Microflora Characteristics of Integrated Rice-Crayfish Farming System in Spring

doi:10.11924/j.issn.1000-6850.casb2022-0817

Abstract

Abstract:

To analyze the composition of microbial community in integrated rice-crayfish farming system at different time in spring, Illumina Miseq high-throughput sequencing technology was used to analyze the bacterial community composition in the intestinal tract and culture environment of Procambarus clarkii. The results showed that a total of 16966 operational taxonomic units (OTUs) were detected in all samples. The maximum OTUs of sediment samples in April were 3677, and the minimum OTUs of intestine were 757. Alpha diversity analysis showed that the abundance and diversity of the sediment microflora were high. The dominant bacteria groups in the integrated rice-crayfish farming system were Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes. Proteobacteria was the predominant group in all samples in April and May, and Firmicutes was the predominant group in P. clarkii intestinal tract in June. The proportion of Actinomycetes in water was higher than that in intestinal tract and sediment. Principal coordinates analysis (PCoA) and unweighted pair group method with arithmatic mean (UPGMA) analysis showed that, microbial communities of the sediment and water in different months were clustered together according to species, but the microbial community structure of intestines and the sediment in June were relatively similar. These results suggested that in spring integrated rice-crayfish farming system, the composition of intestinal microflora of P. clarkii was correlated with the external culture environment. The diversity and composition of microflora in each sample were different but relatively stable in different months.

Key words: integrated rice-crayfish farming system, Procambarus clarkii, high-throughput sequencing, microflora

SHAN Jinfeng, WANG Feifei, WANG Xinhai. Microflora Characteristics of Integrated Rice-Crayfish Farming System in Spring[J]. Chinese Agricultural Science Bulletin, 2023, 39(28): 158-164.

Figures/Tables 6

References 30

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组别	有效序列/条	抽平数列/条	操作分类单元	测序深度/%
A₁	60626	48044	757	99.35
B₁	209884	48044	3677	99.27
C₁	92233	48044	905	99.66
A₂	133900	48044	826	99.39
B₂	107195	48044	3290	99.74
C₂	94534	48044	1235	99.5
A₃	48044	48044	1787	99.58
B₃	95673	48044	3079	99.63
C₃	185887	48044	1410	99.42

组别	有效序列/条	抽平数列/条	操作分类单元	测序深度/%
A₁	60626	48044	757	99.35
B₁	209884	48044	3677	99.27
C₁	92233	48044	905	99.66
A₂	133900	48044	826	99.39
B₂	107195	48044	3290	99.74
C₂	94534	48044	1235	99.5
A₃	48044	48044	1787	99.58
B₃	95673	48044	3079	99.63
C₃	185887	48044	1410	99.42

样品	Chao指数	Observed sopecies指数	PD_whole_tree指数	Shannon指数	Simpson指数
A₁	920.14	757	59.65	4.31	0.832
B₁	4426.11	3677	195.11	10.03	0.997
C₁	1353.08	904	70.85	5.83	0.952
A₂	1068.06	826	67.27	4.61	0.875
B₂	3683.1	3079	180.2	9.62	0.995
C₂	1887.1	1235	95.64	6.25	0.97
A₃	2038.75	1787	108.69	7.69	0.977
B₃	3932.89	3290	170.6	9.37	0.994
C₃	1943.73	1409	100.46	6.82	0.976

样品	Chao指数	Observed sopecies指数	PD_whole_tree指数	Shannon指数	Simpson指数
A₁	920.14	757	59.65	4.31	0.832
B₁	4426.11	3677	195.11	10.03	0.997
C₁	1353.08	904	70.85	5.83	0.952
A₂	1068.06	826	67.27	4.61	0.875
B₂	3683.1	3079	180.2	9.62	0.995
C₂	1887.1	1235	95.64	6.25	0.97
A₃	2038.75	1787	108.69	7.69	0.977
B₃	3932.89	3290	170.6	9.37	0.994
C₃	1943.73	1409	100.46	6.82	0.976

菌群	A₁	B₁	C₁	A₂	B₂	C₂	A₃	B₃	C₃
Curvibacter	38.4	2.65	0.56	23.42	6.27	1.33	0.62	0.12	1.27
hgcI clade	—	—	17.74	—	—	16.05	0.02	0.01	27.55
Limnohabitans	0.29	0.38	12.46	0.09	0.22	7.18	0.05	0.19	5.94
Sphingomonas	2.96	0.11	0.08	18.64	0.9	0.36	0.2	0.03	0.12
Polynucleobacter	0.01	0.01	5.09	—	0.01	7.72	0.05	0.01	6.68
Candidatus Bacilloplasma	5.22	—	—	3.29	0	0.06	8.79	0.01	—
Flavobacterium	0.02	0.52	14.12	0.02	0.1	1.95	0.13	0.11	0.23
Phyllobacterium	0.01	1.19	0.01	15.13	0.09	0.16	0.11	0.01	0.01
Skeletonema pseudocostatum	0.01	0.06	4.48	—	0.05	0.02	—	0.07	0.19
Other	8.78	54.39	9.82	8.77	56.55	24.15	29.03	54.29	19.07