Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats

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.     

环境DNA(eDNA)宏条形码技术对枝角类浮游动物物种鉴定及其生物量监测研究

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。     

基于eDNA技术的渭河浮游动物多样性及关键种生态位特征

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B_i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.     

基于生物导向的水生态健康监测及评估概述

环境监测是水生态健康监测与评估的重要环节,基于物理、化学监测的传统水质监测通常仅能提供独立的数据信息,不能全面、直观地反映水环境状况。基于生物等生命体导向的水生态监测通过生物对环境的响应,能够直接反应复杂水体状况,在水环境健康监测与评估中占据重要地位。基于病原微生物、指示生物介绍了生物监测中的常规生物指标,总结了包括藻类、无脊椎动物和鱼类在内的常见指示生物在不同类型污染水体中的环境指示作用。从生物毒性效应出发介绍了常用的毒性效应测试方法、分析了污染物在不同生物学水平的响应,从而指明生物毒性效应在水环境健康评估中的发展优势。再从生态完整性角度阐述了生态完整性评价的一般方法和新兴分子生物学技术在水生态健康评估中的应用。重点指出环境毒理学和分子生物学在水环境监测的优势,以期为更加科学精确地进行水生态健康监测预警提供支撑。     

环境DNA宏条形码监测湖泊真核浮游植物的精准性

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18 S-V9 ...     

Use of environmental DNA in assessment of fish functional and phylogenetic diversity

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.     

浮游藻类环境DNA宏条形码监测引物的比较与验证

环境DNA (eDNA)宏条形码技术通量高、重复性好,在未来生态环境监测中有巨大的应用潜力。目前,浮游藻类环境DNA监测仍处在发展阶段,尚缺乏统一的浮游藻类扩增引物。利用同一个野外环境样本,比较8对通用引物在浮游藻类环境DNA监测中的差异,为初步建立规范化的浮游藻类环境DNA监测方法提供支撑。结果表明,不同引物对浮游藻类扩增存在明显偏好性,靶向扩增16S rDNA的引物主要检出硅藻,其次是隐藻和绿藻;靶向扩增18S rDNA的1391、AD3和ANF 3对引物具有较高的浮游藻类扩增效率和物种辨识度,分别检出67、62、63个浮游藻属,其检出的浮游藻类的相对丰度排序均为硅藻>绿藻>隐藻>金藻>甲藻,可以作为通用引物用于浮游藻类环境DNA宏条形码监测。     

The use of environmental DNA in invasive species surveillance of the Great Lakes commercial bait trade

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     

Using environmental DNA to assess population‐wide spatiotemporal reserve use

Scientists increasingly rely on protected areas to assist in biodiversity conservation, yet the efficacy of these areas is rarely systematically assessed, often because of underfunding. Still, adaptive management strategies to maximize conservation success often rely on understanding the temporal and spatial dynamism of populations therein. Examination of environmental DNA (eDNA) is a time and cost‐effective way to monitor species’ distribution, and quantitative polymerase chain reaction (qPCR) provides information on organismal abundance. To date, however, such techniques remain underused for population assessments in protected areas. We determined eDNA concentration of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) to describe its occurrence, range, and use of the Tian e‐Zhou National Nature Reserve in Hubei, China, across seasons and hydrological depths. Despite the observation that total eDNA concentrations were highest in surface waters in summer, finless porpoise eDNA concentrations were significantly higher in deeper waters than in surface waters in summer. During the breeding season (spring), eDNA signals were site specific and restricted to the core area of the reserve. However, postbreeding eDNA concentrations were widespread across the reserve, encompassing sites previously thought to be unfrequented by the species. Our results suggest spatiotemporal idiosyncrasies in site, depth, and seasonal use of the reserve and a propensity for postbreeding population dispersal. With eDNA and qPCR we were able to assess an entire population's use of a protected area. Illuminating nuances in habitat use via eDNA could be valuable to set pragmatic conservation goals for this, and other, species.     

BALB／C鼠睾丸组织中冷诱导RNA结合蛋白的cDNA克隆与序列分析

冷诱导RNA结合蛋白(Cold inducible RNA-binding protein,CIRP)在多种冷应激细胞(包括重组中国仓鼠卵巢细胞)中被发现.迄今为止,冷应激对活体生物基凶表达的影响还未见报道.和细胞相比,生物体具有更加复杂的冷应激调节机制.本研究以冷处理的BALB/C鼠为实验动物,从其睾丸组织巾克隆出了CIRP的cDNA.结果表明,CIRP在生物体中能够被低温诱导,可能防止生物体遭受冷损伤.根据克隆的cDNA所推测的氨基酸序列与GenBank上公布的小鼠、大鼠、人类、牛蛙、美西螈、非洲爪蟾胚胎细胞和卵母细胞的CIRP氨基酸序列同源性分别为100%、99.40%、95.5%、67.4%、58.4%、76.9%和79.1%.这表明CIRP在生物进化过程中是高度保守的,可能具有多种生理功能.因此,这一研究将为探索人类和动物冷应激分子机制创立系统试验模型和奠定新的实践基础.图5参14