赤水河鱼类资源的现状与保护

赤水河是长江上游右岸一级支流,为长江上游珍稀特有鱼类国家级自然保护区的重要组成部分。为了了解赤水河鱼类资源现状,于2007年4-10月在赤水河流域进行了鱼类资源调查。在干、支流共51个采样点采集了鱼类标本;对茅台镇、赤水市和合江县三个江段的渔获物进行了统计和分析。共采集到鱼类119种(亚种),隶属于5目16科75属。其中25种为该水域的新记录;34种为长江上游特有鱼类,尤其是宽唇华缨鱼(Sinocrossocheilus labiatus)仅分布于赤水河。在上、中、下游分别采集到鱼类36、61和100种。宽鳍鱲(Zacco platypus)、中华倒刺鲃(Spinibarbus sinensis)、光泽黄颡鱼(Pelteobagrus nitidus)、张氏(Hemiculter tchangi)和蛇鮈(Saurogobio dabryi)为赤水河中主要的经济鱼类,同时,各江段渔获物的组成也存在一定的差别。本研究表明,赤水河流域鱼类种类相对丰富,但过度捕捞和涉水活动导致鱼类资源出现了一定程度的衰减。     

基于eDNA metabarcoding探究北京市主要河流鱼类分布及影响因素

使用eDNA宏条形码(eDNA metabarcoding)和地笼法检测了北京市3条水系在夏季和秋季两个季节的鱼类多样性, 旨在研究北京市鱼类群落的空间格局特征, 探索适用于北京鱼类生物多样性监测及保护的新方法。结果表明: 在北京市的34个采样点中, 利用eDNA metabarcoding共检测出鱼类55种, 显著高于传统方法所捕获的鱼类种数(35种), 鱼类组成以鲤形目和鲈形目为主。山区河流清水鱼的多样性要显著高于城区河流, 城区河流(北运河水系)群落结构较为单一, 以鲫(Carassius auratus)、麦穗鱼(Pseudorasbora parva)、泥鳅(Misgurnus anguillicaudatus)等耐污种为优势种; 山区河流(潮白河水系及大清河水系)以宽鳍鱲(Zacco platypus)、拉氏鱥(Rhynchocypris lagowskii)、马口鱼(Opsariichthys uncirostris)等为优势种。不同季节影响清水鱼群落结构的环境因子不同, 夏季主要是总溶解固体和电导率, 秋季主要是海拔和温度。清水鱼丰富度与环境因子及人类活动的相关性表明, 清水鱼的丰富度随着总溶解固体及灯光指数增加而显著降低, 且均与海拔、温度等存在显著相关性。本研究证明了eDNA metabarcoding方法用于监测北京市鱼类多样性及其时空分布的可行性。     

环境DNA技术在鱼类生态学中的应用研究进展

全球渔业衰退是21世纪人类面临的重要挑战之一。为了有效地遏制鱼类资源的衰退,精确的鱼类生态调查是其首要任务。传统的鱼类监测以渔获物采集与形态学鉴定为主,往往耗时耗力且效果不佳,已无法满足现阶段大尺度上的精确调查。环境DNA （eDNA）技术作为一种近年来新兴的鱼类生态调查方法,其与传统方法相比具有灵敏度高、经济高效、采样受限小且对生态系统无干扰的优势,目前其已被广泛地应用于鱼类物种监测、多样性调查、生物量评估以及繁殖活动监测等方面的研究。然而,eDNA技术在鱼类生态学研究的具体应用中暴露出的一些问题将会影响其监测结果的精确性,诸如操作流程的不规范、基因数据库的不完善以及eDNA在环境中生态学过程的不明确等。鉴于上述原因,首先对eDNA技术的发展历程、分析流程以及eDNA技术在鱼类生态学研究领域中的研究进展进行了综述,而后着重分析了eDNA技术的发展当前所面临的困难与挑战,并提出了相应的解决方案,最后对eDNA技术未来在鱼类生态学研究领域中的发展趋势做出了展望。通过本研究,以期能够为eDNA技术在鱼类生态学领域中的准确应用提供理论基础。     

环境DNA技术在长江口鱼类多样性分析中的应用

研究采用高通量测序技术对长江口水域环境DNA(Environmental DNA, eDNA)样品进行分析,并与传统渔业资源调查结果对比,阐述长江口鱼类群落在其生境内的多样性特征,探讨eDNA技术在长江口水域鱼类多样性研究中的应用前景。结果显示, eDNA技术共检测到10目21科41属45种鱼类,各站点鱼类丰富度之间无显著差异,而多样性之间存在显著差异性。底拖网法共捕获11目16科29属33种鱼类。有18种鱼类在两种方法中均检测到,占鱼类总数的30%。两种方法检测到的鱼类中均以鲈形目(Perciformes)最多,其次是鲤形目(Cypriniformes),两种方法的结果均表明刀鲚(Coilia nasus)和凤鲚(Coilia mystus)为优势物种。研究表明环境DNA技术在长江口水域渔业资源监测中具有可行性,在禁捕环境下可根据实际情况采用不同方法对渔业资源进行监测。     

基于环境DNA宏条形码的洱海鱼类多样性研究

研究使用环境DNA宏条形码(eDNA metabarcoding)检测洱海鱼类多样性,探索适用于洱海鱼类多样性监测和保护的新方法。通过水样采集、过滤、eDNA提取、遗传标记扩增、测序与生物信息分析的环境DNA宏条形码标准化分析流程,从洱海16个采样点中获得可检测的9个采样点数据,共检测出17种鱼类,其中土著种5种、外来种12种;鲫(Carassius auratus)、鳙(Hypophthalmichthys nobilis)、麦穗鱼(Pseudorasbora parva)、泥鳅(Misgurnus anguillicaudatus)和食蚊鱼(Gambusia affinis)为优势种。研究结果表明虽然环境DNA宏条形码无法完全替代传统的鱼类监测方法,但作为一种新兴的生物多样性监测手段,其可用于快速检测洱海鱼类多样性及其空间分布。     

独龙江流域冬季鱼类多样性及其分布特点

2004年10—11月,对独龙江的鱼类资源进行了调查,根据不同的海拔及生境在整个独龙江流域共计设置了26个采样点,采集鱼类标本883号。对各采集点渔获物的统计分析的结果显示:(1)独龙江干流、支流的鱼类生物量、物种多样性,随海拔的上升呈下降趋势;(2)干流的Shannon-Wiener指数、物种均匀性指数均高于支流;(3)除了独龙裂腹鱼、大鳍异齿在整个独龙江流域均有分布外,其余5种鱼类的分布与海拔因子的变化有明显的关系。     

黄浦江和苏州河上游鱼类多样性组成的时空特征

为初步了解黄浦江和苏州河的鱼类多样性组成及其时空分布特征,2005年6月至2006年5月,对黄浦江上游河段的淀峰、松浦大桥两个站点,以及苏州河上游河段的白鹤、黄渡两个站点进行了逐月的鱼类监测。四个站点共采集到鱼类44种,隶属10目14科35属,其中苏州河上游30种,隶属6目10科25属,黄浦江上游39种,隶属10目13科32属。黄浦江上游鱼类的物种多样性明显高于苏州河上游,白鹤、松浦大桥、淀峰之间的鱼类群落为中等相似,黄渡与松浦大桥、淀峰之间的鱼类群落为中等不相似。各站点的鱼类具明显的季节性变化,夏、秋季大于冬、春季。四个站点的鱼类均以杂食性和定居性的物种为主,杂食性鱼类物种数占51.5–62.5%。松浦大桥站的江海洄游性和河湖洄游性鱼类数量明显多于其他站点。鱼类物种的时空重现率计算结果反映了黄浦江、苏州河上游各水域的鱼类群落具相对独立性。初步研究结果表明长期恶化的水质问题和较差的水系连通度可能是影响苏州河上游鱼类多样性的关键因素,而黄浦江具更大水域面积,以及较好水质状况和水系连通度,有利于丰富鱼类多样性。     

长江下游秋季近岸鱼类群落特征

为了解长江下游秋季近岸鱼类群落特征,于2016年9月分区对长江干流下游近岸水域进行了鱼类调查.结果 表明:共采集鱼类38种,隶属于6目11科31属,其中鲤科鱼类为绝对优势物种,占总物种数的63.2％;群落组成中以小型鱼类占绝对优势,其占总物种数和总渔获数量的比例分别为81.6％和98.0％;群落优势种为贝氏鳖(Hemi...     

浅谈鱼类繁殖的多样性

鱼类的怀卵量和产卵量差别很大。如虎鲨每次产卵2枚 ;中华多刺鱼怀卵量百余粒 ,银鱼怀卵量 2 0 3～34 5 2 0粒 ,银鲳怀卵量 8万～ 30万粒 ,江鳕怀卵量 5万～30 0万粒 ,青鱼怀卵量 2 6万～ 6 95万粒 ,翻车鱼屯怀卵量竟高达 3亿粒。同为鱼类 ,相差如此悬珠。日常雌鱼满肚怀卵现象非常普遍 ,然而灰星鲨腹中怀的却是小鲨鱼 ,这些都说明鱼类的生殖方式是多种多样的。其生殖方式可归纳为3种类型 :1　卵生大多数鱼类的生殖方式是卵生。其卵一般无卵壳保护 ,卵子产出体外 ,能否受精、孵化、成活 ,往往是“听天由命”,所以产卵量很大 ,成活率却很低。…     

青藏高原鱼类的多样性

青藏高原有着特殊的生态环境,孕育着特殊的鱼类多样性.裂腹鱼类是青藏高原的优势类群,其演化过程与青藏高原的隆起密切相关;高原鳅属鱼类和鮡科鱼类也是青藏高原鱼类区系的重要成分.高原鱼类在藏族人民中有着自身的文化和历史意义,很多地方群众"敬鱼为神".目前,青藏高原地区的鱼类面临着过度捕捞、环境破坏和外来鱼种的威胁,资源量明显下降,亟待有效地加以保护.     

Assessment of fish communities using environmental DNA: Effect of spatial sampling design in lentic systems of different sizes

Freshwater fish biodiversity is quickly decreasing and requires effective monitoring and conservation. Environmental DNA (eDNA)‐based methods have been shown to be highly sensitive and cost‐efficient for aquatic biodiversity surveys, but few studies have systematically investigated how spatial sampling design affects eDNA‐detected fish communities across lentic systems of different sizes. We compared the spatial patterns of fish diversity determined using eDNA in three lakes of small (SL; 3 ha), medium (ML; 122 ha) and large (LL; 4,343 ha) size using a spatially explicit grid sampling method. A total of 100 water samples (including nine, 17 and 18 shoreline samples and six, 14 and 36 interior samples from SL, ML and LL, respectively) were collected, and fish communities were analysed using eDNA metabarcoding of the mitochondrial 12S region. Together, 30, 35 and 41 fish taxa were detected in samples from SL, ML, and LL, respectively. We observed that eDNA from shoreline samples effectively captured the majority of the fish diversity of entire waterbodies, and pooled samples recovered fewer species than individually processed samples. Significant spatial autocorrelations between fish communities within 250 m and 2 km of each other were detected in ML and LL, respectively. Additionally, the relative sequence abundances of many fish species exhibited spatial distribution patterns that correlated with their typical habitat occupation. Overall, our results support the validity of a shoreline sampling strategy for eDNA‐based fish community surveys in lentic systems but also suggest that a spatially comprehensive sampling design can reveal finer distribution patterns of individual species.     

Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding

Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. Our objective was to determine whether environmental DNA (eDNA) sampling and metabarcoding analysis can be used to accurately measure species diversity in aquatic assemblages with differing structures. We manipulated the density and relative abundance of eight fish and one amphibian species in replicated 206‐L mesocosms. Environmental DNA was filtered from water samples, and six mitochondrial gene fragments were Illumina‐sequenced to measure species diversity in each mesocosm. Metabarcoding detected all nine species in all treatment replicates. Additionally, we found a modest, but positive relationship between species abundance and sequencing read abundance. Our results illustrate the potential for eDNA sampling and metabarcoding approaches to improve quantification of aquatic species diversity in natural environments and point the way towards using eDNA metabarcoding as an index of macrofaunal species abundance.     

Species‐level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization

DNA extraction from environmental samples (environmental DNA; eDNA) for metabarcoding‐based biodiversity studies is gaining popularity as a noninvasive, time‐efficient, and cost‐effective monitoring tool. The potential benefits are promising for marine conservation, as the marine biome is frequently under‐surveyed due to its inaccessibility and the consequent high costs involved. With increasing numbers of eDNA‐related publications have come a wide array of capture and extraction methods. Without visual species confirmation, inconsistent use of laboratory protocols hinders comparability between studies because the efficiency of target DNA isolation may vary. We determined an optimal protocol (capture and extraction) for marine eDNA research based on total DNA yield measurements by comparing commonly employed methods of seawater filtering and DNA isolation. We compared metabarcoding results of both targeted (small taxonomic group with species‐level assignment) and universal (broad taxonomic group with genus/family‐level assignment) approaches obtained from replicates treated with the optimal and a low‐performance capture and extraction protocol to determine the impact of protocol choice and DNA yield on biodiversity detection. Filtration through cellulose‐nitrate membranes and extraction with Qiagen's DNeasy Blood & Tissue Kit outperformed other combinations of capture and extraction methods, showing a ninefold improvement in DNA yield over the poorest performing methods. Use of optimized protocols resulted in a significant increase in OTU and species richness for targeted metabarcoding assays. However, changing protocols made little difference to the OTU and taxon richness obtained using universal metabarcoding assays. Our results demonstrate an increased risk of false‐negative species detection for targeted eDNA approaches when protocols with poor DNA isolation efficacy are employed. Appropriate optimization is therefore essential for eDNA monitoring to remain a powerful, efficient, and relatively cheap method for biodiversity assessments. For seawater, we advocate filtration through cellulose‐nitrate membranes and extraction with Qiagen's DNeasy Blood & Tissue Kit or phenol‐chloroform‐isoamyl for successful implementation of eDNA multi‐marker metabarcoding surveys.     

Effects of sampling seasons and locations on fish environmental DNA metabarcoding in dam reservoirs

Environmental DNA (eDNA) analysis has seen rapid development in the last decade, as a novel biodiversity monitoring method. Previous studies have evaluated optimal strategies, at several experimental steps of eDNA metabarcoding, for the simultaneous detection of fish species. However, optimal sampling strategies, especially the season and the location of water sampling, have not been evaluated thoroughly. To identify optimal sampling seasons and locations, we performed sampling monthly or at two‐monthly intervals throughout the year in three dam reservoirs. Water samples were collected from 15 and nine locations in the Miharu and Okawa dam reservoirs in Fukushima Prefecture, respectively, and five locations in the Sugo dam reservoir in Hyogo Prefecture, Japan. One liter of water was filtered with glass‐fiber filters, and eDNA was extracted. By performing MiFish metabarcoding, we successfully detected a total of 21, 24, and 22 fish species in Miharu, Okawa, and Sugo reservoirs, respectively. From these results, the eDNA metabarcoding method had a similar level of performance compared to conventional long‐term data. Furthermore, it was found to be effective in evaluating entire fish communities. The number of species detected by eDNA survey peaked in May in Miharu and Okawa reservoirs, and in March and June in Sugo reservoir, which corresponds with the breeding seasons of many of fish species inhabiting the reservoirs. In addition, the number of detected species was significantly higher in shore, compared to offshore samples in the Miharu reservoir, and a similar tendency was found in the other two reservoirs. Based on these results, we can conclude that the efficiency of species detection by eDNA metabarcoding could be maximized by collecting water from shore locations during the breeding seasons of the inhabiting fish. These results will contribute in the determination of sampling seasons and locations for fish fauna survey via eDNA metabarcoding, in the future.     

环境DNA metabarcoding及其在生态学研究中的应用

环境DNA metabarcoding(eDNA metabarcoding)是指利用环境样本(如土壤、水、粪便等)中分离的DNA进行高通量的多个物种(或高级分类单元)鉴定的方法。近年来,该方法引起了学者的广泛关注,逐渐应用于生物多样性研究、水生生物监测、珍稀濒危物种和外来入侵物种检测等生态学领域。介绍环境DNA metabarcoding的含义和研究方法;重点介绍环境DNA metabarcoding在物种监测、生物多样性研究和食性分析等生态学领域中的应用;总结环境DNA metabarcoding应用于生态学研究领域面临的挑战并对该方法的发展进行展望。     

Assessment of littoral algal diversity from the northern Gulf of Mexico using environmental DNA metabarcoding

Traditional methods for algal biodiversity monitoring are costly and time inefficient because they rely on high‐level taxonomic expertise to address species identity problems involving phenotypic plasticity and morphological convergence. These problems are exacerbated in regions such as the Gulf of Mexico, that has a limited history of phycological exploration, but that are economically important or threatened by numerous anthropogenic stressors. Given the high pace of disturbance to natural systems, there is a critical need for expedient and cost‐effective tools for the study of benthic algal communities. Here we document the use of environmental DNA metabarcoding, using the partial LSU rDNA and 23S rDNA plastid molecular markers, to elucidate littoral algal diversity in the Northern Gulf of Mexico. We assigned 73.7% of algal OTUs to genus and 59.6% to species ranks. Our current study detected molecular signals for 35 algal/protist species with no previous reports in the Gulf of Mexico, thus providing an important, molecular‐validated, baseline of species richness for this region. We also make several bioinformatic recommendations for the efficient use of high‐throughput sequence data to assess biological communities.     

Metabarcoding技术在真菌多样性研究中的应用

由于受到气候变化、土地利用变化及环境污染等诸多因素的干扰, 真菌多样性受到不容忽视的威胁, 亟需得到保护。构建物种数据库是实现真菌多样性研究和保护的重要前提。近年来兴起的DNA条形码及metabarcoding技术能够在很大程度上弥补传统鉴定方法的缺陷, 可对真菌物种进行大规模、准确、快速、高效地鉴定。本文梳理了metabarcoding技术在真菌物种多样性评估、真菌多样性影响机制和真菌古生态重建等研究中的应用, 同时强调了metabarcoding技术用于真菌多样性研究尚处于初期阶段, 在构建有效参照数据库、优化实验流程以及升级生物信息学工具等方面仍需要进一步的完善。建议加强真菌分类学家、生态学家以及计算机工具研发工程师之间的合作, 共同解决metabarcoding技术在真菌多样性研究及应用中面临的问题, 为宏观尺度上真菌多样性保护提供更加科学的依据。     

Seasonal and spatial variability of zooplankton diversity in the Poyang Lake Basin using DNA metabarcoding

Freshwater ecosystems face multiple threats to their stability globally. Poyang Lake is the largest lake in China, but its habitat has been seriously degraded because of human activities and natural factors (e.g. climate change), resulting in a decline in freshwater biodiversity. Zooplankton are useful indicators of environmental stressors because they are sensitive to external perturbations. DNA metabarcoding is an approach that has gained significant traction by aiding ecosystem conservation and management. Here, the seasonal and spatial variability in the zooplankton diversity were analyzed in the Poyang Lake Basin using DNA metabarcoding. The results showed that the community structure of zooplankton exhibited significant seasonal and spatial variability using DNA metabarcoding, where the community structure was correlated with turbidity, water temperature, pH, total phosphorus, and chlorophyll‐a. These results indicated habitat variations affected by human activities and seasonal change could be the main driving factors for the variations of zooplankton community. This study also provides an important reference for the management of aquatic ecosystem health and conservation of aquatic biodiversity.