Comparison of the composition and functional potentials of bacterial communities in different tissues from Crassostrea sikamea, Crassostrea angulata and Crassostrea gigas

Ye Jing; Dai Wenfang; Liu Sheng; Lin Zhihua; Xue Qinggang

doi:10.12284/hyxb2022144

Volume 44 Issue 8

Aug. 2022

Turn off MathJax

Article Contents

Article Navigation > Haiyang Xuebao > 2022 > 44(8): 66-77

Ye Jing，Dai Wenfang，Liu Sheng, et al. Comparison of the composition and functional potentials of bacterial communities in different tissues from Crassostrea sikamea, Crassostrea angulata and Crassostrea gigas[J]. Haiyang Xuebao，2022, 44(8)：66–77 doi: 10.12284/hyxb2022144

Citation:

Ye Jing，Dai Wenfang，Liu Sheng, et al. Comparison of the composition and functional potentials of bacterial communities in different tissues from Crassostrea sikamea, Crassostrea angulata and Crassostrea gigas[J]. Haiyang Xuebao，2022, 44(8)：66–77 doi: 10.12284/hyxb2022144

Citation:

PDF( 1467 KB)

Comparison of the composition and functional potentials of bacterial communities in different tissues from Crassostrea sikamea, Crassostrea angulata and Crassostrea gigas

doi: 10.12284/hyxb2022144

Ye Jing^{1, 3
,},
Dai Wenfang^{2, 3},
Liu Sheng^{2, 3},
Lin Zhihua^{2, 3},
Xue Qinggang^{2, 3
,
,}

1.
National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
2.
Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai 315604, China
3.
Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China

Received Date: 2021-12-24
Rev Recd Date: 2022-03-22

Available Online: 2022-08-15

Publish Date: 2022-08-15

Abstract

Abstract

To explore the differences in the composition, diversity, and functions of bacterial communities in tissues from two-year old and healthy Crassostrea sikamea, Crassostrea angulata and Crassostrea gigas, the bacterial community structures and functional potentials among three oysters by combining the Illumina MiSeq high-throughput sequencing technology and phylogenetic investigation of communities by reconstruction of unobserved states 2 (PICRUSt2) was compared in this paper. The results showed that a total of 6 020 OTUs were identified in the five tissues from the three oysters, among which the numbers of shared OTUs accounted for 42.4% of total OTUs. The γ-proteobacteria, α-proteobacteria, Tenericutes and Firmicutes were dominant in five tissues of three oysters. The relative abundance of Vibrio genus was significantly higher in the gill, mantle, hepatopancreas and hemolymph tissues of C. sikamea than in the five tissues of C. angulata and C. gigas. Compared to other tissues, the relative abundance of Vibrio genus was the highest in the mantle of C. sikamea, the gonad of C. angulata and the hemolymph of C. gigas, but was lowest in the hepatopancreas of all three oysters. The diversity of bacterial communities was different among the five tissues of three oysters. Compared to other tissues, the bacterial community α-diversity was higher in the gill of C. sikamea, the mantle of C. angulata and the hemolymph of C. gigas, respectively, but was lowest in the hemolymph of C. sikamea, the gonad of C. angulata and the hepatopancreas of C. gigas. Regardless of tissue types, the bacterial community structures differed significantly (r=0.661, p<0.001) among the three oysters. Additionally, the abundances of bacterial-mediated functional pathways involved in the energy metabolism were significantly higher in the hepatopancreas of C. sikamea, the gill of C. angulata and the hemolymph of C. gigas than that in other tissues of corresponding oysters. Our findings suggested that the structure and composition of bacterial communities were different among five tissues of C. sikamea, C. angulata and C. gigas, and the bacterial-mediated functional potentials ware affected by oyster species and tissue types.
- oyster,
- high-throughput sequencing,
- bacterial community,
- function prediction

FullText(HTML)

References(43)

References

[1]	Clerissi C, de Lorgeril J, Petton B, et al. Diversity and stability of microbiota are key factors associated to healthy and diseased Crassostrea gigas oysters[J]. BioRxiv, 2018, doi: 10.1101/378125.
[2]	Wang Yanting, Wang Kai, Huang Lei, et al. Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle[J]. Microbiome, 2020, 8(1): 106. doi: 10.1186/s40168-020-00879-w
[3]	Semova I, Carten J D, Stombaugh J, et al. Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish[J]. Cell Host & Microbe, 2012, 12(3): 277−288.
[4]	Modak T H, Gomez-Chiarri M. Contrasting immunomodulatory effects of probiotic and pathogenic bacteria on eastern oyster, Crassostrea virginica, larvae[J]. Vaccines, 2020, 8(4): 588. doi: 10.3390/vaccines8040588
[5]	Kesarcodi-Watson A, Miner P, Nicolas J L, et al. Protective effect of four potential probiotics against pathogen-challenge of the larvae of three bivalves: Pacific oyster (Crassostrea gigas), flat oyster (Ostrea edulis) and scallop (Pecten maximus)[J]. Aquaculture, 2012, 344−349: 29−34. doi: 10.1016/j.aquaculture.2012.02.029
[6]	全为民, 张锦平, 平仙隐, 等. 巨牡蛎对长江口环境的净化功能及其生态服务价值[J]. 应用生态学报, 2007, 18(4): 871−876. doi: 10.3321/j.issn:1001-9332.2007.04.028 Quan Weimin, Zhang Jinping, Ping Xianyin, et al. Purification function and ecological services value of Crassostrea sp. in Yangtze River Estuary[J]. Chinese Journal of Applied Ecology, 2007, 18(4): 871−876. doi: 10.3321/j.issn:1001-9332.2007.04.028
[7]	Lokmer A, Kuenzel S, Baines J F, et al. The role of tissue-specific microbiota in initial establishment success of Pacific oysters[J]. Environmental Microbiology, 2016, 18(3): 970−987. doi: 10.1111/1462-2920.13163
[8]	Sohn S, Lundgren K M, Tammi K, et al. Probiotic strains for disease management in hatchery larviculture of the eastern oyster Crassostrea virginica[J]. Journal of Shellfish Research, 2016, 35(2): 307−317. doi: 10.2983/035.035.0205
[9]	Ruiz-Ponte C, Samain J F, Sánchez J L, et al. The benefit of a roseobacter species on the survival of scallop larvae[J]. Marine Biotechnology, 1999, 1(1): 52−59. doi: 10.1007/PL00011751
[10]	Stevick R J, Sohn S, Modak T H, et al. Bacterial community dynamics in an oyster hatchery in response to probiotic treatment[J]. Frontiers in Microbiology, 2019, 10: 1060. doi: 10.3389/fmicb.2019.01060
[11]	Dubert J, Barja J L, Romalde J L. New insights into pathogenic vibrios affecting bivalves in hatcheries: present and future prospects[J]. Frontiers in Microbiology, 2017, 8: 762. doi: 10.3389/fmicb.2017.00762
[12]	江海洋, 李磊, 莫宝庆, 等. 贝类污染副溶血性弧菌与海水水质相关性研究[J]. 中国卫生检验杂志, 2008, 18(12): 2502−2504. doi: 10.3969/j.issn.1004-8685.2008.12.018 Jiang Haiyang, Li Lei, Mo Baoqing, et al. Relationship between Vibrio parahaemolyticus concentration in shellfish and sea water quality[J]. Chinese Journal of Health Laboratory Technology, 2008, 18(12): 2502−2504. doi: 10.3969/j.issn.1004-8685.2008.12.018
[13]	Larsen A M, Mohammed H H, Arias C R. Characterization of the gut microbiota of three commercially valuable warmwater fish species[J]. Journal of Applied Microbiology, 2014, 116(6): 1396−1404. doi: 10.1111/jam.12475
[14]	Zhang Xuechen, Li Xiaohui, Lu Jiaqi, et al. Quantifying the importance of external and internal sources to the gut microbiota in juvenile and adult shrimp[J]. Aquaculture, 2021, 531: 735910. doi: 10.1016/j.aquaculture.2020.735910
[15]	孙雪莹. 虾夷扇贝幼体及育苗池水体细菌群落动态及潜在益生菌筛选[D]. 大连: 大连海洋大学, 2016. Sun Xueying. Dynamics of bacterial communities associated with yesso scallop (Patinopecten yessoensisis) larvae and in the water of larval-rearing tanks, and selection of potential probiotics[D]. Dalian: Dalian Ocean University, 2016.
[16]	陈琼, 李贵阳, 罗坤, 等. 凡纳滨对虾(Litopenaeus vannamei)亲虾繁殖期水体微生物多样性[J]. 海洋与湖沼, 2017, 48(1): 130−138. Chen Qiong, Li Guiyang, Luo Kun, et al. Microbial diversity in broodstock waters of the two genders of Litopenaeus vannamei[J]. Oceanologia et Limnologia Sinica, 2017, 48(1): 130−138.
[17]	Zhang Zhen, Lu Zhimeng, Zhang Weiwei, et al. Comparative analysis of midgut bacterial community under Vibrio splendidus infection in Apostichopus japonicus with hindgut as a reference[J]. Aquaculture, 2019, 513: 734427. doi: 10.1016/j.aquaculture.2019.734427
[18]	郁维娜, 戴文芳, 陶震, 等. 健康与患病凡纳滨对虾肠道菌群结构及功能差异研究[J]. 水产学报, 2018, 42(3): 399−409. Yu Weina, Dai Wenfang, Tao Zhen, et al. Characterizing the compositional and functional structures of intestinal microflora between healthy and diseased Litopenaeus vannamei[J]. Journal of Fisheries of China, 2018, 42(3): 399−409.
[19]	Wei Yongjun, Ren Tianqi, Zhang Lei. Dix-seq: an integrated pipeline for fast amplicon data analysis[J]. BioRxiv, 2020, doi: 10.1101/2020.05.11.089748.
[20]	Magoč T, Salzberg S L. FLASH: fast length adjustment of short reads to improve genome assemblies[J]. Bioinformatics, 2011, 27(21): 2957−2963. doi: 10.1093/bioinformatics/btr507
[21]	Edgar R C. Search and clustering orders of magnitude faster than BLAST[J]. Bioinformatics, 2010, 26(19): 2460−2461. doi: 10.1093/bioinformatics/btq461
[22]	Caporaso J G, Bittinger K, Bushman F D, et al. PyNAST: a flexible tool for aligning sequences to a template alignment[J]. Bioinformatics, 2010, 26(2): 266−267. doi: 10.1093/bioinformatics/btp636
[23]	Pierce M L, Ward J E. Gut microbiomes of the eastern oyster (Crassostrea virginica) and the blue mussel (Mytilus edulis): temporal variation and the influence of marine aggregate-associated microbial communities[J]. mSphere, 2019, 4(6): e00730−19.
[24]	王鑫毅, 谢骁, 金珊, 等. 基于高通量测序的缢蛏及其养殖池塘菌群结构的季节变化[J]. 应用生态学报, 2019, 30(12): 4267−4276. Wang Xinyi, Xie Xiao, Jin Shan, et al. Seasonal variation of microflora in Sinonovacula constricta and its aquacultural pond based on high-throughput sequencing[J]. Chinese Journal of Applied Ecology, 2019, 30(12): 4267−4276.
[25]	Pimentel Z T, Dufault-Thompson K, Russo K T, et al. Microbiome analysis reveals diversity and function of mollicutes associated with the eastern oyster, Crassostrea virginica[J]. mSphere, 2021, 6(3): e00227−21.
[26]	Tanaka R, Ootsubo M, Sawabe T, et al. Biodiversity and in situ abundance of gut microflora of abalone (Haliotis discus hannai) determined by culture-independent techniques[J]. Aquaculture, 2004, 241(1/4): 453−463.
[27]	徐嘉康, 王劲松, 方怡涵, 等. 厚壳贻贝肠道细菌的生物被膜对其幼虫和稚贝附着的影响[J]. 海洋学报, 2021, 43(9): 81−91. Xu Jiakang, Wang Jinsong, Fang Yihan, et al. Effects of intestinal bacterial biofilms on settlement process of larvae and plantigrades in Mytilus coruscus[J]. Haiyang Xuebao, 2021, 43(9): 81−91.
[28]	Karimi E, Keller-Costa T, Slaby B M, et al. Genomic blueprints of sponge-prokaryote symbiosis are shared by low abundant and cultivatable Alphaproteobacteria[J]. Scientific Reports, 2019, 9(1): 1999. doi: 10.1038/s41598-019-38737-x
[29]	李玲玲, 谢超伊, 宋宏策, 等. 长牡蛎(Crassostrea gigas)黑色壳表面微生物多样性的研究[J]. 海洋与湖沼, 2021, 52(6): 1418−1429. doi: 10.11693/hyhz20210400082 Li Lingling, Xie Chaoyi, Song Hongce, et al. Microbial diversity on surface of black-shell Crassostrea gigas[J]. Oceanologia et Limnologia Sinica, 2021, 52(6): 1418−1429. doi: 10.11693/hyhz20210400082
[30]	邹建威. 岩扇贝内脏团和肠道可培养微生物及其宏基因多样性分析[D]. 大连: 大连海洋大学, 2019. Zou Jianwei. Diversity analysis of culturable microorganisms and their macrogenes in rock scallop viscera and intestine[D]. Dalian: Dalian Ocean University, 2019.
[31]	Wang Hailiang, Sun Bochao, Xie Guosi, et al. Spotlight on a novel bactericidal mechanism and a novel SXT/R391-like integrative and conjugative element, carrying multiple antibiotic resistance genes, in Pseudoalteromonas flavipulchra strain CDM8[J]. Microbiological Research, 2021, 242: 126598. doi: 10.1016/j.micres.2020.126598
[32]	Bairagi A, Ghosh K S, Sen S K, et al. Evaluation of the nutritive value of Leucaena leucocephala leaf meal, inoculated with fish intestinal bacteria Bacillus subtilis and Bacillus circulans in formulated diets for rohu, Labeo rohita (Hamilton) fingerlings[J]. Aquaculture Research, 2004, 35(5): 436−446. doi: 10.1111/j.1365-2109.2004.01028.x
[33]	Dai Wenfang, Dong Yinghui, Ye Jing, et al. Gut microbiome composition likely affects the growth of razor clam Sinonovacula constricta[J]. Aquaculture, 2022, 550: 737847. doi: 10.1016/j.aquaculture.2021.737847
[34]	Gradoville M R, Crump B C, Häse C C, et al. Environmental controls of oyster-pathogenic Vibrio spp. in oregon estuaries and a shellfish hatchery[J]. Applied and Environmental Microbiology, 2018, 84(9): e02156−17.
[35]	Beaz-Hidalgo R, Balboa S, Romalde J L, et al. Diversity and pathogenecity of Vibrio species in cultured bivalve molluscs[J]. Environmental Microbiology Reports, 2010, 2(1): 34−43. doi: 10.1111/j.1758-2229.2010.00135.x
[36]	Le Roux F, Wegner K M, Polz M F. Oysters and vibrios as a model for disease dynamics in wild animals[J]. Trends in Microbiology, 2016, 24(7): 568−580. doi: 10.1016/j.tim.2016.03.006
[37]	郑国兴, 李何, 黄宁宇, 等. 文蛤病原菌(溶藻弧菌)的分离与性状及病文蛤组织的电镜观察[J]. 水产学报, 1991, 15(2): 85−95. Zheng Guoxing, Li He, Huang Ningyu, et al. Characteristics of Vibrio alginolyticus isolated from diseased clam Meretrix meretrix and histopathological observations on diseased clam by electron microscope[J]. Journal of Fisheries of China, 1991, 15(2): 85−95.
[38]	高晓建, 姚东瑞, 孙晶晶, 等. 4株长牡蛎(Crassostrea gigas)致病性哈维氏弧菌(Vibrio harveyi)鉴定及其毒力基因检测[J]. 海洋湖沼通报, 2015(3): 87−96. Gao Xiaojian, Yao Dongrui, Sun Jingjing, et al. Identification of 4 pathogenic Vibrio harveyi strains isolated from diseased oyster (Crassostrea gigas) and detection of their virulence genes[J]. Transactions of Oceanology and Limnology, 2015(3): 87−96.
[39]	胡慧雯. 浙江省贝类海产品副溶血弧菌污染的风险识别与评估[D]. 杭州: 浙江大学, 2017. Hu Huiwen. Risk identification and assessment of Vibro parahaemolyticus in shellfish seafood in Zhejiang[D]. Hangzhou: Zhejiang University, 2017.
[40]	Arfken A, Song B, Allen Jr S K, et al. Comparing larval microbiomes of the eastern oyster (Crassostrea virginica) raised in different hatcheries[J]. Aquaculture, 2021, 531: 735955. doi: 10.1016/j.aquaculture.2020.735955
[41]	柴英辉, 高菲, 王金锋, 等. 仿刺参(Apostichopus japonicus)肠道菌群的地域性差异与共性研究[J]. 海洋与湖沼, 2019, 50(5): 1127−1137. doi: 10.11693/hyhz20190200044 Chai Yinghui, Gao Fei, Wang Jinfeng, et al. Intestinal microbiota in Apostichopus japonicus: regional difference and common feature[J]. Oceanologia et Limnologia Sinica, 2019, 50(5): 1127−1137. doi: 10.11693/hyhz20190200044
[42]	Fernández N T, Mazón-Suástegui J M, Vázquez-Juárez R, et al. Changes in the composition and diversity of the bacterial microbiota associated with oysters (Crassostrea corteziensis, Crassostrea gigas and Crassostrea sikamea) during commercial production[J]. FEMS Microbiology Ecology, 2014, 88(1): 69−83. doi: 10.1111/1574-6941.12270
[43]	张令帅. 海洋酸化对长牡蛎(Crassostrea gigas)肝胰腺生理功能和能量供给策略的影响[D]. 北京: 中国科学院海洋研究所, 2020. Zhang Lingshuai. Impact of ocean acidification on hepatopancreas physiological function and energy supply of Pacific oyster (Crassostrea gigas)[D]. Beijing: Institute of Oceanology, Chinese Academy of Sciences, 2020.