·kg^-1)
D	39.53± 0.32 c	6.73± 0.01 b	2.45± 0.01 c	56.30± 0.40 c	235.00± 0.15 a	20.20± 0.27 c	2.96± 0.04 a	1.89± 0.09 a	19.23± 0.32 a
M	41.00± 0.27 b	6.94± 0.02 a	2.50± 0.40 b	63.63± 0.40 b	229.00± 0.06 a	22.30± 0.66 b	2.54± 0.04 c	1.07± 0.05 b	18.43± 0.29 b
N	42.90± 0.17 a	6.93± 0.01 a	2.56± 0.01 a	73.70± 0.79 a	204.00± 0.06 a	24.60± 1.15 a	2.86± 0.02 b	1.97± 0.03 a	19.40± 0.27 a

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