Essay - The role of ecological theory in microbial ecology

Microbial ecology is currently undergoing a revolution, with repercussions spreading throughout microbiology, ecology and ecosystem science. The rapid accumulation of molecular data is uncovering vast diversity, abundant uncultivated microbial groups and novel microbial functions. This accumulation of data requires the application of theory to provide organization, structure, mechanistic insight and, ultimately, predictive power that is of practical value, but the application of theory in microbial ecology is currently very limited. Here we argue that the full potential of the ongoing revolution will not be realized if research is not directed and driven by theory, and that the generality of established ecological theory must be tested using microbial systems.

The imprint of the geographical, evolutionary and ecological context on species-area relationships

Species-area relationships (SAR) are fundamental in the understanding of biodiversity patterns and of critical importance for predicting species extinction risk worldwide. Despite the enormous attention given to SAR in the form of many individual analyses, little attempt has been made to synthesize these studies. We conducted a quantitative meta-analysis of 794 SAR, comprising a wide span of organisms, habitats and locations. We identified factors reflecting both pattern-based and dynamic approaches to SAR and tested whether these factors leave significant imprints on the slope and strength of SAR. Our analysis revealed that SAR are significantly affected by variables characterizing the sampling scheme, the spatial scale, and the types of organisms or habitats involved. We found that steeper SAR are generated at lower latitudes and by larger organisms. SAR varied significantly between nested and independent sampling schemes and between major ecosystem types, but not generally between the terrestrial and the aquatic realm. Both the fit and the slope of the SAR were scale-dependent. We conclude that factors dynamically regulating species richness at different spatial scales strongly affect the shape of SAR. We highlight important consequences of this systematic variation in SAR for ecological theory, conservation management and extinction risk predictions.

Soil resource supply influences faunal size-specific distributions in natural food webs

The large range of body-mass values of soil organisms provides a tool to assess the ecological organization of soil communities. The goal of this paper is to identify graphical and quantitative indicators of soil community composition and ecosystem functioning, and to illustrate their application to real soil food webs. The relationships between log-transformed mass and abundance of soil organisms in 20 Dutch meadows and heathlands were investigated. Using principles of allometry, maximal use can be made of ecological theory to build and explain food webs. The aggregate contribution of small invertebrates such as nematodes to the entire community is high under low soil phosphorus content and causes shifts in the mass-abundance relationships and in the trophic structures. We show for the first time that the average of the trophic link lengths is a reliable predictor for assessing soil fertility responses. Ordered trophic link pairs suggest a self-organizing structure of food webs according to resource availability and can predict environmental shifts in ecologically meaningful ways.

Interaction strengths in food webs: issues and opportunities

1. Recent efforts to understand how the patterning of interaction strength affects both structure and dynamics in food webs have highlighted several obstacles to productive synthesis. Issues arise with respect to goals and driving questions, methods and approaches, and placing results in the context of broader ecological theory.

Biodiversity and ecosystem processes in shallow coastal waters: an experimental approach

The relationship between biodiversity and ecological processes is currently the focus of considerable research effort, made all the more urgent by the rate of biodiversity loss world-wide. Rigorous experimental approaches to this question have been dominated by terrestrial ecologists, but shallow-water marine systems offer great opportunities by virtue of their relative ease of manipulation, fast response times and well-understood effects of macrofauna on sediment processes. In this paper, we describe a series of experiments whereby species richness has been manipulated in a controlled way and the concentrations of nutrients (ammonium, nitrate and phosphate) in the overlying water measured under these different treatments. The results indicate variable effects of species and location on ecosystem processes, and are discussed in the context of emerging mainstream ecological theory on biodiversity and ecosystem relations. Extensions of the application of the experimental approach to species-rich, large-scale benthic systems are discussed and the potential for novel analyses of existing data sets is highlighted. (C) 2002 Elsevier Science B.V. All rights reserved.

A new statistical framework for the quantification of covariate associations with species distributions

Identifying processes that shape species geographical ranges is a prerequisite for understanding environmental change. Currently, species distribution modelling methods do not offer credible statistical tests of the relative influence of climate factors and typically ignore other processes (e.g. biotic interactions and dispersal limitation). We use a hierarchical model fitted with Markov Chain Monte Carlo to combine ecologically plausible niche structures using regression splines to describe unimodal but potentially skewed response terms. We apply spatially explicit error terms that account for (and may help identify) missing variables. Using three example distributions of European bird species, we map model results to show sensitivity to change in each covariate. We show that the overall strength of climatic association differs between species and that each species has considerable spatial variation in both the strength of the climatic association and the sensitivity to climate change. Our methods are widely applicable to many species distribution modelling problems and enable accurate assessment of the statistical importance of biotic and abiotic influences on distributions.

Interchange of entire communities: microbial community coalescence

Microbial communities are enigmatically diverse. We propose a novel view of processes likely affecting microbial assemblages, which could be viewed as the Great American Interchange en miniature: the wholesale exchange among microbial communities resulting from moving pieces of the environment containing entire assemblages. Incidental evidence for such ‘community coalescence’ is accumulating, but such processes are rarely studied, likely because of the absence of suitable terminology or a conceptual framework. We provide the nucleus for such a conceptual foundation for the study of community coalescence, examining factors shaping these events, links to bodies of ecological theory, and we suggest modeling approaches for understanding coalescent communities. We argue for the systematic study of community coalescence because of important functional and applied consequences.

Tracing early stages of species differentiation: Ecological, morphological and genetic divergence of Galapagos sea lion populations

Background: Oceans are high gene flow environments that are traditionally believed to hamper the build-up of genetic divergence. Despite this, divergence appears to occur occasionally at surprisingly small scales. The Galápagos archipelago provides an ideal opportunity to examine the evolutionary processes of local divergence in an isolated marine environment. Galápagos sea lions (Zalophus wollebaeki) are top predators in this unique setting and have an essentially unlimited dispersal capacity across the entire species range. In theory, this should oppose any genetic differentiation.
Results: We find significant ecological, morphological and genetic divergence between the western colonies and colonies from the central region of the archipelago that are exposed to different ecological conditions. Stable isotope analyses indicate that western animals use different food sources than those from the central area. This is likely due to niche partitioning with the second Galápagos eared seal species, the Galápagos fur seal (Arctocephalus galapagoensis) that exclusively dwells in the west. Stable isotope patterns correlate with significant differences in foraging-related skull morphology. Analyses of mitochondrial sequences as well as microsatellites reveal signs of initial genetic differentiation.
Conclusion: Our results suggest a key role of intra- as well as inter-specific niche segregation in the evolution of genetic structure among populations of a highly mobile species under conditions of free movement. Given the monophyletic arrival of the sea lions on the archipelago, our study challenges the view that geographical barriers are strictly needed for the build-up of genetic divergence. The study further raises the interesting prospect that in social, colonially breeding mammals additional forces, such as social structure or feeding traditions, might bear on the genetic partitioning of populations.

Lake restoration in terms of ecological resilience: a numerical study of biomanipulations under bistable conditions

An abstract version of the comprehensive aquatic simulation model (CASM) is found to exhibit bistability under intermediate loading of nutrient input, supporting the alternative-stable-states theory and field observations for shallow lakes. Our simulations of biomanipulations under the bistable conditions reveal that a reduction in the abundance of zooplanktivorous fish cannot switch the system from a turbid to a clear state. Rather, a direct reduction of phytoplankton and detritus was found to be most effective to make this switch in the present model. These results imply that multiple manipulations may be effective for practical restorations of lakes. We discuss the present results of biomanipulations in terms of ecological resilience in multivariable systems or natural systems.

Body size in ecological networks

Body size determines a host of species traits that can affect the structure and dynamics of food webs, and other ecological networks, across multiple scales of organization. Measuring body size provides a relatively simple means of encapsulating and condensing a large amount of the biological information embedded within an ecological network. Recently, important advances have been made by incorporating body size into theoretical models that explore food web stability, the patterning of energy fluxes, and responses to perturbations. Because metabolic constraints underpin bodysize scaling relationships, metabolic theory offers a potentially useful new framework within which to develop novel models to describe the structure and functioning of ecological networks and to assess the probable consequences of biodiversity change.