Towards a Molecular Taxonomy for Protists: Benefits,Risks, and Applications in Plankton Ecology

The increasing use of genetic information for the development of methods to study the diversity, distributions, and activities of protists in nature has spawned a new generation of powerful tools. For ecologists, one lure of these approaches lies in the potential for DNA sequences to provide the only immediately obvious means of normalizing the diverse criteria that presently exist for identifying and counting protists. A single, molecular taxonomy would allow studies of diversity across a broad range of species, as well as the detection and quantification of particular species of interest within complex, natural assemblages; goals that are not feasible using traditional methods. However, these advantages are not without their potential pitfalls and problems. Conflicts involving the species concept, disagreements over the true (physiological/ecological) meaning of genetic diversity, and a perceived threat by some that sequence information will displace knowledge regarding the morphologies, functions and physiologies of protistan taxa, have created debate and doubt regarding the efficacy and appropriateness of some genetic approaches. These concerns need continued discussion and eventual resolution as we move toward the irresistible attraction, and potentially enormous benefits, of the application of genetic approaches to protistan ecology.     

The Philosophical Dullness of Classical Ecology, and a Levinsian Alternative

Ecology has had a lower profile in Biology & Philosophy than one might expect on the basis of the attention ecology is given in public discussions in relation to environmental issues. Our tentative explanation is that ecology appears theoretically redundant within biology and, consequently, philosophically challenging problemsrelated to biology are commonly supposed to be somewhere else, particularly in the molecular sphere. Richard Levins has recognized the genuine challenges posed by ecology for theoretical and philosophical thinking in biology. This essay sets the stage for appreciating his work; it was preceded by four articles published in Biology & Philosophy 15(2),and is followed by a personal reminiscent.     

空间分子生态学——分子生态学与空间生态学相结合的新领域

分子标记、基因流、种群空间动态是当前生命科学研究中的热点领域。RFLPs、RAPDs、微卫星等新的分子标记的不断涌现,促进了这些领域的飞速发展。对种群空间动态研究中的等级岛屿模型、距离隔离模型、脚踏石模型、集合种群模型等方面许多令人瞩目的进展做了介绍。同时还介绍了遗传距离、基因流及其测度、基因突变模型、3S技术、空间精确性种群模型和基因频率的空间自相关等热点领域。最后,就空间分子生态学存在的问题与前景进行了讨论,指出了空间分子生态学可能的发展方向。     

林带和牧草地水量平衡的研究

本文从水量平衡观点对林带、牧草地和裸露地的水量平衡各分量的变化规律进行了探讨。林带、牧草地和裸露地水量平衡各分量的分配比例分别为:降水均为100%;蒸发散96.4%、95.7%和89.5%;坡地径流3.6%、4.3%和10.5%。由于林带有林冠和林地两个作用面组成,分别对它们的水量平衡各分量的组成及其变化规律作了分析。还论述了林带对河川径流的影响。     

3S技术及其在生态学研究中的应用

随着国民经济的迅速发展,人类对资源环境的需求越来越高,及时、准确、动态地获取资源现状及其变化信息对资源、生态环境的保护及可持续发展具有重要意义。本文综述了3S技术即遥感(RS)、地理信息系统(GIS)、全球定位系统(GPS)的概念、特点及其研究进展,探讨了3S技术在景观生态学及景观异质性研究、空间格局分析与模拟的应用;并对3S技术在群落生态学、植被调查、生物多样性研究、植被制图以及其它生态学领域中的应用作了展望。     

区域生态学的特点、学科定位及其与相邻学科的关系

区域生态学作为生态学的一门重要分支学科,起源于20世纪70年代的区域综合科学考察和环境污染调查,旨在研究区域生态环境问题形成背景和驱动因子,探讨区域生态环境问题解决的思路和方法。基于前人研究成果和文献综述,系统分析了区域生态学研究的特点,剖析了区域生态学的性质和学科定位。在此基础上进一步比较了区域生态学与景观生态学、生态系统生态学、区域自然地理学和宏观生态学的共性与差异。认为:(1)区域生态学研究对象是具有特定生态环境属性的区域生态综合体,既具有特定要素主导下的空间均质性,也具有多种要素耦合作用下的空间异质性特征,是一门问题导向的应用性基础学科;(2)区域生态学研究需要具有多元综合、问题导向和系统集成的思维,从多层次、多视角探讨区域生态环境问题的解决方案;(3)区域生态学属于宏观生态学研究的范畴,处于分子生态学、个体生态学、种群生态学、群落生态学、生态系统生态学、景观生态学、区域生态学和全球生态学这个生态学学科体系的较高层次。     

生态学的科学概念及其演变与当代生态学学科体系之商榷

生态学既是生物学的分支学科,也是环境科学、地球系统科学的重要组成部分,其研究成果可直接服务于植物、动物、微生物的生物多样性保护、生物资源利用及生物产业管理等应用领域.生态系统概念将经典生态学或者基础生态学研究扩展到了生态系统生态学或者生态系统科学的新阶段,奠定了大尺度及全球生态环境科学研究的理论基础,促进了生物学、地理...     

分子微生物生态学及其研究进展

分子微生物生态学是分子生物学实验技术应用于微生物生态学研究领域而发展形成的一门交叉学科,在研究微生物生态系统组成结构、功能的分子机理以及微生物与生物和非生物环境之间相互关系等方面显示了巨大的潜力．十几年来分子微生物生态学研究所取得的成就证明：分子生物学研究技术向微生物生态学领域的不断渗透,为微生物生态学研究领域注入了新的活力,尤其在微生物多样性、微生物区系分子组成及变化规律以及微生物系统进化研究方面取得了重大突破．本文根据近年分子微生物生态学的研究进展,就分子微生物生态学概念的提出、发展历程、主要研究领域、主要研究方法以及未来研究热点领域作以简要综述。     

Neutral theory and community ecology

I review the mathematical and biological aspects of Hubbell's (2001) neutral theory of species abundance for ecological communities, and clarify its historical connections with closely related approaches in population genetics. A selective overview of the empirical evidence for and against this theory is provided, with a special emphasis on tropical plant communities. The neutral theory predicts many of the basic patterns of biodiversity, confirming its heuristic power. The strict assumption of equivalence that defines neutrality, equivalence among individuals, finds little empirical support in general. However, a weaker assumption holds for stable communities, the equivalence of average fitness among species. One reason for the surprising success of the neutral theory is that all the theories of species coexistence satisfying the fitness equivalence assumption, including many theories of niche differentiation, generate exactly the same patterns as the neutral theory. Hubbell's neutral theory represents an important synthesis and a much needed demonstration of the pivotal role of intraspecific variability in ecology. Further improvements should lead to an explicit linking to niche‐based processes. This research programme will depend crucially on forthcoming theoretical and empirical achievements.     

Parallel changes in the taxonomical structure of bacterial communities exposed to a similar environmental disturbance

Bacterial communities play a central role in ecosystems, by regulating biogeochemical fluxes. Therefore, understanding how multiple functional interactions between species face environmental perturbations is a major concern in conservation biology. Because bacteria can use several strategies, including horizontal gene transfers (HGT), to cope with rapidly changing environmental conditions, potential decoupling between function and taxonomy makes the use of a given species as a general bioindicator problematic. The present work is a first step to characterize the impact of a recent polymetallic gradient over the taxonomical networks of five lacustrine bacterial communities. Given that evolutionary convergence represents one of the best illustration of natural selection, we focused on a system composed of two pairs of impacted and clean lakes in order to test whether similar perturbation exerts a comparable impact on the taxonomical networks of independent bacterial communities. First, we showed that similar environmental stress drove parallel structural changes at the taxonomic level on two independent bacterial communities. Second, we showed that a long-term exposure to contaminant gradients drove significant taxonomic structure changes within three interconnected bacterial communities. Thus, this model lake system is relevant to characterize the strategies, namely acclimation and/or adaptation, of bacterial communities facing environmental perturbations, such as metal contamination.     

Pyrogeography,historical ecology,and the human dimensions of fire regimes

In our 2011 synthesis (Bowman et al., Journal of Biogeography, 2011, 38 , 2223–2236), we argued for a holistic approach to human issues in fire science that we term ‘pyrogeography’. Coughlan & Petty (Journal of Biogeography, 2013, 40 , 1010–1012) critiqued our paper on the grounds that our ‘pyric phase’ model was built on outdated views of cultural development, claiming we developed it to be the unifying explanatory framework for all human–fire sciences. Rather, they suggest that ‘historical ecology’ could provide such a framework. We used the ‘pyric transition’ for multiple purposes but did not offer it as an exclusive explanatory framework for pyrogeography. Although ‘historical ecology’ is one of many useful approaches to studying human–fire relationships, scholars should also look to political and evolutionary ecology, ecosystems and complexity theories, as well as empirical generalizations to build an interdisciplinary fire science that incorporates human, ecological and biophysical dimensions of fire regimes.     

基因工程生物的生态影响及其评价

随着基因工程技术的迅速发展,基因工程产生的生物将被广泛地应用于非受控的自然环境中,这将带来诸多的环境和生态方面的问题。本文概述了基因工程生物在非受控环境下可能产生的生态影响,提出了“基因工程生态学”这一新的应用生态学分支领域,探讨了该分支学科的概念、主要研究内容和目标,以及当前应采取的研究策略,并就发展基因工程生态学的有关问题提出了建议。     

The growing contributions of molecular biology and immunology to protistan ecology: molecular signatures as ecological tools

Modern genetic and immunological techniques have become important tools for assessing protistan species diversity for both the identification and quantification of specific taxa in natural microbial communities. Although these methods are still gaining use among ecologists, the new approaches have already had a significant impact on our understanding of protistan diversity and biogeography. For example, genetic studies of environmental samples have uncovered many protistan phylotypes that do not match the DNA sequences of any cultured organisms, and whose morphological identities are unknown at the present time. Additionally, rapid and sensitive methods for detecting and enumerating taxa of special importance (e.g. bloom-forming algae, parasitic protists) have enabled much more detailed distributional and experimental studies than have been possible using traditional methods. Nevertheless, while the application of molecular approaches has advanced some aspects of aquatic protistan ecology, significant issues still thwart the widespread adoption of these approaches. These issues include the highly technical nature of some of the molecular methods, the reconciliation of morphology-based and sequence-based species identifications, and the species concept itself.     

Integrated pest management theory and practice

Integration in pest management may be conceived at three distinct levels: (a) integration of tactics, (b) integration of the effects of multiple pest stresses, and (c) systems integration. The ecological basis of each is found in population, community or ecosystems processes, respectively. Most current IPM programs are attempts to integrate control tactics into management strategies and therefore only require knowledge of species and population ecology. Further advancement of IPM will require higher levels of integration but the experimental basis of and information on community and ecosystems processes are insufficient to permit reaching these levels. Mostly entomological examples in the grain legumes are used to demonstrate achievements of IPM at level a (tactical integration), and the difficulties involved in advancing towards integration of multiple pest stresses and systems integration (levels b and c). General requisites towards the design and implementation of IPM programs are outlined.     

Mark retention and fish survival associated with a low-cost marking technique for common carp Cyprinus carpio (Linnaeus, 1758)

Common carp (Cyprinus carpio, [Linnaeus, 1758]) have long been established in the United States and in some cases their populations can be very dense, leading biologists to expend significant effort towards reducing numbers of common carp in some populations. Estimating abundance of common carp prior to removal efforts would be useful in evaluating success of these removal efforts, but marking large numbers of fish can be expensive. Therefore, a low-cost tagging option is needed. In this study, we used tank and field experiments to determine the retention and longevity of hole-punch marks in the opercula of common carp. For the tank experiment, fish were double marked with a size-3 self-piercing tag and an operculum hole-punch mark (using a paper hole-punch tool with a hole diameter of 6.4 mm) on opposite sides of the fish. Over the entirety of the 180–day tank experiment, retention of the self-piercing tags and hole-punch marks was 100% and no marking mortality was observed. For the field experiment, 883 common carp were tagged at random in two groups, a double-marked group (n = 416, both self-piercing tags and hole-punch) and a single-mark group (n = 467, self-piercing tag). Fish were sampled monthly for 398 days. Because the length distribution sampled was bimodal, we evaluated tag retention of fish <330 mm TL (small fish, n = 273) and > 331 mm TL (large fish, n = 143), separately. Hole-punch mark retention was high for both size classes throughout most of the field experiment. For large fish, retention of hole-punch marks was 100% for the entire 398-day experiment. For small fish, retention of hole-punch marks was 100% through 184-day and remained above 93% through 328-days, but declined to 0% by day 398. Our results suggest that the operculum hole-punch mark is a valuable low-cost, long-term technique for tagging common carp.     

转型期城市生态学前沿研究进展

城市是一类以人类活动为中心听社会－经济－自然复合生态系统。城市人类活动对局地、区域和全球环境的胁迫效应,自然生态系统的响应机制,城市时、空、量、构、序的耦合规律、动力学机制和控制论方法是当前国际社会和学术界关注的热点。介绍了转型期城市人类生态影响研究的一些主要国际科学计划,如ＳＣＯＰＥ及ＩＨＤＰ等,综述了城市生态学研究三大前沿领域的国际研究动向和案例,即人居生态学、产业生态学和城镇生命支持系统生态     

Environmental and socio‐economic factors related to urban bird communities

Urban fauna communities may be strongly influenced by environmental and socio‐economic factors, but the relative importance of these factors is poorly known. Most research on urban fauna has been conducted in large cities and it is unclear if the patterns found in these locations coincide with those from smaller human settlements. We examined the relative importance of environmental and socio‐economic factors in explaining variation in urban bird communities across 72 neighbourhoods in 18 regional towns in south‐eastern Australia. Native bird species richness varied from 6 to 32 across neighbourhoods and was higher in neighbourhoods with more nectar‐rich plants. Variation in bird species diversity across neighbourhoods was also strongly positively related to the density of nectar‐rich plants, but was higher also in neighbourhoods with higher socio‐economic status (reflecting higher levels of disposal income, education and home ownership). The density of native birds across neighbourhoods per season varied from 1 to 15 birds per hectare and was lower in neighbourhoods with a greater cover of impervious surfaces. The density of exotic birds (introduced to Australia) per season also varied across neighbourhoods (0–13 birds per hectare) and was lower in neighbourhoods with more nectar‐rich plants and higher in neighbourhoods with greater impervious surface cover. Our results demonstrated that the vegetation characteristics of household gardens, along streetscapes and in urban parklands had a strong influence on the richness and diversity of urban bird communities. The density of native and exotic birds varied primarily in response to changes in the built environment (measured through impervious surface cover). Socio‐economic factors had relatively little direct influence on urban birds, but neighbourhood socio‐economics may influence bird communities indirectly through the positive relationship between socio‐economic status and vegetation cover recorded in our study area.     

Getting specific: making taxonomic and ecological sense of large sequencing data sets

Eukaryotic microbes comprise a diverse collection of phototrophic and heterotrophic creatures known to play fundamental roles in ecological processes. Some can be identified by light microscopy, generally the largest and with conspicuous shapes, while the smallest can be counted by epifluorescence microscopy or flow cytometry but remain largely unidentified. Microbial diversity studies greatly advanced with the analysis of phylogenetic markers sequenced from natural assemblages. Molecular surveys began in 1990 targeting marine bacterioplankton (Giovannoni et al. 1990 ) and first approached microbial eukaryotes in three studies published in 2001 (Díez et al. 2001 ; López‐García et al. 2001 ; Moon‐van der Staay et al. 2001 ). These seminal studies, based on cloning and Sanger sequencing the complete 18S rDNA, were critical for obtaining broad pictures of microbial diversity in contrasted habitats and for describing novel lineages by robust phylogenies, but were limited by the number of sequences obtained. So, inventories of species richness in a given sample and community comparisons through environmental gradients were very incomplete. These limitations have been overcome with the advent of high‐throughput sequencing (HTS) methods, initially 454‐pyrosequencing, today Illumina and soon others to come. In this issue of Molecular Ecology, Egge et al. ( 2015 ) show a nice example of the use of HTS to study the biodiversity and seasonal succession of a particularly important group of marine microbial eukaryotes, the haptophytes. Temporal changes were analysed first at the community level, then at the clade level, and finally at the lowest rank comparable to species. Interesting and useful ecological insights were obtained at each taxonomic scale. Haptophyte diversity differed along seasons in a systematic manner, with some species showing seasonal preferences and others being always present. Many of these species had no correspondence with known species, pointing out the high level of novelty in microbial assemblages, only accessible by molecular tools. Moreover, the number of species detected was limited, agreeing with a putative scenario of constrained evolutionary diversification in free‐living small eukaryotes. This study illustrates the potential of HTS to address ecological relevant questions in an accessible way by processing large data sets that, nonetheless, need to be treated with a fair understanding of their limitations.