基于环境DNA metabarcoding的西轩岛近海鱼类多样性研究

鱼类多样性的保护对于生态系统的科学管理和资源的可持续利用至关重要。环境DNA metabarcoding技术的出现和应用为水生生物的调查与监测带来了强有力的技术革新。本研究以浙江舟山近海岛屿——西轩岛为例,设计了4个不同采样站位,先后于2019年2月(冬季)、5月(春季)和11月(秋季)共采集水样12个,通过环境DNA提取、扩增、高通量测序以及生物信息学分析,对西轩岛近海鱼类多样性进行了分析,同时评估了鱼类多样性的时空差异。结果显示,共监测到鱼类33种,隶属于12目26科32属,其中,鲈形目(Perciformes)种类最多,共19种,约占所有种类的57.6%。不同采样季节的多样性指数和均匀度指数均存在显著差异,表明季节可能是影响西轩岛近海鱼类多样性的因素之一。综合时间和空间分析的结果显示,在繁殖季节且远离舟山本岛一侧的采样点监测到的鱼种数量更多。通过比对之前传统渔业资源调查的结果发现,不同季节优势种存在较大变化,可能与采样点数量较少且集中有关。进化树富集结果显示,各季节的优势鱼种与传统调查手段的结果有较大差异,表明目前环境DNA仍不能完全替代传统调查方法,但可以将环境DNA方法与传统的调查方法相结合,以确保监测结果的准确性和可靠性。     

应用环境DNA技术对邵伯湖浮游动物物种检测的初步研究

为掌握邵伯湖浮游动物物种组成,利用环境DNA技术于2018年11月对其浮游动物群落进行了监测.在邵伯湖15个采样点同步进行了水样采集,抽滤后进行了DNA提取,利用线粒体DNA 12S rRNA引物进行PCR扩增,并进行了高通量测序.结果 显示,从二代测序的1114482条DNA序列中,比对得到浮游动物OTUs数68个....     

Introduction of exotic fish species and decline of native species in the lower Po basin,north‐eastern Italy

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Comparison of traditional and environmental DNA survey methods for detecting rare and abundant freshwater fish

1. Detecting rare species is often a necessity for conservation and management, yet challenging for many field survey methods. Environmental DNA (eDNA) is a highly promising solution that has been shown to outperform many established survey methods.
2. Macquarie perch (Macquaria australasica) is an endangered native species that has declined significantly in range and abundance. Detection of M. australasica was compared with an abundant alien fish species (Oncorhynchus mykiss) using eDNA and three conventional survey methods: gill nets, electrofishing and fyke nets.
3. eDNA occupancy estimates for both fish species were compared using four different models to investigate what effect these differences have on false positives and false negatives for the rare and common fish species. These models used unadjusted eDNA detections in water samples, eDNA detections that have been screened using a limit of detection method to remove potential false positives, eDNA data supplemented with a second survey method, or eDNA data augmented with sequencing of positive polymerase chain reaction replicates.
4. eDNA surveying as a single detection method was found to be more efficient and sensitive compared with each capture method separately and combined. Occupancy estimates for the common and rare species did not vary significantly between the four site occupancy-detection models, suggesting that supplementary data may not have as much effect on occupancy estimates compared with other approaches such as temporal or spatial sampling.
5. We conclude that eDNA outperforms the three established survey methods for both a rare and common freshwater fish species. Although there was no significant effect of augmenting eDNA survey methods with other survey data, additional data may improve confidence in detection, and provide confirmatory evidence for unexpected or new detections of a species.

     

人工模拟条件下环境DNA宏条形码技术的定量分析初探

近年来,环境DNA宏条形码技术(eDNA metabarcoding)在水生生态系统生物多样性评估等相关领域中得到广泛应用,因其具有快速测算群落中物种丰度的潜能,eDNA宏条形码技术成为资源保护和管理中颇具应用前景的调查工具.虽然大量证据表明eDNA高通量测序获得的reads数与自然环境中生物相对数量具有相关性,但一直...     

长江中下游干流环境DNA样本鱼类物种检测的初步研究

为开发适用于长江鱼类的环境DNA检测体系,在长江中下游干流24个采样点同步采集水样,抽滤后提取环境DNA,利用线粒体细胞色素B简并引物进行PCR扩增,扩增产物克隆测序得到419条序列,通过在Gen Bank核酸序列数据库进行BLAST序列比对确定物种信息,从来源于17个采样点的115条匹配成功的序列中,共检测到10种鱼类序列,代表15种鱼类。     

Fish diversity assessment in the headwaters of the Volga River using environmental DNA metabarcoding

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Novel tools for early detection of a global aquatic invasive,the zebra mussel Dreissena polymorpha

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Validation of environmental DNA (eDNA) as a detection tool for at‐risk freshwater pearly mussel species (Bivalvia: Unionidae)

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A simple,rapid method for detecting seven common invasive fish species in Europe from environmental DNA

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环境DNA在水域生态中的研究进展

环境DNA(environmental DNA,eDNA)是指生物通过皮肤脱落、唾液、配子、粪便以及分泌物等方式向环境中释放的游离DNA。环境DNA具有敏感性、准确性以及容易操作等诸多优势,更能实时地反映物种多样性以及生物量等,近两三年受到了世界各地学者们的大量关注。水域环境高度复杂,环境DNA在水域生态领域具有重要的应用价值。本文主要从环境DNA在水域生态的应用以及研究方法方面对环境DNA的研究做一小结,同时介绍环境DNA在其他生境的应用,以期为水域生态的研究提供参考。     

Using occupancy and species distribution models to assess the conservation status and habitat use of the goldline darter (Percina aurolineata) in Georgia,USA

The goldline darter (Percina aurolineata) is threatened by recent increases in urbanisation in the Coosawattee River watershed, but no studies have addressed their current status. Similarly, limited data on habitat use make it difficult to understand factors that may impact this species. We compared occurrence data before (1996–2000) and after (2009–2011) a period of rapid development and population growth within the watershed. Single‐season occupancy models were built to account for imperfect species detection and to identify habitat covariates. MaxEnt was used to identify important stream reaches for conservation and to understand landscape scale factors correlated with the distribution of goldline darters. Our results indicate a high proportion of sites occupied upstream of Carters Lake during the historic and recent time periods, with no evidence of decline. However, occurrences of goldline darters for sites in Talking Rock Creek and the lower Coosawattee River were sparse in the historic period and absent during the recent period. The probability of detecting goldline darters is low and was positively associated with the occurrence of small substrate. Species distribution models were strongly influenced by watershed area and elevation and indicated a high probability of suitable habitat within the Coosawattee River and large tributaries upstream of Carters Lake. While goldline darter occupancy is currently stable upstream of Carters Lake, continued urbanisation is a threat to long‐term persistence. We recommend additional monitoring and describe a protocol that allows for precise estimates of species occupancy while minimising the risk of sampling‐related mortality.     

Sound discrimination of two sympatric,threatened fish species allows for their in situ mapping

1. Human impacts on marine ecosystems are increasing and the number of fish species listed in the Red List is constantly growing. In the Mediterranean Sea, seven of the 10 bony fishes defined as Threatened by the IUCN are known to be vocal, including the target species of this study: the shi drum (Umbrina cirrosa Linnaeus, 1758) and the brown meagre (Sciaena umbra Linnaeus, 1758). As a result, non-invasive passive acoustic monitoring (PAM) can be used to pinpoint their distribution at sea. However, for PAM to be effective, reliable acoustic discrimination is required because the sounds they emit during reproduction are remarkably similar (i.e. short broadband pulsed sounds).
2. The shi drum and the brown meagre are closely related, elusive, vocal sciaenids, partially overlapping in their ecological niche. During summer 2019, three PAM surveys were conducted along the tidal inlets of the Venice lagoon (Italy). Here, the calls of both species have been recognized according to their temporal features: shi drum sounds were made up of a lower number of longer pulses with a different envelope, repeated at a lower rate than those of the brown meagre. Further, shi drum and brown meagre sounds of different origins (aquaculture and semi-natural conditions) were analysed and compared with those collected during the survey of the study area in order to validate the field collected data.
3. Call discrimination allowed for a fine-scale species mapping, showing a partially overlapping distribution of the two species along the inlets. This is the first case in which two sciaenids have been documented to share their reproductive habitat in the Mediterranean Sea.
4. This study demonstrates that it is feasible to acoustically monitor the target species even in those parts of the Mediterranean Sea where they co-exist. This, in its turn, could provide managers with the required data for effective conservation measures to be implemented.

     

The sceptical optimist: challenges and perspectives for the application of environmental DNA in marine fisheries

Application of environmental DNA (eDNA) analysis has attracted the attention of researchers, advisors and managers of living marine resources and biodiversity. The apparent simplicity and cost‐effectiveness of eDNA analysis make it highly attractive as species distributions can be revealed from water samples. Further, species‐specific analyses indicate that eDNA concentrations correlate with biomass and abundance, suggesting the possibility for quantitative applications estimating abundance and biomass of specific organisms in marine ecosystems, such as for stock assessment. However, the path from detecting occurrence of an organism to quantitative estimates is long and indirect, not least as eDNA concentration depends on several physical, chemical and biological factors which influence its production, persistence and transport in marine ecosystems. Here, we provide an overview of basic principles in relation to eDNA analysis with potential for marine fisheries application. We describe fundamental processes governing eDNA generation, breakdown and transport and summarize current uncertainties about these processes. We describe five major challenges in relation to application in fisheries assessment, where there is immediate need for knowledge building in marine systems, and point to apparent weaknesses of eDNA compared to established marine fisheries monitoring methods. We provide an overview of emerging applications of interest to fisheries management and point to recent technological advances, which could improve analysis efficiency. We advise precaution against exaggerating the present scope for application of eDNA analysis in fisheries monitoring, but also argue that with informed insights into strengths and limitations, eDNA analysis can become an integrated tool in fisheries assessment and management.     

Biodiversity values of remnant freshwater floodplain lagoons in agricultural catchments: evidence for fish of the Wet Tropics bioregion,northern Australia

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First application in Turkey of the European Non‐native Species in Aquaculture Risk Analysis Scheme to evaluate the farmed non‐native fish,striped catfish Pangasianodon hypophthalmus

The European Non‐native Species in Aquaculture Risk Analysis Scheme (ENSARS) was used to assess one of the most popular aquaculture species in the world, the striped catfish Pangasianodon hypophthalmus (Sauvage, 1878), in two locations of southern Anatolia (Turkey). The overall mean risk score generated for P. hypophthalmus by the ENSARS Organism module (which assesses the risks of introduction, establishment, dispersal and impact) indicated that the species poses a medium risk under current climatic conditions. All other ENSARS modules rendered scores that indicated a moderately low risk under current climatic conditions. However, the risks of introducing novel diseases and the actual use (e.g. deliberate introduction to the natural habitats or food market) of the species both attracted scores indicating a medium risk. Confidence levels were medium or high for all modules except the Socio‐economic, with low confidence values also attributed to the risks for farming process of the organism, and its overall risk of spread into the wild during farming procedures and to marketing impacts. Recommendations are provided for further use of the ENSARS scheme, especially for a a priori assessment of potential aquaculture species in Turkey, where the sector has been remarkably developing in the last decades.     

Living on the edge: Traits of freshwater fish species at risk in Canada

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Environmental DNA as a non‐invasive sampling tool to detect the spawning distribution of European anadromous shads (Alosa spp.)

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环境DNA在长江江豚监测中的应用

为了从水体环境中提取到高质量的eDNA环境DNA(environmentalDNA,eDNA),应用于长江中长江江豚(Neophocaenaphocaenoidesasaeorientalis)的分布调查,本研究比较了滤膜孔径和水样保存方式对eDNA获取的影响,同时对比了eDNA技术与传统调查法对长江江豚的检测结果。结果显示水样抽滤时间与滤膜孔径大小呈负相关关系,且都可以检出目标生物;水样采集后需在6 h内完成抽滤处理,或在冷藏条件下短期保存48 h;长江流域江苏段中观测到长江江豚出现的8个检测点均检测出长江江豚eDNA,而在10个未观测到长江江豚的水域中有3个检测出其eDNA。研究结果表明,相比传统目视监测方法, eDNA技术在长江江豚监测中不仅具有较高的准确性,还具有更高的灵敏性,可作为长江江豚种群调查的有效辅助检测工具。