Exploring the Leaf Beetle Fauna (Coleoptera: Chrysomelidae) of an Ecuadorian Mountain Forest Using DNA Barcoding

Background

Tropical mountain forests are hotspots of biodiversity hosting a huge but little known diversity of insects that is endangered by habitat destruction and climate change. Therefore, rapid assessment approaches of insect diversity are urgently needed to complement slower traditional taxonomic approaches. We empirically compare different DNA-based species delimitation approaches for a rapid biodiversity assessment of hyperdiverse leaf beetle assemblages along an elevational gradient in southern Ecuador and explore their effect on species richness estimates.

Methodology/Principal Findings

Based on a COI barcode data set of 674 leaf beetle specimens (Coleoptera: Chrysomelidae) of 266 morphospecies from three sample sites in the Podocarpus National Park, we employed statistical parsimony analysis, distance-based clustering, GMYC- and PTP-modelling to delimit species-like units and compared them to morphology-based (parataxonomic) species identifications. The four different approaches for DNA-based species delimitation revealed highly similar numbers of molecular operational taxonomic units (MOTUs) (n = 284–289). Estimated total species richness was considerably higher than the sampled amount, 414 for morphospecies (Chao2) and 469–481 for the different MOTU types. Assemblages at different elevational levels (1000 vs. 2000 m) had similar species numbers but a very distinct species composition for all delimitation methods. Most species were found only at one elevation while this turnover pattern was even more pronounced for DNA-based delimitation.

Conclusions/Significance

Given the high congruence of DNA-based delimitation results, probably due to the sampling structure, our study suggests that when applied to species communities on a regionally limited level with high amount of rare species (i.e. ~50% singletons), the choice of species delimitation method can be of minor relevance for assessing species numbers and turnover in tropical insect communities. Therefore, DNA-based species delimitation is confirmed as a valuable tool for evaluating biodiversity of hyperdiverse insect communities, especially when exact taxonomic identifications are missing.     

Epidemiology of leishmaniasis in Ecuador: current status of knowledge -- a review

Although leishmaniasis is regarded as a significant health problem in Ecuador by the Ministry of Health, and the incidence has increased over the last years, an official map on the geographic distribution of disease and sand fly vectors or a control strategy do not exist yet. This article reviews the current situation based on published information to improve our knowledge and understand the epidemiological situation of leishmaniasis in Ecuador in order to help future research and to develop a national control strategy. The disease is endemic in most provinces throughout Pacific coastal region, Amazonian lowlands, and some inter-Andean valleys with a total 21,805 cases reported during 1990-2003. Whereas cutaneous leishmaniasis (CL) is found throughout Ecuador, mucocutaneous leishmaniasis (MCL) appears to be restricted to the Amazon region; one, parasitologically unconfirmed case of visceral form was reported in 1949. Most human infections are caused by Leishmania (Viannia) spp., which is distributed in the subtropical and tropical lowlands; infections due to L. (Leishmania) spp. are found in the Andean highlands and in the Pacific lowlands as well. The proven vectors are Lutzomyia trapidoi and Lu. ayacuchensis. Canis familiaris, Sciurus vulgaris, Potos flavus, and Tamandua tetradactyla have been found infected with Leishmania spp. It is estimated that around 3000-4500 people may be infected every year, and that 3.1 to 4.5 millions people are estimated to be at risk of contracting leishmaniasis.     

Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer

Background

Horizontal gene transfer (HGT) is the stable transmission of genetic material between organisms by means other than vertical inheritance. HGT has an important role in the evolution of prokaryotes but is relatively rare in eukaryotes. HGT has been shown to contribute to virulence in eukaryotic pathogens. We studied the importance of HGT in plant pathogenic fungi by identifying horizontally transferred genes in the genomes of three members of the genus Colletotrichum.

Results

We identified eleven HGT events from bacteria into members of the genus Colletotrichum or their ancestors. The HGT events include genes involved in amino acid, lipid and sugar metabolism as well as lytic enzymes. Additionally, the putative minimal dates of transference were calculated using a time calibrated phylogenetic tree. This analysis reveals a constant flux of genes from bacteria to fungi throughout the evolution of subphylum Pezizomycotina.

Conclusions

Genes that are typically transferred by HGT are those that are constantly subject to gene duplication and gene loss. The functions of some of these genes suggest roles in niche adaptation and virulence. We found no evidence of a burst of HGT events coinciding with major geological events. In contrast, HGT appears to be a constant, albeit rare phenomenon in the Pezizomycotina, occurring at a steady rate during their evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-16-2) contains supplementary material, which is available to authorized users.     

Selection of a suitable plant for phytoremediation in mining artisanal zones

A study was undertaken with the aim of identifying a suitable plant for the phytoremediation of metal-polluted soil from an artisanal mining area in Ecuador. Three zones including a natural zone (NZ), abandoned zone (AZ) and intensively mined zone (IZ) were selected. Three common native plants grown in the three zones were identified and collected, including Miconia zamorensis, Axonopus compressus and Erato polymnioides. The percentage of arbuscular mycorrhizal colonization that benefits their own survival in polluted soil was analyzed in the root samples of these candidate species. Analysis of the soils and plants collected from the different zones showed that the concentrations of Pb, Zn, Cu and Cd were comparatively lower in the NZ, higher in the AZ and IZ, and highest in the AZ for all the metals. The concentration of all these metals in plant tissues was the highest in E. polymnioides. The data analysis including the metal accumulation index, bioconcentration factor and translocation factor strongly identified E. polymnioides as a hyperaccumulator plant suitable for phytoremediation.     

Fluctuations at a Low Mean Temperature Accelerate Dengue Virus Transmission by Aedes aegypti

Background

Environmental factors such as temperature can alter mosquito vector competence for arboviruses. Results from recent studies indicate that daily fluctuations around an intermediate mean temperature (26°C) reduce vector competence of Aedes aeygpti for dengue viruses (DENV). Theoretical predictions suggest that the mean temperature in combination with the magnitude of the diurnal temperature range (DTR) mediate the direction of these effects.

Methodology/Principal Findings

We tested the effect of temperature fluctuations on Ae. aegypti vector competence for DENV serotype-1 at high and low mean temperatures, and confirmed this theoretical prediction. A small DTR had no effect on vector competence around a high (30°C) mean, but a large DTR at low temperature (20°C) increased the proportion of infected mosquitoes with a disseminated infection by 60% at 21 and 28 days post-exposure compared to a constant 20°C. This effect resulted from a marked shortening of DENV extrinsic incubation period (EIP) in its mosquito vector; i.e., a decrease from 29.6 to 18.9 days under the fluctuating vs. constant temperature treatment.

Conclusions

Our results indicate that Ae. aegypti exposed to large fluctuations at low temperatures have a significantly shorter virus EIP than under constant temperature conditions at the same mean, leading to a considerably greater potential for DENV transmission. These results emphasize the value of accounting for daily temperature variation in an effort to more accurately understand and predict the risk of mosquito-borne pathogen transmission, provide a mechanism for sustained DENV transmission in endemic areas during cooler times of the year, and indicate that DENV transmission could be more efficient in temperate regions than previously anticipated.     

Shifts in leaf litter breakdown along a forest–pasture–urban gradient in Andean streams

Tropical montane ecosystems of the Andes are critically threatened by a rapid land‐use change which can potentially affect stream variables, aquatic communities, and ecosystem processes such as leaf litter breakdown. However, these effects have not been sufficiently investigated in the Andean region and at high altitude locations in general. Here, we studied the influence of land use (forest–pasture–urban) on stream physico‐chemical variables (e.g., water temperature, nutrient concentration, and pH), aquatic communities (macroinvertebrates and aquatic fungi) and leaf litter breakdown rates in Andean streams (southern Ecuador), and how variation in those stream physico‐chemical variables affect macroinvertebrates and fungi related to leaf litter breakdown. We found that pH, water temperature, and nutrient concentration increased along the land‐use gradient. Macroinvertebrate communities were significantly different between land uses. Shredder richness and abundance were lower in pasture than forest sites and totally absent in urban sites, and fungal richness and biomass were higher in forest sites than in pasture and urban sites. Leaf litter breakdown rates became slower as riparian land use changed from natural to anthropogenically disturbed conditions and were largely determined by pH, water temperature, phosphate concentration, fungal activity, and single species of leaf‐shredding invertebrates. Our findings provide evidence that leaf litter breakdown in Andean streams is sensitive to riparian land‐use change, with urban streams being the most affected. In addition, this study highlights the role of fungal biomass and shredder species (Phylloicus; Trichoptera and Anchytarsus; Coleoptera) on leaf litter breakdown in Andean streams and the contribution of aquatic fungi in supporting this ecosystem process when shredders are absent or present low abundance in streams affected by urbanization. Finally, we summarize important implications in terms of managing of native vegetation and riparian buffers to promote ecological integrity and functioning of tropical Andean stream ecosystems.     

Effects of Fluctuating Daily Temperatures at Critical Thermal Extremes on Aedes aegypti Life-History Traits

Background

The effect of temperature on insect biology is well understood under constant temperature conditions, but less so under more natural, fluctuating conditions. A fluctuating temperature profile around a mean of 26°C can alter Aedes aegypti vector competence for dengue viruses as well as numerous life-history traits, however, the effect of fluctuations on mosquitoes at critical thermal limits is unknown.

Methodology/Principal Findings

We investigated the effects of large and small daily temperature fluctuations at low (16°C) and high (35–37°C) mean temperatures, after we identified these temperatures as being thresholds for immature development and/or adult reproduction under constant temperature conditions. We found that temperature effects on larval development time, larval survival and adult reproduction depend on the combination of mean temperature and magnitude of fluctuations. Importantly, observed degree-day estimates for mosquito development under fluctuating temperature profiles depart significantly (around 10–20%) from that predicted by constant temperatures of the same mean. At low mean temperatures, fluctuations reduce the thermal energy required to reach pupation relative to constant temperature, whereas at high mean temperatures additional thermal energy is required to complete development. A stage-structured model based on these empirical data predicts that fluctuations can significantly affect the intrinsic growth rate of mosquito populations.

Conclusions/Significance

Our results indicate that by using constant temperatures, one could under- or over-estimate values for numerous life-history traits compared to more natural field conditions dependent upon the mean temperature. This complexity may in turn reduce the accuracy of population dynamics modeling and downstream applications for mosquito surveillance and disease prevention.     

Conversion of Andean montane forests into plantations: Effects on soil characteristics,microorganisms, and microarthropods

Tropical montane forests in the Andes are subjected to deforestation and subsequent transformation into pastures. Abandoned pastures are frequently reforested by planting monoculture timber plantations, resulting in reduced aboveground diversity and changes in soil characteristics compared to primary forests. In this study, we evaluated differences in soil properties (litter layer thickness, pH, water content, and C-to-N ratio) between degraded primary montane forest and monoculture pine (Pinus patula) and alder (Alnus acuminata) plantations and their effects on density, diversity, and community structure of litter and soil-living mesofauna, with focus on oribatid mites (Acariformes). The study was performed in a montane region in the southern Ecuadorian Andes (2,000–2,600 m a.s.l.). C-to-N ratios in the litter and upper 5 cm soil layer were higher in pine plantations, while other soil characteristics were similar between vegetation types. Surprisingly, microbial biomass and density of soil mesofauna in the litter layer did not differ between vegetation types, while density and species richness of oribatid mites were higher in pine plantations. Community structure of oribatid mites differed between vegetation types with only a few species overlapping. The results indicate that quality and diversity of litter were not the major factors regulating the mesofauna community. Instead, soil animals benefited from increased habitat structure in thicker litter layers and potentially increased availability of root-derived resources. Overall, the results suggest that from a soil animal perspective, monoculture plantations are less detrimental than commonly assumed and enrichment of abandoned plantations with native tree species may help to restore tropical montane forests.     

PCR detection and identification of Leishmania parasites in clinical specimens in Ecuador: a comparison with classical diagnostic methods

A simplified polymerase chain reaction (PCR)-based assay was used for detection and typing of Leishmania parasites in clinical specimens from patients suspected of cutaneous leishmaniasis. Using cultures as the reference standard, our PCR detection method was more sensitive (92%) than classical diagnostic techniques, including microscopy (42% sensitivity), histologic staining (33%), and IgG enzyme-linked immunosorbent (20%). The PCR assay was also 100% specific. Parasites in both lesion biopsies and isolates cultured from lesion aspirates were identified as Leishmania braziliensis by PCR. In this study, we have demonstrated the suitability of simplified PCR assays for the simultaneous diagnosis and typing of parasites causing cutaneous leishmaniasis in a developing country where leishmaniasis is endemic.     

Plastid Genome Assembly Using Long-read data

Although plastid genome (plastome) structure is highly conserved across most seed plants, investigations during the past two decades have revealed several disparately related lineages that experienced substantial rearrangements. Most plastomes contain a large inverted repeat and two single-copy regions, and a few dispersed repeats; however, the plastomes of some taxa harbour long repeat sequences (>300 bp). These long repeats make it challenging to assemble complete plastomes using short-read data, leading to misassemblies and consensus sequences with spurious rearrangements. Single-molecule, long-read sequencing has the potential to overcome these challenges, yet there is no consensus on the most effective method for accurately assembling plastomes using long-read data. We generated a pipeline, plastid Genome Assembly Using Long-read data (ptGAUL), to address the problem of plastome assembly using long-read data from Oxford Nanopore Technologies (ONT) or Pacific Biosciences platforms. We demonstrated the efficacy of the ptGAUL pipeline using 16 published long-read data sets. We showed that ptGAUL quickly produces accurate and unbiased assemblies using only ~50× coverage of plastome data. Additionally, we deployed ptGAUL to assemble four new Juncus (Juncaceae) plastomes using ONT long reads. Our results revealed many long repeats and rearrangements in Juncus plastomes compared with basal lineages of Poales. The ptGAUL pipeline is available on GitHub: https://github.com/Bean061/ptgaul .