Effects of Four Annual Rotation Patterns on Soil Microbial Community

doi:10.11924/j.issn.1000-6850.casb2021-0809

Abstract

Abstract:

To clarify the changes of soil microbial community in the cultivated layer under different crop rotation patterns, and to reveal the potential mechanism of paddy and dry crop rotation which is beneficial to the sustainable production of vegetables, in this paper, we designed 4 common crop rotation patterns, fixed the test plots in the same geographic area for long-term crop rotation experiments, and used high-throughput sequencing technology to determine the sequence of the ITS1 region of fungi in the soil and the V3-V4 variable region sequence of the 16S rDNA of bacteria. Soil microbial diversity analysis was conducted. Alpha diversity analysis shows that the soil fungal community diversity in the cultivated layer changes significantly under the four annual rotation patterns, and the Shannon index of the water and dry rotation pattern (SH) is significantly higher than that of the graft pattern (JJ) and vegetable rotation LZ pattern (LZ), and has no significant difference with vegetable rotation LD pattern (LD). The diversity and richness of soil bacterial communities in the cultivated layer change significantly. The Shannon index and ACE index of the SH pattern are significantly higher than those of the LD pattern, and the Shannon index of the SH pattern is significantly higher than that of other patterns. The principal coordinate analysis shows that among the four annual rotation patterns, the soil microbial communities in the cultivated layer are significantly differentiated. The SH and LZ patterns are grouped separately, and the JJ and LD patterns are grouped together. Significant analysis of species differences between groups shows that the SH pattern has 7 genera of fungi and 26 genera of bacteria that are significantly richer than other patterns; the LD and LZ have 4 genera of fungi and 7 genera of bacteria, respectively, their abundance is significantly higher than other patterns; only one genus of bacteria in JJ pattern has significantly higher abundance than other patterns. Significant changes take place in the soil microbial communities in the cultivated layer under long-term annual rotations of different crop rotation patterns. Long-term paddy-upland rotation could increase the diversity of soil microbial communities, enrich the types and relative abundance of beneficial bacteria, and is more conducive to the sustainable production of vegetables.

Key words: paddy-upland rotation, microbial diversity, high-throughput sequencing, cucumber, blight, Fusarium

CLC Number:

S154.36

ZHANG Heqing, WU Jie, HAN Shuai, XI Yadong, LI Yuejian, LIANG Genyun. Effects of Four Annual Rotation Patterns on Soil Microbial Community[J]. Chinese Agricultural Science Bulletin, 2022, 38(20): 73-80.

Figures/Tables 7

References 30

[1]	BERENDSEN R L, PIETERSE C M J, Bakker P A. The rhizosphere microbiome and plant health[J]. Trends in plant science, 2012, 17(8):478-486. doi: 10.1016/j.tplants.2012.04.001 URL
[2]	SCHLATTER D, KINKEL L, THOMASHOW L, et al. Disease suppressive soils: new insights from the soil microbiome[J]. Phytopathology, 2017, 107(11):1284-1297. doi: 10.1094/PHYTO-03-17-0111-RVW URL
[3]	王孝林, 王二涛. 根际微生物促进水稻氮利用[J]. 植物学报, 2019, 54(3):285-287. doi: 10.11983/CBB19060
[4]	薛英龙, 李春越, 王苁蓉, 等. 丛枝菌根真菌促进植物摄取土壤磷的作用机制[J]. 水土保持学报, 2019, 33(6):10-20.
[5]	NUMAN M, BASHIR S, KHAN Y, et al. Plant growth promoting bacteria as an alternative strategy for salt tolerance in plants: a review[J]. Microbiological research, 2018, 209:21-32. doi: 10.1016/j.micres.2018.02.003 URL
[6]	BHARTI N, BARNAWAL D. Amelioration of salinity stress by PGPR:ACC deaminase and ROS scavenging enzymes activity. In: PGPR Amelioration in Sustainable Agriculture[M]. Woodhead publishing, 2019:85-106.
[7]	黄化刚, 吕立新, 张艳茗, 等. 微生物帮助烟草抗旱的机理及其应用[J]. 应用生态学报, 2017, 28(9):3099-3110. doi: 10.13287/j.1001-9332.201709.013
[8]	MENDES R, RAAIJMAKERS J M. Cross-kingdom similarities in microbiome functions[J]. The ISME journal, 2015, 9(9):1905-1907. doi: 10.1038/ismej.2015.7 URL
[9]	PUTTEN W H, BRADFORD M A, BRINKMAN E P, et al. Where, when and how plant-soil feedback matters in a changing world[J]. Functional ecology, 2016, 30(7):1109-1121. doi: 10.1111/1365-2435.12657 URL
[10]	HAAS D, DéFago G. Biological control of soil-borne pathogens by fluorescent pseudomonads[J]. Nature reviews microbiology, 2005, 3(4):307-319. doi: 10.1038/nrmicro1129 URL
[11]	MAKATE C, WANG R, MAKATE M, et al. Crop diversification and livelihoods of smallholder farmers in Zimbabwe: adaptive management for environmental change[J]. SpringerPlus, 2016, 5(1):1135. doi: 10.1186/s40064-016-2802-4 URL
[12]	ZHANG L C, HUANG W, XIAO W, et al. Comparison of Soil Enzyme Activity and Microbial Community Structure between Rapeseed-Rice and Rice-Rice Plantings[J]. International journal of agriculture and bioligy, 2018, 20(8):1801-1808.
[13]	HOU P F, CHIEN C H, CHIANG-HSIEH Y F, et al. Paddy-upland rotation for sustainable agriculture with regards to diverse soil microbial community[J]. Scientific reports, 2018, 8(1):1-9.
[14]	STEINAUER K, CHATZINOTAS A, EISENHAUER N. Root exudate cocktails: the link between plant diversity and soil microorganisms?[J]. Ecology and Evolution, 2016, 6(20):7387-7396. doi: 10.1002/ece3.2454 URL
[15]	GRUNERT O, ROBLES-AGUILAR A A, HERNANDEZ-SANABRIA E, et al. Tomato plants rather than fertilizers drive microbial community structure in horticultural growing media[J]. Scientific reports, 2019, 9(1):1-15. doi: 10.1038/s41598-018-37186-2 URL
[16]	ZHOU X G, ZHANG J, PAN D, et al. p-Coumaric can alter the composition of cucumber rhizosphere microbial communities and induce negative plant-microbial interactions[J]. Biology and fertility of soils, 2018, 54:363-372. doi: 10.1007/s00374-018-1265-x URL
[17]	ZHOU X G, WU F. Vanillic acid changed cucumber (Cucumis sativus L.) seedling rhizosphere total bacterial, Pseudomonas and Bacillus spp. communities[J]. Scientific reports, 2018, 8:4929. doi: 10.1038/s41598-018-23406-2 URL
[18]	AIL-ALI A, DERAVEL J, KRIER F,et al. Biofilm formation is determinant in tomato rhizosphere colonization by Bacillus velezensis FZB42[J]. Environmental science and pollution research, 2018,25, 30:29910-29920.
[19]	ALAM K M, ZHANG T, YAN Y L, et al. Transcriptional Analysis of Pseudomonas stutzeri A1501 Associated with Host Rice[J]. Advances in microbiology, 2016, 6(3):210-221. doi: 10.4236/aim.2016.63021 URL
[20]	SUGIYAMA A, YAZAKI K. Root exudates of legume plants and their involvement in interactions with soil microbes. Secretions and exudates in biological systems[M]. Springer, Berlin,Heidelberg, 2012:27-48.
[21]	DACHEV M, BíNa D, SOBOTKA R, et al. Unique double concentric ring organization of light harvesting complexes in Gemmatimonas phototrophica[J]. PLoS biology, 2017, 15(12):e2003943. doi: 10.1371/journal.pbio.2003943 URL
[22]	DAIMS H, LEBEDEVA E V, PJEVAC P, et al. Complete nitrification by Nitrospira bacteria[J]. Nature, 2015, 528(7583):504-509. doi: 10.1038/nature16461 URL
[23]	TANGAROMSUK J, POKETHITIYOOK P, KRUATRACHUE M, et al. Cadmium biosorption by Sphingomonas paucimobilis biomass[J]. Bioresource Technology, 2002, 85(1):103-105. doi: 10.1016/S0960-8524(02)00066-4 URL
[24]	LIU S W, XU M, TUO L, et al. Phycicoccus endophyticus sp. nov., an endophytic actinobacterium isolated from Bruguiera gymnorhiza[J]. International journal of systematic and evolutionary microbiology, 2016, 66(3):1105-1111. doi: 10.1099/ijsem.0.000842 URL
[25]	JIN D C, KONG X, LI H H, et al. Patulibacter brassicae sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris)[J]. International journal of systematic and evolutionary microbiology, 2016, 66(12):5056-5060. doi: 10.1099/ijsem.0.001469 URL
[26]	何英, 张屹, 朱菲莹, 等. 西瓜枯萎病不同发病阶段根际微生物群落结构分析[J]. 湖南农业科学, 2019(9):47-50.
[27]	HUYNH T T T. Biocontrol potential of Bradyrhizobium japonicum against soybean sudden death syndrome[D]. Iowa State: Iowa State university department of plant pathology and microbiology, 2019:11-50.
[28]	OSHKIN I Y, KULICHEVSKAYA I S, RIJPSTRA W I C, et al. Granulicella sibirica sp. nov., a psychrotolerant acidobacterium isolated from an organic soil layer in forested tundra, West Siberia[J]. International journal of systematic and evolutionary microbiology, 2019, 69(4):1195-1201. doi: 10.1099/ijsem.0.003290 URL
[29]	GROSSI C E M, FANTINO E, SERRAL F, et al. Methylobacterium sp. 2A is a plant growth-promoting rhizobacteria that has the potential to improve potato crop yield under adverse conditions[J]. Frontiers in plant science, 2020, 11:1-15. doi: 10.3389/fpls.2020.00001 URL
[30]	尹彦舒, 崔曼, 崔伟国, 等. 大蒜连作障碍形成机理的研究进展[J]. 生物资源, 2018, 40(2):141-147.

群落	轮作模式	OTU数	ACE指数	Shannon指数
土壤真菌群落	JJ	171.00±37.55a	182.92±37.36a	3.30±0.23a
	LD	192.25±9.20a	200.11±7.09a	3.72±0.12ab
	LZ	226.50±21.27a	231.30±21.86a	3.23±0.17a
	SH	246.75±30.13a	265.26±25.85a	3.92±0.08b
土壤细菌群落	JJ	891.50±154.48ab	915.18±164.09ab	5.33±0.15a
	LD	825.00±53.66a	849.55±58.00a	5.01±0.13a
	LZ	991.75±46.32ab	1030.53±54.98ab	5.23±0.10a
	SH	1147.00±15.25b	1176.49±11.94b	5.89±0.11b

群落	轮作模式	OTU数	ACE指数	Shannon指数
土壤真菌群落	JJ	171.00±37.55a	182.92±37.36a	3.30±0.23a
	LD	192.25±9.20a	200.11±7.09a	3.72±0.12ab
	LZ	226.50±21.27a	231.30±21.86a	3.23±0.17a
	SH	246.75±30.13a	265.26±25.85a	3.92±0.08b
土壤细菌群落	JJ	891.50±154.48ab	915.18±164.09ab	5.33±0.15a
	LD	825.00±53.66a	849.55±58.00a	5.01±0.13a
	LZ	991.75±46.32ab	1030.53±54.98ab	5.23±0.10a
	SH	1147.00±15.25b	1176.49±11.94b	5.89±0.11b

轮作模式	属	相对丰度值/%				轮作模式	属	相对丰度值/%
轮作模式	属	JJ	LD	LZ	SH	轮作模式	属	JJ	LD	LZ	SH
LD	Trichoderma	3	7.64	2.82	3.35	SH	Acrostalagmus	0	0.01	0	0.16
	Talaromyces	0.15	0.5	0.05	0.05		Dactylella	0	0	0.01	0.25
	Symmetrospora	0	0.15	0.01	0.03		Ilyonectria	0	0.03	0.14	0.45
	Spencerozyma	0	0.18	0	0		Oidiodendron	0.08	0.28	0.11	1.1
LZ	Ramicandelaber	0	0	0.16	0.03		Simplicillium	0	0	0.01	0.23
	Pyrenochaetopsis	0.01	0	1.39	0.37		Ustilaginoidea	0	0	0.23	1.1
	Nigrospora	0	0	3.94	0.62		Rhizophagus	0.01	0.01	0	0.07
	Conlarium	0.05	0.04	0.18	0.06

轮作模式	属	相对丰度值/%				轮作模式	属	相对丰度值/%
轮作模式	属	JJ	LD	LZ	SH	轮作模式	属	JJ	LD	LZ	SH
LD	Trichoderma	3	7.64	2.82	3.35	SH	Acrostalagmus	0	0.01	0	0.16
	Talaromyces	0.15	0.5	0.05	0.05		Dactylella	0	0	0.01	0.25
	Symmetrospora	0	0.15	0.01	0.03		Ilyonectria	0	0.03	0.14	0.45
	Spencerozyma	0	0.18	0	0		Oidiodendron	0.08	0.28	0.11	1.1
LZ	Ramicandelaber	0	0	0.16	0.03		Simplicillium	0	0	0.01	0.23
	Pyrenochaetopsis	0.01	0	1.39	0.37		Ustilaginoidea	0	0	0.23	1.1
	Nigrospora	0	0	3.94	0.62		Rhizophagus	0.01	0.01	0	0.07
	Conlarium	0.05	0.04	0.18	0.06

轮作模式	属	相对丰度值/%				轮作模式	属	相对丰度值/%
轮作模式	属	JJ	LD	LZ	SH	轮作模式	属	JJ	LD	LZ	SH
SH	p_Acidobacteria	0.252	0.058	0.360	1.680	SH	Reyranella	0.109	0.060	0.235	0.613
	f_Acidobacteriaceae	0.020	0.019	0.109	0.737		Phenylobacterium	0.175	0.072	0.185	0.405
	f_Blastocatellaceae	0.011	0.004	0.010	0.289		Steroidobacter	0.015	0.000	0.045	0.227
	Blastocatellaceae_RB41	0.035	0.000	0.016	0.219		Altererythrobacter	0.083	0.064	0.061	0.190
	p_Acidobacteria_o_Subgroup_7	0.009	0.000	0.010	0.173		Polycyclovorans	0.011	0.000	0.016	0.186
	p_Acidobacteria_c_Subgroup_6	0.014	0.002	0.029	0.144		f_Comamonadaceae	0.005	0.011	0.008	0.174
	Phycicoccus	0.060	0.028	0.020	0.249		f_BIrii41	0.035	0.013	0.033	0.173
	Iamia	0.006	0.000	0.015	0.134		Dokdonella	0.017	0.010	0.016	0.172
	Patulibacter	0.008	0.000	0.019	0.116		Nitrosospira	0.038	0.014	0.026	0.115
	Gaiella	0.018	0.024	0.011	0.103		o_Chthoniobacterales	0.022	0.000	0.030	0.180
	Chitinophaga	0.034	0.014	0.049	0.444	LD	Mizugakiibacter	8.547	12.341	5.829	3.952
	Niastella	0.002	0.000	0.027	0.192		p_Saccharibacteria	2.129	4.213	1.068	1.912
	Flavisolibacter	0.018	0.011	0.019	0.108		f_ODP1230B8.23	0.919	3.105	1.084	0.450
	p_Chloroflexi_c_KD4-96	0.451	0.253	0.661	0.999		f_Acetobacteraceae	1.073	1.599	1.093	0.784
	f_Anaerolineaceae	0.018	0.005	0.021	0.364		f_Rhodospirillaceae	0.899	1.355	0.689	0.845
	Nitrolancea	0.164	0.179	0.177	0.321		Alkanibacter	0.162	0.260	0.077	0.016
	Chloroflexi	0.026	0.021	0.020	0.116		Bdellovibrio	0.143	0.223	0.059	0.090
	Gemmatimonas	0.789	0.319	0.750	1.656	LZ	p_Acidobacteria	1.081	1.569	6.140	0.402
	Gemmatirosa	0.106	0.066	0.041	0.323		Acidibacter	1.781	1.975	3.208	1.923
	p_Latescibacteria	0.026	0.000	0.034	0.397		Aquicella	0.545	0.800	1.505	0.549
	Nitrospira	0.222	0.183	0.519	1.013		Bradyrhizobium	0.463	0.404	1.070	0.737
	o_Nitrospirales_f_0319-6A21	0.022	0.000	0.022	0.185		Granulicella	0.266	0.398	0.846	0.404
	Sphingomonas	1.255	1.107	1.645	3.771		Methylovirgula	0.045	0.084	0.180	0.057
	f_Nitrosomonadaceae	0.217	0.074	0.415	2.433		Roseiarcus	0.018	0.021	0.142	0.079
	Pseudolabrys	0.692	0.439	1.039	1.503	JJ	Methylobacterium	0.127	0.030	0.011	0.006
	Haliangium	0.308	0.209	0.392	1.094