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.

Red-shifts and red herrings in geographical ecology

I draw attention to the need for ecologists to take spatial structure into account more seriously in hypothesis testing. If spatial autocorrelation is ignored, as it usually is, then analyses of ecological patterns in terms of environmental factors can produce very misleading results. This is demonstrated using synthetic but realistic spatial patterns with known spatial properties which are subjected to classical correlation and multiple regression analyses. Correlation between an autocorrelated response variable and each of a set of explanatory variables is strongly biased in favour of those explanatory variables that are highly autocorrelated - the expected magnitude of the correlation coefficient increases with autocorrelation even if the spatial patterns are completely independent. Similarly, multiple regression analysis finds highly autocorrelated explanatory variables "significant" much more frequently than it should. The chances of mistakenly identifying a "significant" slope across an autocorrelated pattern is very high if classical regression is used. Consequently, under these circumstances strongly autocorrelated environmental factors reported in the literature as associated with ecological patterns may not actually be significant. It is likely that these factors wrongly described as important constitute a red-shifted subset of the set of potential explanations, and that more spatially discontinuous factors (those with bluer spectra) are actually relatively more important than their present status suggests. There is much that ecologists can do to improve on this situation. I discuss various approaches to the problem of spatial autocorrelation from the literature and present a randomisation test for the association of two spatial patterns which has advantages over currently available methods.

Hierarchical Bayesian models in ecology: Reconstructing species interaction networks from non-homogeneous species abundance data

The relationships among organisms and their surroundings can be of immense complexity. To describe and understand an ecosystem as a tangled bank, multiple ways of interaction and their effects have to be considered, such as predation, competition, mutualism and facilitation. Understanding the resulting interaction networks is a challenge in changing environments, e.g. to predict knock-on effects of invasive species and to understand how climate change impacts biodiversity. The elucidation of complex ecological systems with their interactions will benefit enormously from the development of new machine learning tools that aim to infer the structure of interaction networks from field data. In the present study, we propose a novel Bayesian regression and multiple changepoint model (BRAM) for reconstructing species interaction networks from observed species distributions. The model has been devised to allow robust inference in the presence of spatial autocorrelation and distributional heterogeneity. We have evaluated the model on simulated data that combines a trophic niche model with a stochastic population model on a 2-dimensional lattice, and we have compared the performance of our model with L1-penalized sparse regression (LASSO) and non-linear Bayesian networks with the BDe scoring scheme. In addition, we have applied our method to plant ground coverage data from the western shore of the Outer Hebrides with the objective to infer the ecological interactions. (C) 2012 Elsevier B.V. All rights reserved.

Spatial and temporal ecology of Scots pine ectomycorrhizas

Spatial analysis was used to explore the distribution of individual species in an ectomycorrhizal (ECM) fungal community to address: whether mycorrhizas of individual ECM fungal species were patchily distributed, and at what scale; and what the causes of this patchiness might be. Ectomycorrhizas were extracted from spatially explicit samples of the surface organic horizons of a pine plantation. The number of mycorrhizas of each ECM fungal species was recorded using morphotyping combined with internal transcribed spacer (ITS) sequencing. Semivariograms, kriging and cluster analyses were used to determine both the extent and scale of spatial autocorrelation in species abundances, potential interactions between species, and change over time. The mycorrhizas of some, but not all, ECM fungal species were patchily distributed and the size of patches differed between species. The relative abundance of individual ECM fungal species and the position of patches of ectomycorrhizas changed between years. Spatial and temporal analysis revealed a dynamic ECM fungal community with many interspecific interactions taking place, despite the homogeneity of the host community. The spatial pattern of mycorrhizas was influenced by the underlying distribution of fine roots, but local root density was in turn influenced by the presence of specific fungal species.

Identifying optimal sites for natural recovery and restoration of impacted biogenic habitats in a special area of conservation using hydrodynamic and habitat suitability modelling

Selection of sites for successful restoration of impacted shellfish populations depends on understanding the dispersion capability and habitat requirements of the species involved. In Strangford Lough, Northern Ireland, the horse mussel (Modiolus modiolus) biogenic reefs cover only a fraction of their historical range with the remaining reefs badly damaged and requiring restoration. Previous experimental trials suggest that translocation of horse mussels accelerates reef recovery and has therefore been proposed as a suitable restoration technique. We used a series of coupled hydrodynamic and particle dispersal models to assess larval dispersion from remnant and translocated populations to identify suitable areas for adult live M. modiolus translocation in Strangford Lough, Northern Ireland. A maximum entropy model (MAXENT) was used to identify if dispersing larvae could reach habitat suitable for adult M. modiolus. From these we predicted if translocated mussels will reseed themselves or be able to act as larval sources for nearby reefs. The dispersal models showed that the remnant M. modiolus populations are largely self-recruiting with little connectivity between them. The majority of larvae settled near the sources and movement was largely dependent on the tides and not influenced by wind or waves. Higher reef elevation resulted in larvae being able to disperse further away from the release point. However, larval numbers away from the source population are likely to be too low for successful recruitment. There was also little connectivity between the Irish Sea and Strangford Lough as any larvae entering the Lough remained predominantly in the Strangford Narrows. The areas covered by these self-seeding populations are suitable for M. modiolus translocation according to the MAXENT model. As a result of this work and in conjunction with other field work we propose a combination of total protection of all remaining larval sources and small scale translocations onto suitable substrata in each of the identified self-recruiting areas.

The effects of winter ice cover on the trophic ecology of whitefish (Coregonus lavaretus L.) in subarctic lakes

Lakes in Arctic and subarctic regions display extreme levels of seasonal variation in light, temperature and ice cover. Comparatively little is known regarding the effects of such seasonal variation on the diet and resource use of fish species inhabiting these systems. Variation in the diet of European whitefish Coregonus lavaretus (L.) during periods of ice cover in this region is often regarded as 'common knowledge'; however, this aspect of the species' ecology has not been examined empirically. Here, we outline the differences in invertebrate community structure, fish activity, and resource use of monomorphic whitefish populations between summer (August-September) and winter (February-March) in three subarctic lakes in Finnish Lapland. Benthic macroinvertebrate densities did not exhibit measurable differences between summer and winter. Zooplankton diversity and abundance, and activity levels of all fish species (measured as catch per unit effort) were lower in winter. The summer diet of C. lavaretus was typical of a generalist utilising a variety of prey sources. In winter, its dietary niche was significantly reduced, and the diet was dominated by chironomid larvae in all study sites. Pelagic productivity decreases during winter, and fish species inhabiting these systems are therefore restricted to feeding on benthic prey. Sampling time has strong effect on our understanding of resource utilisation by whitefish in subarctic lakes and should be taken into account in future studies of these systems. © 2012 John Wiley & Sons A/S.

Community convergence and recruitment of keystone species as performance indicators of artificial reefs

An experimental artificial reefwas constructed in Strangford Lough, Northern Ireland as part of trials to regenerate damaged biogenic reefs formed by the horse mussel Modiolus modiolus. Experimental reef plots were constructed using Pecten maximus shell as cultch. Clumps of live adult M. modiolus were translocated from nearby natural reefs into cultchwith a high profile (elevated cultch), cultch with a lowprofile (flattened cultch), as well as directly into the seafloor. The aim of the study was to test the hypothesis that translocated mussel clumps would increase habitat complexity thus accelerating community succession and enhancing natural recruitment of M. modiolus spat. These effects were predicted to be greater on elevated cultch due to greater protection from
predators and increased accessibility to food resources. Within the artificial reef array the translocated clumps had a significant positive effect on recruitment compared to cultch without mussels with average densities of spat settled on the translocated M. modiolus clumps ranging from 100 to 200 individuals m-2 compared to 4 to 52 spat m-2 on cultch without mussels. Recruitment of M. modiolus spat was also significantly higher on translocated horse mussels when compared to natural reefs where densities of 8–36 spat m-2 were recorded.
Reef elevation appeared to provide some degree of protection from predators but differences in translocated M. modiolus survival on the different elevation treatments were not significant. In total, 223 taxa were recorded 12 months after reef construction. The presence of translocated clumps ofM. modiolus was the main driver of the increases in faunal diversity and species abundance. Application of objective criteria to assess the performance of artificial reefs suggested that translocation of M. modiolus clumps alone achieved most of the restoration objectives. Consequently this pilot study demonstrates a straightforward and realistic intervention technique that could be used to kick start the regeneration and expansion of impacted mussel and similar biogenic reefs elsewhere.

The spatial ecology of the whiskered bat (Myotis mystacinus) at the western extreme of its range provides evidence of regional adaptation

Although widespread, the ecology of the whiskered bat, Myotis mystacinus in Europe remains poorly understood. Ireland is positioned at the most western extreme of this species' range. To ascertain the ecology of M. mystacinus at its geographic range extreme, the roosting behaviour, home range and habitat use of females in a maternity roost in Ireland was investigated by radio-tracking. M. mystacinus were active in a diversity of habitats: namely, mixed woodland, riparian vegetation, arable land and rough grassland. However, only mixed woodland and riparian habitats were selected as core foraging areas. This is in contrast to a previous study from Britain where only pasture was utilised but is in agreement with data from Slovakia, where woodland was also selected, whilst riparian areas were also utilised by this species in Germany. A high degree of overlap in the foraging areas of individuals was observed. A total of seven roosts were utilised by tracked bats and roost switching behaviour was observed. We discuss our contrasting results in respect to range limitations, regional variability in landscape structure and the composition of bat communities. The present results have implications for the conservation of M. mystacinus within Ireland and other parts of its range, highlighting the need for range wide ecological studies. Regional variability in the ecology of bats related to landscape factors is an important consideration for bat conservation and therefore must be incorporated into future management plans. (C) 2012 Deutsche Gesellschaft fur Saugetierkunde. Published by Elsevier GmbH. All rights reserved.

"Angels and Demons in Cromwellian and Restoration Ireland: Heresy and the Supernatural"

This essay explores accounts of supernatural activity in Cromwellian and Restoration Ireland. Religious life in Cromwellian Ireland was driven by expectations of the unusual—including audible voices from heaven, material encounters with angels, and spiritual encounters with demons. Some conservative Protestants linked this activity to the development and dissemination of heretical belief, while some who had such encounters were confident that it was compatible with the Cromwellian religious mainstream. Crawford Gribben explores the flexibility in the discourse of the marvelous in Ireland and the ways in which the administration contributed to it, and the alignment of the supernatural with various confessional convictions and postures, as well as theological radicalism. After the Restoration, accounts of supernatural encounters were remembered as ghost stories, not as matters for theological debate, a cultural transition linked to the development of a historiography that has continued to invest the Irish Cromwellian past with Gothic tropes.

Adolescents' educational outcomes in a social ecology of parenting, family, and community risks in Northern Ireland

This study examines the influence of social ecological risks within the domains of parenting, family environment, and community in the prediction of educational outcomes for 770 adolescents (49% boys, 51% girls, M = 13.6 years, SD = 2.0) living in a setting of protracted political conflict, specifically working class areas of Belfast, Northern Ireland. Controlling for religious community, age, and gender, youths' lower academic achievement was associated with family environments characterized by high conflict and low cohesion. School behaviour problems were related to greater exposure to community violence, or sectarian and nonsectarian antisocial behaviour. Youths' expectations about educational attainment were undermined by conflict in the family environment and antisocial behaviour in the community, as well as parenting low in warmth and behavioural control. Findings underscore the importance of considering family and community contributions to youths' educational outcomes. Suggestions regarding targeted interventions toward promoting resilience are discussed, such as assessing both child and family functioning, developing multidimensional interventions for parents, and building community partnerships, among others.

A low-cost solution for the restoration of femoral head centre during total hip arthroplasty

Restoration of joint centre during total hip arthroplasty is critical. While computer-aided navigation can improve accuracy during total hip arthroplasty, its expense makes it inaccessible to the majority of surgeons. This article evaluates the use, in the laboratory, of a calliper with a simple computer application to measure changes in femoral head centres during total hip arthroplasty. The computer application was designed using Microsoft Excel and used calliper measurements taken pre- and post-femoral head resection to predict the change in head centre in terms of offset and vertical height between the femoral head and newly inserted prosthesis. Its accuracy was assessed using a coordinate measuring machine to compare changes in preoperative and post-operative head centre when simulating stem insertion on 10 sawbone femurs. A femoral stem with a modular neck was used, which meant nine possible head centre configurations were available for each femur, giving 90 results. The results show that using this technique during a simulated total hip arthroplasty, it was possible to restore femoral head centre to within 6?mm for offset (mean 1.67?±?1.16?mm) and vertical height (mean 2.14?±?1.51?mm). It is intended that this low-cost technique be extended to inform the surgeon of a best-fit solution in terms of neck length and neck type for a specific prosthesis.

Advancing impact prediction and hypothesis testing in invasion ecology using a comparative functional response approach

Invasion ecology urgently requires predictive methodologies that can forecast the ecological impacts of existing, emerging and potential invasive species. We argue that many ecologically damaging invaders are characterised by their more efficient use of resources. Consequently, comparison of the classical ‘functional response’ (relationship between resource use and availability) between invasive and trophically analogous native species may allow prediction of invader ecological impact. We review the utility of species trait comparisons and the history and context of the use of functional responses in invasion ecology, then present our framework for the use of comparative functional responses. We show that functional response analyses, by describing the resource use of species over a range of resource availabilities, avoids many pitfalls of ‘snapshot’ assessments of resource use. Our framework demonstrates how comparisons of invader and native functional responses, within and between Type II and III functional responses, allow testing of the likely population-level outcomes of invasions for affected species. Furthermore, we describe how recent studies support the predictive capacity of this method; for example, the invasive ‘bloody red shrimp’ Hemimysis anomala shows higher Type II functional responses than native mysids and this corroborates, and could have predicted, actual invader impacts in the field. The comparative functional response method can also be used to examine differences in the impact of two or more invaders, two or more populations of the same invader, and the abiotic (e.g. temperature) and biotic (e.g. parasitism) context-dependencies of invader impacts. Our framework may also address the previous lack of rigour in testing major hypotheses in invasion ecology, such as the ‘enemy release’ and ‘biotic resistance’ hypotheses, as our approach explicitly considers demographic consequences for impacted resources, such as native and invasive prey species. We also identify potential challenges in the application of comparative functional responses in invasion ecology. These include incorporation of numerical responses, multiple predator effects and trait-mediated indirect interactions, replacement versus non-replacement study designs and the inclusion of functional responses in risk assessment frameworks. In future, the generation of sufficient case studies for a meta-analysis could test the overall hypothesis that comparative functional responses can indeed predict invasive species impacts.

The predictive science of community ecology

Body mass measures provide a tantalizing tool for explaining both variation in emergent community-level patterns and as a mechanistic basis for fundamental processes such as metabolism, consumption and competition. The unification of body mass, abundance and food web (ecological network) structure in community ecology is an effective way to explore future scenarios of environmental change. However, constraints over the availability of data against which to validate model predictions limit the application of size-based approaches. Here, I explore issues over the use of body size for predicting interaction strengths and hence the dynamics of natural ecosystems. The advantages, disadvantages, opportunities and limitations of such approaches are explored. © 2011 The Author. Journal of Animal Ecology © 2011 British Ecological Society.