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1.
环境DNA(eDNA)宏条形码(Metabarcoding)技术越来越多地被应用于环境中物种定性识别,但如何定量监测物种在环境中的丰度尚未得到解决。本研究以太湖流域常见的5种浮游动物拟同形溞、大型溞、蚤状溞、多刺裸腹溞、老年低额溞为研究对象,建立了一种基于eDNA宏条形码技术的物种定量方法,并与实时荧光定量PCR(qPCR)相比较,研究了eDNA宏条形码技术多物种定量的准确性。结果表明,PCR引物对eDNA宏条形码的物种检测和定量影响显著。313 bp COI313引物对浮游动物物种覆盖度高,但是物种间DNA扩增的偏好性大,不适用于eDNA宏条形码定量检测。基于COI序列重新设计的短COI116引物能够同时检测出所有5个物种。荧光定量PCR(qPCR)物种拷贝数与物种相对占比呈正相关。eDNA宏条形码所检出每个物种的序列数与qPCR定量拷贝数高度一致。综上,eDNA宏条形码技术可实现对浮游动物物种的半定量检测,在生物多样性监测和生物完整性评价有显著的应用价值。  相似文献   
2.
Conservation and management of marine biodiversity depends on biomonitoring of marine habitats, but current approaches are resource-intensive and require different approaches for different organisms. Environmental DNA (eDNA) extracted from water samples is an efficient and versatile approach to detecting aquatic animals. In the ocean, eDNA composition reflects local fauna at fine spatial scales, but little is known about the effectiveness of eDNA-based monitoring of marine communities at larger scales. We investigated the potential of eDNA to characterize and distinguish marine communities at large spatial scales by comparing vertebrate species composition among marine habitats in Qatar, the Arabian Gulf (also known as the Persian Gulf), based on eDNA metabarcoding of seawater samples. We conducted species accumulation analyses to estimate how much of the vertebrate diversity we detected. We obtained eDNA sequences from a diverse assemblage of marine vertebrates, spanning 191 taxa in 73 families. These included rare and endangered species and covered 36% of the bony fish genera previously recorded in the Gulf. Sites of similar habitat type were also similar in eDNA composition. The species accumulation analyses showed that the number of sample replicates was insufficient for some sampling sites but suggested that a few hundred eDNA samples could potentially capture >90% of the marine vertebrate diversity in the study area. Our results confirm that seawater samples contain habitat-characteristic molecular signatures and that eDNA monitoring can efficiently cover vertebrate diversity at scales relevant to national and regional conservation and management.  相似文献   
3.
环境DNA(eDNA)技术作为水生态系统生物多样性监测的新手段,能够从微观角度对生物群落结构特征进行分析.基于渭河干流eDNA浮游动物OTUs分类信息数据及水环境参数,采用多样性指数、非度量多维尺度分析、聚类分析和关联网络分析等方法,探究了浮游动物的多样性和群落结构变化特征,揭示了关键种的生态位分化及其环境适应性.结果表明,浮游动物群落在物种组成、丰度、多样性和空间异质性方面均存在显著差异(P<0.01).Chao1指数、ACE指数、Shannon指数和Simpson指数的均值分别为22.25、22.38、2.32和0.68,下游生物多样性明显高于上游.群落中的关键种与其他物种间连接度较高,具有高节点度、中心性和模块化特征.关键种(类)的OTUs生态位宽度Bi变化范围为0.38~0.80,中生态位种类占全部关键种(类)的63%,生态位重叠程度总体较高.水环境要素与浮游动物群落结构和生态位变化密切相关,其中总氮和水温是其主要限制因子,对浮游动物群落结构变化具有重要影响.  相似文献   
4.
长江生物多样性在人为影响下面临严重威胁,物种监测是生物多样性保护的基础,为完善长江水生态监测体系,实现高效无损伤的物种监测,在长江中下游干流3个江段(新滩、安庆和芜湖)采集水样,建立长江水样环境DNA宏条形码物种检测体系并评估其有效性.结果表明:①长江中下游环境DNA宏条形码检测到32个物种,包括20种鱼类、1种水生哺乳动物(长江江豚)和11种陆生动物,其中鱼类物种包括鲤形目、鲇形目、鲈形目和鲱形目,其种数占鱼类总种数的比例分别为60%、25%、10%和5%.②长江中下游渔获物中资源量居首位的鲤形目在环境DNA调查中序列数最多,占鱼类总序列的96.2%,其次为鲱形目(占比为3.5%),鲇形目和鲈形目占比较低,分别为0.2%和0.1%,4个类目序列相对丰度与渔获物种资源量组成差异较大.③环境DNA调查次数约占传统渔获物调查次数的几十至几百分之一,采样时间不足努力量最少的渔获物调查的1%,检测到的鱼类种数为传统调查总数的31%~49%.④安庆采样点位于长江中下游长江江豚密度最高的江段,其环境DNA检出率和序列相对丰度在3个采样点中均最高.研究显示:长江水样环境DNA包含水陆复合生态系统的生物多样性信息,利用水样环境DNA宏条形码可检测不同类群的水生和陆生物种;对于鱼类物种检测,环境DNA宏条形码比传统调查方法效率更高,可对传统调查结果进行补充;环境DNA宏条形码生物多样性检测主要受分子标记体系和核酸序列数据库限制,获取全面的物种多样性和资源量信息需要对检测分析方法进行进一步完善.   相似文献   
5.
Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment‐based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in the tropics. We constructed a record of afro‐alpine plants retrieved from DNA preserved in sediment cores from 2 volcanic crater sites in the Albertine Rift, eastern Africa. The record extended well beyond the onset of substantial anthropogenic effects on tropical mountains. To ensure high‐quality taxonomic inference from the sedaDNA sequences, we built an extensive DNA reference library covering the majority of the afro‐alpine flora, by sequencing DNA from taxonomically verified specimens. Comparisons with pollen records from the same sediment cores showed that plant diversity recovered with sedaDNA improved vegetation reconstructions based on pollen records by revealing both additional taxa and providing increased taxonomic resolution. Furthermore, combining the 2 measures assisted in distinguishing vegetation change at different geographic scales; sedaDNA almost exclusively reflects local vegetation, whereas pollen can potentially originate from a wide area that in highlands in particular can span several ecozones. Our results suggest that sedaDNA may provide information on restoration targets and the nature and magnitude of human‐induced environmental changes, including in high conservation priority, biodiversity hotspots, where understanding of preanthropogenic impact (or reference) conditions is highly limited. Uso de ADN Sedimentario Antiguo como una Herramienta Novedosa de Conservación para la Biodiversidad Tropical de Grandes Altitudes  相似文献   
6.
环境DNA宏条形码监测湖泊真核浮游植物的精准性   总被引:3,自引:1,他引:2       下载免费PDF全文
环境DNA(eDNA)宏条形码(metabarcoding)技术是一种基于分子的生物多样性高效监测手段,近年来越来越多地被应用于生态环境中生物要素的监测和评估.开展eDNA宏条形码监测技术的标准化和规范化研究,是将其业务化推广应用的前提.本研究以高原湖泊滇池和抚仙湖的真核浮游藻类为研究对象,探究了基于18S-V9宏条形码测序深度对生物多样性监测的影响;通过分析平行样本间物种分类单元的交叉率及α多样性的变异率(coefficient of variation,CV),评估了eDNA宏条形码监测真核浮游藻类结果的精确性.并采用eDNA宏条形码监测数据评估了滇池和抚仙湖北的真核藻类多样性.结果表明:①测序深度显著影响宏条形码技术检出物种的数目,适合滇池和抚仙湖北的eDNA真核藻类多样性分析的测序深度为≥30000条;②重复样品(n=3)间遗传分类单元(OTU)交叉率达到45.97%±1.67%,可注释分类单元(属)交叉率达到64.21%±3.25%,α多样性的变异率<10%.③基于现有DNA条码数据库,滇池和抚仙湖北分别鉴定出真核藻类75属和90属,覆盖本地历史记录形态学物种的62.5%和71.05%.④滇池不同水深的真核藻类多样性无明显差异,抚仙湖的真核藻类多样性具有显著垂直分布特征.和抚仙湖北部相比,滇池真核藻类多样性显著偏低,滇池南部的生物多样性明显高于中部和北部(P<0.05).综上,本研究建立了eDNA宏条形码技术监测结果的精确性评价方法,验证了基于18S-V9引物监测真核浮游植物多样性的可行性,结果可促进eDNA宏条形码监测技术推广与应用.  相似文献   
7.
环境DNA宏条形码技术在蓝藻群落监测中的应用   总被引:1,自引:0,他引:1       下载免费PDF全文
全球气候变化下的蓝藻水华大规模暴发成为重要的环境问题,对蓝藻准确、高效和实时的监测是蓝藻水华防控的关键.近年来,环境DNA(environmental DNA,eDNA)宏条形码技术开始应用于蓝藻群落监测,弥补了显微镜镜检法物种鉴定难和受主观经验影响大的缺点.eDNA宏条形码为快速和大规模蓝藻群落监测提供了可能,其应用尚处于初步探索阶段,数据处理方法尚不成熟,因此有必要从引物选择、序列聚类、注释方法和绝对定量4个层面系统综述eDNA宏条形码技术在蓝藻群落监测中的研究进展,以推进eDNA宏条形码在蓝藻群落监测中的应用.引物选择应针对目标蓝藻类群,16S rRNA基因数据库涵盖蓝藻物种范围广,是最常用的eDNA宏条形码,但16S-23S rRNA基因间隔区域(internal transcribed spacer,ITS)和功能基因在属内物种间具有较好的区分效果,为eDNA宏条形码在蓝藻物种水平注释提供可能.序列聚类一般通过设定物种间分类阈值进行OTUs聚类,但可能丢失序列相似度高于分类阈值的不同物种;序列差异低至单核苷酸变异方法的应用进一步区分了隐蔽的物种和生态型,产生的序列具有生物学意义,可以实现跨数据集间的比较分析.在注释方法上,基于数据库参考序列距离相似度的注释方法,注释结果的分辨率和准确度不高;基于系统进化位置的注释方法,提升了注释结果的准确度,反映了物种间的进化关系.加入外源DNA的内标法,以及基于细胞体积和基因拷贝数目关系的细胞体积校正系数法为eDNA宏条形码物种丰度的绝对定量提供了可能.   相似文献   
8.
Assessing the impact of global changes and protection effectiveness is a key step in monitoring marine fishes. Most traditional census methods are demanding or destructive. Nondisturbing and nonlethal approaches based on video and environmental DNA are alternatives to underwater visual census or fishing. However, their ability to detect multiple biodiversity factors beyond traditional taxonomic diversity is still unknown. For bony fishes and elasmobranchs, we compared the performance of eDNA metabarcoding and long-term remote video to assess species’ phylogenetic and functional diversity. We used 10 eDNA samples from 30 L of water each and 25 hr of underwater videos over 4 days on Malpelo Island (pacific coast of Colombia), a remote marine protected area. Metabarcoding of eDNA detected 66% more molecular operational taxonomic units (MOTUs) than species on video. We found 66 and 43 functional entities with a single eDNA marker and videos, respectively, and higher functional richness for eDNA than videos. Despite gaps in genetic reference databases, eDNA also detected a higher fish phylogenetic diversity than videos; accumulation curves showed how 1 eDNA transect detected as much phylogenetic diversity as 25 hr of video. Environmental DNA metabarcoding can be used to affordably, efficiently, and accurately census biodiversity factors in marine systems. Although taxonomic assignments are still limited by species coverage in genetic reference databases, use of MOTUs highlights the potential of eDNA metabarcoding once reference databases have expanded.  相似文献   
9.
张莉  张远  林佳宁  王书平 《环境科学》2019,40(9):4052-4060
微型真核浮游植物是海洋生态系统中能量流动和物质循环的关键环节,对维持海洋生态系统的稳定发挥着关键的作用.本研究首次应用DNA metabarcoding技术探讨黄海微型真核浮游植物的物种组成及多样性,对比分析ITS、18S r DNA V4和18S r DNA V9扩增子条件下微型真核浮游植物的群落结构及多样性水平,并探讨了其多样性与温度、盐度的响应关系.结果表明:①基于ITS扩增子获得的微型真核浮游植物中绿藻门所占比例较高,而基于18S r DNA V4和18S r DNA V9扩增子获得的甲藻门相对丰度较高.②基于18S r DNA V9扩增子获得的微型真核浮游植物的ACE、Chao1、Shannon和Simpson指数较ITS和18S r DNA V4扩增子更高,而且其门、纲、目和科的数目较高.③黄海微型真核浮游植物的Shannon指数与温度呈现出显著正相关的关系(P 0. 01),而与盐度呈现出显著负相关的关系(P 0. 05).本研究通过对比不同扩增子条件下黄海微型真核浮游植物的群落结构及丰度特征,丰富了黄海微型真核浮游植物的认识,可为今后该海域微型真核浮游植物的生态学研究、生物多样性监测、生物资源动态变化及持续开发生产等方面的分析提供科学依据.  相似文献   
10.
Over 180 non‐native species have been introduced in the Laurentian Great Lakes region, many posing threats to native species and ecosystem functioning. One potential pathway for introductions is the commercial bait trade; unknowing or unconcerned anglers commonly release unused bait into aquatic systems. Previous surveillance efforts of this pathway relied on visual inspection of bait stocks in retail shops, which can be time and cost prohibitive and requires a trained individual that can rapidly and accurately identify cryptic species. Environmental DNA (eDNA) surveillance, a molecular tool that has been used for surveillance in aquatic environments, can be used to efficiently detect species at low abundances. We collected and analyzed 576 eDNA samples from 525 retail bait shops throughout the Laurentian Great Lake states. We used eDNA techniques to screen samples for multiple aquatic invasive species (AIS) that could be transported in the bait trade, including bighead (Hypophthalmichthys nobilis) and silver carp (H. molitrix), round goby (Neogobius melanostomus), tubenose goby (Proterorhinus marmoratus), Eurasian rudd (Scardinius erythrophthalmus), and goldfish (Carassius auratus). Twenty‐seven samples were positive for at least one target species (4.7% of samples), and all target species were found at least once, except bighead carp. Despite current regulations, the bait trade remains a potential pathway for invasive species introductions in the Great Lakes region. Alterations to existing management strategies regarding the collection, transportation, and use of live bait are warranted, including new and updated regulations, to prevent future introductions of invasive species in the Great Lakes via the bait trade. El Uso del ADN Ambiental en la Vigilancia de Especies Invasoras del Mercado de Carnada Comercial de los Grandes Lagos  相似文献   
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