渔业科学进展  2025, Vol. 46 Issue (3): 160-169  DOI: 10.19663/j.issn2095-9869.20240328001
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引用本文 

吕若萱, 王秀华, 王美凤, 连新宇, 李晨, 许华, 尹伟力, 贾鹏, 杨冰. 对虾养殖池塘沉积物中IHHNV DNA检测方法的评估与应用[J]. 渔业科学进展, 2025, 46(3): 160-169. DOI: 10.19663/j.issn2095-9869.20240328001.
LÜ Ruoxuan, WANG Xiuhua, WANG Meifeng, LIAN Xinyu, LI Chen, XU Hua, YIN Weili, JIA Peng, YANG Bing. Infectious Hypodermal and Hematopoietic Necrosis Virus Detection in Shrimp Farming Pond Sediments[J]. Progress in Fishery Sciences, 2025, 46(3): 160-169. DOI: 10.19663/j.issn2095-9869.20240328001.

基金项目

中国水产科学研究院中央级公益性科研院所基本科研业务费专项资金(2024GH02)、现代农业产业技术体系专项资金(CARS48)、国家重点研发计划(2023YFD2400705)、中国水产科学研究院黄海水产研究所基本科研业务费(20603022023025)、海关总署揭榜挂帅项目(2021KH001)和深圳市农业发展专项资金项目:基于eDNA技术的高通量无创渔业病害监测关键技术研发及示范应用(1302)共同资助

作者简介

吕若萱,Email: lvruoxuanora@163.com

通讯作者

杨冰,研究员,Email: yangbing@ysfri.ac.cn

文章历史

收稿日期:2024-03-28
收修改稿日期:2024-04-16
对虾养殖池塘沉积物中IHHNV DNA检测方法的评估与应用
吕若萱 1, 王秀华 2, 王美凤 1, 连新宇 2, 李晨 2, 许华 2, 尹伟力 3, 贾鹏 4, 杨冰 2     
1. 上海海洋大学水产与生命学院 上海 201306;
2. 海水养殖生物育种与可持续产出全国重点实验室(中国水产科学研究院黄海水产研究所) 青岛海洋科技中心海洋渔业科学与食物产出过程功能实验室 青岛市海水养殖流行病学与生物安保重点实验室 山东 青岛 266071;
3. 烟台海关技术中心 山东 烟台 264000;
4. 深圳技术大学 广东 深圳 518118
摘要:对虾传染性皮下和造血组织坏死病毒(IHHNV)是虾类疫病重要病原之一,对对虾养殖业造成危害,其主要检测方法通常通过捕获个体进行分子生物学检测。环境DNA (eDNA)技术可直接从环境样本中快速、经济地监测到目标病原,在水生动物病原检测方面的应用得到快速发展。为了评估eDNA技术检测虾类疾病病原IHHNV的有效性和可行性,本研究以不同粒径底质池塘沉积物作为研究对象,结合3种试剂盒进行提取条件优化,评估不同底质下eDNA的提取效果,利用荧光定量PCR检测方法检测IHHNV最低核酸检出量。结果显示,优化的方法对于沙底沉积物中IHHNV的检测灵敏度可达1.52×102 copies/μL,泥底沉积物中IHHNV的检测灵敏度为1.32×102 copies/μL,该方法灵敏度较高,方便可行,不同的池塘沉积物成分最低检测限浓度相差不到一个数量级,对提取效果差异不明显,可用于沉积物中IHHNV的检测。应用优化的eDNA技术和养殖对虾组织样品qPCR方法对养殖环境中IHHNV的存在情况进行调查。结果显示,调查点养殖池塘沉积物和养殖对虾样品中均有IHHNV检出,且存在一定对应关系。该研究对对虾养殖池塘沉积物中IHHNV DNA检测方法的评估与应用提供了可靠的技术手段,为监测养殖动物健康状态提供了科学依据,同时丰富并完善了eDNA方法在虾类病原监测中的应用。
关键词IHHNV    环境DNA    沉积物    
Infectious Hypodermal and Hematopoietic Necrosis Virus Detection in Shrimp Farming Pond Sediments
LÜ Ruoxuan 1, WANG Xiuhua 2, WANG Meifeng 1, LIAN Xinyu 2, LI Chen 2, XU Hua 2, YIN Weili 3, JIA Peng 4, YANG Bing 2     
1. College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China;
2. State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao 266071, China;
3. Technology Center of Yantai Customs, Yantai 264000, China;
4. Shenzhen Technology University, Shenzhen 518118, China
Abstract: Infectious hypodermal and hematopoietic necrosis virus (IHHNV) is a shrimp disease that poses a substantial threat to the shrimp farming industry. Owing to the significant economic impact of IHHNV on the global shrimp farming industry, the World Organization for Animal Health (WOAH) has listed IHHNV as a notifiable crustacean pathogen. The primary IHHNV detection method usually involves capturing individual shrimp for molecular biological testing. Using environmental DNA (eDNA) technology, which allows rapid and economical pathogen monitoring directly from environmental samples, has rapidly developed for aquatic animal pathogen detection applications. eDNA is used to detect aquatic pathogens, such as external parasites in fish and crustacean diseases, including white spot syndrome virus (WSSV), Enterocytozoon hepatopenaei (EHP), and IHHNV. For instance, for a method has been developed for detecting Cyprinid herpesvirus 3 (CyHV-3) in environmental waters using virus concentration methods and TaqMan polymerase chain reaction (PCR). The concentration-PCR method achieved an average concentration recovery rate of 67.11% for IHHNV detection in environmental waters based on eDNA principles and techniques. Shrimp carrying the IHHNV pathogen can spread the disease to healthy populations, inducing epidemics. Monitoring pathogens in the water environment is a more direct and effective method compared with testing cultivated shrimp for biosecurity investigations and risk assessments. While such eDNA methods are well-studied, research regarding such applications for soil and sediment is limited. Viruses can persist in pond soil and sediments, serving as natural virus reservoirs and providing potential pathways for virus transmission. However, no studies have monitored the presence of IHHNV in natural environment sediments, which is accompanied by a lack of reliable detecting and quantifying IHHNV detection methods for environmental sediments. eDNA methods enable an effective understanding of pathogen transmission mechanisms and the timely establishment of control measures during disease outbreaks. As a promising tool, eDNA detection has significant application prospects in monitoring aquatic animal diseases. This study aimed to evaluate the effectiveness and feasibility of using eDNA technology to detect the shrimp disease pathogen, IHHNV. Different particle size substrates of pond sediments were selected as study subjects. Extraction conditions were optimized using three commercial kits to evaluate the eDNA extraction effects under different substrates and to detect the lowest nucleic acid detection limit of IHHNV using real-time fluorescent quantitative PCR (RT-qPCR). To verify nucleic acid extraction effectiveness from sediments, three different kits were applied to extract DNA from shrimp tissue in both mud and sand substrates, followed by PCR amplification. Considering factors such as kit price, extraction effect, and duration, Kit B and A were selected for nucleic acid extraction from sand and mud sediments, respectively. RT-qPCR amplification of IHHNV in two types of substrate sediments at different addition volumes were observed. As the addition volume of IHHNV-containing shrimp tissue homogenate decreased, the viral load of IHHNV decreased accordingly. The minimum detectable addition volume for IHHNV in sand sediments was 5 μL, with a viral load of 1.52×102 copies/μL; whereas the minimum detectable addition was 10 μL for mud sediments, with a viral load of 1.32×102 copies/μL. The original viral load in 5 μL and 10 μL homogenate volumes were 9.94×102 and 1.72×103 copies/μL, respectively. Compared to the original viral load added, the recovery rate in sand and mud sediments were approximately 15.30% and 7.70%, respectively. The minimum detection limit concentration of different pond sediment components varied by less than an order of magnitude, showing no significant difference in extraction effects, making it suitable for IHHNV detection in sediments. The optimized eDNA technique and RT-qPCR method for cultured shrimp tissue samples were applied to investigate the presence of IHHNV in the farming environment. IHHNV positives were detected in both sediment and shrimp farming ponds between July and September; however, the positive detection rate was lower in sediment than in shrimp (Penaeus vannamei). The study demonstrates that the detection results of pond sediments and cultured P. vannamei samples are consistent, indicating that pond sediments effectively reflect the IHHNV infection status of shrimp farms. IHHNV RT-qPCR detection in pond sediments during the cultivation period from July to September 2022 were observed. IHHNV loads reached 102 copies/μL level in all six farming ponds. Notably, the IHHNV load in the sediment of pond 6-1 reached up to 4.88×102 copies/μL. Viral loads in shrimp tissue samples reached up to 102–103 copies/μL, indicating that IHHNV loads in shrimp tissue samples were higher than those in pond sediments. This study provides a reliable technical method to evaluate IHHNV detection methods in shrimp farming pond sediments, offering a scientific basis for monitoring the health status of cultured animals and supporting the application of eDNA methods for monitoring shrimp pathogens.
Key words: Infectious hypodermal and hematopoietic necrosis virus (IHHNV)    Environmental DNA (eDNA)    Sediment    

随着水产养殖业的不断发展,水生动物疫病发生率呈逐年上升的趋势。危害严重的重大和新发虾类疫病每年会给对虾养殖业造成巨大的经济损失。白斑综合征(white spot disease, WSD)、虾肝肠胞虫病(Enterocytozoon hepatopenaei disease, EHPD)、对虾传染性皮下和造血组织坏死病(infectious hypodermal and haematopoietic necrosis, IHHN)、急性肝胰腺坏死病(acute hepatopancreatic necrosis disease, AHPND)等疾病(Aranguren et al, 2017; Xu et al, 2016; Strand et al, 2011)是当前对虾养殖业的重要疾病,受到全球关注。

对虾传染性皮下和造血组织坏死病毒(IHHNV)是已知虾类病原中最小的病毒,病毒粒子长度为3.9 kb (GenBank检索号:NC-002190),为线性单链DNA (Lightner et al, 2011)。IHHNV能引起凡纳对虾(Penaeus vannamei)和斑节对虾(P. monodon)生长缓慢、大小不均和池塘产量低,可造成对虾养殖业50%的经济损失(Lightner et al, 2011)。存在IHHNV的对虾养殖场典型特点为具有较高的流行率(Aly et al, 2021; Chayaburakul et al, 2004)。IHHNV对世界对虾养殖业造成的经济影响巨大,已被世界动物卫生组织(World Organization for Animal Health, WOAH)列为须向其申报的甲壳类动物病原之一(WOAH, 2023)。

环境DNA(environmental DNA, eDNA)研究始于1987年,被定义为可检测到的短DNA/RNA片段。这些片段来自活体生物的细胞成分或其分泌到周围环境(水、空气、沉积物)的非生物成分短核酸片段(Bass et al, 2015; Díaz-Ferguson et al, 2014; Thomsen et al, 2015)。近年来,eDNA技术已被应用于生态系统的物种多样性研究、资源生物量检测以及濒危物种和入侵物种检测(单秀娟等, 2018; 张浩博等, 2024; 牟铭等; 2021)。在水样、土壤及沉积物等环境中检测eDNA,对于深入了解和保护水生动物生态具有巨大潜力(Goldberg et al, 2015)。对于生物安全调查和风险评估,监测水环境中的病原比监测养殖动物更直接、有效(Jin et al, 2014; Qiao et al, 2016)。近几年对于环境水体中利用eDNA技术检测水生动物病原的研究较为广泛,如鱼类体外寄生虫大西洋鲑鱼三代虫(Gyrodactylus salaris) (Rusch et al, 2018; Fossøy et al, 2020)和鲑鱼甲病毒(salmon alphavirus, SAV) 3亚型(SAV3)(Weli et al, 2021; Bernhardt et al, 2021),甲壳类动物疫病中的对虾白斑综合征病毒(WSSV)、虾肝肠胞虫(EHP)和对虾传染性皮下和造血组织坏死病毒(IHHNV)等病原(Wang et al, 2022; 张娜等, 20212022)。在土壤沉积物方面研究较少,已有研究证明,池塘土壤和沉积物中的病毒可长期存在,是天然病毒库,为病毒传播提供了可能的途径(Honjo et al, 2012; Natividad et al, 2008)。携带IHHNV病原的对虾,可将疾病传播给健康群体,进而导致流行病发生。然而,尚未有研究监测自然环境沉积物中IHHNV的存在,且缺乏可靠的检测和量化环境沉积物中IHHNV的方法。

eDNA技术有助于水生动物疫病主动监测,尤其是宿主在疫病入侵或宿主感染病原后无临床症状的情况下。通过eDNA技术可以有效地了解病原的传播机制并及时制定疾病暴发时的控制措施。对于稀有或具有价值的水生动物等,环境采样优于动物采样,且eDNA检测方法符合动物福利国际标准的需求。综上,eDNA检测在水生动物疫病监测方面具有重要的应用前景。

本研究尝试优化并利用eDNA技术,结合普通PCR和荧光定量PCR (RT-qPCR),比对并优化不同试剂盒提取沉积物核酸效果,同时对对虾养殖池塘沉积物中IHHNV开展核酸检测与评估,以期为养殖动物健康状态提供科学依据,丰富并完善eDNA技术的应用,为其作为标准方法提供可靠数据支持。

1 材料与方法 1.1 样品采集与处理

不同底质沉积物样品:分别采自山东滨州和青岛沿海区域。对采集地点沙底和泥底沉积物进行虾类病原检测,确保无IHHNV等病原。分别将两种底质沉积物过筛,确定其颗粒直径。

对虾养殖池塘沉积物样品:采集自滨州一对虾养殖场。沉积物采集自6个养殖池塘,编号分别为3-1、3-3、3-6、3-8、6-1和6-3,每个池塘随机取6个位点,每个点位共采集3份等体积沉积物样本。使用650 mm× 13.6 mm (长度×孔径)的不锈钢管抓取表层深度约2 cm的沉积物,将底泥混匀后取50 g装入密封袋中。独立包装及编号,干冰保存运输,–80 ℃冰箱冰冻保存。实验前烘干过筛,确定其组成后备用。

感染IHHNV的凡纳对虾阳性组织样品及IHHNV阴性组织样品均为本实验室保存。试剂盒A:土壤DNA提取试剂盒购自天根生化科技(北京)有限公司;试剂盒B:土壤DNA提取试剂盒购自北京索莱宝科技有限公司;试剂盒C:柱式土壤DNA提取试剂盒(BTN71205)购自北京百奥莱博科技有限公司。

1.2 3种DNA提取试剂盒对对虾DNA扩增的有效性比较

实验分为沙底组和泥底组,沉积物灭菌干燥后,每组样品分别取250 mg。向每份沉积物样品中加入对虾组织匀浆液(95%乙醇),添加量分别为200、150、100、50、25、10和5 μL,室温晾干10~15 min,挥发乙醇。分别使用试剂盒A、B和C提取样品(具体提取方法见说明书),50 μL洗脱缓冲液洗脱。试剂盒A的提取方法修改内容为:1)加入250 mg土壤样本步骤,涡旋振荡2 min;2)向样本中加入60 μL缓冲液SC,涡旋振荡20 min至样本混匀,其余步骤与说明书一致。

提取凡纳对虾组织DNA进行十足目(Decapoda)内参PCR扩增。引物由生工生物工程(上海)有限公司合成,扩增片段为848 bp。引物序列:143F 5’-TGC-CTT-ATC-AGCTNT-CGA-TTG-TAG-3’和145R 5’-TTC-AGN-TTT-GCA-ACC-ATA-CTT-CCC-3’。扩增体系:10×PCR buffer 2.5 μL,MgCl2(25 mmol/L) 1.5 μL,上、下游引物(10 μmol/L)各2.5 μL,dNTPs (2.5 mmol/L) 2.0 μL,Taq DNA聚合酶0.1 μL,DNA 1 μL,双蒸水12.9 μL,总体积25 μL。扩增程序:94 ℃ 4 min;94 ℃ 1 min,55 ℃ 1 min,72 ℃ 2 min,39个循环;72 ℃ 5 min。将6 μL PCR扩增产物经1.5%的琼脂糖凝胶电泳。

1.3 回收率测试组织样品制备

为确定使用筛选的试剂盒提取沉积物中DNA后IHHNV和组织样品的回收率之间的关系,将感染IHHNV的凡纳对虾阳性组织样品组织匀浆机匀浆,加入95%乙醇,分别取5 μL和10 μL,室温晾干10~ 15 min,挥发乙醇,使用海洋动物组织基因组DNA提取试剂盒(天根生化科技有限公司)提取DNA,提取方法参考试剂盒说明书,按1.5的方法进行IHHNV RT-qPCR检测。

1.4 沉积物中IHHNV定量检测样品制备

将采集的沙底沉积物和泥底沉积物样品灭菌烘干,称取250 mg分装至1.5 mL离心管中。将含有IHHNV的对虾组织匀浆液(95%乙醇)分别添加至分装好的沉积物中,添加量分别为200、150、100、50、25、10、5 μL,每份样品设3个平行,室温晾干10~ 15 min,挥发乙醇。阴性对照为无IHHNV的对虾组织样品,同时设立无任何添加的沉积物样品对照。沙底沉积物使用试剂盒B,泥底沉积物使用条件优化的试剂盒A,均使用50 μL洗脱缓冲液洗脱。

1.5 实时荧光定量PCR

使用RT-qPCR方法检测IHHNV,引物、探针、反应体系和扩增程序等信息见表 1

表 1 IHHNV引物及探针信息(WOAH, 2023) Tab.1 Pathogenic primers and probe information (WOAH, 2023)

引物和TaqMan探针由生工生物工程(上海)股份有限公司合成。PCR体系:Luna Universal Probe qPCR Mix 10 μL,10 μmol/L的上下游引物各0.8 μL,10 μmol/L的探针0.4 μL,无核酸酶水7 μL,DNA模板1 μL,总体积20 μL。IHHNV反应程序:95 ℃预变性5 min;95 ℃变性15 s,60 ℃延伸30 s,共40个循环。每份样品设置3个平行,同时设立空白对照、阴性对照和阳性对照。每份样品的Ct值取平均值,IHHNV病毒拷贝数通过标准曲线计算(公式:Ct= –4.042log(Sq)+46.956,R2=0.995,E=76.8%)。

1.6 对虾养殖池塘沉积物与池塘生物样品中IHHNV DNA评估

对虾养殖池塘沉积物采集自2022年7—9月凡纳对虾6个养殖池塘,采样位置及采样方式见图 1,自池塘四周及中部随机选择6个采样位置,每个池塘6份沉积物样品,每个位置3个平行,共108份,称取250 mg分装至1.5 mL离心管中,采用本研究筛选优化的eDNA方法对样品开展IHHNV监测。

图 1 对虾养殖池塘采样照片 Fig.1 Sampling points photographs of shrimp farming pond a:3-1对虾养殖池塘,b:用不锈钢管采样,c:沉积物样品,d:采样点模式图。 a: No.3-1 shrimp farming pond; b: Sampling using stainless steel tubes; c: Sample of sediments; d: Sampling pattern diagram.
1.7 对虾养殖池塘凡纳对虾IHHNV检测

对采集自与1.6中同一对虾养殖池塘的凡纳对虾进行IHHNV RT-qPCR检测,取对虾鳃样品30 mg,使用海洋动物组织基因组DNA提取试剂盒(天根生化科技有限公司)提取DNA,提取方法参考试剂盒说明书,按1.5的方法进行IHHNV RT-qPCR检测。

1.8 统计分析

实验数据以平均值±标准差($ \bar x $±SD)表示。使用Excel 2016和IBM SPSS Statistics 27软件进行统计分析。

2 结果 2.1 池塘沉积物中核酸提取方法及底质对DNA获取效果的影响

分别取50 g两种底质沉积物过筛,确定泥底沉积物粒径约为0.09 mm,沙底沉积物粒径约为0.18 mm。为验证从沉积物中提取核酸的有效性,针对泥底和沙底两种底质应用3种试剂盒提取对虾组织DNA,进行PCR扩增,1.5%的琼脂糖凝胶电泳结果见图 23图 2显示,在沙底大粒径沉积物中,试剂盒A、B均可提取到添加量为5 μL的对虾组织匀浆液中的DNA(试剂盒B提取的条带更亮),试剂盒C只检测到添加量为50 μL的对虾组织匀浆液中的DNA。图 3显示,在泥底小粒径沉积物中,试剂盒A可提取到添加量为5 μL的对虾组织匀浆液中的DNA,但是条带较弱,试剂盒B和C均可提取到添加量为50 μL的对虾组织匀浆液中的DNA,但前者比后者条带更亮。由于提取样本为泥沙环境样本,电泳条带存在不同程度拖带、模糊现象。阴性对照正常,在DNA提取和PCR过程中不存在污染情况。

图 2 沙底沉积物不同试剂盒提取DNA的十足目内参基因的PCR检测结果 Fig.2 PCR detection results of internal reference gene (848 bp) of Decapoda from DNA extracted by different kits from sand sediments M:Marker 2000 DNA标记;1~7:试剂盒B样品添加量依次为200、150、100、50、25、10、5 μL;
8~14:试剂盒A样品添加量依次为200、150、100、50、25、10、5 μL;
15~21:试剂盒C样品添加量依次为200、150、100、50、25、10、5 μL;N:阴性对照。
M: Marker 2000; 1~7: The amount of sample added to kit B was 200, 150, 100, 50, 25, 10, and 5 μL.
8~14: The amount of sample added to kit A is 200, 150, 100, 50, 25, 10, and 5 μL;
15~21: The amount of sample added to kit C was 200, 150, 100, 50, 25, 10, and 5 μL; N: Negative control.
图 3 泥底沉积物不同试剂盒提取DNA的十足目内参基因的PCR检测结果 Fig.3 PCR detection results of internal reference gene (848 bp) of Decapoda from DNA extracted by different kits from mud sediments M:Marker 2000 DNA标记;1~7:试剂盒B样品添加量依次为200、150、100、50、25、10、5 μL;
8~14:试剂盒A样品添加量依次为200、150、100、50、25、10、5 μL;
15~21:试剂盒C样品添加量依次为200、150、100、50、25、10、5 μL;N:阴性对照。
M: Marker 2000; 1~7: The amount of sample added to kit B was 200, 150, 100, 50, 25, 10, and 5 μL.
8~14: The amount of sample added to kit A is 200, 150, 100, 50, 25, 10, and 5μL;
15~21: The amount of sample added to kit C was 200, 150, 100, 50, 25, 10, and 5 μL; N: Negative control.

根据试剂盒价格、提取效果、时长等因素综合考虑,选取试剂盒B进行沙底沉积物核酸提取,试剂盒A进行泥底沉积物核酸提取。

2.2 不同底质沉积物中IHHNV检测效果的评估

应用2.1筛选的结果量化评估沙底和泥底池塘沉积物中IHHNV的检测灵敏度。不同添加量在两种底质沉积物中IHHNV RT-qPCR扩增结果如图 4图 5所示,两种底质提取效果比较见图 6。结果显示,随含IHHNV的对虾组织匀浆液添加量的减少,IHHNV病毒载量呈降低趋势,含IHHNV的沙底沉积物中最低检测添加量为5 μL,病毒载量为1.52×102 copies/μL;含IHHNV的泥底沉积物中最低检测添加量为10 μL,病毒载量为1.32×102 copies/μL。5 μL和10 μL体积的匀浆液中的原始病毒载量分别为9.94×102 copies/μL和1.72×103 copies/μL。与添加后提取出来的病毒载量相比,沙底沉积物回收率约为15.30%,泥底沉积物回收率约为7.70%。IHHNV最低检测限浓度相差不到1个数量级,差异不显著。

图 4 不同对虾组织匀浆液添加量下试剂盒B提取含IHHNV沙底沉积物DNA中IHHNV的qPCR扩增动力曲线 Fig.4 RT-qPCR amplification kinetic curves of IHHNV in DNA extracted from sand sediments by B kit with different addition amounts of IHHNV-containing shrimp tissue homogenate 1~7:添加量依次200、150、100、50、25、10、5 μL;P:阳性对照;N:阴性对照。下图同。 1~7: 200, 150, 100, 50, 25, 10, and 5 μL; P: Positive control; N: Negative control. The same below.
图 5 不同对虾组织匀浆液添加量下试剂盒A提取泥底沉积物DNA中IHHNV的qPCR扩增动力曲线 Fig.5 RT-qPCR amplification kinetic curves of IHHNV in DNA extracted from mud sediments by kit A with different addition amounts of IHHNV-containing shrimp tissue homogenate
图 6 不同添加量下两种底质沉积物病毒载量比较 Fig.6 The viral load of the two substrate sediments was extracted under different addition amounts
2.3 对虾养殖池塘沉积物中IHHNV病原检出情况与评估

为了对对虾养殖池塘沉积物中IHHNV病原检出情况与池塘凡纳对虾的对应关系进行综合评估,采用试剂盒A对108份池塘养殖沉积物进行核酸提取和IHHNV检测,结果见图 7,7—9月,对虾养殖池塘沉积物和凡纳对虾中均有阳性检出,且存在一定对应关系。研究表明,池塘沉积物和养殖凡纳对虾样品检测结果一致,养殖池塘沉积物能有效地反映出对虾养殖场IHHNV的感染情况。

图 7 对虾养殖周期池塘沉积物和凡纳对虾中IHHNV病原检出情况 Fig.7 Detection of IHHNV pathogens in pond sediments and P. vannamei during shrimp culture cycle 3-1、3-3、3-6、3-8、6-1、6-3表示采样对虾养殖池塘编号。 3-1, 3-3, 3-6, 3-8, 6-1, and 6-3 indicate shrimpfarming pond number.

对虾养殖池塘7—9月份养殖期间沉积物中IHHNV RT-qPCR检测结果见表 2,结果显示,6个养殖池塘沉积物中IHHNV载量均可达到102 copies/μL;其中6-1池沉积物中IHHNV载量最大,达到4.88× 102 copies/μL。养殖凡纳对虾样品中IHHNV RT-qPCR检测结果见表 3,对虾组织样品中IHHNV载量可达到102~103数量级copies/μL,且对虾组织样品中IHHNV载量较高于养殖池塘沉积物中IHHNV载量。

表 2 各采样池不同时间沉积物中IHHNVRT-qPCR检测结果 Tab.2 The results of IHHNV RT-qPCR detection in sediments at different month in each sampling pool
表 3 各采样池不同时间凡纳对虾中IHHNVRT-qPCR检测结果 Tab.3 The results of IHHNV RT-qPCR detection in P. vannamei shrimp at different month in each sampling pond
3 讨论

目前,养殖水生动物疾病监测工作需要对养殖动物进行致死性采样和筛查,以检测目标病原。eDNA技术的优势即无需采集动物样本便可确定水生系统(例如池塘)的感染状态。随着研究的不断深入,eDNA技术正在持续改进,在其广泛应用并实施动物保护目的之前,需要进行充分的技术评估及有效性的系统评价方法。本研究测试并优化了3种常用的土壤DNA提取试剂盒,通过PCR方法扩增甲壳类动物内参848引物来完成提取效果评价,同时将IHHNV eDNA定量与沙底及泥底沉积物进行比较。筛选使用最有效的提取方法来确定eDNA技术是否可在对虾养殖池塘中应用,以提供准确的数据支持IHHNV存在和流行。

病毒与沉积物颗粒结合导致从沉积物中定量提取病毒比较困难。Metcalf等(1995)已在公共卫生领域开发了从污水污泥和沉积物中提取病毒的方法。增加样品体积可以提高该方法的检测灵敏度。近年来,使用表面活化剂或珠磨机均质化的商业DNA提取试剂盒已可用于从土壤中提取DNA。使用试剂盒提取核酸相对快速且便捷,但病毒类型和样本不同导致适合方法不同(LaBelle et al, 1979)。

传统的eDNA沉积物的提取方法步骤繁琐,耗时长,目前国际使用较多的试剂盒主要有Power Soil试剂盒,且研究结果表明不存在PCR抑制(Eichmiller et al, 2016)。本研究从经济实用的角度出发,针对研究对象选用3种国产土壤DNA提取试剂盒进行实际应用评估。研究结果表明,该3种商品化试剂盒均能成功地从沉积物中检测到IHHNV,但各有其优缺点。在eDNA提取物质量相当的情况下,针对泥底沉积物,天根土壤基因组DNA提取试剂盒比索莱宝土壤基因组DNA提取试剂盒获得更高的eDNA浓度,而二者在沙底沉积物的提取效果相当,高浓度的提取物可能包含更多的物种信息,有利于后续开展有关水生动物疫病监测方面的研究。由于同一种试剂盒对不同目标的研究具有不同效果(Deiner et al, 2015),因此,需要针对特定研究对象筛选出适合的提取方法。本研究优化了天根土壤基因组DNA提取试剂盒的关键步骤,由于泥底沉积物颗粒直径较小,与试剂混合充分较困难,若涡旋时间较短,导致结果平行较差及提取病毒较困难等。根据反复实验结果明确了增加涡旋时间,可获得较高的DNA产量,将涡旋时间优化为加入250 mg土壤时,涡旋振荡2 min;加入60 μL缓冲液SC时,涡旋振荡20 min,取得了明显的改进效果。

非生物因素(如氧气供应、颗粒大小和矿物成分、有机物质负荷)和生物因素(如脱氧核糖核酸酶的降解率)是影响DNA中遗传信息保存的重要限制因素(Coolen et al, 2004; Dell'Anno et al, 2005; Manske et al, 2008)。有研究表明,从环境沉积物中回收锦鲤疱疹病毒(Cyprinid herpesvirus 3,CyHV-3)的回收率为(0.79±0.59)%,超滤法对水体中的CyHV-3浓缩回收率约为(50±3)%(Honjo et al, 20102012)。所以,在水体中的回收率较沉积物中的回收率高,研究表明,采用切向流超滤浓缩水样中IHHNV的平均回收率为67.11%(Wang et al, 2022)。本研究针对5 μL和10 μL的IHHNV阳性对虾组织匀浆液中的原始病毒载量与添加于两种沉积物后提取出来的病毒载量进行比较,沙底沉积物回收率约为15.30%,泥底沉积物中回收率约为7.70%,均有不同程度的损失,粒径的大小对回收率具有一定影响,本研究结果对于不同粒径沉积物中病毒的检测具有一定参考价值。

eDNA产量、回收率、最大化的去除PCR抑制剂等均是评价一种提取方法是否有效的重要因素(Eichmiller et al, 2016)。从水生生态系统采集的eDNA沉积物中含有大量的腐殖质和其他物质,腐殖质和酚类化合物是常见的PCR抑制剂,会对PCR产生抑制,从而减少PCR产物并影响检测率(Kolby et al, 2015; Harper et al, 2019)。有研究表明,从沉积物中提取不同病毒DNA的过程中,因病毒DNA的损失会产生不同的产量(Goldberg et al, 2016)。本研究中,将已知量的对虾组织样品添加到每个沉积物样品中作为外标,可以更准确地计算环境沉积物中IHHNV的浓度,且提取DNA的载量与添加量呈正相关。该方法也可用于评估环境沉积物中其他病毒的载量。

在疫病发生初期,养殖对虾尚未出现临床症状,是疾病早期监测预警的关键阶段,目前国内外还未有关于对养殖池塘沉积物中IHHNV核酸提取和病原检测的相关研究报道。本研究对对虾养殖期内的108份沉积物样品进行IHHNV检测,沉积物中阳性检出率与池塘养殖生物中IHHNV的检测结果一致,对虾组织样品中IHHNV载量较高于养殖池塘沉积物中的IHHNV载量,表明在养殖过程中,携带IHHNV的养殖动物确实可以通过多种途径将病毒传播到养殖环境中。该方法可用于确定养殖过程中养殖池塘是否存在IHHNV。有些采样池的沉积物中IHHNV的RT-qPCR结果与养殖池塘中的养殖生物PCR结果未表现出一致性,可能是由于在沉积物中病毒不是均匀存在的,且沉积物样品比组织样品病毒含量低,难以检出,出现组织样品有阳性检出但沉积物样品呈阴性的情况;若沉积物样品中有阳性检出但养殖生物组织样品未检出则可能是由于沉积物中的病毒存活时间较长(钱瑭毅等, 2021),或者养殖池塘中其他生物样品如蟹类、浮游生物等携带相关病原。eDNA载量可以指示疫病发生的情况,若eDNA样品中的低载量表示感染动物的密度或脱落率较低或者即将发生,eDNA样品中的高载量则表示疫病已经发生。本研究表明,eDNA技术能有效地监测沉积物中的病原体,该技术在水生动物疫病的监测中具有重要的应用价值。调查结果显示,沉积物成为IHHNV的潜在储存库。沉积物中IHHNV的感染活性、存活时间、环境因素的影响等方面有待后续的深入研究。

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