Challenges in modelling complexity of fungal entomopathogens in semi-natural populations of insects

The use of fungal entomopathogens as microbial control agents has driven studies into their ecology in crop ecosystems. Yet, there is still a lack of understanding of the ecology of these insect pathogens in semi-natural habitats and communities. We review the literature on prevalence of fungal entomopathogens in insect populations and highlight the difficulties in making such measurements. We then describe the theoretical host-pathogen models available to examine the role that fungal entomopathogens could play in regulating insect populations in semi-natural habitats, much of the inspiration for which has been drawn from managed systems, particularly forests. We further emphasise the need to consider the complexity, and particularly the heterogeneity, of semi-natural habitats within the context of theoretical models and as a framework for empirical studies. We acknowledge that fundamental gaps in understanding fungal entomopathogens from an ecological perspective coupled with a lack of empirical data to test theoretical predictions is impeding progress. There is an increasing need, especially under current rapid environmental change, to improve our understanding of the role of fungi in insect population dynamics beyond the context of forestry and agriculture.     

Habitat�Cperformance relationships: finding the right metric at a given spatial scale

The field of habitat ecology has been muddled by imprecise terminology regarding what constitutes habitat, and how importance is measured through use, selection, avoidance and other bio-statistical terminology. Added to the confusion is the idea that habitat is scale-specific. Despite these conceptual difficulties, ecologists have made advances in understanding ‘how habitats are important to animals’, and data from animal-borne global positioning system (GPS) units have the potential to help this clarification. Here, we propose a new conceptual framework to connect habitats with measures of animal performance itself—towards assessing habitat–performance relationship (HPR). Long-term studies will be needed to estimate consequences of habitat selection for animal performance. GPS data from wildlife can provide new approaches for studying useful correlates of performance that we review. Recent examples include merging traditional resource selection studies with information about resources used at different critical life-history events (e.g. nesting, calving, migration), uncovering habitats that facilitate movement or foraging and, ultimately, comparing resources used through different life-history strategies with those resulting in death. By integrating data from GPS receivers with other animal-borne technologies and combining those data with additional life-history information, we believe understanding the drivers of HPRs will inform animal ecology and improve conservation.     

Hybridization and the colonization of novel habitats by annual sunflowers

Although invasive plant species often have a hybrid ancestry, unambiguous evidence that hybridization has stimulated the evolution of invasive behaviors has been difficult to come by. Here, we briefly review how hybridization might contribute to the colonization of novel habitats, range expansions, and invasiveness and then describe work on hybrid sunflowers that forges a direct link between hybridization and ecological divergence. We first discuss the invasion of Texas by the common sunflower and show that the introgression of chromosomal segments from a locally adapted species may have facilitated range expansion. We then present evidence that the colonization of sand dune, desert floor, and salt marsh habitats by three hybrid sunflower species was made possible by selection on extreme or “transgressive” phenotypes generated by hybridization. This body of work corroborates earlier claims regarding the role of hybridization in adaptive evolution and provides an experimental and conceptual framework for ongoing studies in this area.     

Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes: molecular and cultivation studies

The aim of this review is to interpret recent studies in which molecular methods were used to identify and characterize prokaryotes in lake sediments and related habitats. In the first part studies based on the phylogenetic diversity of prokaryotes found in lacustrine habitats are summarized. The application of various cultivation-independent methods for the characterization of distinct groups of sediment bacteria is exemplified with morphologically conspicuous, colorless sulfur bacteria in the second part of this review. Finally, traditional and recently developed methods are described which could be used for linking the function of microbial populations with their identification. The potential of these approaches for the study of lake sediments is discussed in order to give a perspective for future studies in this habitat.     

Using stable isotope biogeochemistry to study marine mammal ecology

Stable isotope analysis (SIA) has emerged as a common tool in ecology and has proven especially useful in the study of animal diet, habitat use, movement, and physiology. SIA has been vigorously applied to the study of marine mammals, because most species live in habitats or undergo large migrations/movements that make them difficult to observe. Our review supplies a complete list of published SIA contributions to marine mammal science and highlights informative case examples in four general research areas: (1) physiology and fractionation, (2) foraging ecology and habitat use, (3) ecotoxicology, and (4) historic ecology and paleoecology. We also provide a condensed background of isotopic nomenclature, highlight several physiological considerations important for accurate interpretation of isotopic data, and identify research areas ripe for future growth. Because it is impossible to conduct controlled laboratory experiments on most marine mammal species, future studies in marine mammal ecology must draw on isotopic data collected from other organisms and be cognizant of key assumptions often made in the application of SIA to the study of animal ecology. The review is designed to be accessible to all audiences, from students unfamiliar with SIA to those who have utilized it in published studies.     

Palearctic passerines in Afrotropical environments: a review

Previous ecological studies of Palearctic passerine migrants in Africa have claimed to reveal some general features with respect to habitat use, foraging ecology and interspecific relationships with Afrotropical residents. In this review we discuss apparent contradictions between earlier generalisations and more recent results from more detailed field studies and explore in which areas our ecological knowledge and theoretical understanding remain poor and have given rise to misconceptions. For example, it has been claimed that migrants use structurally more diverse and open habitats and that they forage higher and in more peripheral parts of the vegetation than their ecologically similar Afrotropical counterparts, yet in the past these characteristics were often not clearly defined and not always correlated in practice. It has also been stated that migrants are more flexible in habitat use, occupying a wider range of habitat types and employing a higher diversity of foraging techniques, both of which were assumed to be adaptations to permit coexistence with Afrotropical residents by using untapped resources that are only seasonally available. Yet results from studies of the role of competition in shaping migrant-resident communities remain largely unconvincing. While flexibility may facilitate migrant-resident coexistence, it may also favour the evolution of migration because specialists are less able to use their advantages in different environments. We note that definitions of flexibility and specialisation may themselves depend on the ecological or evolutionary approach adopted by researchers. We conclude that few generalisations can safely be made about the ecology of Palearctic migrants in Africa and that adaptive explanations for the behaviours observed are largely lacking, as are studies of the fitness consequences of different migrant strategies such as have been conducted in the Nearctic-Neotropical migration system.     

The water economy of South American desert rodents: from integrative to molecular physiological ecology

Rodents from arid and semi-arid habitats live under conditions where the spatial and temporal availability of free water is limited, or scarce, thus forcing these rodents to deal with the problem of water conservation. The response of rodents to unproductive desert environments and water deficits has been intensively investigated in many deserts of the world. However, current understanding of the cellular, systemic and organismal physiology of water economy relies heavily on short-term, laboratory-oriented experiments, which usually focus on responses at isolated levels of biological organization. In addition, studies in small South American mammals are scarce. Indeed xeric habitats have existed in South America for a long time and it is intriguing why present day South American desert rodents do not show the wide array of adaptive traits to desert life observed for rodents on other continents. Several authors have pointed out that South American desert rodents lack physiological and energetic specialization for energy and water conservation, hypothesizing that their success is based more on behavioral and ecological strategies. We review phenotypic flexibility and physiological diversity in water flux rate, urine osmolality, and expression of water channels in South American desert-dwelling rodents. As far as we know, this is the first review of integrative studies at cellular, systemic and organismal levels. Our main conclusion is that South American desert rodents possess structural as well as physiological systems for water conservation, which are as remarkable as those found in "classical" rodents inhabiting other desert areas of the world.     

Plumular Protection and some related aspects of seedling behaviour

Summary

The habitats available to ferns and their allies in Scotland have been almost totally altered. From the first agricultural incursions on the wildwood to the progressive management of the whole country, ferns have filled any available niches in a characteristically opportunist fashion. More recently, large areas of the landscape have been reconstructed to provide reservoirs, an extensive network of roads with verges and walls and many other man-made installations. While there has undoubtedly been a loss of many types of habitats, especially of wetland, this is a brief review of some areas which would not otherwise have existed and yet offer suitable conditions for a wide variety of species.     

Sustainable pest regulation in agricultural landscapes: a review on landscape composition, biodiversity and natural pest control

Agricultural intensification has resulted in a simplification of agricultural landscapes by the expansion of agricultural land, enlargement of field size and removal of non-crop habitat. These changes are considered to be an important cause of the rapid decline in farmland biodiversity, with the remaining biodiversity concentrated in field edges and non-crop habitats. The simplification of landscape composition and the decline of biodiversity may affect the functioning of natural pest control because non-crop habitats provide requisites for a broad spectrum of natural enemies, and the exchange of natural enemies between crop and non-crop habitats is likely to be diminished in landscapes dominated by arable cropland. In this review, we test the hypothesis that natural pest control is enhanced in complex patchy landscapes with a high proportion of non-crop habitats as compared to simple large-scale landscapes with little associated non-crop habitat. In 74% and 45% of the studies reviewed, respectively, natural enemy populations were higher and pest pressure lower in complex landscapes versus simple landscapes. Landscape-driven pest suppression may result in lower crop injury, although this has rarely been documented. Enhanced natural enemy activity was associated with herbaceous habitats in 80% of the cases (e.g. fallows, field margins), and somewhat less often with wooded habitats (71%) and landscape patchiness (70%). The similar contributions of these landscape factors suggest that all are equally important in enhancing natural enemy populations. We conclude that diversified landscapes hold most potential for the conservation of biodiversity and sustaining the pest control function.     

Aliens in caves: the global dimension of biological invasions in subterranean ecosystems

Alien species are a significant threat to natural ecosystems and human economies. Despite global efforts to address this challenge, the documented number of alien species is rapidly increasing worldwide. However, the magnitude of the impact of alien species may vary significantly across habitats. For example, some habitats are naturally less prone to biological invasions due to stringent abiotic and biotic characteristics, selecting for a limited number of introduced species possessing traits closely related to the native organisms. Subterranean ecosystems are quintessential examples of habitats with strong environmental filters (e.g. lack of light and scarcity of food), driving convergent adaptations in species that have successfully adapted to life in darkness. Despite these stringent environmental constraints, the number of records of alien species in subterranean ecosystems has increased in recent decades, but the relevant literature remains largely fragmented and mostly anecdotal. Therefore, even though caves are generally considered very fragile ecosystems, their susceptibility to impacts by alien species remains untested other than for some very specific cases. We provide the first systematic literature survey to synthesise available knowledge on alien species in subterranean ecosystems globally. This review is supported by a database summarising the available literature, aiming to identify gaps in the distribution and spread of alien invertebrate species in subterranean habitats, and laying the foundations for future management practices and interventions. First, we quantitatively assessed the current knowledge of alien species in subterranean ecosystems to shed light on broader questions about taxonomic biases, geographical patterns, modes of dispersal, pathways for introductions and potential impacts. Secondly, we collected species-specific traits for each recorded alien species and tested whether subterranean habitats act as ecological filters for their establishment, favouring organisms with pre-adaptive traits suitable for subterranean life. We found information on the presence of 246 subterranean alien species belonging to 18 different classes. The dominant alien species were invertebrates, especially insects and arachnids. Most species were reported in terrestrial subterranean habitats from all continents except Antarctica. Palaearctic and Nearctic biogeographic regions represented the main source of alien species. The main routes of introductions into the recipient country are linked to commercial activities (84.3% of cases for which there was information available). Negative impacts have been documented for a small number of case studies (22.7%), mostly related to increased competition with native species. For a limited number of case studies (6.1%), management strategies were reported but the effectiveness of these interventions has rarely been quantified. Accordingly, information on costs is very limited. Approximately half of the species in our database can be considered established in subterranean habitats. According to our results, the presence of suitable traits grants access to the stringent environmental filter posed by subterranean environments, facilitating establishment in the new habitat. We recommend that future studies deepen the understanding of invasiveness into subterranean habitats, raising public and scientific community awareness of preserving these fragile ecosystems.     

Poor design of behavioural experiments gets poor results: examples from intertidal habitats

Many patterns of distribution and abundance of intertidal animals are explained by processes of movements of animals, selecting particular habitats or levels on the shore, or interacting with other species. Movements of intertidal animals have therefore been studied over many years. During this long history, much intertidal ecology has changed in focus from broad-scale to small-scale patterns and processes, although there has been recent refocus on a combination of many scales. Simultaneously, there has been an increase in the incidence of field experiments and growing recognition that behaviour is more flexible than originally thought. This review examines changes in the ways that experiments on movements on intertidal animals have been and are being done, taking into account these changes in emphasis. Although some progress has been made, there is still a long way to go. The idea is still prevalent that behaviour is simple, rather invariant and that the animals respond to broad-scale cues that have traditionally been of interest to many investigators. This means that many experiments are still designed to minimise (or ignore) natural variation in behaviour rather than to measure it and that any associated disturbances are considered irrelevant and therefore not evaluated. Understanding the role that behaviour has in establishing and maintaining many of the patterns observed on intertidal shores is crucial to our understanding of the ecology of these habitats. Better experiments, designed logically with appropriate controls to evaluate realistic processes and to measure how behaviour varies among places and from time to time can only improve this understanding.     

Competitive effects of non-native plants are lowest in native plant communities that are most vulnerable to invasion

Despite widespread acknowledgment that disturbance favors invasion, a hypothesis that has received little attention is whether non-native invaders have greater competitive effects on native plants in undisturbed habitats than in disturbed habitats. This hypothesis derives from the assumption that competitive interactions are more persistent in habitats that have not been recently disturbed. Another hypothesis that has received little attention is whether the effects of non-native plants on native plants vary among habitats that differ in soil fertility. We documented habitat occurrences of 27 non-native plant species and 377 native plant species encountered in numerous study plots in a broad sample of ecosystems in MS (USA). We then reviewed experimental and regression-based field studies in the scientific literature that specifically examined potential competitive (or facilitative) effects of these non-native species on native species and characterized the habitats in which effects were the greatest. As expected, the non-native species examined here in general were more likely to be associated with severely disturbed habitats than were the native species as a group. In contrast, we found that non-native species with competitive effects on natives were more likely to be associated with undisturbed habitats than with disturbed habitats. When longer term studies involving more resident species were given more weight in the analysis, competitive effects appeared to be the greatest in undisturbed habitats with low soil fertility. These results reinforce the notion that invasion is not synonymous with impact. The environmental conditions that promote invasion may limit competitive effects of invaders on native plant communities following invasion.     

The pitfalls of extrapolation in conservation: movements and habitat use of a threatened toad are different in the boreal forest

Widely distributed species often vary geographically in their ecology. Thus, results of studies done in one part of their range cannot necessarily be extrapolated readily to populations elsewhere. This problem is particularly important for threatened species whose ecology has been studied in a few disconnected locations. The Canadian toad Bufo ( Anaxyrus ) hemiophrys occupies a large geographic range in western North America, but most studies of its ecology have been done in the prairies, where the species is considered to be closely associated with aquatic habitats. However, B. hemiophrys also occurs in boreal forest, where it faces threats from logging activities, especially if it uses upland habitats far from ponds and lakes. We radio-tracked 29 toads in the boreal forest of northern Alberta, Canada to determine their patterns of movement and habitat use. Most movements between fixes were <50 m, but toads sometimes made longer movements exceeding 100 m. Over time, however, these short-term movements combined into large-scale directional movements that were highly variable among toads in both tortuosity and timing, but which generally took toads into upland forested habitats. Putative hibernacula also were located in upland sites. However, despite this terrestriality, toads still were associated with wetlands, using them significantly more often than would be expected based on their proportionate areal contribution to the landscape. Nonetheless, use of upland sites and long-distance terrestrial movements differentiate this population of B. hemiophrys from those studied in prairie environments. Conservation plans based on what we know about the species elsewhere therefore would be inappropriate in this region. Management often requires site-specific information, which can be obtained only from natural-history studies of the populations in question.     

Vacant habitats in the Universe

The search for life on other planets usually makes the assumption that where there is a habitat, it will contain life. On the present-day Earth, uninhabited habitats (or vacant habitats) are rare, but might occur, for example, in subsurface oils or impact craters that have been thermally sterilized in the past. Beyond Earth, vacant habitats might similarly exist on inhabited planets or on uninhabited planets, for example on a habitable planet where life never originated. The hypothesis that vacant habitats are abundant in the Universe is testable by studying other planets. In this review, I discuss how the study of vacant habitats might ultimately inform an understanding of how life has influenced geochemical conditions on Earth.     

Global methods for protein glycosylation analysis by mass spectrometry

Mass spectrometry has been an analytical tool of choice for glycosylation analysis of individual proteins. Over the last 5 years several previously and newly developed mass spectrometry methods have been extended to global glycoprotein studies. In this review we discuss the importance of these global studies and the advances that have been made in enrichment analyses and fragmentation methods. We also briefly describe relevant sample preparation methods that have been used for the analysis of a single glycoprotein that could be extrapolated to global studies. Finally this review covers aspects of improvements and advances on the instrument front which are important to future global glycoproteomic studies.     

Geomicrobiology in oceanography: microbe-mineral interactions at and below the seafloor

Oceanography is inherently interdisciplinary and, since its inception, has included the study of microbe-mineral interactions. From early studies of manganese nodules, to the discovery of hydrothermal vents, it has been recognized that microorganisms are involved at various levels in the transformation of rocks and minerals at and below the seafloor. Recent studies include mineral weathering at low temperatures and microbe-mineral interactions in the subseafloor "deep biosphere". A common characteristic of seafloor and subseafloor geomicrobiological processes that distinguishes them from terrestrial or near-surface processes is that they occur in the dark, one or more steps removed from the sunlight that fuels the near-surface biosphere on Earth. This review focuses on geomicrobiological studies and energy flow in dark, deep-ocean and subseafloor rock habitats.     

Effects of global environmental changes on parasitoid–host food webs and biological control

Global environmental changes threaten biodiversity and the interactions between species, and food-web approaches are being used increasingly to measure their community-wide impacts. Here we review how parasitoid–host food webs affect biological control, and how their structure responds to environmental change. We find that land-use intensification tends to produce webs with low complexity and uneven interaction strengths. Dispersal, spatial arrangement of habitats, the species pool and community differences across habitats have all been found to determine how webs respond to landscape structure, though clear effects of landscape complexity on web structure remain elusive. The invasibility of web structures and response of food webs to invasion have been the subject of theoretical and empirical work respectively, and nutrient enrichment has been widely studied in the food-web literature, potentially driving dynamic instability and altering biomass ratios of different trophic levels. Combined with food-web changes observed under climate change, these responses of food webs could signal changes to biological control, though there have been surprisingly few studies linking food-web structure to pest control, and these have produced mixed results. However, there is strong potential for food-web approaches to add value to biological control research, as parasitoid–host webs have been used to predict indirect effects among hosts that share enemies, to study non-target effects of biological control agents and to quantify the use of alternative prey resources by enemies. Future work is needed to link food-web interactions with evolutionary responses to the environment and predator–prey interactions, while incorporating recent advances in predator biodiversity research. This holistic understanding of agroecosystem responses and functioning, made possible by food-web approaches, may hold the key to better management of biological control in changing environments.     

Ecological traps: current evidence and future directions

Ecological traps, which occur when animals mistakenly prefer habitats where their fitness is lower than in other available habitats following rapid environmental change, have important conservation and management implications. Empirical research has focused largely on assessing the behavioural effects of traps, by studying a small number of geographically close habitat patches. Traps, however, have also been defined in terms of their population-level effects (i.e. as preferred habitats of sufficiently low quality to cause population declines), and this is the scale most relevant for management. We systematically review the ecological traps literature to (i) describe the geographical and taxonomic distribution of efforts to study traps, (ii) examine how different traps vary in the strength of their effects on preference and fitness, (iii) evaluate the robustness of methods being used to identify traps, and (iv) determine whether the information required to assess the population-level consequences of traps has been considered. We use our results to discuss key knowledge gaps, propose improved methods to study traps, and highlight fruitful avenues for future research.