Metabolic Flexibility as a Major Predictor of Spatial Distribution in Microbial Communities

A better understand the ecology of microbes and their role in the global ecosystem could be achieved if traditional ecological theories can be applied to microbes. In ecology organisms are defined as specialists or generalists according to the breadth of their niche. Spatial distribution is often used as a proxy measure of niche breadth; generalists have broad niches and a wide spatial distribution and specialists a narrow niche and spatial distribution. Previous studies suggest that microbial distribution patterns are contrary to this idea; a microbial generalist genus (Desulfobulbus) has a limited spatial distribution while a specialist genus (Methanosaeta) has a cosmopolitan distribution. Therefore, we hypothesise that this counter-intuitive distribution within generalist and specialist microbial genera is a common microbial characteristic. Using molecular fingerprinting the distribution of four microbial genera, two generalists, Desulfobulbus and the methanogenic archaea Methanosarcina, and two specialists, Methanosaeta and the sulfate-reducing bacteria Desulfobacter were analysed in sediment samples from along a UK estuary. Detected genotypes of both generalist genera showed a distinct spatial distribution, significantly correlated with geographic distance between sites. Genotypes of both specialist genera showed no significant differential spatial distribution. These data support the hypothesis that the spatial distribution of specialist and generalist microbes does not match that seen with specialist and generalist large organisms. It may be that generalist microbes, while having a wider potential niche, are constrained, possibly by intrageneric competition, to exploit only a small part of that potential niche while specialists, with far fewer constraints to their niche, are more capable of filling their potential niche more effectively, perhaps by avoiding intrageneric competition. We suggest that these counter-intuitive distribution patterns may be a common feature of microbes in general and represent a distinct microbial principle in ecology, which is a real challenge if we are to develop a truly inclusive ecology.     

Trophic niche width,offspring condition and immunity in a raptor species

Strategies developed by organisms to maximize foraging efficiency have a strong influence on fitness. The way in which the range of food resources is exploited has served to classify species, populations and individuals from more specialist (narrow trophic niche) to more generalist (broad trophic niche). Recent studies have provided evidence that many of the considered generalist species/populations are actually composed of different specialist individuals (individual specialization). Even the existence of generalism as an adaptive strategy has been questioned. In this study, we investigated the relationship between trophic niche width, individual quality and offspring viability in a population of common kestrel Falco tinnunculus during 4 years. We showed that the diet of kestrels varied significantly among years and that individuals of better quality fed their offspring with a higher diversity of prey species and a higher amount of food. Moreover, body condition and immune response of nestlings were positively correlated with diversity of prey delivered by parents. Our study suggests that generalism has the potential to increase fitness and that broadening the trophic niche may be an adaptive strategy in unpredictable environments.     

Reconsidering the Specialist-Generalist Paradigm in Niche Breadth Dynamics: Resource Gradient Selection by Canada Lynx and Bobcat

The long-standing view in ecology is that disparity in overall resource selection is the basis for identifying niche breadth patterns, with species having narrow selection being classified “specialists” and those with broader selection being “generalists”. The standard model of niche breadth characterizes generalists and specialists as having comparable levels of overall total resource exploitation, with specialists exploiting resources at a higher level of performance over a narrower range of conditions. This view has gone largely unchallenged. An alternate model predicts total resource use being lower for the specialized species with both peaking at a comparable level of performance over a particular resource gradient. To reconcile the niche breadth paradigm we contrasted both models by developing range-wide species distribution models for Canada lynx, Lynx canadensis, and bobcat, Lynx rufus. Using a suite of environmental factors to define each species’ niche, we determined that Canada lynx demonstrated higher total performance over a restricted set of variables, specifically those related to snow and altitude, while bobcat had higher total performance across most variables. Unlike predictions generated by the standard model, bobcat level of exploitation was not compromised by the trade-off with peak performance, and Canada lynx were not restricted to exploiting a narrower range of conditions. Instead, the emergent pattern was that specialist species have a higher total resource utilization and peak performance value within a smaller number of resources or environmental axes than generalists. Our results also indicate that relative differences in niche breadth are strongly dependent on the variable under consideration, implying that the appropriate model describing niche breadth dynamics between specialists and generalists may be more complex than either the traditional heuristic or our modified version. Our results demonstrate a need to re-evaluate traditional, but largely untested, assumptions regarding resource utilization in species with broad and narrow niches.     

Niche width impacts vertebrate diversification

Aim The size of the climatic niche of a species is a major factor determining its distribution and evolution. In particular, it has been proposed that niche width should be associated with the rate of species diversification. Here, we test whether species niche width affects the speciation and extinction rates of three main clades of vertebrates: amphibians, mammals and birds. Location Global. Methods We obtained the time‐calibrated phylogenies, IUCN conservation status, species distribution maps and climatic data for 2340 species of amphibians, 4563 species of mammals and 9823 species of birds. We computed the niche width for each species as the mean annual temperature across the species range. We estimated speciation, extinction and transition rates associated with lineages with either narrow (specialist) or wide (generalist) niches using phylogeny‐based birth–death models. We also tested if current conservation status was correlated with the niche width of species. Results We found higher net diversification rates in specialist species than in generalist species. This result was explained by both higher speciation rates (for the three taxonomic groups) and lower extinction rates (for mammals and birds only) in specialist than in generalist species. In contrast, current specialist species tended to be more threatened than generalist species. Main conclusions Our diversification analysis shows that the width of the climatic niche is strongly associated with diversification rates and may thus be a crucial factor for understanding the emergence of diversity patterns in vertebrates. The striking difference between our diversification results and current conservation status suggests that the current extinction process may be different from extinction rates estimated from the whole history of the group.     

Multi-Axis Niche Examination of Ecological Specialization: Responses to Heat,Desiccation and Starvation Stress in Two Species of Pit-Building Antlions

Classical ecological studies discussing specialization usually focus on species’ performance along one niche axis. This approach may overlook niche differentiation evident in another dimension which could explain species co-occurrence. The present research exemplifies a comprehensive approach to examining local adaptation. Specifically, we examined multiple niche axes by subjecting a model organism to various experimental conditions to monitor responses to extreme stress associated with heat, desiccation and starvation. Our model system comprised two pit-building antlions: the habitat generalist Myrmeleon hyalinus and the habitat specialist Cueta lineosa. Previous research has shown that the foraging performance of the generalist is better than that of the specialist, even in the latter’s characteristic habitat. We illustrate that this apparent superiority of the habitat generalist does not manifest itself along other niche axes; rather, the habitat specialist holds a set of traits that provide an advantage under harsh environmental conditions. Specifically, C. lineosa has an advantage over M. hyalinus at high temperatures, exhibiting a higher survival rate and improved foraging success (i.e., high-temperature specialist). C. lineosa is also more efficient in its energy budget, losing less mass during starvation and gaining mass more efficiently during feeding. This superior efficiency is a result of physiological adaptations as well as behavioural responses to harsh conditions. In conclusion, our results imply that the habitat specialization of C. lineosa has not led it towards an evolutionary dead-end.     

Scale‐invariance of niche breadth in fleas parasitic on small mammals

The resource specialization or niche breadth of a species is not fixed across populations, but instead varies over geographical space. A species may be a local specialist but a regional generalist, if it uses locally few resources that are substitutable across locations. In contrast, a species is a local generalist and a regional specialist if it uses locally many resources that cannot be substituted from 1 location to the next. Scale‐dependence can thus be a major factor in estimation of niche breadth. Here, we test for relationships between local and global estimates of host specificity (a measure of niche breadth for parasites) in fleas (Siphonaptera) parasitic on small mammals from 49 different regions within the Holarctic. Across all fleas, we found a strong, positive relationship between the number of host species that a flea uses in 1 locality and the number of different host species that can serve as the flea's principal host (i.e. the one supporting the most fleas in a region) among all regions. Also, we observed a strong positive relationship between the taxonomic distinctness of the host species used in 1 locality and that of all known principal hosts among all localities. These relationships held after correcting for potentially confounding phylogenetic influences. We discuss the implications of scale‐independent host specificity and its association with geographical range size and species‐specific patterns of host use.     

The effect of positional error on fine scale species distribution models increases for specialist species

Species occurrences inherently include positional error. Such error can be problematic for species distribution models (SDMs), especially those based on fine-resolution environmental data. It has been suggested that there could be a link between the influence of positional error and the width of the species ecological niche. Although positional errors in species occurrence data may imply serious limitations, especially for modelling species with narrow ecological niche, it has never been thoroughly explored. We used a virtual species approach to assess the effects of the positional error on fine-scale SDMs for species with environmental niches of different widths. We simulated three virtual species with varying niche breadth, from specialist to generalist. The true distribution of these virtual species was then altered by introducing different levels of positional error (from 5 to 500 m). We built generalized linear models and MaxEnt models using the distribution of the three virtual species (unaltered and altered) and a combination of environmental data at 5 m resolution. The models’ performance and niche overlap were compared to assess the effect of positional error with varying niche breadth in the geographical and environmental space. The positional error negatively impacted performance and niche overlap metrics. The amplitude of the influence of positional error depended on the species niche, with models for specialist species being more affected than those for generalist species. The positional error had the same effect on both modelling techniques. Finally, increasing sample size did not mitigate the negative influence of positional error. We showed that fine-scale SDMs are considerably affected by positional error, even when such error is low. Therefore, where new surveys are undertaken, we recommend paying attention to data collection techniques to minimize the positional error in occurrence data and thus to avoid its negative effect on SDMs, especially when studying specialist species.     

Niche breadth predicts geographical range size: a general ecological pattern

The range of resources that a species uses (i.e. its niche breadth) might determine the geographical area it can occupy, but consensus on whether a niche breadth–range size relationship generally exists among species has been slow to emerge. The validity of this hypothesis is a key question in ecology in that it proposes a mechanism for commonness and rarity, and if true, may help predict species' vulnerability to extinction. We identified 64 studies that measured niche breadth and range size, and we used a meta‐analytic approach to test for the presence of a niche breadth–range size relationship. We found a significant positive relationship between range size and environmental tolerance breadth (z = 0.49), habitat breadth (z = 0.45), and diet breadth (z = 0.28). The overall positive effect persisted even when incorporating sampling effects. Despite significant variability in the strength of the relationship among studies, the general positive relationship suggests that specialist species might be disproportionately vulnerable to habitat loss and climate change due to synergistic effects of a narrow niche and small range size. An understanding of the ecological and evolutionary mechanisms that drive and cause deviations from this niche breadth–range size pattern is an important future research goal.     

Niche breadth and biodiversity change derived from marine Amphipoda species off Iceland

Understanding the ecological requirements and thresholds of individual species is crucial to better predict potential outcomes of climate change on species distribution. In particular, species optima and lower and upper limits along resource gradients require attention. Based on Huisman‐Olff‐Fresco (HOF) models, we determined species‐specific responses along gradients of nine environmental parameters including depth in order to estimate niche attributes of 30 deep‐sea benthic amphipods occurring around Iceland. We, furthermore, examined the relationships between niche breadth, occupancy, and geographic range assuming that species with a wider niche are spatially more widely dispersed and vice versa. Overall, our results reveal that species react very differently to environmental gradients, which is independent of the family affiliation of the respective species. We could infer a strong relationship between occupancy and geographic range and also relate this to differences in niche breadth; that is specialist species with a narrow niche had a more limited distribution and may thus be more threatened by changing environmental conditions than generalist species, which are more widespread. Given the preponderance of rare species in the deep sea, this implies that many species could be at risk. However, this must be carefully weighed against geographical data gaps in this area, given that many deep‐sea areas are severely undersampled and the true distribution of most species is unknown. After all, our results underline that an accurate taxonomic classification is of crucial importance, without which ecological niche properties cannot be determined and which is hence fundamental for the assessment and understanding of changes in biodiversity in the face of increasing human perturbations.     

Jack of all trades, master of all: a positive association between habitat niche breadth and foraging performance in pit-building antlion larvae

Species utilizing a wide range of resources are intuitively expected to be less efficient in exploiting each resource type compared to species which have developed an optimal phenotype for utilizing only one or a few resources. We report here the results of an empirical study whose aim was to test for a negative association between habitat niche breadth and foraging performance. As a model system to address this question, we used two highly abundant species of pit-building antlions varying in their habitat niche breadth: the habitat generalist Myrmeleon hyalinus, which inhabits a variety of soil types but occurs mainly in sandy soils, and the habitat specialist Cueta lineosa, which is restricted to light soils such as loess. Both species were able to discriminate between the two soils, with each showing a distinct and higher preference to the soil type providing higher prey capture success and characterizing its primary habitat-of-origin. As expected, only small differences in the foraging performances of the habitat generalist were evident between the two soils, while the performance of the habitat specialist was markedly reduced in the alternative sandy soil. Remarkably, in both soil types, the habitat generalist constructed pits and responded to prey faster than the habitat specialist, at least under the temperature range of this study. Furthermore, prey capture success of the habitat generalist was higher than that of the habitat specialist irrespective of the soil type or prey ant species encountered, implying a positive association between habitat niche-breadth and foraging performance. Alternatively, C. lineosa specialization to light soils does not necessarily confer upon its superiority in utilizing such habitats. We thus suggest that habitat specialization in C. lineosa is either an evolutionary dead-end, or, more likely, that this species' superiority in light soils can only be evident when considering additional niche axes.     

渔山岛岩礁基质潮间带大型底栖动物优势种生态位

2009年3月至2010年1月期间对渔山岛岩礁基质潮间带大型底栖动物进行定量采样调查,并获得大型底栖动物85种,筛选出全年取样获得优势种30种,隶属5门7纲24科。对获得的30个优势种以Shannon—Wiener指数为基础进行了生态位宽度测定,以Pianka重叠指数为基础进行了生态位重叠值分析,结果显示：潮间带大型底栖动物群落中优势种生态位宽度变化范围为0.18~1.94,值较高的有条纹隔贻贝、覆瓦小蛇螺、角偏顶蛤、日本笠藤壶、鳞笠藤壶和马氏毛粒蟹,均大于1.00,它们对环境适应的能力较强;各优势种的生态位重叠程度不均匀,在0~0.97之间,它们对群落环境资源的利用存在着交叉,潜在的种间竞争压力较大。以密度数据四次开方为基础,利用欧氏距离进行群落物种的系统聚类分析和非度量多维标度排序分析,结果均表明30个优势种可以分为三大类,即狭布种、泛化种和特有种。优势种生态位宽度、优势种之间的生态位重叠值与物种的分布与数量密切相关,生境相似程度高的物种聚类和排序距离就小,大型底栖动物主要通过在资源位上的分布、摄食类群和生活型等的差异缓解竞争。     

Immune defence strategies of generalist and specialist insect herbivores

Ecological immunology examines the adaptive responses of animals to pathogens in relation to other environmental factors and explores the consequences of trade-offs between investment in immune function and other life-history traits. Among species of herbivorous insects, diet breadth may vary greatly, with generalists consuming a wide variety of plant families and specialists restricted to a few species. Generalists may thus be exposed to a wider range of pathogens exerting stronger selection on the innate immune system. To examine whether this produces an increase in the robustness of the immune response, we compared larvae of the generalist herbivore Heliothis virescens and the specialist Heliothis subflexa challenged by entomopathogenic and non-pathogenic bacteria. Heliothis virescens larvae showed lower mortality, a lower number of recoverable bacteria, lower proliferation of haemocytes and higher phagocytic activity. These results indicate a higher tolerance to entomopathogenic bacteria by the generalist, which is associated with a more efficient cell-mediated immune response by mechanisms that differ between these closely related species. Our findings provide novel insights into the consequences of diet breadth and related environmental factors, which may be significant in further studies to understand the ecological forces and investment trade-offs that shape the evolution of innate immunity.     

Summer food of sympatric red fox and pine marten in the German Alps

Based on fecal analyses, we compared summer diet composition and trophic niche breadth for the sympatric red fox Vulpes vulpes (n=55 scats) and pine marten Martes martes (n=64) in the foothills of the German Alps. Mammals accounted for 41 and 51% of the consumed biomass by pine martens and red foxes, respectively, and no single mammal species exceeded 8% of the diet. The larger red fox consumed a wider range of prey sizes than the smaller pine marten, and both consumed large amounts of plants and also insects. Whereas the Levins index suggested that both predators have specialist feeding niches, the Shannon-Wiener index showed that both predators were relatively generalist. Despite its preliminary nature, our study suggests that a strict distinction between generalist and specialist trophic niches is not justified for medium-sized carnivores in the Alps, particularly as results greatly depend on the indices used.     

Contrasting carbon metabolism in saprotrophic and pathogenic microascalean fungi from Protea trees

Protea-associated Knoxdaviesia species grow on decaying inflorescences, yet are closely related to plant pathogens such as Ceratocystis albifundus. C. albifundus also infects Protea, but occupies a distinct niche. We investigated substrate utilization in two Knoxdaviesia saprotrophs, a generalist and a specialist, and the pathogen C. albifundus by integrating phenome and whole-genome data. On shared substrates, the generalist grew slightly better than its specialist counterpart, alluding to how it has maintained its Protea host range. C. albifundus grew on few substrates and had limited cell wall-degrading enzymes. It did not utilize sucrose, but may prefer soluble oligosaccharides. Nectar monosaccharides are likely important carbon sources for early colonizing Knoxdaviesia species. Once the inflorescence ages, they could switch to degrading cell wall components. C. albifundus likely uses its limited cell wall-degrading arsenal to gain access to plant cells and exploit internal resources. Overall, carbon metabolism and gene content in three related fungi reflected their ecological adaptations.     

Specialist versus generalist life histories and nucleotide diversity in Caenorhabditis nematodes

Species with broad ecological amplitudes with respect to a key focal resource, niche generalists, should maintain larger and more connected populations than niche specialists, leading to the prediction that nucleotide diversity will be lower and more subdivided in specialists relative to their generalist relatives. This logic describes the specialist-generalist variation hypothesis (SGVH). Some outbreeding species of Caenorhabditis nematodes use a variety of invertebrate dispersal vectors and have high molecular diversity. By contrast, Caenorhabditis japonica lives in a strict association and synchronized life cycle with its dispersal host, the shield bug Parastrachia japonensis, itself a diet specialist. Here, we characterize sequence variation for 20 nuclear loci to investigate how C. japonica''s life history shapes nucleotide diversity. We find that C. japonica has more than threefold lower polymorphism than other outbreeding Caenorhabditis species, but that local populations are not genetically disconnected. Coupled with its restricted range, we propose that its specialist host association contributes to a smaller effective population size and lower genetic variation than host generalist Caenorhabditis species with outbreeding reproductive modes. A literature survey of diverse organisms provides broader support for the SGVH. These findings encourage further testing of ecological and evolutionary hypotheses with comparative population genetics in Caenorhabditis and other taxa.     

THE EVOLUTION OF ENVIRONMENTAL TOLERANCE AND RANGE SIZE: A COMPARISON OF GEOGRAPHICALLY RESTRICTED AND WIDESPREAD MIMULUS

The geographic ranges of closely related species can vary dramatically, yet we do not fully grasp the mechanisms underlying such variation. The niche breadth hypothesis posits that species that have evolved broad environmental tolerances can achieve larger geographic ranges than species with narrow environmental tolerances. In turn, plasticity and genetic variation in ecologically important traits and adaptation to environmentally variable areas can facilitate the evolution of broad environmental tolerance. We used five pairs of western North American monkeyflowers to experimentally test these ideas by quantifying performance across eight temperature regimes. In four species pairs, species with broader thermal tolerances had larger geographic ranges, supporting the niche breadth hypothesis. As predicted, species with broader thermal tolerances also had more within‐population genetic variation in thermal reaction norms and experienced greater thermal variation across their geographic ranges than species with narrow thermal tolerances. Species with narrow thermal tolerance may be particularly vulnerable to changing climatic conditions due to lack of plasticity and insufficient genetic variation to respond to novel selection pressures. Conversely, species experiencing high variation in temperature across their ranges may be buffered against extinction due to climatic changes because they have evolved tolerance to a broad range of temperatures.     

Panmixia across elevation in thermally sensitive Andean dung beetles

Janzen's seasonality hypothesis predicts that organisms inhabiting environments with limited climatic variability will evolve a reduced thermal tolerance breadth compared with organisms experiencing greater climatic variability. In turn, narrow tolerance breadth may select against dispersal across strong temperature gradients, such as those found across elevation. This can result in narrow elevational ranges and generate a pattern of isolation by environment or neutral genetic differentiation correlated with environmental variables that are independent of geographic distance. We tested for signatures of isolation by environment across elevation using genome‐wide SNP data from five species of Andean dung beetles (subfamily Scarabaeinae) with well‐characterized, narrow thermal physiologies, and narrow elevational distributions. Contrary to our expectations, we found no evidence of population genetic structure associated with elevation and little signal of isolation by environment. Further, elevational ranges for four of five species appear to be at equilibrium and show no decay of genetic diversity at range limits. Taken together, these results suggest physiological constraints on dispersal may primarily operate outside of a stable realized niche and point to a lower bound on the spatial scale of local adaptation.     

Diet breadth and its relationship with genetic diversity and differentiation: the case of southern beech aphids (Hemiptera: Aphididae)

Herbivorous insect species with narrow diet breadth are expected to be more prone to genetic differentiation than insect species with a wider diet breadth. However, a generalist can behave as a local specialist if a single host-plant species is locally available, while a specialist can eventually behave as a generalist if its preferred host is not available. These problems can be addressed by comparing closely related species differing in diet breadth with overlapping distributions of insect and host populations. In this work, diet breadth, genetic diversity and population differentiation of congeneric aphid species from southern beech forests in Chile were compared. While at the species level no major differences in genetic diversity were found, a general trend towards higher genetic diversity as diet breadth increased was apparent. The aphid species with wider diet breadth, Neuquenaphis edwardsi (Laing), showed the highest genetic diversity, while the specialist Neuquenaphis staryi Quednau & Remaudière showed the lowest. These differences were less distinct when the comparisons were made in the same locality and over the same host. Comparison of allopatric populations indicates that genetic differentiation was higher for the specialists, Neuquenaphis similis Hille Ris Lambers and N. staryi, than for the generalist N. edwardsi. Over the same host at different locations, genetic differentiation among populations of N. edwardsi was higher than among populations of N. similis. The results support the assumption that specialists should show more pronounced genetic structuring than generalists, although the geographical distribution of host plants may be playing an important role.     

Habitat specialization of birds in the Czech Republic: comparison of objective measures with expert opinion

Capsule Expert‐based classification of bird species as habitat specialists and as generalists agrees with objective measures of species’ habitat requirements based on large‐scale monitoring data.

Aims To compare habitat specialization of 137 common bird species breeding in the Czech Republic using three different measures and to test their relationships to species’ abundance and habitat associations.

Methods Data on bird abundance and surveyed habitats were collected through a standardized monitoring scheme of common breeding species in the Czech Republic. From these data we calculated a quantitative species specialization index (SSI). Canonical correspondence analysis (CCA) was applied to calculate species’ habitat niche breadth and the level of association of each species to the main habitats. A panel of 11 local bird experts classified each species as habitat generalist or habitat specialist.

Results Species classified as habitat specialists by expert opinion showed higher habitat specialization according to the SSI, as well as according to CCA‐based habitat niche breadth. These species were also more closely associated with one of the main habitat types. These relationships were significant even after controlling for abundance.

Conclusions As expert opinion accords with the level of species’ habitat specialization expressed using two quantitative objective measures, we suggest that these characteristics reflect real interspecific variation in the breadth of habitat requirements in birds. Interspecific differences in habitat specialization are not caused solely by the variability in abundance among species.