DNA宏条形码（metabarcoding）技术在浮游植物群落监测研究中的应用

保护生物多样性和生态系统健康是维持生态系统功能和实现人类可持续发展的必要条件。浮游植物作为水生生态系统的初级生产者发挥着重要的生态功能,同时有毒藻类的爆发也会威胁水生态安全。然而,基于形态学的物种鉴定方法难以满足日益增长的水生态环境监测的需求。DNA条形码技术利用基因组特定基因上、短的DNA序列来鉴别生物物种,目前已广泛用于快速物种鉴别。然而其在水生生态系统浮游植物群落的监测中才刚刚起步。由于浮游植物物种多样性高,单基因DNA条形码往往不足以识别所有浮游植物种类;近年来,采用多基因条形码、全叶绿体基因组序列的超级条形码,以及特定DNA条形码方法在单物种和群落水平上区分浮游植物种类的潜力很大。本文综述了浮游植物DNA条形码技术在物种鉴别研究方面的进展,以及DNA宏条形码技术（DNA metabarcoding）在水生浮游植物环境监测的应用现状及前景。     

浮游动物DNA宏条形码标志基因比较研究

DNA宏条形码技术作为一种新型生物监测方法,在未来生态环境监测中有巨大的应用潜力。目前,浮游动物DNA宏条形码监测仍在发展阶段,需要首先对其(采样方法、引物选择和数据分析等)进行标准化和调整,然后才能用于常规流域生态监测。其中,如何选择合适的PCR扩增引物是DNA宏条形码生物监测标准化的关键问题之一。本研究比较了COI、18SV9和16S通用引物在浮游动物DNA宏条形码监测中的差异,为初步建立规范化的浮游动物DNA宏条形码监测方法提供技术支撑。结果表明,16S引物对浮游动物具有更好的特异性,其产生的操作分类单元(operational taxonomic unit, OTU)有88.1%属于浮游动物。虽然18SV9引物具有更高的物种覆盖度,不仅能扩增出浮游动物,还能扩增出大量藻类和真菌,但其物种识别敏感性较差,不适合浮游动物物种水平多样性监测。COI引物的浮游动物物种特异性、物种覆盖度和物种识别敏感性都适中,检出的浮游动物物种数量高于18SV9引物和16S引物,更加适合浮游动物DNA宏条形码监测。     

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。     

土地利用变化对生物多样性的影响

土地利用变化对生物多样性影响是生物多样性受到威胁的重要因素.文章对土地利用变化对基因多样性、物种多样性、生态系统多样性影响方面的研究进行了总结分析,并提出了新的展望.土地利用变化对基因多样性的影响涉及了对物种生境的隔离、农牧业活动对物种改良和生境条件的改变方面,目前还主要集中在对少数物种繁殖过程方面影响的研究;土地利用变化对物种多样性影响包括对物种优势度和丰富度、种间关系、物种分布格局、物种入侵和灭绝方面的影响,目前对物种丰富性和多样性影响方面研究较多,对物种灭绝、物种入侵和种间关系影响方面的研究极少,且还限于大型动物和植物,对微生物和小型动植物研究却很少;土地利用变化对生态系统的影响涉及了对生态系统结构组成及分布方面的影响.另外,目前缺少土地利用变化对基因多样性、物种多样性和生态系统多样性综合影响方面的研究,难以量化和预测土地利用变化对生物多样性影响效应.未来需要综合考虑基因多样性、物种多样性和生态系统多样性方面,系统开展土地利用变化对生物多样性影响的趋势和机制方面的研究,定量预测土地利用变化对生物多样性的影响.     

生物多样性保护及其研究进展（综述）

由于人口的增长和人类经济活动的加剧,致使生物多样性受到了严重的威胁,引起国际社会的普遍关注．生物多样性是生物及其与环境形成的生态复合体以及与此相关的各种生态过程的总和,具有十分重要的价值,是人类生存的物质基础．各国政府和有关的国际组织积极投入到保护生物多样性的全球行动中．为了促进保护工作,国内外都开展了相关的研究工作．综观该领域的研究现状,可以看出以下７个方面已成为当前生物多样性研究的热点：①生物多样性的调查、编目及信息系统的建立;②人类活动对生物多样性的影响;③生物多样性的生态系统功能;④生物多样性的长期动态监测;⑤物种濒危机制及保护对策的研究;⑥栽培植物与家养动物及其野生近缘的遗传多样性研究;⑦生物多样性保护技术与对策．结合我国的具体情况,建议优先考虑以下４个方面的研究：①生物多样性的调查、编目与动态监测;②物种濒危机制及保护对策的研究;③生物多样性的生态系统功能与生态系统管理;④栽培植物与家养动物及其野生近缘的遗传多样性研究．     

气候变化对生物多样性的影响:脆弱性和适应

气候变化对生物多样性影响及其适应直接关系着未来生物多样性的保护.气候变化对生物多样性影响、生物多样性在气候变化影响下的脆弱性、生物多样性适应气候变化方面进行了总结分析,对存在的问题进行了讨论,对今后研究提出了一些建议.过去的气候变化已使物种物候、分布和丰富度等改变,使一些物种灭绝、部分有害生物危害强度和频率增加,使一些生物入侵范围扩大、生态系统结构与功能改变等.未来的气候变化仍将使物种物候和行为、分布和丰富度等改变,使一些物种灭绝、使有害生物爆发频率和强度增加,并将可能使生态系统结构与功能发生改变等.生物多样性适应气候变化包括了自然适应和人为适应两个方面,自然适应体现在物种适应性进化、迁移、生态系统稳定性和弹性等,人为适应体现在种质基因保存、物种异地保护、自然保护区规划设计、生态系统适应性管理、生态恢复和气候灾害防御等.目前,生物多样性对气候变化影响的脆弱性、生物多样性自然适应和人为适应气候变化方面的研究都还不系统深入,需要加强生物多样性自然适应和人为适应气候变化方面的研究.     

DNA条形码识别 Ⅵ：基于微型DNA条形码的果实蝇物种鉴定

选用双翅目实蝇科12属36种55个样本为材料,将其DNA条形码(mtDNACOI基因648 bp)与微型DNA条形码(mtDNACOI基因50～200 bp)数据进行比较分析,探讨微型DNA条形码对果实蝇物种鉴定的可行性.采用虚拟实验(Silico analysis),将BOLD数据库中49个样本的序列分别拆成648 bp、160 bp、50 bp三个片段,通过构建NJ树,并进行遗传距离分析,得出每个片段鉴定物种的准确性依次为100%、94%、84%.同时做了实体实验(Empirical test),得到了果实蝇属6个物种的COI序列,将其与虚拟实验中的49个样本序列合并,以DNA-barcode指定序列5'端160 bp序列为分析基础,通过遗传距离分析,得出其鉴定物种的准确性为94%,验证了虚拟实验结果.即微型DNA条形码(Minimalist-barcode)鉴定果实蝇物种的准确性与DNA条形码基本一致,均可作为果实蝇物种鉴定的有效依据.图2表1参29附1     

浮游植物程序性细胞死亡研究进展

浮游植物是水生生态系统的基础,在生物地化循环中起着非常重要的作用,浮游植物的死亡势必引起水生生态系统的改变。近年来的研究表明,浮游植物的死亡是浮游植物水华衰退的一个重要原因。浮游植物中是否存在与后生动物类似的程序性细胞死亡（Programmed cell death,PCD）途径,也因此成了一个热点问题。文章对近年来浮游植物死亡表型、PCD生化证据、诱发条件、分子基础方面研究进行了总结。大量证据表明,浮游植物中存在类似细胞凋亡、类凋亡、自噬等途径的PCD,但Caspase基因除具有死亡执行者功能外,还可能具有看家功能。活性氧（ROS）和一氧化氮（NO）在浮游植物PCD过程中可能起到死亡信号分子的作用。部分浮游植物的PCD可以改善种群生存,但其生态学意义总体而言仍存在许多争论。     

我国水生生物遗传资源保护现状与策略

我国水产品总产量连续30年高居世界首位,满足了国民30%的动物蛋白需求。水生生物遗传资源是水产优质蛋白有效供给的重要物质基础,更是未来世界应对食物短缺、保障食物安全的有效途径。水生生物遗传资源与物种多样性和遗传多样性直接相关,活体资源、标本资源、组织资源和基因资源是水生生物遗传资源收集保存和开发利用的主要形式。当前,水生生物种类数量急剧减少、精准鉴定尚未大规模开展、利用效率相对较低、保护设施不够完善等因素成为制约水生生物遗传资源高效开发的瓶颈。该文系统总结了我国水生生物遗传资源基本状况,分析了面临的主要问题,凝练了遗传资源保护的基本思路和总体目标,提出了加强水生生物遗传资源保护的发展战略和研究工作,以期为我国水生生物遗传资源强国建设提供借鉴和参考。     

植物功能多样性及其与生态系统功能关系研究进展

生物多样性影响生态系统的多种功能。生物多样性的急剧丧失使得对其影响评定尤为重要和紧迫,因此,生物多样性与生态系统功能关系成为生态学研究的热点问题之一,其中功能多样性与生态系统功能关系的研究成为近十年该领域研究的重点。文章首先概括了植物功能多样性的多种定义,并详细介绍了目前被广泛接受的定义"功能多样性是某一群落内物种间功能特征的变化范围或指特定生态系统中所有物种功能特征的数值和范围"。其次重点阐述了围绕植物功能多样性开展的5个重要研究论题:(1)分别从功能丰富度、功能均匀度、功能离散度3个方面介绍了功能多样性算法,并强调要注重多指数相结合以综合描述功能多样性;(2)植物功能性状间主要体现为权衡关系,植物功能性状受到了气候、土壤、海拔、地形地貌、放牧、土地利用方式等一系列因素的影响;(3)基于植物功能性状更有利于探讨环境过滤和相似性限制对群落构建的驱动作用;(4)功能多样性与物种多样性间呈现正相关、负相关和饱和曲线等一系列关系,之所以呈现不同关系与资源状况和外界干扰密切相关;(5)尽管很多研究都证明了功能多样性对生态系统功能具有正效应,但依然存在两个主要的争议,一方面是物种多样性、功能多样性在生态系统功能维持中的相对重要性,另一方面是选择效应与互补效应在功能多样性与生态系统功能关系中的适用性。最后,提出了该领域需要进一步深入开展的4个研究方向:开展多尺度研究、重视多营养级研究,加强野外观测与受控实验相结合的研究、深化生态系统多功能性的研究。     

Utility of Mitochondrial DNA Barcodes in Species Conservation

Abstract:  Molecular tools are a standard part of many conservation studies and can be informative at many different levels of analysis, although there are inherent limitations and strengths of different genes or parts of genes to inform specific questions. Animal DNA barcodes, 600- to 800-base-pair segments of the mitochondrial gene cytochrome oxidase I, have been proposed as a means to quantify global biodiversity. Although mitochondrial (mt) DNA has a long history of use at the species level, recent analyses suggest that the use of a single gene, particularly mitochondrial, is unlikely to yield data that are balanced, universally acceptable, or sufficient in taxonomic scope to recognize many species lineages. Mitochondrial and nuclear genomes have different patterns of evolution and modes of inheritance, which can result in very different assessments of biodiversity. The ramifications of choosing a particular definition of species (species concept) need to be carefully considered because current efforts have designated DNA barcodes as the universal species concept without demonstrating its superiority over preexisting concepts. The results of such a barcoding paradigm may include a failure to recognize significant portions of biodiversity or nuclear/mitochondrial mixed lineages and could spuriously focus conservation resources on populations with relatively minor mtDNA divergence. DNA barcodes are most likely to provide potentially useful information for groups that are already well studied, and such taxa do not constitute the majority of biodiversity or those in most need of research attention. DNA barcode-length sequences are an important source of data but, when used alone or out of context, may offer only a fraction of the information needed to characterize species while taking resources from broader studies that could produce information essential to robust and informed conservation decisions.     

Transforming ecology and conservation biology through genome editing

As the conservation challenges increase, new approaches are needed to help combat losses in biodiversity and slow or reverse the decline of threatened species. Genome-editing technology is changing the face of modern biology, facilitating applications that were unimaginable only a decade ago. The technology has the potential to make significant contributions to the fields of evolutionary biology, ecology, and conservation, yet the fear of unintended consequences from designer ecosystems containing engineered organisms has stifled innovation. To overcome this gap in the understanding of what genome editing is and what its capabilities are, more research is needed to translate genome-editing discoveries into tools for ecological research. Emerging and future genome-editing technologies include new clustered regularly interspaced short palindromic repeats (CRISPR) targeted sequencing and nucleic acid detection approaches as well as species genetic barcoding and somatic genome-editing technologies. These genome-editing tools have the potential to transform the environmental sciences by providing new noninvasive methods for monitoring threatened species or for enhancing critical adaptive traits. A pioneering effort by the conservation community is required to apply these technologies to real-world conservation problems.     

Zooplankton biodiversity and lake trophic state: explanations invoking resource abundance and distribution

While empirical studies linking biodiversity to local environmental gradients have emphasized the importance of lake trophic status (related to primary productivity), theoretical studies have implicated resource spatial heterogeneity and resource relative ratios as mechanisms behind these biodiversity patterns. To test the feasibility of these mechanisms in natural aquatic systems, the biodiversity of crustacean zooplankton communities along gradients of total phosphorus (TP) as well as the vertical heterogeneity and relative abundance of their phytoplankton resources were assessed in 18 lakes in Quebec, Canada. Zooplankton community richness was regressed against TP, the spatial distribution of phytoplankton spectral groups, and the relative biomass of spectral groups. Since species richness does not adequately capture ecological function and life history of different taxa, features which are important for mechanistic theories, relationships between zooplankton functional diversity (FD) and resource conditions were examined. Zooplankton species richness showed the previously established tendency to a unimodal relationship with TP, but functional diversity declined linearly over the same gradient. Changes in zooplankton functional diversity could be attributed to changes in both the spatial distribution and type of phytoplankton resource. In the studied lakes, spatial heterogeneity of phytoplankton groups declined with TP, even while biomass of all groups increased. Zooplankton functional diversity was positively related to increased heterogeneity in cyanobacteria spatial distribution. However, a smaller amount of variation in functional diversity was also positively related to the ratio of biomass in diatoms/chrysophytes to cyanobacteria. In all observed relationships, a greater variation of functional diversity than species richness measures was explained by measured factors, suggesting that functional measures of zooplankton communities will benefit ecological research attempting to identify mechanisms behind environmental gradients affecting diversity.     

富营养化水体降磷对浮游植物群落结构特征的影响

浮游植物是水生态系统中物质循环和能量流动的基础,作为初级生产者,浮游植物的群落结构直接影响着水生态系统的结构和功能。在水产养殖生产中,如何根据养殖生物对生活环境的需求开展精准培水、定向培水,培养养殖生物所需要的浮游植物,在维持养殖水域生态平衡的同时又能为养殖生物提供一定的饵料资源,这一直是摆在水产科技工作者面前的重要难题和研究热点。已有的资料大都是通过添加磷的方式研究磷改变对浮游植物生长的影响,而有关富营养化水体降磷对浮游植物群落结构影响的研究尚未见报道。为此,试验通过向取自富营养化湖泊的水体中加入磷去除剂,采用Pielou均匀度指数、Mcnaughton优势度指数和Shannon多样性指数,研究自然水体中的磷被降低后水体浮游植物群落结构的变化情况。结果表明,所取富营养化水体中共检出绿藻（Chlorophyta）、硅藻（Bacillariophyta）、蓝藻（Cyanophyta）、裸藻（Euglenophyta）、隐藻（Cryptophyta）、甲藻（Pyrrophyta）6门29种（包括变种和变型）;其中绿藻、蓝藻、硅藻、隐藻、裸藻、甲藻分别有7、4、2、1、1种,分别占总种数的24.13%、13.79%、6.90%、3.45%、3.45%。富营养化水体降磷后,虽然试验组和对照组在浮游植物种类组成上没有差异,但浮游植物群落结构特征发生了很大变化,浮游植物数量明显降低,由13 238.8×104cells·L-1降低至3 997.5×104cells·L-1,下降了69.8%;浮游植物优势种从1门（蓝藻（Cyanophyta））6种增加到3门（绿藻（Chlorophyta）、硅藻（Bacillariophyta）、蓝藻（Cyanophyta））12种,优势度指数从97.29%降低至86.30%,优势种门数和优势种种数远远高于对照组,优势度明显低于对照组;同时,浮游植物多样性指数和均匀度分别从1.85和0.38升高至2.60和0.54,显示出试验组浮游植物多样性和均匀度优于对照组。研究表明富营养化水体降磷对浮游植物群落结构产生了明显影响,使群落结构处于更加复杂、完整和稳定的状态。     

汞在海洋浮游植物中的生物累积和毒性效应

浮游植物是海洋生态系统的主要初级生产者,同时作为食物也是许多水生生物摄取汞的主要途径。本文综述了近年来汞在海洋浮游植物中的最新研究进展,包括汞在浮游植物中的吸收、累积规律及其影响因素,汞对浮游植物的毒性效应(生长抑制、光合作用影响)以及生物的适应机制(汞的还原、螯合解毒、矿化固定等),最后对浮游植物中汞累积和毒性的未来研究方向进行了展望。     

Evaluating the efficacy of restoration plantings through DNA barcoding of frugivorous bird diets

Frugivores are critical components of restoration programs because they are seed dispersers. Thus, knowledge about bird–plant trophic relationships is essential in the evaluation of the efficacy of restoration processes. Traditionally, the diet of frugivores is characterized by microscopically identifying plant residues in droppings, which is time‐consuming, requires botanical knowledge, and cannot be used for fragments lacking detectable morphological characteristics (e.g., fragmented seeds and skins). We examined whether DNA barcoding can be used as a universal tool to rapidly characterize the diet of a frugivorous bird, Eurasian blackcap (Sylvia atricapilla). We used the DNA barcoding results to assess restoration efforts and monitor the diversity of potentially dispersed plants in a protected area in northern Italy. We collected 642 Eurasian Blackcap droppings at the restored site during the autumn migration over 3 years. Intact seeds and fragmented plant material were analyzed at 2 plastidial barcode loci (rbcL and trnH‐psbA), and the resulting plant identifications were validated by comparison with a reference molecular data set of local flora. At least 17 plant species, including 7 of the 11 newly transplanted taxa, were found. Our results demonstrate the potential for DNA barcoding to be used to monitor the effectiveness of restoration plantings and to obtain information about fruit consumption and dispersal of invasive or unexpected plant species. Such an approach provides valuable information that could be used to study local plant biodiversity and to survey its evolution over time.     

Large-scale biodiversity patterns in freshwater phytoplankton

Our planet shows striking gradients in the species richness of plants and animals, from high biodiversity in the tropics to low biodiversity in polar and high-mountain regions. Recently, similar patterns have been described for some groups of microorganisms, but the large-scale biogeographical distribution of freshwater phytoplankton diversity is still largely unknown. We examined the species diversity of freshwater phytoplankton sampled from 540 lakes and reservoirs distributed across the continental United States and found strong latitudinal, longitudinal, and altitudinal gradients in phytoplankton biodiversity, demonstrating that microorganisms can show substantial geographic variation in biodiversity. Detailed analysis using structural equation models indicated that these large-scale biodiversity gradients in freshwater phytoplankton diversity were mainly driven by local environmental factors, although there were residual direct effects of latitude, longitude, and altitude as well. Specifically, we found that phytoplankton species richness was an increasing saturating function of lake chlorophyll a concentration, increased with lake surface area and possibly increased with water temperature, resembling effects of productivity, habitat area, and temperature on diversity patterns commonly observed for macroorganisms. In turn, these local environmental factors varied along latitudinal, longitudinal, and altitudinal gradients. These results imply that changes in land use or climate that affect these local environmental factors are likely to have major impacts on large-scale biodiversity patterns of freshwater phytoplankton.