Mapping the root systems of individual trees in a natural community using genotyping-by-sequencing

•The architecture of root systems is an important driver of plant fitness, competition and ecosystem processes. However, the methodological difficulty of mapping roots hampers the study of these processes. Existing approaches to match individual plants to belowground samples are low throughput and species specific. Here, we developed a scalable sequencing-based method to map the root systems of individual trees across multiple species. We successfully applied it to a tropical dry forest community in the Brazilian Caatinga containing 14 species. • We sequenced all 42 individual shrubs and trees in a 14 × 14 m plot using double-digest restriction site-associated sequencing (ddRADseq). We identified species-specific markers and individual-specific haplotypes from the data. We matched these markers to the ddRADseq data from 100 mixed root samples from across the centre (10 × 10 m) of the plot at four different depths using a newly developed R package. • We identified individual root samples for all species and all but one individual. There was a strong significant correlation between belowground and aboveground size measurements, and we also detected significant species-level root-depth preference for two species. • The method is more scalable and less labour intensive than the current techniques and is broadly applicable to ecology, forestry and agricultural biology

Molecular phylogenetics and temporal diversification in the genus Aeromonas based on the sequences of five housekeeping genes

Several approaches have been developed to estimate both the relative and absolute rates of speciation and extinction within clades based on molecular phylogenetic reconstructions of evolutionary relationships, according to an underlying model of diversification. However, the macroevolutionary models established for eukaryotes have scarcely been used with prokaryotes. We have investigated the rate and pattern of cladogenesis in the genus Aeromonas (γ-Proteobacteria, Proteobacteria, Bacteria) using the sequences of five housekeeping genes and an uncorrelated relaxed-clock approach. To our knowledge, until now this analysis has never been applied to all the species described in a bacterial genus and thus opens up the possibility of establishing models of speciation from sequence data commonly used in phylogenetic studies of prokaryotes. Our results suggest that the genus Aeromonas began to diverge between 248 and 266 million years ago, exhibiting a constant divergence rate through the Phanerozoic, which could be described as a pure birth process

Transitions between biomes are common and directional in Bombacoideae (Malvaceae)

This is the final version. Available from Wiley via the DOI in this record.Aim: To quantify evolutionary transitions between tropical evergreen rain forest and seasonally dry biomes, to test whether biome transitions affect lineage diversification and to examine the robustness of these results to methodological choices. Location: The tropics. Time period: The Cenozoic. Major taxa studied: The plant subfamily Bombacoideae (Malvaceae). Methods: We inferred ancestral biomes based on a fossil-dated molecular phylogeny of 103 species (59% of the clade) and recorded the number of transitions among biomes using biogeographical stochastic mapping based on the dispersal-extinction-cladogenesis model. We then estimated diversification rates using state-specific speciation and extinction rate (SSE) methods. Furthermore, we tested the sensitivity of the results to model choice, phylogenetic uncertainty, measurement error and biome definition. Results: We found numerous transitions from evergreen rain forest to seasonally dry biomes, and fewer in the opposite direction. These results were robust to methodological choices. Biome type did not influence diversification rates, although this result was subject to uncertainty, especially related to model choice and biome definition. Main conclusions: Our results contradict the idea of evolutionary biome conservatism in Bombacoideae, and support previous findings that evergreen rain forests serve as a source for the flora of seasonally dry biomes. The impact of biome classification and biome definition on the results suggest caution when using a biome concept for biogeographical reconstruction and diversification rate analysis.German Research FoundationKnut and Alice Wallenberg FoundationSwedish Foundation for Strategic ResearchRoyal Botanic GardensKew. CDBSwedish Research Counci

Mapping the root systems of individual trees in a natural community using genotyping-by-sequencing.

This is the final version. Available from Wiley via the DOI in this record.The architecture of root systems is an important driver of plant fitness, competition and ecosystem processes. However, the methodological difficulty of mapping roots hampers the study of these processes. Existing approaches to match individual plants to belowground samples are low throughput and species specific. Here, we developed a scalable sequencing-based method to map the root systems of individual trees across multiple species. We successfully applied it to a tropical dry forest community in the Brazilian Caatinga containing 14 species. We sequenced all 42 individual shrubs and trees in a 14 × 14 m plot using double-digest restriction site-associated sequencing (ddRADseq). We identified species-specific markers and individual-specific haplotypes from the data. We matched these markers to the ddRADseq data from 100 mixed root samples from across the centre (10 × 10 m) of the plot at four different depths using a newly developed R package. We identified individual root samples for all species and all but one individual. There was a strong significant correlation between belowground and aboveground size measurements, and we also detected significant species-level root-depth preference for two species. The method is more scalable and less labour intensive than the current techniques and is broadly applicable to ecology, forestry and agricultural biology.Natural Environment Research Council (NERC)Natural Environment Research Council (NERC)Fundação de Amparo à Pesquisa do Estado de São Paul

Phytogeographical patterns of dry forests sensu stricto in northern Minas Gerais State, Brazil

The Deciduous Complex that occurs in northern Minas Gerais State, Brazil, raises questions about the floristic affinities of these formations in relation to neighboring phytogeographical domains. Little is known about the identity of the seasonal forest formations that comprise this complex, or about its relationships to abiotic components, such as soils, topography and climate. This study aimed to recognize the patterns of floristic similarity of all studied fragments of dry forest of northern Minas Gerais with soil and climate attributes, based on the available database. Cluster analysis indicated the existence of two floristic groups that had clear associations with either the Koppen's BSh (semi-arid) or Aw (seasonal tropical) climates. Likewise, the subdivisions of these groups showed clear associations with the dominant soil classes in the region. The Red-Yellow Latosol is the dominant soil classes in the BSh climatic domain, seconded by alluvial areas associated with Fluvic Neosols. The Aw domain comprised a much varied set of soils: Nitosols, Argisols, Cambisols and Litholic Neosols, most derived from the Bambuí limestone/slate formation. The ecotonal nature of northern Minas Gerais State provides a complex interaction between the flora of neighboring phytogeographical domains. This, allied to pedogeomorphological factors, allowed a better understanding of the effects of late Quaternary climate changes for the Deciduous Complex evolution. We conclude that the Latosols under present-day semi-arid climates (BSh) are relicts of former wetter climates, during which humid forest (semideciduous) expansion took place. Later, these semideciduous forests were subjected to a much drier climate, when selection for deciduousness led to the present-days Deciduous Complex scenario

Multi-antigen print immunoassay (MAPIA)-based evaluation of novel recombinant Leishmania infantum antigens for the serodiagnosis of canine visceral leishmaniasis

Background: Domestic dogs are the principal reservoir hosts of Leishmania infantum in regions where visceral leishmaniasis (VL) is endemic. Although serologic methods are frequently used for the screening of infected dogs, antibody-based tests require further assessment, due to lack of sensitivity and specificity. In this study, we employed a multi-antigen printing immunoassay (MAPIA) to compare the antibody responses to novel recombinant proteins of L. infantum with the potential for the detection of canine VL. Findings: MAPIA strips were prepared employing 12 recombinant proteins. Antibody reactivity to these antigens was compared using a panel of sera collected from clinically asymptomatic (n = 16) and symptomatic (n = 41) culture-positive animals. Our findings showed that the canine immune response to antigen differs between dogs and depends on infection status. Using this screening assay, when five out of the 12 antigens were combined, an overall 81% detection rate of L. infantum-infected dogs was achieved. Conclusions: We conclude that MAPIA is an effective screening tool to rapidly select multiple antigens of diagnostic utility to be used in a more sensitive point of care diagnostic test such as the Dual-Path Platform (DPP) multiplex test for the rapid detection of infected dogs

Low prevalence of H. pylori Infection in HIV-Positive Patients in the Northeast of Brazil

<p>Abstract</p> <p>Background</p> <p>This study conducted in Northeastern Brazil, evaluated the prevalence of <it>H. pylori </it>infection and the presence of gastritis in HIV-infected patients.</p> <p>Methods</p> <p>There were included 113 HIV-positive and 141 age-matched HIV-negative patients, who underwent upper gastrointestinal endoscopy for dyspeptic symptoms. <it>H. pylori </it>status was evaluated by urease test and histology.</p> <p>Results</p> <p>The prevalence of <it>H. pylori </it>infection was significantly lower (p < 0.001) in HIV-infected (37.2%) than in uninfected (75.2%) patients. There were no significant differences between <it>H. pylori </it>status and gender, age, HIV viral load, antiretroviral therapy and the use of antibiotics. A lower prevalence of <it>H. pylori </it>was observed among patients with T CD4 cell count below 200/mm³; however, it was not significant. Chronic active antral gastritis was observed in 87.6% of the HIV-infected patients and in 780.4% of the control group (p = 0.11). <it>H. pylori </it>infection was significantly associated with chronic active gastritis in the antrum in both groups, but it was not associated with corpus chronic active gastritis in the HIV-infected patients.</p> <p>Conclusion</p> <p>We demonstrated that the prevalence of <it>H. pylori </it>was significantly lower in HIV-positive patients compared with HIV-negative ones. However, corpus gastritis was frequently observed in the HIV-positive patients, pointing to different mechanisms than <it>H. pylori </it>infection in the genesis of the lesion.</p