Bacterial communities of Bartonella-positive fleas: diversity and community assembly patterns

We investigated the bacterial communities of nine Bartonella-positive fleas (n = 6 Oropsylla hirsuta fleas and n = 3 Oropsylla montana fleas), using universal primers, clone libraries, and DNA sequencing. DNA sequences were used to classify bacteria detected in a phylogenetic context, to explore community assembly patterns within individual fleas, and to survey diversity patterns in dominant lineages.     

Latitudinal gradients in diversity: real patterns and random models

Mid-domain models have been argued lo provide a default explanation for the best known spatial pattern in biodiversity, namely the latitudinal gradient in species richness. These models assume no environmental gradients, but merely a random latitudinal association between the size and placement of the geographic ranges of species. A mid-domain peak in richness is generated because when the latitudinal extents of species in a given taxonomic group are bounded to north and south, perhaps by a physical constraint such as a continental edge or perhaps by a climatic constraint such as a critical temperature or precipitation threshold, then the number of ways in which ranges can be distributed changes systematically between the bounds. In addition, such models make predictions about latitudinal variation in the latitudinal extents of the distributions of species, and in beta diversity (the spatial turnover in species identities). Here we test how well five mid-domain models predict observed latitudinal patterns of species richness, latitudinal extent and beta diversity in two groups of birds, parrots and woodpeckers, across the New World. Whilst both groups exhibit clear gradients in richness and beta diversity and the general trend in species richness is acceptably predicted (but not accurately, unless substantial empirical information is assumed), the fit of these models is uniformly poor for beta diversity and latitudinal range extent. This suggests either that, at least for these data, as presently formulated mid-domain models are too simplistic, or that in practice the mid-domain effect is not significant in determining geographical variation in diversity.     

Comparing Allee effect-based and dispersal-based neutral models for species abundance distribution patterns

Dispersal is important for biodiversity maintenance in both neutral and niche theories. However, little is known about the potential role of Allee effect at the community level. In the present study, we developed neutral models for quantifying the separate and joint influences of the Allee effect and dispersal process, respectively, on species abundance distribution (SAD) patterns. Tree census data from Barro Colorado Island (BCI), Panama were used as the case to compare different neutral SAD models. Results showed that Allee effects were not detected in the BCI tree SAD curve. By contrast, the neutral models with the incorporation of dispersal process (including both immigration and emigration) can remarkably improve the fitting power of neutral models on the BCI tree SAD curve. Finally, even though the influence is not detectable, the Allee effect-based SAD models still might be alternative SAD models for model comparison and null hypothesis testing.     

The community and ecosystem consequences of intraspecific diversity: a meta‐analysis

Understanding the relationships between biodiversity and ecosystem functioning has major implications. Biodiversity–ecosystem functioning relationships are generally investigated at the interspecific level, although intraspecific diversity (i.e. within‐species diversity) is increasingly perceived as an important ecological facet of biodiversity. Here, we provide a quantitative and integrative synthesis testing, across diverse plant and animal species, whether intraspecific diversity is a major driver of community dynamics and ecosystem functioning. We specifically tested (i) whether the number of genotypes/phenotypes (i.e. intraspecific richness) or the specific identity of genotypes/phenotypes (i.e. intraspecific variation) in populations modulate the structure of communities and the functioning of ecosystems, (ii) whether the ecological effects of intraspecific richness and variation are strong in magnitude, and (iii) whether these effects vary among taxonomic groups and ecological responses. We found a non‐linear relationship between intraspecific richness and community and ecosystem dynamics that follows a saturating curve shape, as observed for biodiversity–function relationships measured at the interspecific level. Importantly, intraspecific richness modulated ecological dynamics with a magnitude that was equal to that previously reported for interspecific richness. Our results further confirm, based on a database containing more than 50 species, that intraspecific variation also has substantial effects on ecological dynamics. We demonstrated that the effects of intraspecific variation are twice as high as expected by chance, and that they might have been underestimated previously. Finally, we found that the ecological effects of intraspecific variation are not homogeneous and are actually stronger when intraspecific variation is manipulated in primary producers than in consumer species, and when they are measured at the ecosystem rather than at the community level. Overall, we demonstrated that the two facets of intraspecific diversity (richness and variation) can both strongly affect community and ecosystem dynamics, which reveals the pivotal role of within‐species biodiversity for understanding ecological dynamics.     

Mid-domain models as predictors of species diversity patterns: bathymetric diversity gradients in the deep sea

Geometric constraints represent a class of null models that describe how species diversity may vary between hard boundaries that limit geographic distributions. Recent studies have suggested that a number of large scale biogeographic patterns of diversity (e.g. latitude, altitude, depth) may reflect boundary constraints. However, few studies have rigorously tested the degree to which mid-domain null predictions match empirical patterns or how sensitive the null models are to various assumptions. We explore how variation in the assumptions of these models alter null depth ranges and consequently bathymetric variation in diversity, and test the extent to which bathymetric patterns of species diversity in deep sea gastropods, bivalves, and polychaetes match null predictions based on geometric constraints.
Range–size distributions and geographic patterns of diversity produced by these null models are sensitive to the relative position of the hard boundaries, the specific algorithms used to generate range sizes, and whether species are continuously or patchily distributed between range end points. How well empirical patterns support null expectations is highly dependent on these assumptions. Bathymetric patterns of species diversity for gastropods, bivalves and polychaetes differ substantially from null expectations suggesting that geometric constraints do not account for diversity–depth patterns in the deep sea benthos.     

Global patterns of diversity and community structure in marine bacterioplankton

Because of their small size, great abundance and easy dispersal, it is often assumed that marine planktonic microorganisms have a ubiquitous distribution that prevents any structured assembly into local communities. To challenge this view, marine bacterioplankton communities from coastal waters at nine locations distributed world-wide were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes, used as operational taxonomic units (OTU). Our survey and analyses show that there were marked differences in the composition and richness of OTUs between locations. Remarkably, the global marine bacterioplankton community showed a high degree of endemism, and conversely included few cosmopolitan OTUs. Our data were consistent with a latitudinal gradient of OTU richness. We observed a positive relationship between the relative OTU abundances and their range of occupation, i.e. cosmopolitans had the largest population sizes. Although OTU richness differed among locations, the distributions of the major taxonomic groups represented in the communities were analogous, and all local communities were similarly structured and dominated by a few OTUs showing variable taxonomic affiliations. The observed patterns of OTU richness indicate that similar evolutionary and ecological processes structured the communities. We conclude that marine bacterioplankton share many of the biogeographical and macroecological features of macroscopic organisms. The general processes behind those patterns are likely to be comparable across taxa and major global biomes.     

Assembly rules and community models for unicellular organisms: patterns in diatoms of boreal streams

1. Many studies have addressed either community models (e.g. Clementsian versus Gleasonian gradients) or assembly rules (e.g. nestedness, checkerboards) for higher plant and animal communities, but very few studies have examined different non‐random distribution patterns simultaneously with the same data set. Even fewer studies have addressed generalities in the distribution patterns of unicellular organisms, such as diatoms. 2. We studied non‐randomness in the spatial distribution and community composition of stream diatoms. Our data consisted of diatom surveys from 47 boreal headwater streams and small rivers in northern Finland. Our analytical approaches included ordinations, cluster analysis, null model analyses, and associated randomisation tests. 3. Stream diatom communities did not follow discrete Clementsian community types, where multiple species occur exclusively in a single community type. Rather, diatom species showed rather individualistic responses, leading to continuous Gleasonian variability in community composition. 4. Although continuous variability was the dominating pattern in the data, diatoms also showed significant nestedness and less overlap in species distribution than expected by chance. However, these patterns were probably only secondary signals from species’ individualistic responses to the environment. 5. Although unicellular organisms, such as diatoms, differ from multicellular organisms in several biological characteristics, they nevertheless appear to show largely similar non‐random distribution patterns previously found for higher plants and metazoans.     

Reconciling classical and individual-based approaches in theoretical population ecology: a protocol for extracting population parameters from individual-based models

The two main approaches in theoretical population ecology-the classical approach using differential equations and the approach using individual-based modeling-seem to be incompatible. Linked to these two approaches are two different timescales: population dynamics and behavior or physiology. Thus, the question of the relationship between classical and individual-based approaches is related to the question of the mutual relationship between processes on the population and the behavioral timescales. We present a simple protocol that allows the two different approaches to be reconciled by making explicit use of the fact that processes operating on two different timescales can be treated separately. Using an individual-based model of nomadic birds as an example, we extract the population growth rate by deactivating all demographic processes-in other words, the individuals behave but do not age, die, or reproduce. The growth rate closely matches the logistic growth rate for a wide range of parameters. The implications of this result and the conditions for applying the protocol to other individual-based models are discussed. Since in physics the technique of separating timescales is linked to some concepts of self-organization, we believe that the protocol will also help to develop concepts of self-organization in ecology.     

Abundance, diversity and body size: patterns from a grassland arthropod community

1. The empirical relationships among body size, species richness and number of individuals may give insight into the factors controlling species diversity and the relative abundances of species. To determine these relationships, we sampled the arthropods of grasslands and savannahs at Cedar Creek, MN using sweep nets (90 525 individuals of 1225 species) and pitfall traps (12 721 individuals of 92 species). Specimens were identified, enumerated and measured to determine body size.
2. Both overall and within abundant taxonomic orders, species richness and numbers of individuals peaked at body sizes intermediate for each group. Evolution could create unimodal diversity patterns by random diversification around an ancestral body size or from size-dependent fitness differences. Local processes such as competition or predation could also create unimodal diversity distributions.
3. The average body size of a species depended significantly on its taxonomic order, but on contemporary trophic role only within the context of taxonomic order.
4. Species richness ( S _i) within size classes was related to the number of individuals ( I _i) as S _i =  I i^0·5. This relationship held across a 100 000-fold range of body sizes. Within size classes, abundance distributions of size classes were all similar power functions. A general rule of resource division, together with similar minimum population sizes, is sufficient to generate the relationship between species richness and number of individuals.
5. Smaller bodied species had slightly shallower abundance distributions and may, in general, persist at lower densities than larger species.
6. Our results suggest there may be fewer undescribed small arthropod species than previously thought and that most undescribed species will be smaller than arthropods.     

Comparing patterns of taxonomic,functional and phylogenetic diversity in reef coral communities

Coral Reefs - Biodiversity defines the variety of living organisms on this planet and is often quantified by the total number of species. However, species richness is insufficient in accounting for...     

Effects of diversity on diversity: consequences of competition and facilitation

Diversity in one group of species or genotypes is often correlated with diversity in a second group – prominent examples including native vs exotic species, and genetic diversity in a focal species vs species diversity in the rest of the community. I used simulation models to investigate the roles of competition and facilitation among species or genotypes in creating diversity–diversity relationships, with a focus on facilitation, which has received little theoretical attention. When competitive interactions dominate, increasing diversity in one group reduces diversity in the second group via filling of available niche space. Facilitation can create positive diversity–diversity relationships via a sampling effect, whereby a strong facilitator of the second group is more likely to be present as diversity increases in the first group, and also via one group acting as a source of biotic heterogeneity (i.e. diversifying selection) on the second group. However, the biotic heterogeneity effect is expected only under restricted conditions – with asymmetric facilitation, only during a transient period, or only over a small range of species diversity levels – and therefore seems unlikely to operate within trophic levels in natural communities. More generally, the simultaneous operation of competition and facilitation results in several different diversity–diversity relationships and underlying mechanisms. The results clarify the potential roles of positive and negative interactions in creating diversity–diversity relationships, and in determining the outcome of community dynamics in general. This study also highlights some important difficulties in incorporating facilitation into ecological theory for communities with many species.     

Towards global patterns in the diversity and community structure of ectomycorrhizal fungi

Global species richness patterns of soil micro-organisms remain poorly understood compared to macro-organisms. We use a global analysis to disentangle the global determinants of diversity and community composition for ectomycorrhizal (EcM) fungi-microbial symbionts that play key roles in plant nutrition in most temperate and many tropical forest ecosystems. Host plant family has the strongest effect on the phylogenetic community composition of fungi, whereas temperature and precipitation mostly affect EcM fungal richness that peaks in the temperate and boreal forest biomes, contrasting with latitudinal patterns of macro-organisms. Tropical ecosystems experience rapid turnover of organic material and have weak soil stratification, suggesting that poor habitat conditions may contribute to the relatively low richness of EcM fungi, and perhaps other soil biota, in most tropical ecosystems. For EcM fungi, greater evolutionary age and larger total area of EcM host vegetation may also contribute to the higher diversity in temperate ecosystems. Our results provide useful biogeographic and ecological hypotheses for explaining the distribution of fungi that remain to be tested by involving next-generation sequencing techniques and relevant soil metadata.     

Spatial patterns of diatom diversity and community structure in ancient Lake Ohrid

For effective lakes’ management, high-frequent water quality data on a synoptic scale are essential. The aim of this study is to test the suitability of the latest generation of satellite sensors to provide information on lake water quality parameters for the five largest Italian subalpine lakes. In situ data of phytoplankton composition, chlorophyll-a (chl-a) concentration and water reflectance were used in synergy with satellite observations to map some algal blooms in 2016. Chl-a concentration maps were derived from satellite data by applying a bio-optical model to satellite data, previously corrected for atmospheric effects. Results were compared with in situ data, showing good agreement. The shape and magnitude of water reflectance from different satellite data were consistent. Output chl-a concentration maps, show the distribution within each lake during blooming events, suggesting a synoptic view is required for these events monitoring. Maps show the dynamic of bloom events with concentration increasing from 2 up to 7 mg m^?3 and dropping again to initial value in less than 20 days. Latest generation sensors were shown to be valuable tools for lakes monitoring, thanks to frequent, free of charge data availability over long time periods.     

Theozymes and compuzymes: theoretical models for biological catalysis

A theozyme is a theoretical enzyme constructed by computing the optimal geometry for transition-state stabilization by functional groups. It is created in order to permit quantitative assessment of catalytic function. Theozymes have been used to elucidate the role of transition-state stabilization in the mechanisms underlying enzyme- and antibody-catalyzed hydroxyepoxide cyclizations, eliminations and decarboxylations, peptide and ester hydrolyses, and pericyclic and radical reactions. The enzymes studied include orotodine monophosphate decarboxylase, HIV protease and ribonucleotide reductase.     

Legume diversity patterns in west central Africa: influence of species biology on distribution models

Objectives

Species Distribution Models (SDMs) are used to produce predictions of potential Leguminosae diversity in West Central Africa. Those predictions are evaluated subsequently using expert opinion. The established methodology of combining all SDMs is refined to assess species diversity within five defined vegetation types. Potential species diversity is thus predicted for each vegetation type respectively. The primary aim of the new methodology is to define, in more detail, areas of species richness for conservation planning.

Methodology

Using Maxent, SDMs based on a suite of 14 environmental predictors were generated for 185 West Central African Leguminosae species, each categorised according to one of five vegetation types: Afromontane, coastal, non-flooded forest, open formations, or riverine forest. The relative contribution of each environmental variable was compared between different vegetation types using a nonparametric Kruskal-Wallis analysis followed by a post-hoc Kruskal-Wallis Paired Comparison contrast. Legume species diversity patterns were explored initially using the typical method of stacking all SDMs. Subsequently, five different ensemble models were generated by partitioning SDMs according to vegetation category. Ecological modelers worked with legume specialists to improve data integrity and integrate expert opinion in the interpretation of individual species models and potential species richness predictions for different vegetation types.

Results/Conclusions

Of the 14 environmental predictors used, five showed no difference in their relative contribution to the different vegetation models. Of the nine discriminating variables, the majority were related to temperature variation. The set of variables that played a major role in the Afromontane species diversity model differed significantly from the sets of variables of greatest relative important in other vegetation categories. The traditional approach of stacking all SDMs indicated overall centers of diversity in the region but the maps indicating potential species richness by vegetation type offered more detailed information on which conservation efforts can be focused.     

Ecological consequences of genetic diversity

Understanding the ecological consequences of biodiversity is a fundamental challenge. Research on a key component of biodiversity, genetic diversity, has traditionally focused on its importance in evolutionary processes, but classical studies in evolutionary biology, agronomy and conservation biology indicate that genetic diversity might also have important ecological effects. Our review of the literature reveals significant effects of genetic diversity on ecological processes such as primary productivity, population recovery from disturbance, interspecific competition, community structure, and fluxes of energy and nutrients. Thus, genetic diversity can have important ecological consequences at the population, community and ecosystem levels, and in some cases the effects are comparable in magnitude to the effects of species diversity. However, it is not clear how widely these results apply in nature, as studies to date have been biased towards manipulations of plant clonal diversity, and little is known about the relative importance of genetic diversity vs. other factors that influence ecological processes of interest. Future studies should focus not only on documenting the presence of genetic diversity effects but also on identifying underlying mechanisms and predicting when such effects are likely to occur in nature.     

Sample pooling obscures diversity patterns in intertidal ciliate community composition and structure

The aim of this study was to assess the effect of sample pooling on the portrayal of ciliate community structure and composition in intertidal sediment samples. Molecular ciliate community profiles were obtained from nine biological replicates distributed in three discrete sampling plots and from samples that were pooled prior to RNA extraction using terminal restriction fragment polymorphism (T-RFLP) analyses of SSU rRNA. Comparing the individual replicates of one sampling plot with each other, we found a differential variability among the individual biological replicates. T-RFLP profiles of pooled samples displayed a significantly different community composition compared with the cumulative individual biological replicate samples. We conclude that sample pooling obscures diversity patterns in ciliate and possibly also other microbial eukaryote studies. However, differences between pooled samples and replicates were less pronounced when community structure was analyzed. We found that the most abundant T-RFLP peaks were generally shared between biological replicates and pooled samples. Assuming that the most abundant taxa in an ecosystem under study are also the ones driving ecosystem processes, sample pooling may still be effective for the analyses of ecological key players.