基于环境DNA-宏条形码技术的底栖动物监测及水质评价研究进展

底栖动物是淡水生态系统中物种多样性最高的类群,也是应用最广泛的水质监测指示生物之一。传统的底栖动物监测以形态学为基础,耗时费力,无法满足流域尺度大规模监测的需求。环境DNA-宏条形码技术是一种新兴的生物监测方法,其与传统方法相比优势在于采样方法简单、低成本、高灵敏度,不受生物样本和环境状况的影响,不依赖分类专家和鉴定资料,能够快速准确地对多个类群进行大规模、高通量的物种鉴定。然而,在实际应用中该方法的效果受诸多因素的影响,不同的方法、流程往往会产生差异较大的结果。鉴于此,着重分析总结了应用环境DNA-宏条形码技术监测底栖动物的关键影响因素,包括样品采集与处理流程、分子标记选择、引物设计、PCR偏好性、参考数据库的完整性及相应的优化。并基于此探讨了提高环境DNA-宏条形码技术在底栖动物监测效率和准确率的途径,以期为底栖动物环境DNA-宏条形码监测方案的制定提供可靠的参考。最后对该技术在底栖动物监测和水质评价中的最新发展方向进行了展望。     

我国外来水生生物入侵现状及其影响

生物入侵已经被公认是造成生物多样性丧失的重要因素之一，它对生态系统的结构和功能的严重影响已经引起全世界的高度重视。外来水生生物是生物入侵的重要组成部分：因此，从生物入侵的基本概念及入侵物种的传播途径着手，分析我国水生外来物种及其对水生生态系统和渔业可持续发展的影响。     

基于环境DNA宏条形码技术的辽东湾典型围海养殖池塘内水母多样性研究

研究使用环境DNA宏条形码技术(eDNA metabarcoding)检测辽东湾东北部河口区围海养殖池塘水母种类多样性,探索适用于水母种类物种鉴定和监测的新方法。利用环境DNA宏条形码技术,分别基于18S rDNA和COI宏条形码检测了辽东湾东北部河口区围海养殖池塘水母种类多样性,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,从围海养殖池塘7个采样点中获得可检测的采样点数据。结果显示,基于18S rDNA宏条形码检测出8种水母种类,其中钵水母纲大型水母2种、水螅水母总纲小型水母6种;基于COI宏条形码技术共检测出19种水母种类,其中钵水母纲大型水母5种、水螅水母总纲小型水母14种;两种DNA条形码标记都显示养殖种类海蜇(Rhopilema esculentum)为优势种。研究结果表明,环境DNA宏条形码技术作为一种新兴的生物多样性监测手段可用于快速检测水母种类多样性,在水母类物种鉴定、监测及早期预警中有较大的应用潜能。     

中国入侵生物学学科的构建与发展

自英国生态学家查尔斯.艾尔顿1958年撰写的《动植物的入侵生态学》出版至今,半个世纪已经过去,这部著作被公认为是生物入侵在科学研究方面的开端。这期间生物入侵研究经历了萌芽期（20世纪80年代之前）、成长期（20世纪80年代）和快速发展期（20世纪90年代末期至今）。在这个过程中,越来越多的概念、假说、方法和技术被提出和整合到生物入侵研究之中,由此催生了一门生态学领域的新兴学科——入侵生物学。本文在对近50年来生物入侵专著和论文的统计分析基础上,介绍了国际生物入侵研究的发展脉络和现状。同时综述了中国入侵生物学在基础和应用研究方面的相关进展,着重阐述了主要科学问题（＂入侵潜力与成功入侵的关系＂、＂入侵种种群的扩张与扩散＂、＂入侵种的生态适应性与进化＂及＂本地生态系统对入侵的响应及可入侵性＂）和预防与控制的技术体系（风险评估与早期预警、检测与监测、狙击与灭除、生物防治、生态修复与干扰调控）,并进一步介绍了中国入侵生物学学科体系的构建和框架,提出入侵生物学是研究外来物种的入侵性与生态系统的可入侵性,以及外来物种预防与控制的科学,是一门多领域交叉的学科。最后展望和讨论了中国入侵生物学学科发展可能遇到的一些问题。     

我国外来入侵生物防控科技进展

随着全球经济一体化的发展,外来入侵生物的危害日益加重。我国针对当前各类重大外来生物的入侵,按照基础研究、共性关键技术与重大产品研发、典型应用示范3个层面,部署了一系列项目,并取得了一定成果:揭示了入侵生物的入侵特性和入侵机理,以及入侵植物与脆弱生态系统的相互作用机制;研发了重大新发农业入侵物种风险评估及防控技术,建立了生物威胁数据库和生物入侵突发事件可视化智能决策支持平台,以及重大入侵动植物的治理模式和技术体系;建立了主要入侵生物标本资源库。今后应以跨境动植物有害生物为主要目标,开展入侵扩散与成灾机制、早期预防预警、快速检测监测、识别追踪溯源、点面拦截狙击、区域防灾减灾等技术研究。     

网络理论在入侵生物学中的应用研究现状

生物入侵是一个动态有序的过程,其发生和危害存在异质性,通常由来源地、入侵地和它们之间的连接构成的系统中的自然、生物、社会等因素所决定。网络理论是研究复杂系统的一种新方法,本质是从复杂的信息中抽象出规律、揭示系统的结构特征共性。近20年,网络理论已被应用于生物入侵研究。本研究综述了网络理论在生物入侵研究中的应用进展,明确了主要的研究方向和前沿热点,认为:2000年以来国际上已开展的研究集中在评估外来物种入侵风险和入侵后对生态系统影响2个方面;外来物种随运输网络入侵的风险评估和景观连接性对入侵物种扩散的影响、外来物种入侵对本地物种间互作网络的影响及生态群落可入侵性是网络理论应用的热点;研究热点具有明显的时间发展特征,2013年以前多是对生态系统的影响,近10年来主要是风险评估。我国利用网络理论研究外来物种入侵较少且集中于对生态系统的危害,未来应加强对外来物种的时空定量传入和扩散风险评估,为我国制定和提升外来入侵物种早期监测预警、阻止新的入侵、抑制进一步扩散的管理措施提供依据。     

海洋外来物种入侵生态学研究

海洋外来物种入侵已成为最为严重的全球性环境问题之一。海洋生态系统类型多样、环境复杂,其生物入侵的监测、控制与管理难度相对较大。我国对陆地外来生物的入侵已开展了较为深入的研究,但对于海洋外来生物的入侵研究仍处于起步阶段,对其入侵监测、入侵机制、入侵危害的程度以及防治等问题缺乏基础数据。本文在分析国内外海洋外来生物入侵现状的基础上,概述其入侵生态学研究形势及相关成果,包括海洋外来物种的入侵途径、入侵过程、入侵生态效应以及全球变化对入侵的影响等。海洋外来生物的入侵可能对海洋生态系统造成直接或间接的影响,如种间竞争破坏生态环境、与土著种杂交造成遗传污染、病原生物及有毒藻类导致海洋生态灾害加剧等。此外,从政策和法规、入侵风险评估、监测和公共宣传教育、生物信息系统和有效管理机制等方面提出对我国海洋外来物种入侵的防治策略。本研究为我国海洋外来物种的进一步研究提供了参考。     

DNA宏条形码技术在海洋浮游动物多样性和生态学研究中的应用

浮游动物是海洋生态系统的关键类群,其覆盖门类广泛,多样性高。传统形态鉴定技术需要检测人员具备专业的形态鉴定知识,且费时费力。宏条形码技术无需分离生物个体,而是提取拖网采集到的浮游动物混合样本的总DNA,或者水体中的环境DNA （eDNA）,依托高通量测序平台测序,能够实现对大规模样本快速、准确、经济的分析,在海洋浮游动物生态学研究中得到越来越广泛的应用。分析了DNA宏条形码技术常用的核糖体和线粒体分子标记,在浮游动物多样性和数量研究中的可靠性和不足,并给出在海洋浮游动物群落监测,食物关系分析及生物入侵早期预警等研究中的应用。未来,开发多基因片段组合条形码,发展完备的参考数据库及实现准确的量化研究是DNA宏条形码技术发展的重要方向。     

我国南方生物入侵的问题与对策

外来物种入侵到新的栖息地,可能给当地造成严重的生态灾难,导致生态灾害爆发及生物多样性的丧失,进而威胁到人类生存环境.目前,生物入侵已给我国造成了非常严重的环境问题和社会危害,带来了巨大的生态和经济损失,仅对我国农林业造成的直接经济损失每年就高达574亿元.文中主要以我国南方外来植物为例,分析了生物入侵的危害、途径、原因,针对生物入侵涉及地域、生态系统类型和涉及物种种类特点,提出了防治对策:重视生物入侵现象,加强与之相关问题的基础研究;加强立法,建立科学的引种制度;加强动植物检疫,建立全国外来物种入侵动态监测网;提高全民防范意识;加强国际合作.     

基于分子生物学方法的外来入侵物种入侵历史重构

生物入侵是一个世界性的问题。全球每年因生物入侵造成的损失超过1万亿美元。探究入侵物种在入侵地的入侵历史对了解生物入侵的生物生态学机制、制定阻截及防除措施有重要意义。分子标记方法的兴起和大规模应用打开了入侵生物入侵历史研究的新天地。采用分子标记的方法可鉴定入侵物种的种类、追溯其来源地、回溯其扩散路径、分析扩散模式及探究物种入侵过程中对入侵种群本身的变化及其对生态系统所造成的各种影响。分子标记的应用使得多个入侵物种的入侵历史得以重现。由于分子标记方法重构的入侵历史受采样范围、采用的分子标记的种类及数量等因素的影响,该方法呈现入侵历史是否是真实发生的入侵过程还存在争议。     

中国近海入侵贝类及其影响

海洋贝类种类繁多,是近海底栖生态系统的优势种,在生态系统物质循环和能量流动中起着极其重要的作用;但因频繁的人类活动导致的贝类入侵问题,往往使该过程不能正常运转。大量研究表明,入侵贝类会抑制原著贝类或其他生物的生长及拓殖,形成单一优势群落,破坏当地生态系统的平衡,也会对海洋渔业生产和近海工程及作业等造成不可预测的危害。目前,欧美等国家针对该问题已开展了大量工作,十分重视入侵贝类的生物学、生态学与行为学特征及特性的研究,并根据其入侵途径与方式的不同开展了检测、监测、防控及管理工作。但在我国,入侵贝类还未引起相关部门及研究机构的足够重视。本文主要简述了我国近海的3种入侵贝类沙筛贝、指甲履螺和地中海贻贝的生物学、生态学及行为学等特征及其对当地生态系统的影响;同时,根据其特性及入侵过程控制的难易,建议在完善我国入侵贝类数据库的基础上加强早期预警与检测,以及安全防控和管理等工作。     

Invasive species in China — an overview

China is a vast country with rich biodiversity, which makes China especially vulnerable to invasive species. It has a long history of introduction of non-native species, especially those with perceived beneficial impacts. Its rapid economic development, including an explosive growth in international trade and transportation, has increased the potential for new introductions. Currently, alien species are widespread in the country, occur in many ecosystems, represent most major taxonomic groups, and are introduced unintentionally as well as intentionally for cultivation. The paper lists various cases of invasive species which have caused significant threats or damages to local natural or artificial ecosystems, and indicates that two example industries (fresh water fisheries and lawn grasses) have brought or tend to bring in many invasive species and hence have caused or will cause changes and loss of biodiversity in local ecosystems. Based on these studies, it is suggested that China combat the problem through enhancing awareness, development of a database on invasive species, strengthening international co-operation, preparing case studies and introducing the necessary legislation, regulations and monitoring.     

Improved Methods for Capture,Extraction, and Quantitative Assay of Environmental DNA from Asian Bigheaded Carp (Hypophthalmichthys spp.)

Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA) is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp.), an invasive fish spreading toward the Laurentian Great Lakes. However, the standard eDNA methods of this program have not advanced since their development in 2010. We developed new, quantitative, and more cost-effective methods and tested them against the standard protocols. In laboratory testing, our new quantitative PCR (qPCR) assay for bigheaded carp eDNA was one to two orders of magnitude more sensitive than the existing endpoint PCR assays. When applied to eDNA samples from an experimental pond containing bigheaded carp, the qPCR assay produced a detection probability of 94.8% compared to 4.2% for the endpoint PCR assays. Also, the eDNA capture and extraction method we adapted from aquatic microbiology yielded five times more bigheaded carp eDNA from the experimental pond than the standard method, at a per sample cost over forty times lower. Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species.     

Environmental DNA detection of aquatic invasive plants in lab mesocosm and natural field conditions

Aquatic invasive plant species cause negative impacts to economies and ecosystems worldwide. Traditional survey methods, while necessary, often do not result in timely detections of aquatic invaders, which can be cryptic, difficult to identify, and exhibit very rapid growth and reproduction rates. Environmental DNA (eDNA) is a relatively new method that has been used to detect multiple types of animals in freshwater and marine ecosystems through tissues naturally shed from the organism into the water column or sediment. While eDNA detection has proven highly effective in the detection of aquatic animals, we know less about the efficacy of eDNA as an effective surveillance tool for aquatic plants. To address this disparity, we designed mesocosm experiments with Elodea species to determine the ability to detect accumulation and degradation of the DNA signal for aquatic plants, followed by field surveillance of the highly invasive Hydrilla verticillata in freshwaters across several U.S. geographic regions. In both lab and field experiments, we designed a high sensitivity quantitative PCR assay to detect the aquatic plant species. In both experiments, plant eDNA detection was successful; we saw accumulation of DNA when plants were introduced to tanks and a decrease in DNA over time after plants were removed. We detected eDNA in the field in areas of known Hydrilla distribution. Employing eDNA detection for aquatic plants will strengthen efforts for early detection and rapid response of invaders in global freshwater ecosystems.     

An assessment of natural and human disturbance effects on Mexican ecosystems: current trends and research gaps

Mexico harbors more than 10% of the planet’s endemic species. However, the integrity and biodiversity of many ecosystems is experiencing rapid transformation under the influence of a wide array of human and natural disturbances. In order to disentangle the effects of human and natural disturbance regimes at different spatial and temporal scales, we selected six terrestrial (temperate montane forests, montane cloud forests, tropical rain forests, tropical semi-deciduous forests, tropical dry forests, and deserts) and four aquatic (coral reefs, mangrove forests, kelp forests and saline lakes) ecosystems. We used semi-quantitative statistical methods to assess (1) the most important agents of disturbance affecting the ecosystems, (2) the vulnerability of each ecosystem to anthropogenic and natural disturbance, and (3) the differences in ecosystem disturbance regimes and their resilience. Our analysis indicates a significant variation in ecological responses, recovery capacity, and resilience among ecosystems. The constant and widespread presence of human impacts on both terrestrial and aquatic ecosystems is reflected either in reduced area coverage for most systems, or reduced productivity and biodiversity, particularly in the case of fragile ecosystems (e.g., rain forests, coral reefs). In all cases, the interaction between historical human impacts and episodic high intensity natural disturbance (e.g., hurricanes, fires) has triggered a reduction in species diversity and induced significant changes in habitat distribution or species dominance. The lack of monitoring programs assessing before/after effects of major disturbances in Mexico is one of the major limitations to quantifying the commonalities and differences of disturbance effects on ecosystem properties.     

我国外来入侵生物防控现状、问题和对策

外来物种入侵已经威胁全球多个国家和地区,严重影响农林牧渔业生产,威胁生态系统稳定,是当前全球生物多样性丧失的主要原因之一,开展入侵物种防控已成为生物多样性保护与农业绿色发展的重点工作。我国已经成为全球遭受生物入侵威胁与损失最为严重的国家之一,截至2018年底,入侵我国的外来物种有近800种,已确认入侵农林生态系统的有638种,全国31个省（区、市）均有外来生物入侵发生并带来危害,半数以上县域都有入侵物种分布,几乎涉及所有类型的生态系统。本文对全球主要发达国家外来入侵物种发生情况及防控进行梳理发现,从国家层面立法开展外来入侵生物防控成为主流,制定长期防控战略并增加投入是入侵物种防控成功的关键。近些年,我国在外来入侵物种防控方面初步建立了工作机制,发布了重点管理外来入侵物种名录,完成了重点入侵物种的调查监测,开展了局部地区的防控措施,积极推动立法工作。根据国外生物入侵防治经验与我国实际情况,本研究提出我国外来入侵物种防控对策建议,包括加强法制建设、开展本底调查和启动重大防控工程等,为我国外来侵入生物的防控提供借鉴。     

小型城市湖泊生态系统预警技术--以武汉市汉阳地区为例

城市湖泊正面临着水体污染和生态系统退化的双重压力 ,对湖泊生态系统的状态进行预警是判定湖泊演化趋势以及制定相应控制对策的重要途径和手段。本文以武汉市汉阳地区的 6个小型城市湖泊为例 ,结合国内外的研究进展 ,从水生生态系统、湖滨生态系统和入湖沟渠生态系统 3方面入手 ,结合生物监测、生物标志物技术 ,综合考虑水文、水质和生态系统以及污染物扩散等因素 ,设计出汉阳地区湖泊生态系统的预警技术体系。该技术体系主要分 5步 :湖泊生态系统现状调研、生物标志物和关键指示因子确定、水质 -生态系统模拟、系统输出和灵敏度检验以及生态系统状态预警及对策、措施     

Putting bryophyte communities in the map: A case study on prioritizing monitoring of human pressure in riverscapes

Freshwater ecosystems support biological communities with high species richness and conservation interest. However, these ecosystems are highly altered by human intervention and threatened worldwide, making them a priority in conservation planning and biodiversity monitoring. Bryophytes, including several conservation-interest taxa, are recognized indicators of ecological status in freshwaters. We aimed to develop a framework for designing monitoring networks to detect trends in aquatic and semi-aquatic bryophyte communities, prioritizing high-conservation interest communities in different contexts of human pressure (specifically, resulting from the intersection of two criteria: (i) protection status and (ii) presence of a potential impact area).The framework consists of three steps: (1) Spatial modelling of biodiversity; (2) Spatial conservation prioritization; and (3) Model-assisted monitoring network design. Community-level modelling was used to model the distribution of the main bryophyte assemblages in the study area. A conservation prioritization software was utilized to identify areas with high conservation value. The monitoring network was designed using stratified random sampling and unequal-probability sampling techniques to target high conservation value sites distributed across different contexts of human pressure.We have identified four distinct community types, each characterized both by a small group of common and dominant species, and by small group of rarer, conservation-interest species. This typification of four species assemblages occurring in the study area, also highlighted those with potentially higher conservation-interest. The most valuable areas for the conservation of aquatic and semi-aquatic bryophyte communities coincide with specific environmental zones: mountainous areas in Lusitania, large watercourses in the Mediterranean North and some locations in the Mediterranean Mountains. Finally, we obtained a potential monitoring network consisting of 64 monitoring points, unequally distributed across different contexts of human pressure, privileging locations with higher conservation value.The framework presented here illustrates the potential of combining biodiversity modelling, spatial conservation prioritization and monitoring design in the development of monitoring networks. Namely, this framework allowed us to counter data deficiencies, to identify high priority areas to monitor and to design a monitoring network considering different scenarios of human pressure at a regional scale.This framework can also be valuable for conservation efforts as an approach to monitoring conservation-interest biodiversity features in anthropogenically modified riverscapes, which present different degrees of human pressure and the cumulative effects of these different impact elements. Moreover, this approach allows for the comprehensive monitoring of biodiversity values important for management at the national and regional levels. In addition, this framework is one of the first efforts in the development of monitoring networks that target aquatic and semi-aquatic bryophyte communities, a long-neglected plant group of high ecological and conservation importance in freshwater ecosystems.     

Growth of Hydrilla verticillata (L.f.) Royle under controlled conditions

Aquatic macrophytes are important resources for the maintenance of trophic chains and in biogeochemical processes, but they can also be deleterious for several uses if present in excess. Hydrilla verticillata was found in the Paraná River (Brazil) after 2005, which requires monitoring owing to the invasive potential of this species. In this study, we measured the growth of H. verticillata under controlled conditions and compared the growth dynamics for the two development strategies (branch and tuber). We show that this species has great potential to develop in tropical (Brazilian) aquatic ecosystems. The parameters from the modelling of the growth kinetics indicated a doubling time of 19.8 days for H. verticillata growing from stems; however, the growth from tubers were much faster, with doubling times ranging from 2.5 to 11 days. The delay for the tubers to sprout caused a decrease in the number of branches of H. verticillata stems. From the growth parameters obtained from the experiments under controlled conditions, we concluded that the high temperature and light availability in most South American reservoirs (including the Porto Primavera Reservoir where it was first recorded) are suitable for H. verticillata to compete and probably displace other native aquatic macrophytes, such as Egeria najas, Egeria densa, and Cerathophyllum demersum. This is a matter of concern because these and other submersed species are commonly found in several natural and man-made South-American aquatic ecosystems, where they are key for biodiversity maintenance.