Examination of Taxonomic Uncertainties Surrounding Brucella abortus bv. 7 by Phenotypic and Molecular Approaches

Brucella taxonomy is perpetually being reshuffled, at both the species and intraspecies levels. Biovar 7 of Brucella abortus was suspended from the Approved Lists of Bacterial Names Brucella classification in 1988, because of unpublished evidence that the reference strain 63/75 was a mixture of B. abortus biovars 3 and 5. To formally clarify the situation, all isolates previously identified as B. abortus bv. 7 in the AHVLA and ANSES strain collections were characterized by classical microbiological and multiple molecular approaches. Among the 14 investigated strains, including strain 63/75, only four strains, isolated in Kenya, Turkey, and Mongolia, were pure and showed a phenotypic profile in agreement with the former biovar 7, particularly agglutination with both anti-A/anti-M monospecific sera. These results were strengthened by molecular strategies. Indeed, genus- and species-specific methods allowed confirmation that the four pure strains belonged to the B. abortus species. The combination of most approaches excluded their affiliation with the recognized biovars (biovars 1 to 6 and 9), while some suggested that they were close to biovar 3.These assays were complemented by phylogenetic and/or epidemiological methods, such as multilocus sequence analysis (MLSA) and variable-number tandem repeat (VNTR) analysis. The results of this polyphasic investigation allow us to propose the reintroduction of biovar 7 into the Brucella classification, with at least three representative strains. Interestingly, the Kenyan strain, sharing the same biovar 7 phenotype, was genetically divergent from other three isolates. These discrepancies illustrate the complexity of Brucella taxonomy. This study suggests that worldwide collections could include strains misidentified as B. abortus bv. 7, and it highlights the need to verify their real taxonomic position.     

Species delimitation and phylogeny in the genus Nasutitermes (Termitidae: Nasutitermitinae) in French Guiana

Species delimitation and identification can be arduous for taxa whose morphologic characters are easily confused, which can hamper global biodiversity assessments and pest species management. Exploratory methods of species delimitation that use DNA sequence as their primary information source to establish group membership and estimate putative species boundaries are useful approaches, complementary to traditional taxonomy. Termites of the genus Nasutitermes make interesting models for the application of such methods. They are dominant in Neotropical primary forests but also represent major agricultural and structural pests. Despite the prevalence, pivotal ecological role and economical impact of this group, the taxonomy of Nasutitermes species mainly depends on unreliable characters of soldier external morphology. Here, we generated robust species hypotheses for 79 Nasutitermes colonies sampled throughout French Guiana without any a priori knowledge of species affiliation. Sequence analysis of the mitochondrial cytochrome oxidase II gene was coupled with exploratory species‐delimitation tools, using the automatic barcode gap discovery method (ABGD) and a generalized mixed Yule‐coalescent model (GMYC) to propose primary species hypotheses (PSHs). PSHs were revaluated using phylogenetic analyses of two more loci (mitochondrial 16S rDNA and nuclear internal transcribed spacer 2) leading to 16 retained secondary species hypotheses (RSSH). Seven RSSHs, represented by 44/79 of the sampled colonies, were morphologically affiliated to species recognized as pests in the Neotropics, where they represent a real invasive pest potential in the context of growing ecosystem anthropization. Multigenic phylogenies based on combined alignments (1426–1784 bp) were also reconstructed to identify ancestral ecological niches and major‐pest lineages, revealing that Guyanese pest species do not form monophyletic groups.     

The effect of mating system on invasiveness: some genetic load may be advantageous when invading new environments

The role of adaptation in determining invasion success has been acknowledged recently, notably through the accumulation of case studies of rapid evolution during bioinvasions. Despite this growing body of empirical evidence, there is still a need to develop the theoretical background of invasions with adaptation. Specifically, the impact of mating system on the dynamics of adaptation during invasion of a new environment remains only partially understood. Here, we analyze a simulation demo-genetic model of bioinvasion accounting for partial asexuality rates. We simulate two levels of recurrent immigration from a source population at mutation–drift–selection equilibrium to a new empty environment with a different adaptive landscape (black-hole sink). Adaptation relies on a quantitative trait coded explicitly by 10 loci under mutation, selection and genetic drift. Using this model, we confirm previous results on the positive effects on invasiveness of migration, mutation and similarity of local phenotypic optima. We further show how the invasion dynamics of the introduced population is affected by the rate of asexuality. Purely asexual species have lower invasion success in terms of probability and time to invasion than species with other mating systems. Among species with mixed mating systems, the greatest invasiveness is observed for species with high asexual rates. We suggest that this pattern is due to inflated genetic variance in the source population through the Hill-Robertson effect (i.e., clonal interference). An interesting consequence is that species with the highest genetic load in their source environment have greatest invasiveness in the new environment.     

A comparative analysis of dispersal syndromes in terrestrial and semi‐terrestrial animals

Dispersal, the behaviour ensuring gene flow, tends to covary with a number of morphological, ecological and behavioural traits. While species‐specific dispersal behaviours are the product of each species’ unique evolutionary history, there may be distinct interspecific patterns of covariation between dispersal and other traits (‘dispersal syndromes’) due to their shared evolutionary history or shared environments. Using dispersal, phylogeny and trait data for 15 terrestrial and semi‐terrestrial animal Orders (> 700 species), we tested for the existence and consistency of dispersal syndromes across species. At this taxonomic scale, dispersal increased linearly with body size in omnivores, but decreased above a critical length in herbivores and carnivores. Species life history and ecology significantly influenced patterns of covariation, with higher phylogenetic signal of dispersal in aerial dispersers compared with ground dwellers and stronger evidence for dispersal syndromes in aerial dispersers and ectotherms, compared with ground dwellers and endotherms. Our results highlight the complex role of dispersal in the evolution of species life‐history strategies: good dispersal ability was consistently associated with high fecundity and survival, and in aerial dispersers it was associated with early maturation. We discuss the consequences of these findings for species evolution and range shifts in response to future climate change.     

Environmental Drivers of the Canadian Arctic Megabenthic Communities

Environmental gradients and their influence on benthic community structure vary over different spatial scales; yet, few studies in the Arctic have attempted to study the influence of environmental gradients of differing spatial scales on megabenthic communities across continental-scales. The current project studied for the first time how megabenthic community structure is related to several environmental factors over 2000 km of the Canadian Arctic, from the Beaufort Sea to northern Baffin Bay. Faunal trawl samples were collected between 2007 and 2011 at 78 stations from 30 to 1000 m depth and patterns in biomass, density, richness, diversity, and taxonomic composition were examined in relation to indirect/spatial gradients (e.g., depth), direct gradients (e.g., bottom oceanographic variables), and resource gradients (e.g., food supply proxies). Six benthic community types were defined based on their biomass-based taxonomic composition. Their distribution was significantly, but moderately, associated with large-scale (100–1000 km) environmental gradients defined by depth, physical water properties (e.g., bottom salinity), and meso-scale (10–100 km) environmental gradients defined by substrate type (hard vs. soft) and sediment organic carbon content. We did not observe a strong decline of bulk biomass, density and richness with depth or a strong increase of those community characteristics with food supply proxies, contrary to our hypothesis. We discuss how local- to meso-scale environmental conditions, such as bottom current regimes and polynyas, sustain biomass-rich communities at specific locations in oligotrophic and in deep regions of the Canadian Arctic. This study demonstrates the value of considering the scales of variability of environmental gradients when interpreting their relevance in structuring of communities.     

Long-Distance Wind-Dispersal of Spores in a Fungal Plant Pathogen: Estimation of Anisotropic Dispersal Kernels from an Extensive Field Experiment

Given its biological significance, determining the dispersal kernel (i.e., the distribution of dispersal distances) of spore-producing pathogens is essential. Here, we report two field experiments designed to measure disease gradients caused by sexually- and asexually-produced spores of the wind-dispersed banana plant fungus Mycosphaerella fijiensis. Gradients were measured during a single generation and over 272 traps installed up to 1000 m along eight directions radiating from a traceable source of inoculum composed of fungicide-resistant strains. We adjusted several kernels differing in the shape of their tail and tested for two types of anisotropy. Contrasting dispersal kernels were observed between the two types of spores. For sexual spores (ascospores), we characterized both a steep gradient in the first few metres in all directions and rare long-distance dispersal (LDD) events up to 1000 m from the source in two directions. A heavy-tailed kernel best fitted the disease gradient. Although ascospores distributed evenly in all directions, average dispersal distance was greater in two different directions without obvious correlation with wind patterns. For asexual spores (conidia), few dispersal events occurred outside of the source plot. A gradient up to 12.5 m from the source was observed in one direction only. Accordingly, a thin-tailed kernel best fitted the disease gradient, and anisotropy in both density and distance was correlated with averaged daily wind gust. We discuss the validity of our results as well as their implications in terms of disease diffusion and management strategy.     

Rapid parallel flow cytometry assays of active GTPases using effector beads

We describe a rapid assay for measuring the cellular activity of small guanine triphosphatases (GTPases) in response to a specific stimulus. Effector-functionalized beads are used to quantify in parallel multiple GTP-bound GTPases in the same cell lysate by flow cytometry. In a biologically relevant example, five different Ras family GTPases are shown for the first time to be involved in a concerted signaling cascade downstream of receptor ligation by Sin Nombre hantavirus.     

Unclosed HIV-1 Capsids Suggest a Curled Sheet Model of Assembly

The RNA genome of retroviruses is encased within a protein capsid. To gather insight into the assembly and function of this capsid, we used electron cryotomography to image human immunodeficiency virus (HIV) and equine infectious anemia virus (EIAV) particles. While the majority of viral cores appeared closed, a variety of unclosed structures including rolled sheets, extra flaps, and cores with holes in the tip were also seen. Simulations of nonequilibrium growth of elastic sheets recapitulated each of these aberrations and further predicted the occasional presence of seams, for which tentative evidence was also found within the cryotomograms. To test the integrity of viral capsids in vivo, we observed that ~ 25% of cytoplasmic HIV complexes captured by TRIM5α had holes large enough to allow internal green fluorescent protein (GFP) molecules to escape. Together, these findings suggest that HIV assembly at least sometimes involves the union in space of two edges of a curling sheet and results in a substantial number of unclosed forms.     

Identification of Tribbles-1 as a Novel Binding Partner of Foxp3 in Regulatory T Cells

In a previous study, we identified TRIB1, a serine-threonine kinase-like molecule, as a biomarker of chronic antibody-mediated rejection of human kidneys when measured in peripheral blood mononuclear cells. Here, we focused our analysis on a specific subset of peripheral blood mononuclear cells that play a dominant role in regulating immune responses in health and disease, so-called CD4⁺CD25⁺Foxp3⁺ regulatory T cells (Tregs). We isolated both human and murine Treg and non-Treg counterparts and analyzed TRIB1 and Foxp3 mRNA expression by quantitative PCR on the freshly isolated cells or following 24 h of activation. Physical interaction between the human TRIB1 and Foxp3 proteins was analyzed in live cell lines by protein complementation assay using both flow cytometry and microscopy and confirmed in primary freshly isolated human CD4⁺CD25^hiCD127⁻ Tregs by co-immunoprecipitation. Both TRIB1 and Foxp3 were expressed at significantly higher levels in Tregs than in their CD4⁺CD25⁻ counterparts (p < 0.001). Moreover, TRIB1 and Foxp3 mRNA levels correlated tightly in Tregs (Spearman r = 1.0; p < 0.001, n = 7), but not in CD4⁺CD25⁻ T cells. The protein complementation assay revealed a direct physical interaction between TRIB1 and Foxp3 in live cells. This interaction was impaired upon deletion of the TRIB1 N-terminal but not the C-terminal domain, suggesting an interaction in the nucleus. This direct interaction within the nucleus was confirmed in primary human Tregs by co-immunoprecipitation. These data show a direct relationship between TRIB1 and Foxp3 in terms of their expression and physical interaction and highlight Tribbles-1 as a novel binding partner of Foxp3 in Tregs.