Marine and terrestrial ecology: unifying concepts, revealing differences

The extent to which similar ecological processes operate on land and in the sea has been much debated, with apparently 'fundamental' differences often disappearing when appropriate comparisons are made. However, marine and terrestrial ecology have developed as largely separate intellectual endeavours, which has hampered the search for general patterns and mechanisms. Here, I argue that marine-terrestrial comparative studies can be extremely useful at uncovering mechanisms when they explicitly consider those facets of the environment that are important to a particular hypothesis. Furthermore, the binary 'marine-terrestrial' division misses many opportunities for more interesting comparisons, several of which I highlight here. Increasing the flow of concepts, hypotheses, and data between marine and terrestrial ecologists is essential to reveal those differences that really are important.     

生态学中的尺度问题：内涵与分析方法

尺度问题已成为现代生态学的核心问题之一.尺度问题主要涉及3个方面：尺度概念、尺度分析和尺度推绎.主要评述前两个方面.生态学尺度有三重概念：维数、种类和组分,其中每重概念又包含了多个定义,有必要进行澄清、分类和统一.尺度分析涉及尺度效应分析和多尺度空间格局分析.格局、过程及它们之间的关系,以及某些景观特性均表现出尺度效应,因此多尺度研究非常必要和重要.多尺度空间格局分析（尤其是特征尺度的识别）是进行尺度效应分析和跨尺度推绎的基础.多尺度分析需要特定的方法,景观指数法是最常用和最简单的方法,但也常产生误导;空间统计学方法（如半方差分析法、尺度方差分析法、空隙度指数法和小波分析法等）和分维分析法在最近十几年发展起来,并逐渐应用于生态学,在尺度分析上具有很大的应用潜力.各种方法在尺度分析上各有优势和不足,有必要同时使用两种或两种以上方法进行比较和评估.总之,有关尺度分析的研究需要进一步加强,从而为下一步的尺度推绎提供可靠的依据.     

Xerophytes, xeromorphs and sclerophylls: the history of some concepts in ecology

Research on xeromorphic and sclerophyllous (the literal meanings of which are dry-form and hard-leaved) plants offers a case-history illustrating the nature of progress in one branch of science. The story runs from about 1890–1970, beginning with the birth of ecological concepts, including Warming's 1895 classification of plants into hydrophytes, xerophytes and meso-phytes, Schimper's pioneer work on the sclerophylls, and with the conceptions that lay behind this work; and so on through the main lines of research, concluding with an account of work on the anomalous distribution of the sclerophylls in Australia. This case-history shows how the problems of classification and categorization may be linked to conceptual and empirical problems of substance, and hence are not merely classificatory. Indeed, the hypotheses under test are not formulated explicitly, but are encapsulated in the terminology, as is so often the case in the biological sciences.     

生态预报: 生态学的一个前沿领域

生态预报对于资源,环境的决策和管理将起着越来越重要的作用。计算机科学和定量分析的进步,生态学理论的发展以及新技术的应用增加了人类预测生态系统变化的能力。本文介绍了有关生态预报的内涵,相关研究进展及案例,提出生态预报是生态学的一个重要前沿领域,也将是今后生态学研究的一个重要努力方向。     

Fungi in freshwaters: ecology, physiology and biochemical potential

Research on freshwater fungi has concentrated on their role in plant litter decomposition in streams. Higher fungi dominate over bacteria in terms of biomass, production and enzymatic substrate degradation. Microscopy-based studies suggest the prevalence of aquatic hyphomycetes, characterized by tetraradiate or sigmoid spores. Molecular studies have consistently demonstrated the presence of other fungal groups, whose contributions to decomposition are largely unknown. Molecular methods will allow quantification of these and other microorganisms. The ability of aquatic hyphomycetes to withstand or mitigate anthropogenic stresses is becoming increasingly important. Metal avoidance and tolerance in freshwater fungi implicate a sophisticated network of mechanisms involving external and intracellular detoxification. Examining adaptive responses under metal stress will unravel the dynamics of biochemical processes and their ecological consequences. Freshwater fungi can metabolize organic xenobiotics. For many such compounds, terrestrial fungal activity is characterized by cometabolic biotransformations involving initial attack by intracellular and extracellular oxidative enzymes, further metabolization of the primary oxidation products via conjugate formation and a considerable versatility as to the range of metabolized pollutants. The same capabilities occur in freshwater fungi. This suggests a largely ignored role of these organisms in attenuating pollutant loads in freshwaters and their potential use in environmental biotechnology.     

Physiological ecology of rocky intertidal organisms: a synergy of concepts

The rocky intertidal zone is among the most physically harshenvironments on earth. Marine invertebrates and algae livingin this habitat are alternatively pounded by waves and exposedto thermal extremes during low tide periods (Denny and Wethey,2001). Additionally, they must deal with strong selective pressuresrelated to predation and competition for space (Connell, 1961).As a result, the steep physical gradient and spatially condensedcommunity has made the rocky intertidal zone an ideal "naturallaboratory" to study the coupled role of physical and biologicalfactors in determining the abundance and distribution of organismsin nature (Connell, 1961; Paine, 1966, 1994).     

The role of allelopathy in biochemical ecology: Experience from Taiwan

Allelopathic compounds, including fatty acids, phenolics, flavonoids, terpenoids, and alkaloids, have been found in various plants and soils of different habitats in Taiwan since 1972. For example, in a monoculture of rice plants, phytotoxins were produced during the decomposition of rice residues in soil, suppressed the growth of rice seedlings, and reduced the numbers of tillers and panicles, leading to yield reduction. The allelopathic metabolites are also affected by environmental factors, such as oxygen, temperature, soil moisture, microbial activity, and levels of fertilizers in soil, and allelopathy was pronounced in areas where environmental stresses were severe. Substantial amounts of phytotoxic mimosine and phenolics were released into soil by plant parts of Leucaenaleucocephala, and these suppressed the growth of many understory species except that of L.leucocephala itself. A unique pattern of absence of understory plants was ubiquitous beneathPhyllostachys edulis, due primarily to an allelopathic effect. In a forest pasture intercropping, an aggressive kikuyu grass was planted in a deforested land where Chinese fir grew previously, to help in understanding the mechanism of biological interactions between plants. Aqueous soil leachate and extracts of the grass significantly, retarded the growth of local weeds but not that of the Chinese fir. Allelopathy thus plays an appreciable role in natural vegetation and plantations in Taiwan.     

Barcoding a quantified food web: crypsis, concepts, ecology and hypotheses

The efficient and effective monitoring of individuals and populations is critically dependent on correct species identification. While this point may seem obvious, identifying the majority of the more than 100 natural enemies involved in the spruce budworm (Choristoneura fumiferana--SBW) food web remains a non-trivial endeavor. Insect parasitoids play a major role in the processes governing the population dynamics of SBW throughout eastern North America. However, these species are at the leading edge of the taxonomic impediment and integrating standardized identification capacity into existing field programs would provide clear benefits. We asked to what extent DNA barcoding the SBW food web would alter our understanding of the diversity and connectence of the food web and the frequency of generalists vs. specialists in different forest habitats. We DNA barcoded over 10% of the insects collected from the SBW food web in three New Brunswick forest plots from 1983 to 1993. For 30% of these specimens, we amplified at least one additional nuclear region. When the nodes of the food web were estimated based on barcode divergences (using molecular operational taxonomic units (MOTU) or phylogenetic diversity (PD)--the food web became much more diverse and connectence was reduced. We tested one measure of food web structure (the "bird feeder effect") and found no difference compared to the morphologically based predictions. Many, but not all, of the presumably polyphagous parasitoids now appear to be morphologically-cryptic host-specialists. To our knowledge, this project is the first to barcode a food web in which interactions have already been well-documented and described in space, time and abundance. It is poised to be a system in which field-based methods permit the identification capacity required by forestry scientists. Food web barcoding provided an effective tool for the accurate identification of all species involved in the cascading effects of future budworm outbreaks. Integrating standardized barcodes within food webs may ultimately change the face of community ecology. This will be most poignantly felt in food webs that have not yet been quantified. Here, more accurate and precise connections will be within the grasp of any researcher for the first time.     

Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances

Microbial ecology examines the diversity and activity of micro-organisms in Earth's biosphere. In the last 20 years, the application of genomics tools have revolutionized microbial ecological studies and drastically expanded our view on the previously underappreciated microbial world. This review first introduces the basic concepts in microbial ecology and the main genomics methods that have been used to examine natural microbial populations and communities. In the ensuing three specific sections, the applications of the genomics in microbial ecological research are highlighted. The first describes the widespread application of multilocus sequence typing and representational difference analysis in studying genetic variation within microbial species. Such investigations have identified that migration, horizontal gene transfer and recombination are common in natural microbial populations and that microbial strains can be highly variable in genome size and gene content. The second section highlights and summarizes the use of four specific genomics methods (phylogenetic analysis of ribosomal RNA, DNA-DNA re-association kinetics, metagenomics, and micro-arrays) in analysing the diversity and potential activity of microbial populations and communities from a variety of terrestrial and aquatic environments. Such analyses have identified many unexpected phylogenetic lineages in viruses, bacteria, archaea, and microbial eukaryotes. Functional analyses of environmental DNA also revealed highly prevalent, but previously unknown, metabolic processes in natural microbial communities. In the third section, the ecological implications of sequenced microbial genomes are briefly discussed. Comparative analyses of prokaryotic genomic sequences suggest the importance of ecology in determining microbial genome size and gene content. The significant variability in genome size and gene content among strains and species of prokaryotes indicate the highly fluid nature of prokaryotic genomes, a result consistent with those from multilocus sequence typing and representational difference analyses. The integration of various levels of ecological analyses coupled to the application and further development of high throughput technologies are accelerating the pace of discovery in microbial ecology.     

生态记忆及其在生态学中的潜在应用

生态记忆指群落过去的状态或经验影响其目前或未来生态响应的能力.作为研究生态系统结构和功能的一个新视角,生态记忆在群落演替、生态恢复、生物入侵和自然资源管理等多个领域中受到重视.本文在综述生态记忆的概念、组成、类别的基础上,进一步探讨了生态记忆的可能机制和影响因素,并指出了其潜在应用,以期为理解演替机理和指导生态恢复提供参考.     

Ecological immunology: costly parasite defences and trade-offs in evolutionary ecology

In the face of continuous threats from parasites, hosts have evolved an elaborate series of preventative and controlling measures - the immune system - in order to reduce the fitness costs of parasitism. However, these measures do have associated costs. Viewing an individual's immune response to parasites as being subject to optimization in the face of other demands offers potential insights into mechanisms of life history trade-offs, sexual selection, parasite-mediated selection and population dynamics. We discuss some recent results that have been obtained by practitioners of this approach in natural and semi-natural populations, and suggest some ways in which this field may progress in the near future.     

Ecological lever and interface ecology: epibiosis modulates the interactions between host and environment

The properties of the body surface play a crucial role in most interactions of marine organisms. Critical ecological properties such as drag, morphology, uptake and release of radiation and organic matter are linked to the body surface of an aquatic organism. The properties and functions of this interface may be modified substantially by the presence and activities of epibiotic communities. This, in turn, may lead to substantial modulation of the interactions between the organism bearing epiphytes and its environment, with consequences for the relative fitness of the host organism (basibiont) and its interactors, and ultimately, the structure and functioning of the assemblage. Epibiosis may act as an ecological lever via these indirect effects, greatly amplifying or buffering biotic and abiotic stress.     

Ecological lever and interface ecology: epibiosis modulates the interactions between host and environment

The properties of the body surface play a crucial role in most interactions of marine organisms. Critical ecological properties such as drag, morphology, uptake and release of radiation and organic matter are linked to the body surface of an aquatic organism. The properties and functions of this interface may be modified substantially by the presence and activities of epibiotic communities. This, in turn, may lead to substantial modulation of the interactions between the organism bearing epiphytes and its environment, with consequences for the relative fitness of the host organism (basibiont) and its interactors, and ultimately, the structure and functioning of the assemblage. Epibiosis may act as an ecological lever via these indirect effects, greatly amplifying or buffering biotic and abiotic stress.     

On the ecology of Cephalodella

A material consisting of 66 species of Cephalodella (Rotifera), from diverse waters in south and central Sweden, was analyzed to reveal their possible relationships to substrate and habitat. Most species preferred periphytic environments. Most species have a broad ecological range, only a few being bog specialists. An artificial substrate, white cotton, was colonized by several species, even some without eyes.     

Ecological frames of mind: the role of cognition in behavioral ecology.

Cognitive psychology is the study of how information, from the senses and from memory, is used in the production of behavior. Investigation of the specifics of behavioral adaptation has already led some behavioral ecologists into the domain of animal cognition. I make several arguments for the benefits and the necessity of a sophisticated assessment by ecologists of the cognitive aspects of behavioral adaptation. First, because cognition typically serves to produce adaptive behavior, cognitive structure and function should reflect ecological demands; studies of cognition in ecological contexts are opportunities to understand adaptation. Furthermore, constraints on cognitive properties may help determine how behavior meets the environment. Studies of spatial memory in food-caching corvids exemplify how cognitive aspects of behavior may both reflect and determine specifics of adaptation. Second, many models in behavioral ecology assume certain cognitive abilities, such as timing or counting. Cognitive theory and methodology should be used to determine whether animals possess these abilities. I have provided examples. Third, consideration of cognitive function can lead to original ideas about the details of behavioral adaptation. Without a thorough integration of cognitive psychology with behavioral ecology, our understanding of the relation between behavior and selective pressures will be compromised.     

Eltonian shortfall due to the Grinnellian view: functional ecology between the mismatch of niche concepts

A number of recognized shortfalls currently exist in biology. They are related to 1) a disparity between the species described and the actual number of species; 2) uncertainties in species’ geographical distribution; 3) scarcity of species abundance data and 4) a lack of evolutionary data. Here, we discuss how attempts to solve the Eltonian shortfall (scarcity of knowledge about intra‐ and interspecific interactions, responses of species to environment and the effects of species on ecosystems) based on functional ecology must be aware of the pitfalls of using a Grinnellian view (broad scale) to address local questions (Eltonian scale). Since the characterization of species’ requirements and their effects on the environment (Eltonian niche) is based on functional traits, it is important to recognize that the Grinnellian niche is focused on the requirements but not the effect of species on a given habitat. By neglecting the dichotomy between the Eltonian and Grinnellian niches, choosing traits based on large‐scale datasets to address local questions to describe the niche of a species may lead to two pitfalls. The first applies to situations where traits that may predict potential distribution and coexistence at large scales (Grinnellian view) are often not suitable for explaining coexistence at local scales (Eltonian view). Since the Eltonian niche comprises the requirements and impacts of species at a local scale, the second pitfall is that the selection of traits only based on their significance at coarse scales may ignore the distinction between response and effect traits. We present a theoretical framework that explores the Eltonian shortfall, and discuss possible solutions. We provide a conceptual basis to aid in the choice of traits with respect to niche concepts and population ecology for dealing with the Eltonian shortfall.