Plant-soil feedbacks and invasive spread

Plant invaders have been suggested to change soil microbial communities and biogeochemical cycling in ways that can feedback to benefit themselves. In this paper, we ask when do these feedbacks influence the spread of exotic plants. Because answering this question is empirically challenging, we show how ecological theory on 'pushed' and 'pulled' invasions can be used to examine the problem. We incorporate soil feedbacks into annual plant invasion models, derive the conditions under which such feedbacks affect spread, and support our approach with simulations. We show that in homogeneous landscapes, strong positive feedbacks can influence spreading velocity for annual invaders, but that empirically documented feedbacks are not strong enough to do so. Moreover, to influence spread, invaders must modify the soil environment over a spatial scale larger than is biologically realistic. Though unimportant for annual invader spread in our models, feedbacks do affect invader density and potential impact. We discuss how future research might consider the way landscape structure, dispersal patterns, and the time scales over which plant–soil feedbacks develop regulate the effects of such feedbacks on invader spread.     

Robustness of positional specification by the Hedgehog morphogen gradient

Spatial gradients of Hedgehog signalling play a central role in many patterning events during animal development, regulating cell fate determination and tissue growth in a variety of tissues and developmental stages. Experimental evidence suggests that many of the proteins responsible for regulating Hedgehog signalling and transport are themselves targets of Hedgehog signalling, leading to multiple levels of feedback within the system. We use mathematical modelling to analyse how these overlapping feedbacks combine to regulate patterning and potentially enhance robustness in the Drosophila wing imaginal disc. Our results predict that the regulation of Hedgehog transport and stability by glypicans, as well as multiple overlapping feedbacks in the Hedgehog response network, can combine to enhance the robustness of positional specification against variability in Hedgehog levels. We also discuss potential trade-offs between robustness and additional features of the Hedgehog gradient, such as signalling range and size regulation.     

Integrating ecosystem engineering and food webs

Ecosystem engineering, the physical modification of the environment by organisms, is a common and often influential process whose significance to food web structure and dynamics is largely unknown. In the light of recent calls to expand food web studies to include non‐trophic interactions, we explore how we might best integrate ecosystem engineering and food webs. We provide rationales justifying their integration and present a provisional framework identifying how ecosystem engineering can affect the nodes and links of food webs and overall organization; how trophic interactions with the engineer can affect the engineering; and how feedbacks between engineering and trophic interactions can affect food web structure and dynamics. We use a simple integrative food chain model to illustrate how feedbacks between the engineer and the food web can alter 1) engineering effects on food web dynamics, and 2) food web responses to extrinsic environmental perturbations. We identify four general challenges to integration that we argue can readily be met, and call for studies that can achieve this integration and help pave the way to a more general understanding of interaction webs in nature. Synthesis All species are affected by their physical environment. Because ecosystem engineering species modify the physical environment and belong to food webs, such species are potentially one of the most important bridges between the trophic and non‐trophic. We examine how to integrate the so far, largely independent research areas of ecosystem engineering and food webs. We present a conceptual framework for understanding how engineering can affect food webs and vice versa, and how feedbacks between the two alter ecosystem dynamics. With appropriate empirical studies and models, integration is achievable, paving the way to a more general understanding of interaction webs in nature.     

Plant water uptake modelling: added value of cross-disciplinary approaches

In recent years, research interest in plant water uptake strategies has rapidly increased in many disciplines, such as hydrology, plant ecology and ecophysiology. Quantitative modelling approaches to estimate plant water uptake and spatiotemporal dynamics have significantly advanced through different disciplines across scales. Despite this progress, major limitations, for example, predicting plant water uptake under drought or drought impact at large scales, remain. These are less attributed to limitations in process understanding, but rather to a lack of implementation of cross-disciplinary insights into plant water uptake model structure. The main goal of this review is to highlight how the four dominant model approaches, that is, Feddes approach, hydrodynamic approach, optimality and statistical approaches, can be and have been used to create interdisciplinary hybrid models enabling a holistic system understanding that, among other things, embeds plant water uptake plasticity into a broader conceptual view of soil–plant feedbacks of water, nutrient and carbon cycling, or reflects observed drought responses of plant–soil feedbacks and their dynamics under, that is, drought. Specifically, we provide examples of how integration of Bayesian and hydrodynamic approaches might overcome challenges in interpreting plant water uptake related to different travel and residence times of different plant water sources or trade-offs between root system optimization to forage for water and nutrients during different seasons and phenological stages.     

The fundamental role of ecological feedback mechanisms for the adaptive management of seagrass ecosystems – a review

Seagrass meadows are vital ecosystems in coastal zones worldwide, but are also under global threat. One of the major hurdles restricting the success of seagrass conservation and restoration is our limited understanding of ecological feedback mechanisms. In these ecosystems, multiple, self‐reinforcing feedbacks can undermine conservation efforts by masking environmental impacts until the decline is precipitous, or alternatively they can inhibit seagrass recovery in spite of restoration efforts. However, no clear framework yet exists for identifying or dealing with feedbacks to improve the management of seagrass ecosystems. Here we review the causes and consequences of multiple feedbacks between seagrass and biotic and/or abiotic processes. We demonstrate how feedbacks have the potential to impose or reinforce regimes of either seagrass dominance or unvegetated substrate, and how the strength and importance of these feedbacks vary across environmental gradients. Although a myriad of feedbacks have now been identified, the co‐occurrence and likely interaction among feedbacks has largely been overlooked to date due to difficulties in analysis and detection. Here we take a fundamental step forward by modelling the interactions among two distinct above‐ and belowground feedbacks to demonstrate that interacting feedbacks are likely to be important for ecosystem resilience. On this basis, we propose a five‐step adaptive management plan to address feedback dynamics for effective conservation and restoration strategies. The management plan provides guidance to aid in the identification and prioritisation of likely feedbacks in different seagrass ecosystems.     

森林-农业景观格局变化的社会-生态系统模拟模型方法进展

社会-生态系统（SES）模拟模型是景观格局分析和决策的有效工具,能表征景观格局变化的社会-生态效应及景观决策的复杂反馈机制。文献综述了森林-农业景观格局的SES模型方法进展发现：（1）多数模型对景观过程与社会经济决策的反馈关系分析不足;（2）应集成多种情景模拟和景观效应分析方法,完善现有SES模型的理论方法基础;（3）通过集成格局优化模型和自主体模型会有效改进SES模型功能,具体途径包括：集成情景-生态效应的景观格局模拟方法、完善景观决策的理论基础、加强集成模型的不确定性分析、降低模型复杂性和综合定性-定量数据等。研究结果有助于理解多尺度森林-农业景观格局在社会-生态系统中的重要作用,能更好地支持跨学科集成模型开发与应用。     

Ecology after 100 years: Progress and pseudo-progress

Has the science of ecology fulfilled the promises made by the originators of ecological science at the start of the last century? What should ecology achieve? Have good policies for environmental management flowed out of ecological science? These important questions are rarely discussed by ecologists working on detailed studies of individual systems. Until we decide what we wish to achieve as ecologists we cannot define progress toward those goals. Ecologists desire to achieve an understanding of how the natural world operates, how humans have modified the natural world, and how to alleviate problems arising from human actions. Ecologists have made impressive gains over the past century in achieving these goals, but this progress has been uneven. Some sub-disciplines of ecology are well developed empirically and theoretically, while others languish for reasons that are not always clear. Fundamental problems can be lost to view as ecologists fiddle with unimportant pseudo-problems. Bandwagons develop and disappear with limited success in addressing problems. The public demands progress from all the sciences, and as time moves along and problems get worse, more rapid progress is demanded. The result for ecology has too often been poor, short-term science and poor management decisions. But since the science is rarely repeated and the management results may be a generation or two down the line, it is difficult for the public or for scientists to decide how good or bad the scientific advice has been. In ecology over the past 100 years we have made solid achievements in behavioural ecology, population dynamics, and ecological methods, we have made some progress in understanding community and ecosystem dynamics, but we have made less useful progress in developing theoretical ecology, landscape ecology, and natural resource management. The key to increasing progress is to adopt a systems approach with explicit hypotheses, theoretical models, and field experiments on a scale defined by the problem. With continuous feedback between problems, possible solutions, relevant theory and experimental data we can achieve our scientific goals.     

Evaluation Approaches for Advancing Urban Water Goals

Urban areas (especially cities) are challenged in meeting their direct water needs from local sources. They also exert strain on global water resources through their indirect (virtual) water use. Agencies concerned with urban water management have visions and goals for managing direct water use, but indirect use is only inferred in more global visions for sustainable consumption. There is limited quantification of “urban water performance” at the macro urban scale (whole of city) to monitor progress toward these goals. It is constrained by a lack of clarity about the evaluation approaches that best serve them. We ask, How can the evaluation approaches described in literature advance urban water management goals? We reviewed the utility of eight evaluation approaches, including urban water system modeling, urban metabolism (territorial and mass balance), consumption (life cycle assessment, water footprinting, and input‐output analysis), and complex systems (ecological network analysis and systems dynamics) approaches. We found that urban metabolism based on water mass balance is a core method for generating information to inform current goals for direct urban water use, with potential for being “coupled” with the other approaches. Consumption approaches inform the management of indirect water use. We describe this in a framework for urban water evaluation to give greater clarity to this field and flag the further research that would be needed to progress this. It includes the recommendation to differentiate the evaluation of direct and indirect urban water, but to also interpret them together.     

Isolation of mononuclear cells from the central nervous system of rats with EAE

Whether studying an autoimmune disease directed to the central nervous system (CNS), such as experimental autoimmune encephalomyelitis (EAE, 1), or the immune response to an infection of the CNS, such as poliomyelitis, Lyme neuroborreliosis, or neurosyphilis, it is often necessary to isolate the CNS-infiltrating immune cells.In this video-protocol we demonstrate how to isolate mononuclear cells (MNCs) from the CNS of a rat with EAE. The first step of this procedure requires a cardiac perfusion of the rodent with a saline solution to ensure that no blood remains in the blood vessels irrigating the CNS. Any blood contamination will artificially increase the number of apparent CNS-infiltrating MNCs and may alter the apparent composition of the immune infiltrate. We then demonstrate how to remove the brain and spinal cord of the rat for subsequent dilaceration to prepare a single-cell suspension. This suspension is separated on a two-layer Percoll gradient to isolate the MNCs. After washing, these cells are then ready to undergo any required procedure. Mononuclear cells isolated using this procedure are viable and can be used for electrophysiology, flow cytometry (FACS), or biochemistry. If the technique is performed under sterile conditions (using sterile instruments in a tissue culture hood) the cells can also be grown in tissue culture medium. A given cell population can be further purified using either magnetic separation procedures or a FACS.     

Life history and mating systems select for male biased parasitism mediated through natural selection and ecological feedbacks

tlsb-1%Males are often the ‘sicker’ sex with male biased parasitism found in a taxonomically diverse range of species. There is considerable interest in the processes that could underlie the evolution of sex-biased parasitism. Mating system differences along with differences in lifespan may play a key role. We examine whether these factors are likely to lead to male-biased parasitism through natural selection taking into account the critical role that ecological feedbacks play in the evolution of defence. We use a host-parasite model with two-sexes and the techniques of adaptive dynamics to investigate how mating system and sexual differences in competitive ability and longevity can select for a bias in the rates of parasitism. Male-biased parasitism is selected for when males have a shorter average lifespan or when males are subject to greater competition for resources. Male-biased parasitism evolves as a consequence of sexual differences in life-history that produce a greater proportion of susceptible females than males and therefore reduce the cost of avoiding parasitism in males. Different mating systems such as monogamy, polygyny or polyandry did not produce a bias in parasitism through these ecological feedbacks but may accentuate an existing bias.     

Effects of local negative feedbacks on the evolution of species within metacommunities

Local negative feedbacks occur when the occupation of a site by a species decreases the subsequent fitness of related individuals compared to potential competitors. Such negative feedbacks can enhance diversity by changing the spatial structure of the environment. The conditions, however, involve dispersive, environmental and evolutionary processes in complex interactive ways. We introduce a model that accounts for four mechanisms: colonisation‐competition‐extinction ecological dynamics, evolutionary dynamics, local negative feedbacks and environmental averaging. Three qualitatively distinct dynamics are possible, one dominated by specialists, another dominated by generalists and an intermediate situation exhibiting taxon cycles. We discuss how metacommunity diversity, macro‐ecological patterns and environmental patterning are linked to the three qualitative dynamics. The model provides classical shapes for morph‐abundance distributions, or diversity‐area relationships. Diversity can be high when specialists dominate or when taxon cycles happen. Finally, local negative feedbacks often yield fine‐grain environments for taxon cycle dynamics and coarse‐grain environments when generalists dominate.     

Making sense of the combined effect of interleukin-2 and interleukin-4 on lymphocytes using a mathematical model

The cytokines are the information superhighway of the immune system. They are an important component of the integrated behavior of the system. In order to be able to have a good understanding of the immune system, we must be able to model the effect of cytokines and their combined effect. This work is a step in that direction. We study the combined effect of two cytokines: interleukin-2 (IL-2) and interleukin-4 (IL-4) on some cells of the immune system. Interleukin-2 and interleukin-4 are important growth and differentiation factors for B and T cells. Interleukin-4 antagonizes the effect of interleukin-2 on B cells and some T cells while it synergizes with interleukin-2 on other T cells. We build a mathematical model of the interaction of both cytokines on T and B cells as a building block toward a model of the Th1/Th2 cross-regulation. The response of a given cell to the combination of interleukin-2 and interleukin-4 is shown to involve competing dynamical effects which can lead to either antagnostic or synergistic combined effect. Author to whom correspondence should be addressed at Department of Engineering and Public Policy. Work supported by NIH grant nv: Ai31427.     

Cancer vaccines: between the idea and the reality

Whether vaccines are designed to prepare the immune system for the encounter with a pathogen or with cancer, certain common challenges need to be faced, such as what antigen and what adjuvant to use, what type of immune response to generate and how to make it long lasting. Cancer, additionally, presents several unique hurdles. Cancer vaccines must overcome immune suppression exerted by the tumour, by previous therapy or by the effects of advanced age of the patient. If used for cancer prevention, vaccines must elicit effective long-term memory without the potential of causing autoimmunity. This article addresses the common and the unique challenges to cancer vaccines and the progress that has been made in meeting them. Considering how refractory cancer has been to standard therapy, efforts to achieve immune control of this disease are well justified.     

Integrating spatial structure and interspecific and intraspecific plant–soil feedback effects and responses into community structure

Plant–soil feedbacks have important effects on plant communities, but most theory has been derived from experiments on intraspecific plant–soil feedbacks. Much less is known about how interspecific plant–soil feedbacks affect coexistence and plant communities, due in part to experimental and analytical challenges. Here, we propose a framework for evaluating plant–soil feedbacks among multiple interacting species that incorporates 1) the average effect each species has on conspecific and heterospecific neighbors via how they modify soil biota, 2) the average response of each species to the soil modifications made by neighboring species, and 3) intraspecific feedback. We refer to this as the ‘effect–response–intraspecific’ (ERI) model. We used individual‐based models to evaluate the relative importance of intraspecific and interspecific soil feedback in determining species abundance ranks in simulated plant communities. To compare the heuristic value of the ERI model to that of an established model in which effects and responses to soil feedback are not explicitly recognized, we evaluated a ‘full‐factorial’ model in which soil feedbacks among five plant species were measured and then explicitly modeled. The ERI model indicated that the response to interspecific plant–soil feedbacks was the key factor for species’ abundance rank without spatial structure. In contrast, interspecific plant–soil feedback had no impact on species abundance with spatial structure, and intraspecific feedback became dominant. Thus, our models predict that the relative importance of intraspecific and interspecific feedbacks changes as a function of the degree of spatial structure in a system. Overall, the ERI model provides a novel and tractable framework for evaluating complex multi‐species plant–soil feedbacks.     

Glycosylation of mouse and human immune cells: insights emerging from N-glycomics analyses

N-glycans are key players mediating cell-cell communication in the immune system, interacting with glycan-binding proteins. In the present article, we discuss key themes that are emerging from the structural analysis of complex-type N-linked glycans from human and murine immune cell lines, employing high-sensitivity MALDI (matrix-assisted laser desorption ionization)-TOF (time-of-flight) MS technology. Particular focus is given to terminal epitopes, the abundance of multiply branched N-glycans and how glycosylation can affect human health in diseases such as congenital neutropenia and glycogen storage disease.     

Setting Effective and Realistic Restoration Goals: Key Directions for Research

Restoration ecology has made significant advances in the past few decades and stands to make significant contributions both to the practical repair of damaged ecosystems and the development of broader ecological ideas. I highlighted four main areas where progress in research can assist with this. First, we need to enhance the translation of recent advances in our understanding of ecosystem and landscape dynamics into the conceptual and practical frameworks for restoration. Second, we need to promote the development of an ability to correctly diagnose ecosystem damage, identify restoration thresholds, and develop corrective methodologies that aim to overcome such thresholds. This involves understanding which system characteristics are important in determining ecosystem recovery in a range of ecosystem types, and to what extent restoration measures need to overcome threshold and hysteresis effects. A third key requirement is to determine what realistic goals for restoration are based on the ecological realities of today and how these will change in the future, given ongoing changes in climate and land use. Finally, there is a need for a synthetic approach which draws together the ecological and social aspects of the issues surrounding restoration and the setting of restoration goals.     

The epidemiological feedbacks critical to the evolution of host immunity

We examine in detail how epidemiological feedbacks combine with costs and benefits to determine the evolution of resistance by systematically analysing continuously stable strategies (CSS) for different host–parasite frameworks. The mode of resistance (innate versus acquired), the nature of the host (i.e. life‐history and immunological memory) and the nature of the disease (effects on fertility or mortality) all impact on the feedbacks that are critical to the evolution of resistance. By identifying relationships between CSS investment and the underlying epidemiological feedback for each mode of resistance in each framework, we distil complex feedbacks into simple combinations of selection pressures. When the parasite does not affect fertility, CSS investment reflects only the benefit of resistance and we explain why this is markedly different for innate and acquired resistance. If infection has no effect on host fertility, CSS investment in acquired immunity increases with the square of disease prevalence. While in contrast for evolving innate resistance, CSS investment is greatest at intermediate prevalence. When disease impacts fertility, only a fraction of the host population reproduce, and this introduces new ecological feedbacks to both the cost of resistance and the damage from infection. The multiple feedbacks in this case lead to the alternative result that the higher the abundance of infecteds, the higher the investment in innate resistance. A key insight is that maximal investment occurs at intermediate lifespans in a range of different host–parasite interactions, but for disparate reasons which can only be understood by a detailed analysis of the feedbacks. We discuss the extension of our approach to structured host populations and parasite community dynamics.     

From host immunity to pathogen invasion: the effects of helminth coinfection on the dynamics of microparasites

Concurrent infections with multiple parasites are ubiquitous in nature. Coinfecting parasites can interact with one another in a variety of ways, including through the host's immune system via mechanisms such as immune trade-offs and immunosuppression. These within-host immune processes mediating interactions among parasites have been described in detail, but how they scale up to determine disease dynamic patterns at the population level is only beginning to be explored. In this review, we use helminth-microparasite coinfection as a model for examining how within-host immunological effects may influence the ecological outcome of microparasitic diseases, with a specific focus on disease invasion. The current literature on coinfection between helminths and major microparasitic diseases includes many studies documenting the effects of helminths on individual host responses to microparasites. In many cases, the observed host responses map directly onto parameters relevant for quantifying disease dynamics; however, there have been few attempts at integrating data on individual-level effects into theoretical models to extrapolate from the individual to the population level. Moreover, there is considerable variability in the particular combination of disease parameters affected by helminths across different microparasite systems. We develop a conceptual framework identifying some potential sources of such variability: Pathogen persistence and severity, and resource availability to hosts. We also generate testable hypotheses regarding diseases and the environmental contexts when the effects of helminths on microparasite dynamics should be most pronounced. Finally, we use a case study of helminth and mycobacterial coinfection in the African buffalo to illustrate both progress and challenges in understanding the population-level consequences of within-host immunological interactions, and conclude with suggestions for future research that will help improve our understanding of the effects of coinfection on dynamics of infectious diseases.     

Density-dependent linkage of scale-dependent feedbacks: a flume study on the intertidal macrophyte Spartina anglica

Spartina anglica is an autogenic ecosystem engineer. At a local (within-vegetation) scale, it improves plant growth by enhancing sediment accretion through attenuation of hydrodynamic energy with its shoots. This constitutes a short-range positive feedback. The vegetation also shows a long-distance negative feedback through formation of erosion troughs around the tussock, which are restricting lateral expansion. There is a growing recognition of the important role of such scale-dependent feedbacks for landscape structuring and ecosystem stability. By a series of flume studies, we provide direct experimental evidence that 1) both the local positive and the long-distance negative feedback are strongly density-dependent with clear thresholds, and 2) that both feedbacks are inherently linked via their density dependence, partly as the result of conservation laws. The observed thresholds occurred at vegetation densities commonly found in the field. We demonstrate that threshold densities are affected by external hydrodynamic forcing for the long-distance negative feedback. We expect the same to be true for the local positive feedback (sediment accretion), so that under mild hydrodynamic forcing, this local positive feedback may occur in the absence of a long-distance negative feedback (formation of erosion troughs). The density dependence of nearby positive and the long-distance negative feedback and how external conditions affect the linkage of both feedbacks are important factors shaping the vegetated salt-marsh landscape.     

Decidual natural killer cells and the immune microenvironment at the maternal-fetal interface

During early pregnancy,an orchestrated evolutionary maternal adaption toward tolerance of the semiallogeneic fetus is required to ensure decidualization and early embryo development.Remodeling of the immune system involves natural killer cells(NKs),macrophages,T cells and dendritic cells(DCs) altering the microenvironment in the deciduas.In particular,a unique population of NK cells with a CD56~(bright)CD16~- phenotype in the decidua has been proposed to play a key role in the maternal adaptation to pregnancy.However,there is a tendency for pregnancy immunology to reflect transplantation immunology regarding the assumption that the maternal immune system should be suppressed.This tendency is misleading.We discuss how the immune system is formed in early deciduas and the interactions between maternal NK cells and fetal growth.We propose that the maternal immune response must not be fully suppressed and is even necessary for the local response of uterine NK cells.