微生物的遗传多样性

微生物是生物圈中不可或缺的重要组成部分, 维系着自然界生态平衡。随着分子生物学技术的发展, 微生物遗传多样性的研究从形态学水平、蛋白水平进入到了DNA水平。而高通量测序技术和宏基因组技术的发展, 不仅为我们理解微生物的遗传多样性提供了更加丰富的信息和有力的证据, 也对于合理利用生物资源、保护生态平衡等方面具有重要意义。文章就微生物遗传多样性研究的相关内容, 如物种的分离鉴定、微生物群体遗传结构、物种形成以及系统发育和进化等方面的研究进展进行综述。     

The fundamental processes in ecology: a thought experiment on extraterrestrial biospheres

Ecological science is often organised as a hierarchical series of entities: genes, individuals, populations, species, communities, ecosystems and biosphere. Here, I consider an alternative process‐based approach to ecology, and analyse the nature of the fundamental processes in ecology. These fundamental processes are discussed in the context of the following question:‘for any planet with carbon‐based life, which persists over geological time scales, what are the minimum set of ecological processes that must be present?‘I suggest that the following processes would be present on any such planet: energy flow, multiple guilds, ecological tradeo ffs leading to within‐guild biodiversity, ecological hypercycles, merging of organismal and ecological physiology, carbon sequestration and possibly photosynthesis. Nutrient cycling is described as an emergent property of these fundamental processes. I discuss reasons why a biosphere based on a single species with no nutrient cycling is very unlikely to exist. I also describe the concept of ‘Gaian effect’. This suggests that some processes will always tend to extend the lifespan of a biosphere in which they develop (positive Gaian effect) while others could either increase or decrease (negative Gaian effect) such a lifespan. These ideas are discussed in the context of astrobiology, ecosystem services, conservation biology and Gaia theory.     

Physiological dynamics,reproduction‐maintenance allocations,and life history evolution

Allocation of resources to competing processes of growth, maintenance, or reproduction is arguably a key process driving the physiology of life history trade‐offs and has been shown to affect immune defenses, the evolution of aging, and the evolutionary ecology of offspring quality. Here, we develop a framework to investigate the evolutionary consequences of physiological dynamics by developing theory linking reproductive cell dynamics and components of fitness associated with costly resource allocation decisions to broader life history consequences. We scale these reproductive cell allocation decisions to population‐level survival and fecundity using a life history approach and explore the effects of investment in reproduction or tissue‐specific repair (somatic or reproductive) on the force of selection, reproductive effort, and resource allocation decisions. At the cellular level, we show that investment in protecting reproductive cells increases fitness when reproductive cell maturation rate is high or reproductive cell death is high. At the population level, life history fitness measures show that cellular protection increases reproductive value by differential investment in somatic or reproductive cells and the optimal allocation of resources to reproduction is moulded by this level of investment. Our model provides a framework to understand the evolutionary consequences of physiological processes underlying trade‐offs and highlights the insights to be gained from considering fitness at multiple levels, from cell dynamics through to population growth.     

SCALE AND HIERARCHY IN MACROEVOLUTION

Abstract: Scale and hierarchy must be incorporated into any conceptual framework for the study of macroevolution, i.e. evolution above the species level. Expansion of temporal and spatial scales reveals evolutionary patterns and processes that are virtually inaccessible to, and unpredictable from, short‐term, localized observations. These larger‐scale phenomena range from evolutionary stasis at the species level and the mosaic assembly of complex morphologies in ancestral forms to the non‐random distribution in time and space of the origin of major evolutionary novelties, as exemplified by the Cambrian explosion and post‐extinction recoveries of metazoans, and the preferential origin of major marine groups in onshore environments and tropical waters. Virtually all of these phenomena probably involve both ecological and developmental factors, but the integration of these components with macroevolutionary theory has only just begun. Differential survival and reproduction of units can occur at several levels within a biological hierarchy that includes DNA sequences, organisms, species and clades. Evolution by natural selection can occur at any level where there is heritable variation that affects birth and death of units by virtue of interaction with the environment. This dynamic can occur when selfish DNA sequences replicate disproportionately within genomes, when organisms enjoy fitness advantages within populations (classical Darwinian selection), when differential speciation or extinction occurs within clades owing to organismic properties (effect macroevolution), and when differential speciation or extinction occurs within clades owing to emergent, species‐level properties (in the strict sense species selection). Operationally, emergent species‐level properties such as geographical range can be recognized by testing whether their macroevolutionary effects are similar regardless of the different lower‐level factors that produce them. Large‐scale evolutionary trends can be driven by transformation of species, preferential production of species in a given direction, differential origination or extinction, or any combination of these; the potential for organismic traits to hitch‐hike on other factors that promote speciation or damp extinction is high. Additional key attributes of macroevolutionary dynamics within biological hierarchies are that (1) hierarchical levels are linked by upward and downward causation, so that emergent properties at a focal level do not impart complete independence; (2) hierarchical effects are asymmetrical, so that dynamics at a given focal level need not propagate upwards, but will always cascade downwards; and (3) rates are generally, although not always, faster at lower hierarchical levels. Temporal and spatial patterns in the origin of major novelties and higher taxa are significantly discordant from those at the species and genus levels, suggesting complex hierarchical effects that remain poorly understood. Not only are many of the features promoting survivorship during background times ineffective during mass extinctions, but also they are replaced in at least some cases by higher‐level, irreducible attributes such as clade‐level geographical range. The incorporation of processes that operate across hierarchical levels and a range of temporal and spatial scales has expanded and enriched our understanding of evolution.     

Sex in a material world: why the study of sexual reproduction and sex‐specific traits should become more nutritionally‐explicit

Recent advances in nutritional ecology, particularly arising from Ecological Stoichiometry and the Geometric Framework for nutrition, have resulted in greater theoretical coherence and increasingly incisive empirical methodologies that in combination allow for the consideration of nutrient‐related processes at many levels of biological complexity. However, these advances have not been consistently integrated into the study of sexual differences in reproductive investment, despite contemporary emphasis on the material costs associated with sexually selected traits (e.g. condition‐dependence of exaggerated ornaments). Nutritional ecology suggests that material costs related to sex‐specific reproductive traits should be linked to quantifiable underlying differences in the relationship between individuals of each sex and their foods. Here, we argue that applying nutritionally‐explicit thought to the study of sexual reproduction should both deepen current understanding of sex‐specific phenomena and broaden the tractable frontiers of sexual selection research. In support of this general argument, we examine the causes and consequences of sex‐specific nutritional differences, from food selection and nutrient processing to sex‐specific reproductive traits. At each level of biological organization, we highlight how a nutritionally‐explicit perspective may provide new insights and help to identify new directions. Based on predictions derived at the individual level, we then consider how sex‐specific nutrient limitation might influence population growth, and thus potentially broader patterns of life history evolution, using a simple population dynamics model. We conclude by highlighting new avenues of research that may be more accessible from this integrative perspective.     

Stages of transition from precellular organic microsystems to primary prokaryotic communities

Basic provisions of an original concept of biosphere germination are enumerated. Formation of primary microorganisms and communities is considered from the viewpoint of crucial transformations in compartments of organic matter that led to the emergence of fundamental properties of biological systems. The necessary initial condition was the transition of organic microsystems in the bifurcation state which maintained continuing dynamic processes in them. The decisive stage of transformation of microsystems in protobionts (initial forms of life) comprised their acquiring ability to concentrate free energy and information at the expense of fortified reactions to external influences, exerted by the fluctuating hydrothermal environment. The primary biosphere was formed during the evolution of microorganism types in the direction probionts-progenotes-prokaryotes.     

Integrated process optimization: lessons from retrovirus and virus-like particle production

The optimization of production and purification processes is usually approached by engineers from a strictly biotechnological point of view. The present paper envisages the definition and application of an optimization model that takes into account the impact of both biological and technological issues upon the optimization protocols and strategies. For this purpose, the optimization of three analogous but different systems comprising animal cell growth and bioparticle production is presented. These systems were: human immunodeficiency 1 (HIV-1) and porcine parvovirus (PPV) virus-like particles (VLPs) produced in insect cells and retrovirus produced in mammalian cells. For the systematization of the optimization process four levels of optimization were defined-product, technology, design and integration. In this paper, the limits of each of the optimization levels defined are discussed by applying the concept to the systems described. This analysis leads to decisions regarding the production of VLPs and retrovirus as well as on the points relevant for further process development. Finally, the definition of the objective function or performance index, the possible strategies and tools for bioprocess optimization are described. Although developed from the three described processes, this approach can, based on the recent literature evidence reviewed here, be applied more universally for the process development of complex biopharmaceuticals.     

AN AMPLIFICATION OF THE PHYLOGENETIC SPECIES CONCEPT

Abstract— The goal of a phylogenetic species concept is to reveal the smallest units that are analysable by cladistic methods and interpretable as the result of phylogenctic history. We define species as the smallest aggregation of populations (sexual) or lineagcs (asexual) diagnosable by a unique combination of character states in comparable individuals (semaphoronts). A character state is an inherited attribute distributed among all comparable individuals (semaphoronts) of the same historical population, clade, or terminal lineage. This definition of species is character-based and pattern oriented. Evolutionary explanations of phylogenetic species are consistent with contemporary explanations of processes of speciation, but require only the assumption of nested hierarchical pattern. We discuss the compatibility of the phylogenetic species concept with various biological needs for species and justify its use at the exclusion of alternative species concepts.     

Biological hierarchies and the nature of extinction

Hierarchy theory recognises that ecological and evolutionary units occur in a nested and interconnected hierarchical system, with cascading effects occurring between hierarchical levels. Different biological disciplines have routinely come into conflict over the primacy of different forcing mechanisms behind evolutionary and ecological change. These disconnects arise partly from differences in perspective (with some researchers favouring ecological forcing mechanisms while others favour developmental/historical mechanisms), as well as differences in the temporal framework in which workers operate. In particular, long‐term palaeontological data often show that large‐scale (macro) patterns of evolution are predominantly dictated by shifts in the abiotic environment, while short‐term (micro) modern biological studies stress the importance of biotic interactions. We propose that thinking about ecological and evolutionary interactions in a hierarchical framework is a fruitful way to resolve these conflicts. Hierarchy theory suggests that changes occurring at lower hierarchical levels can have unexpected, complex effects at higher scales due to emergent interactions between simple systems. In this way, patterns occurring on short‐ and long‐term time scales are equally valid, as changes that are driven from lower levels will manifest in different forms at higher levels. We propose that the dual hierarchy framework fits well with our current understanding of evolutionary and ecological theory. Furthermore, we describe how this framework can be used to understand major extinction events better. Multi‐generational attritional loss of reproductive fitness (MALF) has recently been proposed as the primary mechanism behind extinction events, whereby extinction is explainable solely through processes that result in extirpation of populations through a shutdown of reproduction. While not necessarily explicit, the push to explain extinction through solely population‐level dynamics could be used to suggest that environmentally mediated patterns of extinction or slowed speciation across geological time are largely artefacts of poor preservation or a coarse temporal scale. We demonstrate how MALF fits into a hierarchical framework, showing that MALF can be a primary forcing mechanism at lower scales that still results in differential survivorship patterns at the species and clade level which vary depending upon the initial environmental forcing mechanism. Thus, even if MALF is the primary mechanism of extinction across all mass extinction events, the primary environmental cause of these events will still affect the system and result in differential responses. Therefore, patterns at both temporal scales are relevant.     

The Hierarchical Structure of Ecosystems: Connections to Evolution

Ecologic systems, which are involved mainly in the processing of energy and materials, are actually nested one inside another—they are simultaneously parts and wholes. This fundamental hierarchical organization is easy to detect in nature but has been undervalued by ecologists as a source of new insights about the structure and development of ecosystems and as a means of understanding the crucial connections between ecologic processes and large-scale evolutionary patterns. These ecologic systems include individual organisms bundled into local populations, populations as functional components of local communities or ecosystems, local systems making up the working parts of larger regional ecosystems, and so on, right up to the entire biosphere. Systems at any level of organization can be described and interpreted based on aspects of scale (size, duration, and “membership” in more inclusive entities), integration (all the vital connections both at a particular focal level and across levels of hierarchical organization), spatiotemporal continuity (the “life history” of each system), and boundaries (either membranes, skins, or some other kind of border criterion). Considering hierarchical organization as a general feature of ecologic systems could reinvigorate theoretical ecology, provide a realistic scaling framework for paleoecologic studies, and – most importantly – forge new and productive connections between ecology and evolutionary theory.     

When things don't add up: quantifying impacts of multiple stressors from individual metabolism to ecosystem processing

Ecosystems are exposed to multiple stressors which can compromise functioning and service delivery. These stressors often co‐occur and interact in different ways which are not yet fully understood. Here, we applied a population model representing a freshwater amphipod feeding on leaf litter in forested streams. We simulated impacts of hypothetical stressors, individually and in pairwise combinations that target the individuals' feeding, maintenance, growth and reproduction. Impacts were quantified by examining responses at three levels of biological organisation: individual‐level body sizes and cumulative reproduction, population‐level abundance and biomass and ecosystem‐level leaf litter decomposition. Interactive effects of multiple stressors at the individual level were mostly antagonistic, that is, less negative than expected. Most population‐ and ecosystem‐level responses to multiple stressors were stronger than expected from an additive model, that is, synergistic. Our results suggest that across levels of biological organisation responses to multiple stressors are rarely only additive. We suggest methods for efficiently quantifying impacts of multiple stressors at different levels of biological organisation.     

The GP problem: quantifying gene-to-phenotype relationships

In this paper we refer to the gene-to-phenotype modeling challenge as the GP problem. Integrating information across levels of organization within a genotype-environment system is a major challenge in computational biology. However, resolving the GP problem is a fundamental requirement if we are to understand and predict phenotypes given knowledge of the genome and model dynamic properties of biological systems. Organisms are consequences of this integration, and it is a major property of biological systems that underlies the responses we observe. We discuss the E(NK) model as a framework for investigation of the GP problem and the prediction of system properties at different levels of organization. We apply this quantitative framework to an investigation of the processes involved in genetic improvement of plants for agriculture. In our analysis, N genes determine the genetic variation for a set of traits that are responsible for plant adaptation to E environment-types within a target population of environments. The N genes can interact in epistatic NK gene-networks through the way that they influence plant growth and development processes within a dynamic crop growth model. We use a sorghum crop growth model, available within the APSIM agricultural production systems simulation model, to integrate the gene-environment interactions that occur during growth and development and to predict genotype-to-phenotype relationships for a given E(NK) model. Directional selection is then applied to the population of genotypes, based on their predicted phenotypes, to simulate the dynamic aspects of genetic improvement by a plant-breeding program. The outcomes of the simulated breeding are evaluated across cycles of selection in terms of the changes in allele frequencies for the N genes and the genotypic and phenotypic values of the populations of genotypes.     

The limited spatial scale of dispersal in soil arthropods revealed with whole‐community haplotype‐level metabarcoding

Soil arthropod communities are highly diverse and critical for ecosystem functioning. However, our knowledge of spatial structure and the underlying processes of community assembly are scarce, hampered by limited empirical data on species diversity and turnover. We implement a high‐throughput sequencing approach to generate comparative data for thousands of arthropods at three hierarchical levels: genetic, species and supra‐specific lineages. A joint analysis of the spatial arrangement across these levels can reveal the predominant processes driving the variation in biological assemblages at the local scale. This multihierarchical approach was performed using haplotype‐level COI metabarcoding of entire communities of mites, springtails and beetles from three Iberian mountain regions. Tens of thousands of specimens were extracted from deep and superficial soil layers and produced comparative phylogeographic data for >1,000 codistributed species and nearly 3,000 haplotypes. Local assemblage composition differed greatly between grasslands and forests and, within each habitat, showed strong spatial structure and high endemicity. Distance decay was high at all levels, even at the scale of a few kilometres or less. The local distance decay patterns were self‐similar for the haplotypes and higher hierarchical entities, and this fractal structure was similar in all regions, suggesting that uniform processes of limited dispersal determine local‐scale community assembly. Our results from whole‐community metabarcoding provide insight into how dispersal limitations constrain mesofauna community structure within local spatial settings over evolutionary timescales. If generalized across wider areas, the high turnover and endemicity in the soil locally may indicate extremely high richness globally, challenging our current estimations of total arthropod diversity on Earth.     

林缘和荒草坡不同草本层盖度小生境中积雪草的等级可塑性

为研究克隆植物在不同生境中对小生境的利用能力和对不同尺度异质性生境的等级可塑性及其格局差异,比较了林缘和荒草坡不同草本层盖度小生境中积雪草(Centella asiatica)分株种群、克隆片段和叶水平的形态和生理特征。在分株种群水平,林缘和荒草坡积雪草被测的分株种群特征差异均不显著,不同草本层盖度小生境间积雪草根冠比差异显著,即在盖度小的小生境中其根冠比显著大于盖度大的小生境。在克隆片段水平,林缘和荒草坡生境显著影响积雪草的根干重、花果干重、一级匍匐茎节间长和总匍匐茎节间长,而不同草本层盖度小生境则显著影响花果干重、根冠比、一级匍匐茎数、二级匍匐茎节间长和总匍匐茎节间长。荒草坡积雪草拥有更大的根干重和花果干重,但一级匍匐茎节间长和总匍匐茎节间长较短。草本层盖度小的小生境中积雪草的根冠比和一级匍匐茎数显著高于盖度大的小生境,而花果干重、二级匍匐茎节间长和总匍匐茎节间长则相反。在叶水平,荒草坡和草本层盖度大的小生境中,积雪草的叶片长、叶片宽和叶面积都较大,而草本层盖度大的小生境中积雪草叶柄长和比叶柄长都显著大于盖度小的小生境;林缘和荒草坡生境与不同草本层盖度小生境对4个叶绿素指标影响均不显著,林缘和荒草坡生境与不同草本层盖度小生境的交互作用对所有测量特征均无显著影响。上述结果表明,积雪草对不同生境和有草本层盖度差异的小生境的反应存在等级可塑性,但是二者的等级差异格局不同;等级反应格局的差异反映出积雪草对不同生境条件有不同的生态适应对策,且对生境小尺度异质性的可塑性强于对大尺度异质性的可塑性。     

Homeostatic mechanisms of biological systems: Development homeostasis

Homeostasis as an ability to maintain structural-functional parameters of the system at the required level is a basic characteristic for providing the stability of any biological system (from biosphere and separate ecosystems to communities, populations, and individuals). The study of homeostatic mechanisms that provide the stability of biological systems is the main task for solving many theoretical and practical questions. The search for criteria of homeostasis estimation and study of homeostatic mechanism ratio at different levels are principally important in this direction. Estimation of the role of homeostatic mechanisms of the organism and population for providing the stability of biological systems of different levels when using the approach based on estimation of the population state from ontogenetic positions (population developmental biology) seems promising.     

生态系统模拟模型的研究进展

从四个方面概述了生态系统模拟模型的发展现状：1)个体及种群,种群动态模型主要模拟在一个生境中单个种的动、植物个体出生或发芽、成长及其死亡过程,还有种内竞争和种间相互作用,主要分析生境中生物之间的相互作用。主要概述了林窗模型和土壤一植物一大气系统模型。2)群落与生态系统,概述了生态系统生产力模型、生物地球化学循环模型及演替模型。主要模拟植物种类在整个生态系统发展过程中的变化,以及植被类型的转变和相关的生物地球化学循环过程的改变,从而反映生物群落对气候变化的响应。3)景观生态系统,景观动态研究包含了时空两个方面的动态变化,一般可分为随机景观模型和基于过程的景观模型。随机模型用于模拟群落格局在演替过程中的动态变化等,基于过程的景观模型深入研究组成景观的各生态系统的空间结构。4)生物圈与地球生态系统,基于过程的陆地生物地球化学模式被用来研究自然生态系统中碳和其它矿物营养物质的潜在通量和蓄积量,较为流行的模式有陆地生态系统模式TEM、CENTURY、法兰克福生物圈模式FBM、Biome-BGC、卡内基-埃姆斯-斯坦福方法CASA等。这些模式己被用于估算自然生态系统对大气CO2加倍及相关气候变化在区域和全球尺度的平衡响应。最后,结合实际工作展望了生态系统模拟模型在各方面的发展方向。     

State of the science in reconciling top‐down and bottom‐up approaches for terrestrial CO2 budget

Robust estimates of CO₂ budget, CO₂ exchanged between the atmosphere and terrestrial biosphere, are necessary to better understand the role of the terrestrial biosphere in mitigating anthropogenic CO₂ emissions. Over the past decade, this field of research has advanced through understanding of the differences and similarities of two fundamentally different approaches: “top‐down” atmospheric inversions and “bottom‐up” biosphere models. Since the first studies were undertaken, these approaches have shown an increasing level of agreement, but disagreements in some regions still persist, in part because they do not estimate the same quantity of atmosphere–biosphere CO₂ exchange. Here, we conducted a thorough comparison of CO₂ budgets at multiple scales and from multiple methods to assess the current state of the science in estimating CO₂ budgets. Our set of atmospheric inversions and biosphere models, which were adjusted for a consistent flux definition, showed a high level of agreement for global and hemispheric CO₂ budgets in the 2000s. Regionally, improved agreement in CO₂ budgets was notable for North America and Southeast Asia. However, large gaps between the two methods remained in East Asia and South America. In other regions, Europe, boreal Asia, Africa, South Asia, and Oceania, it was difficult to determine whether those regions act as a net sink or source because of the large spread in estimates from atmospheric inversions. These results highlight two research directions to improve the robustness of CO₂ budgets: (a) to increase representation of processes in biosphere models that could contribute to fill the budget gaps, such as forest regrowth and forest degradation; and (b) to reduce sink–source compensation between regions (dipoles) in atmospheric inversion so that their estimates become more comparable. Advancements on both research areas will increase the level of agreement between the top‐down and bottom‐up approaches and yield more robust knowledge of regional CO₂ budgets.