“生态系统能量流动”的教学分析与设计

生态系统的存在与发展主要取决于能量持续不断的流动和物质周而复始的循环。生态系统作为一个动态开放系统,具有能量流动、生物生产、物质循环、信息传递等基本功能。其中,物质作为能量的载体,使能量沿着食物链（网）流动;能量作为动力,使物质能够不断地在生物群落和无机环境之间循环往返。     

我国土壤动物群落生态学研究综述

总结了我国土壤动物群落生态学研究的特点,即区域分布集中于中国东部、研究的生态系统类型广泛、研究角度多种多样与应用研究发展迅速。并从土壤动物群落与环境关系、土壤动物群落的组成和多样性、土壤动物群落结构、土壤动物群落功能、土壤动物群落演替与受干扰生态系统的土壤动物群落6个方面综述其最新研究成果。在此基础上指出我国土壤动物群落生态学中有待开拓的研究领域是基础研究、特色区域和生态系统的研究、土地覆盖/土地利用对土壤动物的影响研究、土壤动物多样性及其保护研究、土壤动物在土壤生态系统和陆地生态系统物质循环和能量流动中的作用研究、全球变化响应研究与土壤动物应用研究。     

西藏高原湿地植物和土壤细菌多样性及其影响因素分析

植物和微生物是湿地生态系统的主要组成部分,也是其能量流动和物质循环的重要驱动力。了解湿地植物和土壤微生物的多样性及其关键影响因子,对于维持湿地生态系统的结构和功能有重要意义。本研究对西藏高原26个湿地进行野外调查和实验室分析,以揭示湿地植物与土壤细菌多样性的关系,明确影响植物多样性和土壤细菌多样性的关键因子。结果显示,植物群落特征与土壤细菌多样性显著相关,但驱动土壤细菌多样性变异的主要因素是环境因子而非植物。植物多样性的变异主要受土壤电导率影响,而细菌多样性的变异则与海拔、年降水量、土壤pH值以及植物功能性状（叶片总氮和总碳）相关。     

“生态系统的稳态”中核心概念梳理及案例分析

生态系统稳态的核心是稳定的营养结构和完善的能量流动、物质循环及信息传递。稳态下,生态系统能量与物质的输入与输出保持平衡,生物成分间通过竞争、捕食等种间关系赋予生态系统一定限度的反馈调节。阐述在教学中如何把握这部分知识的核心概念,帮助学生理解生态系统反馈调节的基础和机制,分析生态平衡被打破时的恢复与重建,提高能量利用效率、保持或改善无机环境,并为学生梳理知识体系,纠正理解错误,提高学习效率。     

土壤线虫作为生态指示生物的研究进展

土壤线虫广布于各种类型的土壤中, 在维持土壤生态系统的稳定性、促进物质循环和能量流动等方面发挥着重要的作用, 同时也是理想的环境指示生物。简述了土壤线虫的生活史策略和营养类群的多样性、土壤线虫多样性的生态指数、影响土壤线虫群落多样性的环境因素, 以及线虫作为指示生物在农业生态系统、草地生态系统、森林生态系统的功能作用。提出了全球气候变化背景下对青藏高原高寒草地土壤线虫分类、群落结构特征以及土壤线虫的生物指示作用研究的必要性, 并对土壤线虫未来的发展趋势做了展望。     

中国科学院长白山森林生态系统定位站综合研究概况

中国科学院长白山森林生态系统定位站是从事森林生态系统的结构,功能和生产力研究的科研基地,是中国科学院陆地生态系统科研规划中列入的五个重点生态系统科学研究基地之一。其目的在于用系统生态学的观点和方法研究森林生态系统中物质转化与能量流动的规律,研究各个成分之间的相互关系,阐明森林生态系统的结构与功能及其调节控制的原理,为有效地提高     

在"生态系统能量流动"教学中发展科学思维及强化生命观念

在"生态系统能量流动"一节教学中,组织学生从微观到宏观分别研究各生命系统的能量流动过程,建立、分析、研究能量流动模型,总结归纳生态系统能量流动的概念及能量流动规律,应用规律解决问题,提高节约粮食的意识,教学过程中不断地发展科学思维并形成系统观、物质与能量观.     

啮齿动物的适应性

啮齿动物是哺乳动物中最大的类群,占哺乳动物种数的42%。啮齿动物具有高繁殖力、适应性强、分布广等特点,食性、行为和生理等各个方面也表现出多样性,例如聚群行为既可节省能量消耗,还能改变肠道微生物的组成。啮齿动物是生态系统的重要组成部分,在生态系统的物质和能量流动等过程和功能方面具有不可替代的作用。     

放牧对草地枯落物分解和土壤动物群落及其相互关系的影响

在草地生态系统中,枯落物作为介导土-草界面过程的重要环节,主要调控地上-地下生态系统物质循环与能量流动,其分解对土壤食物网和土壤生物营养结构具有显著影响。土壤动物是枯落物与土壤之间物质循环与能量流动的重要媒介,是枯落物分解与养分释放过程的主要调节者。近年来,国内外学者对枯落物分解与土壤动物多样性的研究逐步深入,取得大量的研究成果。本文通过综述国内外文献,从放牧对枯落物分解过程的影响、放牧对土壤动物的影响及放牧对枯落物分解与土壤动物关系的影响等三个方面,总结分析了放牧通过采食、践踏和排泄行为改变枯落物分解,间接影响土壤动物多样性,从而降低了土壤微食物网的复杂性。另外,食草动物对草地枯落物分解和土壤动物关系的影响复杂,且这种关系往往对放牧强度、放牧季节、家畜种类等做出响应,进而会影响到整个生态系统的结构和功能。     

种间互作网络的结构、生态系统功能及稳定性机制研究

生态群落中不同物种间发生多样化的相互作用, 形成了复杂的种间互作网络。复杂生态网络的结构如何影响群落的生态系统功能及稳定性是群落生态学的核心问题之一。种间互作直接影响到物质和能量在生态系统不同组分之间的流动和循环以及群落构建过程, 使得网络结构与生态系统功能和群落稳定性密切相关。在群落及生态系统水平上开展种间互作网络研究将为群落的构建机制、生物多样性维持、生态系统稳定性、物种协同进化和性状分化等领域提供新的视野。当前生物多样性及生态系统功能受到全球变化的极大影响, 研究种间互作网络的拓扑结构、构建机制、稳定性和生态功能也可为生物多样性的保护和管理提供依据。该文从网络结构、构建机制、网络结构和稳定性关系、种间互作对生态系统功能的影响等4个方面综述当前种间网络研究进展, 并提出在今后的研究中利用机器学习和多层网络等来探究环境变化对种间互作网络结构和功能的影响, 并实现理论和实证研究的有效整合。     

微生物分子生态学技术在湖泊微生物多样性研究中的应用

微生物是湖泊生物圈物质循环和能量流动的主要参与者,在湖泊的生态系统中起着重要的作用。但是,湖泊中存在着大量不可培养的细菌,利用传统的培养技术,无法对湖泊微生物的多样性进行深入而全面的研究,而不依赖培养的分子生物学技术的发展为此方面研究开辟了新的路径。微生物分子生态学作为分子生物学与微生物生态学交叉产生的学科,在研究湖泊微生物多样性方面已经得到了广泛的应用。主要综述了变性梯度凝胶电泳(PCR-DGGE)技术,末端限制性酶切片段长度多态性技术(T-RFLP),16SrDNA克隆文库技术等微生物分子生态学技术在研究湖泊微生物多样性方面的应用情况。     

Free energy simulations: The meaning of the individual contributions from a component analysis

A theoretical analysis is made of the decomposition into contributions from individual interactions of the free energy calculated by thermodynamic integration. It is demonstrated that such a decomposition, often referred to as “component analysis,” is meaningful, even though it is a function of the integration path. Moreover, it is shown that the path dependence can be used to determine the relation of the contribution of a given interaction to the state of the system. To illustrate these conclusions, a simple transformation(Cl^? to Br^? in aqueous solution) is analyzed by use of the Reference Interaction Site Model-Hypernetted Chain Closure integral equation approach; it avoids the calculational difficulties of macromolecular simulation while retaining their conceptual complexity. The difference in the solvation free energy between chloride and bromide is calculated, and the contributions of the Lennard-Jones and electrostatic terms in the potential function are analyzed by the use of suitably chosen integration paths. The model is also used to examine the path dependence of individual contributions to the double free energy differences (ΔΔG or ΔΔA) that are often employed in free energy simulations of biological systems. The alchemical path, as contrasted with the experimental path, is shown to be appropriate for interpreting the effects of mutations on ligand binding and protein stability. The formulation is used to obtain a better understanding of the success of the Poisson-Boltzmann continuum approach for determining the solvation properties of polar and ionic systems. © 1994 Wiley-Liss, Inc.     

The significance of vertebrates in the structure and functioning of ecosystems

A review of published data on the ecology of terrestrial vertebrates and, partly, fishes is used as a basis to show that their communities have only a weak relationship to the structure of phytocenoses. Unlike plants, vertebrates actively choose preferable biotopes and do not die off upon transition between the stages of succession. The role of vertebrates in the functioning of ecosystems is determined by their contribution to matter and energy turnover and effect on the structure of ecosystems of different ranks. The transfer of matter and energy in food chains accelerates their turnover, and the distribution of excrements and corpses within the ranges of animal activity and migrations modulates the pattern of matter and energy fluxes over the Earth’s surface. The spread of plant diaspores by animals and the burrowing and feeding activities of first-order consumers give rise to microsuccessions within macrosuccession stages, thereby contributing to the diversity of vegetation. In some cases, the activities of first-order consumers may result in the cessation of succession.     

生态流的构成和分析方法研究综述

人类活动带来的生态环境和土地利用变化是全球变化研究的重点内容之一。在复杂的自然生态系统中,各组分之间的物质循环、能量流动和信息传递通常以流态形式来表达,其路径、方向、强度、速率等对生态系统产生重要影响。系统分析了生态流的起源与发展,从能流、物质流和信息流三方面对生态流进行了解构,并对相关原理和分析方法进行了总结和述评。在现有研究基础上,以典型半人工半自然的农田生态系统为例,通过生态网络连接度等指标与纯自然生态系统对比分析生态流的流向、路径和强度等,人类活动增强了生态系统的灵活度,但扰乱了原有的稳定性。生态学家一直专注于研究适用于统一计算生态流的方法,其量化已具有一定的研究基础,但仍存在许多问题,在以后的研究中仍需系统地深入探索。     

网络视角下城市物质代谢过程解析——以京津冀13城市为例

城市作为物质吞吐量的集中区,往往存在一定的资源消耗和环境问题。京津冀是中国北方经济规模最大的地区,负载着巨大的资源环境压力。以京津冀地区为例,在计算城市物质输入与输出的基础上,运用生态网络分析方法对代谢系统内部的具体路径和节点关系进行深入探究,并分析其变化。结果表明,京津冀地区97%的流量都集中于各城市内部,各城市之间的优势互补有待加强。2017年京津冀13城市代谢总流量增长为2000年的3.3倍,其中承德、秦皇岛和唐山增长最为迅速,而衡水是唯一一个流量下降的城市。各城市的关键路径中有71.8%呈现流量上升态势,加工制造业为涉及关键路径最多的部门,其中加工制造业-环境为大多数所有城市共有的关键路径。掠夺/控制是京津冀13城市的主导关系类型;2000—2017年间13城市总体的生态关系良性转变少于劣性转变,致使共生关系数量下降,需要从交通运输业、采掘业和加工制造业等重点部门上寻求突破。关键路径及生态关系等代谢网络特征及其变化的识别,有效打破了城市代谢的“黑箱”,为缓解不同城市物质利用所带来的资源环境问题提供可靠理论依据。     

Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method

Background

Many proteins tune their biological function by transitioning between different functional states, effectively acting as dynamic molecular machines. Detailed structural characterization of transition trajectories is central to understanding the relationship between protein dynamics and function. Computational approaches that build on the Molecular Dynamics framework are in principle able to model transition trajectories at great detail but also at considerable computational cost. Methods that delay consideration of dynamics and focus instead on elucidating energetically-credible conformational paths connecting two functionally-relevant structures provide a complementary approach. Effective sampling-based path planning methods originating in robotics have been recently proposed to produce conformational paths. These methods largely model short peptides or address large proteins by simplifying conformational space.

Methods

We propose a robotics-inspired method that connects two given structures of a protein by sampling conformational paths. The method focuses on small- to medium-size proteins, efficiently modeling structural deformations through the use of the molecular fragment replacement technique. In particular, the method grows a tree in conformational space rooted at the start structure, steering the tree to a goal region defined around the goal structure. We investigate various bias schemes over a progress coordinate for balance between coverage of conformational space and progress towards the goal. A geometric projection layer promotes path diversity. A reactive temperature scheme allows sampling of rare paths that cross energy barriers.

Results and conclusions

Experiments are conducted on small- to medium-size proteins of length up to 214 amino acids and with multiple known functionally-relevant states, some of which are more than 13Å apart of each-other. Analysis reveals that the method effectively obtains conformational paths connecting structural states that are significantly different. A detailed analysis on the depth and breadth of the tree suggests that a soft global bias over the progress coordinate enhances sampling and results in higher path diversity. The explicit geometric projection layer that biases the exploration away from over-sampled regions further increases coverage, often improving proximity to the goal by forcing the exploration to find new paths. The reactive temperature scheme is shown effective in increasing path diversity, particularly in difficult structural transitions with known high-energy barriers.

     

Does natural selection organize ecosystems for the maintenance of high productivity and diversity?

Three types of evidence suggest that natural ecosystems are organized for high productivity and diversity: (i) changes not previously experienced by a natural ecosystem, such as novel human disturbances, tend to diminish its productivity and/or diversity, just as 'random' changes in a machine designed for a function usually impair its execution of that function; (ii) humans strive to recreate properties of natural ecosystems to enhance productivity of artificial ones, as farmers try to recreate properties of natural soils in their fields; and (iii) productivity and diversity have increased during the Earth's history as a whole, and after every major biotic crisis. Natural selection results in ecosystems organized to maintain high productivity of organic matter and diversity of species, just as competition among individuals in Adam Smith's ideal economy favours high production of wealth and diversity of occupations. In nature, poorly exploited energy attracts more efficient users. This circumstance favours the opening of new ways of life and more efficient recycling of resources, and eliminates most productivity-reducing 'ecological monopolies'. Ecological dominants tend to be replaced by successors with higher metabolism, which respond to more stimuli and engage in more varied interactions. Finally, increasingly efficient predators and herbivores favour faster turnover of resources.     

Indirect Energy Flows in Niche Model Food Webs: Effects of Size and Connectance

Indirect interactions between species have long been of interest to ecologists. One such interaction type takes place when energy or materials flow via one or more intermediate species between two species with a direct predator-prey relationship. Previous work has shown that, although each such flow is small, their great number makes them important in ecosystems. A new network analysis method, dynamic environ approximation, was used to quantify the fraction of energy flowing from prey to predator over paths of length greater than 1 (flow indirectness or FI) in a commonly studied food web model. Web structure was created using the niche model and dynamics followed the Yodzis-Innes model. The effect of food web size (10 to 40 species) and connectance (0.1 to 0.48) on FI was examined. For each of 250 model realizations run for each pair of size and connectance values, the FI of every predator-prey interaction in the model was computed and then averaged over the whole network. A classification and regression tree (CART) analysis was then used to find the best predictors of FI. The mean FI of the model food webs is 0.092, with a standard deviation of 0.0279. It tends to increase with system size but peaks at intermediate connectance levels. Of 27 potential predictor variables, only five (mean path length, dominant eigenvalue of the adjacency matrix, connectance, mean trophic level and fraction of species belonging to intermediate trophic levels) were selected by the CART algorithm as best accounting for variation in the data; mean path length and the dominant eigenvalue of the adjacency matrix were dominant.