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Unprecedented rates of species extinctions have prompted extensive research into the consequences of biodiversity losses on ecosystem functioning. While aquatic species are most threatened, research with freshwater and marine model systems has lagged behind progress made in terrestrial environments. This editorial to a special feature summarizes the main outcomes of a conference aimed at setting the stage for exploring the potential of aquatic systems to assess the role of biodiversity in ecosystem functioning. This series of papers proposes fresh approaches to the study of biodiversity effects on ecosystem functioning, outlines a new way of analyzing experimental data, presents a model that considers scale as an important factor determining outcomes, explores the effects of multiple stressors on species richness and ecosystem processes, and develops a food-web perspective that relates ecosystem properties to biodiversity. An insightful synthesis of lessons learned from aquatic systems is premature at present, but the papers clearly demonstrate the role that marine and freshwater systems can play in resolving open questions. The implications go well beyond the biodiversity in, and functioning of, ecosystems shaped by free-flowing or standing water. [ABSTRACT FROM AUTHOR]

Research on ecological communities, and plant–pollinator mutualistic networks in particular, has increasingly benefited from the theory and tools of complexity science. Nevertheless, up to now there have been few attempts to investigate the interplay between the structure of real pollination networks and their dynamics. This study is one of the first contributions to explore this issue. Biological invasions, of major concern for conservation, are also poorly understood from the perspective of complex ecological networks. In this paper we assess the role that established alien species play within a host community by analyzing the temporal changes in structural network properties driven by the removal of non-native plants. Three topological measures have been used to represent the most relevant structural properties for the stability of ecological networks: degree distribution, nestedness, and modularity. Therefore, we investigate for a detailed pollination network, 1) how its dynamics, represented as changes in species abundances, affect the evolution of its structure, 2) how topology relates to dynamics focusing on long-term species persistence; and 3) how both structure and dynamics are affected by the removal of alien plant species. Network dynamics were simulated by means of a stochastic metacommunity model. Our results showed that established alien plants are important for the persistence of the pollination network and for the maintenance of its structure. Removal of alien plants decreased the likelihood of species persistence. On the other hand, both the full network and the subset native network tended to lose their structure through time. Nevertheless, the structure of the full network was better preserved than the structure of the network without alien plants. Temporal topological shifts were evident in terms of degree distribution, nestedness, and modularity. However the effects of removing alien plants were more pronounced for degree distribution and modularity of the network. Therefore, elimination of alien plants affected the evolution of the architecture of the interaction web, which was closely related to the higher species loss found in the network where alien plants were removed. [ABSTRACT FROM AUTHOR]

In this paper, we tested whether the spatial distribution of a given species in more or less fragmented and disturbed landscapes depends on the species habitat specialization. We studied 891 spatial replicates from the French Breeding Bird Survey (FBBS) monitored at least two years during 2001–2005, and two independent landscape databases measuring respectively landscape fragmentation and recent landscape disturbance on each FBBS replicate. We used a continuous habitat specialization index for the 105 most common bird species monitored by the FBBS. We further modelled the spatial variation in abundance of each species according to fragmentation and disturbance across FBBS replicates, accounting for habitat differences and spatial trends. We then tested whether more or less specialized species responded to landscape fragmentation and disturbance. We found that the more specialist a species, the more negative its spatial response to landscape fragmentation and disturbance. Although there was a very high variation around these tendencies indicating that there are many other drivers of species distribution, our results suggest that measuring specialization may be helpful in predicting which species are likely to thrive in human degraded landscapes. We also emphasize the need to consider both positive and negative species responses when assessing consequences of habitat change in communities. [ABSTRACT FROM AUTHOR]

Species distributions often show an aggregated pattern, which can be due to a number of endo- and exogenous factors. While autologistic models have been used for modelling such data with statistical rigour, little emphasis has been put on disentangling potential causes of aggregation. In this paper we ask whether it is possible to infer sources of aggregation in species distributions from a single set of occurrence data by comparing the performance of various autologistic models. We create simulated data sets, which show similar occupancy patterns, but differ in the process that causes the aggregation. We model the distribution of these data with various autologistic models, and show how the relative performance of the models is sensitive to the factor causing aggregation in the data. This information can be used when modelling real species data, where causes of aggregation are typically unknown. To illustrate, we use our approach to assess the potential causes of aggregation in data of seven bird species with contrasting statistical patterns. Our findings have important implications for conservation, as understanding the mechanisms that drive population fluctuations in space and time is critical for the development of effective management actions for long-term conservation. [ABSTRACT FROM AUTHOR]

The species–time relationship (STR) describes how the species richness of a community increases with the time span over which the community is observed. This pattern has numerous implications for both theory and conservation in much the same way as the species–area relationship (SAR). However, the STR has received much less attention and to date only a handful of papers have been published on the pattern. Here we gather together 984 community time-series, representing 15 study areas and nine taxonomic groups, and evaluate their STRs in order to assess the generality of the STR, its consistency across ecosystems and taxonomic groups, its functional form, and its relationship to local species richness. In general, STRs were surprisingly similar across major taxonomic groups and ecosystem types. STRs tended to be well fit by both power and logarithmic functions, and power function exponents typically ranged between 0.2 and 0.4. Communities with high richness tended to have lower STR exponents, suggesting that factors increasing richness may simultaneously decrease turnover in ecological systems. Our results suggest that the STR is as fundamental an ecological pattern as the SAR, and raise questions about the general processes underlying this pattern. They also highlight the dynamic nature of most species assemblages, and the need to incorporate time scale in both basic and applied research on species richness patterns. [ABSTRACT FROM AUTHOR]

In this paper we investigate ecological flow networks via graph theory in search of the real sequential chains through which energy passes from producers to consumers in complex food webs. We obtain such fundamental pathways by identifying strongly connected components (SCCs), subsystems that groups species that take part in cycling, and performing topological sorting on the acyclic graphs that are obtained. Topological sorting identifies preferential directions for energy to flow from sources to sinks, while recycling remains confined within each SCC. Resolving food web networks for SCC highlights the possibility that compartments can be found in ecosystems, but this does not seem a general rule. The four aquatic food webs described in detail show a rather clear subdivision between benthic and pelagic subcommunities, a result that is discussed in the light of other studies. Should further research confirm these results, new insight into the way ecosystems use energy will be provided, with implications on cycling, reciprocal dependency of variables and indirect effects. [ABSTRACT FROM AUTHOR]

Human activities have differentially altered biogeochemical cycling at local, regional and global scales. We propose that a stoichiometric approach, examining the fluxes of multiple elements and the ratio between them, may be a useful tool for better understanding human effects on ecosystem processes and services. The different scale of impacts of the elements carbon, nitrogen and phosphorus and the different nature of their biogeochemical cycles, imply a large variation of their stoichiometric ratios in space and time and thus divergent impacts on biota.In this paper, we examine the effects of anthropogenic perturbations on nutrient ratios in ecosystems in two examples and one case study. Altered stoichiometry in agricultural systems (example 1) can affect not only crop yield and quality but also the interactions between plants and their pollinators, pests and pathogens. Human activities have also altered stoichiometry in coastal ecosystems (example 2). Increased N loading has especially lead to increased N:P and reduced Si:N ratios, with detrimental effects on ecosystem services derived from coastal pelagic food webs, such as fish yield and water quality. The terrestrial–aquatic linkage in stoichiometric alterations is illustrated with a case study, the Mississippi River watershed, where anthropogenic activities have caused stoichiometric changes that have propagated through the watershed into the northern Gulf of Mexico.Coupled with altered stoichiometric nutrient inputs are the inherent differences in variation and sensitivity of different ecosystems to anthropogenic disturbance. Furthermore, the connections among the components of a watershed may result in downstream cascades of disrupted functioning. Applying a multiple element perspective to understanding and addressing societal needs is a new direction for both ecological stoichiometry and sustainability. [ABSTRACT FROM AUTHOR]

Studies of microbial communities from aquatic ecosystems provide important insights into relations between various aspects of ecosystem functioning and changes in biodiversity. Aquatic microbial systems provide a valuable counterpoint to studies of terrestrial systems, because patterns reflect consequences of interactions occurring over many generations of community development, and are unlikely to represent artifacts of the initial conditions established in experimental communities. In this paper we re-analyse our previously published data to separate the contributions of temporal and spatial variation to overall variation in ecosystem functioning. A new analysis based on re-sampling confirms a negative relationship between richness and the variability of one ecosystem process, carbon dioxide flux. The negative relationship reflects high variation among communities of low species richness, rather than high temporal variation within communities of low richness. We also review the various transformations and summary statistics proposed as alternate measures of variability in ecosystem functioning, to point out that different measures are often appropriate for different kinds of data. Finally, we conclude that arguments about the cosmopolitan distribution of microbes do not preclude the existence of important relations between microbial species richness and ecosystem functioning. [ABSTRACT FROM AUTHOR]

The relationship between biodiversity and ecosystem functioning has emerged as a major scientific issue today. As experiments progress, there is a growing need for adequate theories and models to provide robust interpretations and generalisations of experimental results, and to formulate new hypotheses. This paper provides an overview of recent theoretical advances that have been made on the two major questions in this area: (1) How does biodiversity affect the magnitude of ecosystem processes (short-term effects of biodiversity)? (2) How does biodiversity contribute to the stability and maintenance of ecosystem processes in the face of perturbations (long-term effects of biodiversity)? Positive short-term effects of species diversity on ecosystem processes, such as primary productivity and nutrient retention, have been explained by two major types of mechanisms: (1) functional niche complementarity (the complementarity effect), and (2) selection of extreme trait values (the selection effect). In both cases, biodiversity provides a range of phenotypic trait variation. In the complementarity effect, trait variation then forms the basis for a permanent association of species that enhances collective performance. In the selection effect, trait variation comes into play only as an initial condition, and a selective process then promotes dominance by species with extreme trait values. Major differences between within-site effects of biodiversity and across-site productivity–diversity patterns have also been clarified. The local effects of diversity on ecosystem processes are expected to be masked by the effects of varying environmental parameters in across-site comparisons. A major reappraisal of the paradigm that has dominated during the last decades seems necessary if we are to account for long-term effects of biodiversity on ecosystem functioning. The classical deterministic, equilibrium approaches to stability do not explain the reduced temporal variability of aggregate ecosystem properties that has been observed in more diverse systems. On the other hand, stochastic, nonequilibrium approaches do show two types of biodiversity effects on ecosystem productivity in a fluctuating environment: (1) a buffering effect, i.e., a reduction in the temporal variance; and (2) a performance-enhancing effect, i.e., an increase in the temporal mean. The basic mechanisms involved in these long-term insurance effects are very similar to those that operate in short-term biodiversity effects: temporal niche complementarity, and selection of extreme trait values. The ability of species diversity to provide an insurance against environmental fluctuations and a reservoir of variation allowing adaptation to changing conditions may be critical in a long-term perspective. These recent theoretical developments in the area of biodiversity and ecosystem functioning suggest that linking community and ecosystem ecology is a fruitful avenue, which paves the way for a new ecological synthesis. [ABSTRACT FROM AUTHOR]