基于环境DNA宏条码和底拖网的珠江河口鱼类多样性

文章采用环境DNA宏条码和底拖网对珠江河口鱼类多样性进行了研究, 并对两种方法进行了比较。利用环境DNA宏条码检测到了175种鱼类, 而利用底拖网采集到了47种鱼类, 结合两种方法共检测出179种鱼类, 隶属于15 目63科128属。其中两种方法共同识别了鱼类43种, 占总检测物种的24.02%, 基于底拖网的调查未能收集到基于环境DNA宏条码检测到的大多数物种。根据Shannon指数和Simpson指数显示, DNA宏条码所检测珠江河口鱼类群落α多样性显著高于底拖网方法(P<0.05)。两种方法的PCoA结果均显示珠江河口鱼类群落存在空间结构, 基于环境DNA宏条码的分析显示空间重叠更多。两种方法基于冗余分析均显示溶解氧和盐度是影响鱼类群落结构的主要环境因子。研究表明, 环境DNA 宏条形码是一种环保且可靠的评估方法, 将其搭载到现有调查可以更好地了解河口鱼类多样性。     

太湖鱼类群落结构及多样性

为了解太湖鱼类群落结构和多样性的分布特征,于2009-2010年利用拖网等网具对该水域的鱼类资源进行了调查.结果表明:本次调查共采获鱼类50种,隶属10目15科40属,其中鲤形目种类最多,占总数的68％;鱼类生态类型以湖泊定居性种类为主,群落优势种为湖鲚(Coilia ectenes taihuensis)、间下鱵(Hyporhamphus intermedius)和陈氏短吻银鱼(Salangichthys jordani)等小型鱼类;与历史资料相比,太湖鱼类的物种数量下降,优势种组成发生较大变化,鱼类群落中体质量＜30 g的小型鱼类占绝对优势,渔业资源小型化趋势明显.由于过度捕捞和湖泊环境恶化,鱼类群落生物多样性指数均表现偏低,物种丰富度指数D为1.54,多样性指数H’N、H’w分别为0.21和0.46,均匀度指数J'N、.J'w分别为0.07和0.14;太湖各湖区间鱼类种群和多样性的差别一定程度上反映出鱼类群落结构与湖泊营养盐、透明度等环境特征相适应的特点.     

黄海山东海域春、秋季鱼类群落多样性

根据2006年春季(5月)和秋季(10月)黄海山东海域疏目变水层双拖网调查数据,作者对该海域鱼类群落多样性、空间分布及长度谱特征进行了研究。调查共捕获鱼类61种,其中鲈形目种类最多(27种),其次为鲱形目(8种)和鲉形目(7种);按摄食类型可分为浮游动物食性、浮游动物/底栖动物食性、底栖动物食性、底栖动物/游泳动物食性、游泳动物食性、杂食性、碎屑食性7个类群,其中浮游动物食性占渔获物重量组成的82.5%。春、秋季鱼类群落均主要由小型种类占优势,春季优势种有3种,为玉筋鱼(Ammodytes personatus)、鳀(Engraulis japonicus)和方氏锦鳚(Pholis fangi),秋季优势种有5种,分别是鳀、青鳞小沙丁鱼(Sardinella zunasi)、玉筋鱼、小黄鱼(Larimichthys polyactis)和赤鼻棱鳀(Thryssa kammalensis)。丰富度指数(D)、Shannon-Wiener多样性指数(H’)、均匀度指数(J’)的空间异质性明显,表现出近岸海域(尤其是青岛-乳山南部近岸海域)较高,深水区较低的态势,但多样性指数的季节间差异不显著。资源量与Shannon-Wiener多样性指数(H’)、均匀度指数(J’)、功能团多样性指数(FD)均呈负相关关系,与种类丰富度指数(D)则无相关关系。春、秋季鱼类群落长度谱曲线斜率均小于-0.2,而截距均大于10,与该海域1985年及2000年的研究结果相比,长度谱斜率显著降低、截距显著增加,这与小型个体种类占优势密切相关。与历史资料相比,黄海山东海域鱼类群落多样性下降,小型个体比例上升,资源呈衰退趋势。     

禁渔后西凉湖鱼类物种和功能多样性时空格局及其与水环境因子的关系

为解析禁渔后西凉湖鱼类群落组成、结构与多样性格局,探明影响鱼类多样性的关键环境因子,于2020年11月和2021年4月在西凉湖开展了鱼类群落与环境因子调查,共设置15个样点,分布于西-西凉湖(XLH1-8)和东-西凉湖(XLH9-15)。结果表明秋季与总氮、叶绿素a和高锰酸盐指数呈正相关,西-西凉湖与总磷和浊度呈正相关。本次调查共采集鱼类31种,隶属6目8科26属,其中鲤形目最多(24种),占77.4%。优势种为似鱎、?、鲫和红鳍原鲌,其中似鱎为主要优势种。非度量多维尺度排序分析(NMDS)结果表明,西凉湖鱼类群落结构具有显著的季节和空间差异(P<0.05)。在秋季,东-西凉湖的Shannon-Wiener指数、Simpson指数和Pielou指数均显著高于西-西凉湖(P<0.05); Margalef指数显著高于西-西凉湖(P<0.05);在秋季,东-西凉湖的功能丰富度指数显著高于西-西凉湖(P<0.05);功能分散度指数显著高于西-西凉湖(P<0.05)。Pearson相关性分析结果表明, Shannon-Wiener指数、Simpson指数、Piel...     

西沙群岛礁栖鱼类物种多样性及其食性特征

通过新的方法(即潜水调查法)调查了西沙群岛浅水区的礁栖鱼类, 并从食性角度分析鱼类群落特征及其对水质环境变化的响应。2006年5-6月, 对西沙群岛6个岛礁(东岛、永兴岛、羚羊礁、金银岛、华光礁和中建岛)共10个站位的礁栖鱼类种类、数量和长度进行了调查, 结合公开资料(FishBase等)确定鱼类食性。共记录到29科71属119种鱼, 其中50种是新记录。至此, 西沙群岛的鱼类总记录已达到717种。从不同站位来看, 永兴岛西的种类数量和Shannon-Wiener多样性指数均最高。多数鱼种分布范围狭小。摄食浮游动物和底栖无脊椎动物的鱼类是优势类群, 而草食性、杂食性和食物链顶端食性的鱼类数量和生物量较低, 反映出西沙群岛珊瑚礁生态系统整体上健康稳定。永兴岛的杂食性鱼类的数量比例和生物量比例均高于其他岛礁, 反映出鱼类群落已对水体富营养化产生响应。     

汉江支流堵河鱼类群落结构及多样性

基于堵河2018年6月-2019年5月渔获物,分析了鱼类群落组成及变化、优势种以及群落多样性时空分布特征,讨论了外界环境扰动作用对鱼类群落结构和生物多样性的影响.结果 表明:调查期间共采集鱼类38种,分属4目8科,其中鲤形目鱼类最多(26种),占总种数的68.4％.群落优势种为鳙(Aristichthys nobili...     

黄河兰州段鱼类多样性与保护

兰州市是黄河唯一穿城而过的省会城市, 是黄河流域综合治理与高质量发展的重要区域, 了解其鱼类多样性现状及变化趋势对黄河流域水生态保护尤为重要。本文于2020年7-10月对黄河干流兰州段及其4条支流(庄浪河、大通河、湟水河和宛川河)开展了鱼类多样性、分布及影响因素调查, 以Shannon-Wiener多样性指数、Pielou均匀度指数、Simpson优势度指数、Cody和Routledge指数、Bray-Curtis相异性系数对黄河兰州段5条河流鱼类群落进行评估, 同时通过相对多度(relative abundance, RA)判定优势种, 利用非度量多维标度排序(non-metric multidimensional scaling, NMDS)展示物种空间分布格局。本次调查获得鱼类20种, 隶属于4目6科15属。其中, 国家II级重点保护野生动物1种, 受威胁鱼类4种, 中国特有鱼类7种, 黄河特有鱼类4种。区系组成属青藏高原区高原西北亚区, 其中鲤形目种类占绝对优势, 优势种为东方高原鳅(Triplophysa orientalis)、粗壮高原鳅(T. robusta)、鲫(Carassius auratus)和麦穗鱼(Pseudorasbora parva)。庄浪河和黄河干流的α多样性较高。β多样性分析结果表明, 黄河干流与庄浪河、大通河、湟水河和宛川河间的鱼类物种明显不相似; 大通河与湟水河之间以及黄河干流与宛川河之间的鱼类物种组成相似性较高。NMDS分析表明, 黄河兰州段鱼类被划分为地理空间上相近的4个地理群。水利设施建设、外来物种和水体污染可能影响了黄河兰州段鱼类多样性和分布。本研究为黄河兰州段鱼类多样性保护和科学管理以及黄河流域生态保护和高质量发展提供了基础调查数据。     

抚河源自然保护区鱼类群落结构及主要物种生长特征

基于2018年5月和7月对江西省抚河源自然保护区的鱼类资源调查数据, 研究了该保护区鱼类群落结构及主要物种生长特征。结果显示, 该保护区鱼类共有4目9科18属20种, 其中鲤形目鱼类最多, 占总种数的55%。优势种为侧条光唇鱼(Acrossocheilus parallens)、鲫(Carassius auratus)、宽鳍鱲(Zacco platypus)。保护区主要以肉食性和杂食性、底层性、定居性鱼类为主。物种多样性分析显示, 杨溪港鱼类多样性指数和丰富度指数最高(H′=1.52; D=2.07), 天井溪鱼类多样性指数和丰富度指数最低(H′=0.84; D=0.99)。主要鱼类的体长体重线性回归拟合方程式分析显示, 侧条光唇鱼(b=2.903)、鲫(b=3.039)和马口鱼(Opsariichthys bidens)(b=2.994)呈等速增长, 银(Squalidus argentatus, b=2.459)和宽鳍鱲(b=3.398)呈异速增长。β多样性分析显示, 杨溪港与桐斜河(β_r=12.3)、横路河(β_r=10.8)、天井溪(β_r=11.6)间的生境差异较大, 鱼类物种分化较大。相似性分析显示, 洪水坑与桐斜河(C_j=0.09)、天井溪(C_j=0.13)、胡洋溪(C_j=0.14)间的鱼类物种组成相似性较低。研究结果补充了保护区鱼类群落结构和主要鱼类生长特征的基础资料, 为抚河源自然保护区鱼类资源的保护和管理提供理论依据。     

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。     

江西柘林水库鱼类群落结构及功能多样性分析

为了解江西柘林水库鱼类群落结构和多样性的时空变化特征,研究鱼类物种多样性和功能多样性的关系,于2020年9月至2021年4月在该水库调查分析了鱼类物种组成、优势度及群落物种多样性和功能多样性。结果表明,共采集鱼类53种,分属于5目12科36属。其中,鲤形目(38种)种类最多,占调查物种数的71.69%,柘林水库上、中、下游库区分别采集到鱼类36、40和32种,各库区均以鲤形目鱼类为主,分别占采集物种数的72.97%、85.00%和75.00%。优势物种主要是■(Hemiculter leucisculus)、鳙(Aristichthys nobilis)和黄尾鲴(Xenocypris davidi),重要种主要是草鱼(Ctenopharyngodon idella)、鲢(Hypophthalmichthys molitrix)、鳊(Parabramis pekinensis)、鲫(Carassius auratus)、蒙古红鲌(Erythroculter mongolicus)等。鱼类群落结构季节性差异大于空间格局差异,主要表现为秋季和冬季之间;生物多样性指数Margalef和功能丰富...     

DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River

The Yangtze River is the longest river in China and is divided into upstream and mid‐downstream regions by the Three Gorges (the natural barriers of the Yangtze River), resulting in a complex distribution of fish. Dramatic changes to habitat environments may ultimately threaten fish survival; thus, it is necessary to evaluate the genetic diversity and propose protective measures. Species identification is the most significant task in many fields of biological research and in conservation efforts. DNA barcoding, which constitutes the analysis of a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence, has been widely used for species identification. In this study, we collected 561 COI barcode sequences from 35 fish from the midstream of the Yangtze River. The intraspecific distances of all species were below 2% (with the exception of Acheilognathus macropterus and Hemibarbus maculatus). Nevertheless, all species could be unambiguously identified from the trees, barcoding gaps and taxonomic resolution ratio values. Furthermore, the COI barcode diversity was found to be low (≤0.5%), with the exception of H. maculatus (0.87%), A. macropterus (2.02%) and Saurogobio dabryi (0.82%). No or few shared haplotypes were detected between the upstream and downstream populations for ten species with overall nucleotide diversities greater than 0.00%, which indicated the likelihood of significant population genetic structuring. Our analyses indicated that DNA barcoding is an effective tool for the identification of cyprinidae fish in the midstream of the Yangtze River. It is vital that some protective measures be taken immediately because of the low COI barcode diversity.     

Comparing local‐ and regional‐scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods

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Genetic diversity and population structure of a cyprinid fish (Ancherythroculter nigrocauda) in a highly fragmented river

In this study, samples of Ancherythroculter nigrocauda, an endemic fish in the upper Yangtze River, were collected above and below dams in the Longxi River, a tributary of the upper Yangtze River, China, to investigate the genetic impacts of dams. The mitochondrial cytochrome b gene (cyt b) and 13 microsatellite (SSR) loci were used to analyze whether dams have resulted in loss of genetic diversity of the two fragmented populations or caused genetic differentiation between them. The results showed that the haplotype diversity (0.488; 0.486), nucleotide diversity (0.084%; 0.082%) and average expected heterozygosity (0.652; 0.676) of the two populations were all at a low level, and recent bottlenecks were detected. However, there was no genetic differentiation detected by the low genetic differentiation index (F_st, cyt b: ?0.1677, p = 0.99707; SSR: 0.00259, p = 0.81427). Besides, 11 pairs of half‐sibling relationship were found between the two populations indicating that there were individual movements and gene flow between them. This could be the larvae moving from upstream to downstream when water spilled over dams in flooding season. Therefore, our analysis showed that the dams have caused a loss of genetic diversity of the populations of A. nigrocauda in the Longxi River, blocked the active upstream movement but allowing passive downstream drift of larvae.     

Environmental DNA detection of rare and invasive fish species in two Great Lakes tributaries

The extraction and characterization of DNA from aquatic environmental samples offers an alternative, noninvasive approach for the detection of rare species. Environmental DNA, coupled with PCR and next‐generation sequencing (“metabarcoding”), has proven to be very sensitive for the detection of rare aquatic species. Our study used a custom‐designed group‐specific primer set and next‐generation sequencing for the detection of three species at risk (Eastern Sand Darter, Ammocrypta pellucida; Northern Madtom, Noturus stigmosus; and Silver Shiner, Notropis photogenis), one invasive species (Round Goby, Neogobius melanostomus) and an additional 78 native species from two large Great Lakes tributary rivers in southern Ontario, Canada: the Grand River and the Sydenham River. Of 82 fish species detected in both rivers using capture‐based and eDNA methods, our eDNA method detected 86.2% and 72.0% of the fish species in the Grand River and the Sydenham River, respectively, which included our four target species. Our analyses also identified significant positive and negative species co‐occurrence patterns between our target species and other identified species. Our results demonstrate that eDNA metabarcoding that targets the fish community as well as individual species of interest provides a better understanding of factors affecting the target species spatial distribution in an ecosystem than possible with only target species data. Additionally, eDNA is easily implemented as an initial survey tool, or alongside capture‐based methods, for improved mapping of species distribution patterns.     

Identifying spawning sites and other critical habitat in lotic systems using eDNA “snapshots”: A case study using the sea lamprey Petromyzon marinus L.

Many aquatic species of conservation concern exist at low densities and are inherently difficult to detect or monitor using conventional methods. However, the introduction of environmental (e)DNA has recently transformed our ability to detect these species and enables effective deployment of limited conservation resources. Identifying areas for breeding, as well as the ecological distribution of species, is vital to the survival or recovery of a conservation species (i.e., areas of critical habitat). In many species, spawning events are associated with a higher relative abundance of DNA released within an aquatic system (i.e., gametes, skin cells etc.), making this the ideal time to monitor these species using eDNA techniques. This study aims to examine whether a “snapshot” eDNA sampling approach (i.e., samples taken at fixed points in chronological time) could reveal areas of critical habitat including spawning sites for our target species Petromyzon marinus. We utilized a species‐specific qPCR assay to monitor spatial and temporal patterns in eDNA concentration within two river catchments in Ireland over three consecutive years. We found that eDNA concentration increased at the onset of observed spawning activity and patterns of concentration increased from downstream to upstream over time, suggesting dispersal into the higher reaches as the spawning season progressed. We found P. marinus to be present upstream of several potential barriers to migration, sometimes in significant numbers. Our results also show that the addition of a lamprey‐specific fish pass at an “impassable” weir, although assisting in ascent, did not have any significant impact on eDNA concentration upstream after the pass had been installed. eDNA concentration was also found to be significantly correlated with both the number of fish and the number of nests encountered. The application of snapshot sampling techniques for species monitoring therefore has substantial potential for the management of low‐density species in fast‐moving aquatic systems.     

Seasonal dynamics of riverine fish communities using eDNA

As fish communities are a major concern in rivers ecosystems, we investigated if their environmental (e)DNA signals vary according to the sampling period or hydromorphological conditions. Three rivers were studied over a year using eDNA metabarcoding approach. The majority of the species (c. 80%) were detected all year round in two rivers having similar hydromorphological conditions, whereas in the river affected by an upstream lake waterflow, more species were detected sporadically (42%). For all the rivers, in more than 98% of the occasional detections, the reads abundance represented <0.4% of the total reads per site and per sampling session. Even if the majority of the fish communities remained similar over the year for each of the three rivers, specific seasonal patterns were observed. We studied if the waterflow or the reproduction period had an effect on the observed dynamics. Waterflow, which influences eDNA downstream transportation, had a global influence in taxonomic richness, while the fishes' reproductive period had only an influence on certain species. Our results may help selecting the best sampling strategy according to research objectives. To study fish communities at local scale, seasons of low waterflow periods are recommended. This particularly helps to restraint effects of external eDNA coming from connections with other aquatic environment (tributaries, lakes, wetlands, sewage effluents, etc.). To obtain a more integrative overview of the fish community living in a river basin, high waterflow or breeding seasons are preferable for enhancing species detection probability, especially for rare species.     

Space invaders: Searching for invasive Smallmouth Bass (Micropterus dolomieu) in a renowned Atlantic Salmon (Salmo salar) river

Humans have the ability to permanently alter aquatic ecosystems and the introduction of species is often the most serious alteration. Non‐native Smallmouth Bass (Micropterus dolomieu) were identified in Miramichi Lake c. 2008, which is a headwater tributary to the Southwest Miramichi River, a renowned Atlantic Salmon (Salmo salar) river whose salmon population is dwindling. A containment programme managed by the Department of Fisheries and Oceans, Canada (DFO) was implemented in 2009 to confine Smallmouth Bass (SMB) to the lake. We utilized environmental DNA (eDNA) as a detection tool to establish the potential escape of SMB into the Southwest Miramichi River. We sampled at 26 unique sites within Miramichi Lake, the outlet of Miramichi Lake (Lake Brook), which flows into the main stem Southwest Miramichi River, and the main stem Southwest Miramichi River between August and October 2017. We observed n = 6 positive detections located in the lake, Lake Brook, and the main stem Southwest Miramichi downstream of the lake. No detections were observed upstream of the confluence of Lake Brook and the main stem Southwest Miramichi. The spatial pattern of positive eDNA detections downstream of the lake suggests the presence of individual fish versus lake‐sourced DNA in the outlet stream discharging to the main river. Smallmouth Bass were later confirmed by visual observation during a snorkeling campaign, and angling. Our results, both eDNA and visual confirmation, definitively show Smallmouth Bass now occupy the main stem of the Southwest Miramichi.     

珠江水系鱼类群落多样性空间分布格局

珠江是我国南方第一大河,是我国重要淡水渔业生产基地和水生生物资源基因库。珠江鱼类在维持生物多样性、提供鱼类种质资源方面举足轻重。但是到目前为止,关于其鱼类空间分布格局的研究甚少。特别是近几十年来各种水工建设和过度捕捞使得渔业资源急剧衰退,鱼类空间分布的研究显得尤为重要。2015年对珠江全流域13个站位进行了全面调查,共采集渔获物10119尾,隶属于94种72属17科。鲤科鱼类占显著优势,其次种类较多的依次为鲿科、鳅科。采用非度量多维标度排序(NMDS)方法对鱼类群落空间分布特征进行了分析,结果表明珠江鱼类被划分为3个类群,即以餐、南方拟餐、黄颡鱼等小型鱼类为主的中上游类群、以赤眼鳟、鲮鱼、广东鲂等中型鱼类为主的中下游类群和以罗非鱼为主的重要支流类群。同时发现中下游物种多样性高,上游及河口江段多样性低的格局。采用冗余分析方法(RDA)分析了鱼类多样性与环境因子的关系,发现年均气温、降雨量、年均径流量、河流宽度与透明度是珠江水系河流鱼类群落结构差异的主要影响因子,其中年均气温是影响鱼类群落分布的最关键因子之一。与历史资料对比后发现,珠江鱼类种类明显减少、空间分布也发生了巨大改变。研究是珠江水系野生渔业资源长期调查的一部分,研究结果将对渔业资源的多样性保护和可持续利用具有指导意义。     

长江三峡上游水域细菌群落结构与功能预测

[目的]揭示三峡附近支流和长江干流细菌群落组成,共现网络特征和对网络有重要作用的中心节点微生物,进一步研究三峡上游水域细菌群落的代谢功能.[方法]本研究于长江北岸四条一级支流和附近干流(香溪河、大宁河、朱衣河、梅溪河、长江干流)采集水样,基于16SrRNA基因Pacbio测序技术和生物信息学方法分析细菌群落结构,Tax...