Bacterial community assessment of drinking water and downstream distribution systems in highland localities of Ecuador.

Bacterial communities in drinking water provide a gauge to measure quality and confer insights into public health. In contrast to urban systems, water treatment in rural areas is not adequately monitored and could become a health risk. We performed 16S rRNA amplicon sequencing to analyze the microbiome present in the water treatment plants at two rural communities, one city, and the downstream water for human consumption in schools and reservoirs in the Andean highlands of Ecuador. We tested the effect of water treatment on the diversity and composition of bacterial communities. A set of physicochemical variables in the sampled water was evaluated and correlated with the structure of the observed bacterial communities. Predominant bacteria in the analyzed communities belonged to Proteobacteria and Actinobacteria. The Sphingobium genus, a chlorine resistance group, was particularly abundant. Of health concern in drinking water reservoirs were Fusobacteriaceae, Lachnospiraceae, and Ruminococcaceae; these families are associated with human and poultry fecal contamination. We propose the latter families as relevant biomarkers for establishing local standards for the monitoring of potable water systems in highlands of Ecuador. Our assessment of bacterial community composition in water systems in the Ecuadorian highlands provides a technical background to inform management decisions.

Intraspecific morphological and genetic variation of common species predicts ranges of threatened ones.

Predicting where threatened species occur is useful for making informed conservation decisions. However, because they are usually rare, surveying threatened species is often expensive and time intensive. Here, we show how regions where common species exhibit high genetic and morphological divergence among populations can be used to predict the occurrence of species of conservation concern. Intraspecific variation of common species of birds, bats and frogs from Ecuador were found to be a significantly better predictor for the occurrence of threatened species than suites of environmental variables or the occurrence of amphibians and birds. Fully 93 per cent of the threatened species analysed had their range adequately represented by the geographical distribution of the morphological and genetic variation found in seven common species. Both higher numbers of threatened species and greater genetic and morphological variation of common species occurred along elevation gradients. Higher levels of intraspecific divergence may be the result of disruptive selection and/or introgression along gradients. We suggest that collecting data on genetic and morphological variation in common species can be a cost effective tool for conservation planning, and that future biodiversity inventories include surveying genetic and morphological data of common species whenever feasible.

Systematics of Sturnira (Chiroptera: Phyllostomidae) in Ecuador, with comments on species boundaries.

Molecular and morphological analyses of variation often conflict with historical species descriptions based on a few characters and small samples sizes. Here we present a molecular phylogeny together with a quantitative morphologica analysis of the species in Sturnira in Ecuador. The 438 terminal taxa or organisms included in the anlaysis occur within a total of 10 ingroup lineages, which contain considerable substructure. Some species, as recognized by their morphologica traits, form paraphyletic arrangements with other taxa. We could not distinguish the close species pairs S. erythromos/S. bogotensis and S. ludovici/S. oporophilum in morphospace and therefore when distinct lineages were recovered genetically, they initially contained mixed membership of specimens identified using morphological criteria. Similarly the qualitative character states that diagnose S. luisi in its original description are not recovered in a quantitative analysis of morphological variation and thus S. luisi cannot be mapped to a single lineage in a molecular phylogeny. We presen additional evidence to corroborate the existence of S. perla as a species. We found a remarkable geographic structure within some species containing sister pairings, with lineages having a clear eastern or western distribution in relation to the Andes. Our analysis demonstrates the potential for conflict between character-based diagnoses, analysis of morphological variation and molecular phylogenetics in the identification of species and supports a combined approach to this problem.

Beta-Lactam Antibiotic Resistance Genes in the Microbiome of the Public Transport System of Quito, Ecuador.

Multidrug-resistant bacteria present resistance mechanisms against ß-lactam antibiotics, such as Extended-Spectrum Beta-lactamases (ESBL) and Metallo-ß-lactamases enzymes (MBLs) which are operon encoded in Gram-negative species. Likewise, Gram-positive bacteria have evolved other mechanisms through mec genes, which encode modified penicillin-binding proteins (PBP2). This study aimed to determine the presence and spread of ß-lactam antibiotic resistance genes and the microbiome circulating in Quito's Public Transport (QTP). A total of 29 station turnstiles were swabbed to extract the surface environmental DNA. PCRs were performed to detect the presence of 13 antibiotic resistance genes and to identify and to amplify 16S rDNA for barcoding, followed by clone analysis, Sanger sequencing, and BLAST search. ESBL genes blaTEM-1 and blaCTX-M-1 and MBL genes blaOXA-181 and mecA were detected along QPT stations, blaTEM being the most widely spread. Two subvariants were found for blaTEM-1, blaCTX-M-1, and blaOXA-181. Almost half of the circulating bacteria found at QPT stations were common human microbiota species, including those classified by the WHO as pathogens of critical and high-priority surveillance. ß-lactam antibiotic resistance genes are prevalent throughout QPT. This is the first report of blaOXA-181 in environmental samples in Ecuador. Moreover, we detected a new putative variant of this gene. Some commensal coagulase-negative bacteria may have a role as mecA resistance reservoirs.

First national assessment of wildlife mortality in Ecuador: An effort from citizens and academia to collect roadkill data at country scale.

Ecuador has both high richness and high endemism, which are increasingly threatened by anthropic pressures, including roads. Research evaluating the effects of roads remains scarce, making it difficult to develop mitigation plans. Here, we present the first national assessment of wildlife mortality on roads that allow us to (1) estimate roadkill rates per species, (2) identify affected species and areas, and (3) reveal knowledge gaps. We bring together data from systematic surveys and citizen science efforts to present a dataset with 5010 wildlife roadkill records from 392 species, and we also provide 333 standardized corrected roadkill rates calculated on 242 species. Systematic surveys were reported by ten studies from five Ecuadorian provinces, revealing 242 species with corrected roadkill rates ranging from 0.03 to 171.72 ind./km/year. The highest rates were for the yellow warbler Setophaga petechia in Galapagos (171.72 ind./km/year), the cane toad Rhinella marina in Manabi (110.70 ind./km/year), and the Galapagos lava lizard Microlophus albemarlensis (47.17 ind./km/year). Citizen science and other nonsystematic monitoring provided 1705 roadkill records representing all 24 provinces in Ecuador and 262 identified species. The common opossum Didelphis marsupialis, the Andean white-eared opossum Didelphis pernigra, and the yellow warbler Setophaga petechia were more commonly reported (250, 104, and 81 individuals, respectively). Across all sources, we found 15 species listed as "Threatened" and six as "Data Deficient" by the IUCN. We recommend stronger research efforts in areas where the mortality of endemic or threatened species could be critical for populations, such as in Galapagos. This first country-wide assessment of wildlife mortality on Ecuadorian roads represents contributions from academia, members of the public, and government, underlining the value of wider engagement and collaboration. We hope these findings and the compiled dataset will guide sensible driving and sustainable planning of infrastructure in Ecuador and, ultimately, contribute to reduce wildlife mortality on roads.

Ecuador tiene gran riqueza y alto endemismo de especies, mismas que están amenazadas por presiones antrópicas como las carreteras. Sin embargo, la investigación en este campo es escasa, dificultando el desarrollo de planes de mitigación. Presentamos la primera evaluación nacional de mortalidad de fauna silvestre en carreteras que nos permite 1) estimar tasas de atropellamiento por especies, 2) identificar especies y áreas afectadas, y 3) revelar vacíos de información. Compilamos datos de estudios sistemáticos y esfuerzos de ciencia ciudadana en Ecuador para presentar una base de datos que comprende 5010 registros de atropellamientos correspondientes a 392 especies, también proveemos 333 tasas de atropellamiento estandarizadas para 242 especies. Monitoreos sistemáticos fueron reportados por diez estudios de cinco provincias del Ecuador, revelando 242 especies con una tasa de mortalidad que varía entre 0.03 y 171.72 ind./km/año. Las tasas de atropellamiento más altas correspondieron a la reinita amarilla Setophaga petechia en Galápagos (171.72 ind./km/año), el sapo de la caña Rhinella marina in Manabí (110.70 ind./km/año), y la lagartija de lava de Galápagos Microlophus albemarlensis (47.17 ind./km/año). La ciencia ciudadana y monitoreos no sistemáticos proporcionaron 1705 registros representando a las 24 provincias de Ecuador y a 262 especies identificadas. La zarigüeya común Didelphis marsupialis, la zarigüeya orejiblanca andina Didelphis pernigra y la reinita amarilla Setophaga petechia fueron las más reportadas (250, 104 y 81 individuos respectivamente). Considerando todas las fuentes de datos encontramos 15 especies clasificadas como amenazadas y seis como datos insuficientes por la UICN. Recomendamos mayores esfuerzos de investigación en áreas donde la mortalidad de especies endémicas o amenazadas puede ser crítica para las poblaciones, como en Galápagos. Esta primera evaluación de mortalidad silvestre en carreteras ecuatorianas representa contribuciones de varios sectores, incluidos la academia, ciudadanía y el gobierno, resaltando el valor de una mayor participación y colaboración. Esperamos que estos hallazgos y la base de datos guíen la planificación sostenible de infraestructuras viales en Ecuador y contribuyan a reducir la mortalidad animal en las carreteras por medio de una conducción vehicular más cautelosa.

The microbiome of the ice-capped Cayambe Volcanic Complex in Ecuador.

A major challenge in microbial ecology is to understand the principles and processes by which microbes associate and interact in community assemblages. Microbial communities in mountain glaciers are unique as first colonizers and nutrient enrichment drivers for downstream ecosystems. However, mountain glaciers have been distinctively sensitive to climate perturbations and have suffered a severe retreat over the past 40 years, compelling us to understand glacier ecosystems before their disappearance. This is the first study in an Andean glacier in Ecuador offering insights into the relationship of physicochemical variables and altitude on the diversity and structure of bacterial communities. Our study covered extreme Andean altitudes at the Cayambe Volcanic Complex, from 4,783 to 5,583 masl. Glacier soil and ice samples were used as the source for 16S rRNA gene amplicon libraries. We found (1) effects of altitude on diversity and community structure, (2) the presence of few significantly correlated nutrients to community structure, (3) sharp differences between glacier soil and glacier ice in diversity and community structure, where, as quantified by the Shannon γ-diversity distribution, the meta-community in glacier soil showed more diversity than in glacier ice; this pattern was related to the higher variability of the physicochemical distribution of variables in the former substrate, and (4) significantly abundant genera associated with either high or low altitudes that could serve as biomarkers for studies on climate change. Our results provide the first assessment of these unexplored communities, before their potential disappearance due to glacier retreat and climate change.

Wildlife roadkill patterns in a fragmented landscape of the Western Amazon.

One of the most evident and direct effects of roads on wildlife is the death of animals by vehicle collision. Understanding the spatial patterns behind roadkill helps to plan mitigation measures to reduce the impacts of roads on animal populations. However, although roadkill patterns have been extensively studied in temperate zones, the potential impacts of roads on wildlife in the Neotropics have received less attention and are particularly poorly understood in the Western Amazon. Here, we present the results of a study on roadkill in the Amazon region of Ecuador; a region that is affected by a rapidly increasing development of road infrastructure. Over the course of 50 days, in the wet season between September and November 2017, we searched for road-killed vertebrates on 15.9 km of roads near the city of Tena, Napo province, for a total of 1,590 surveyed kilometers. We recorded 593 dead specimens, predominantly reptiles (237 specimens, 40%) and amphibians (190, 32%), with birds (102, 17%) and mammals (64, 11%) being less common. Recorded species were assigned to three functional groups, based on their movement behavior and habitat use ("slow," "intermediate," and "fast"). Using Ripley's K statistical analyses and 2D HotSpot Identification Analysis, we found multiple distinct spatial clusters or hotspots, where roadkill was particularly frequent. Factors that potentially determined these clusters, and the prevalence of roadkill along road segments in general, differed between functional groups, but often included land cover variables such as native forest and waterbodies, and road characteristics such as speed limit (i.e., positive effect on roadkill frequency). Our study, which provides a first summary of species that are commonly found as roadkill in this part of the Amazon region, contributes to a better understanding of the negative impacts of roads on wildlife and is an important first step toward conservation efforts to mitigate these impacts.

"Horchata" drink in Southern Ecuador: medicinal plants and people's wellbeing.

BACKGROUND: The "horchata" is a herbal mixture infusion consumed in Southern Ecuador. It remains unknown how vendors group the plant species to sell them at traditional markets. This research documented the following: 1) a list of medicinal plant species sold for the drink; 2) the culturally important medicinal plant species; 3) the agreement among vendors regarding the medicinal plants species and their therapeutic use; and 4) the groups of medicinal plants sold for the preparation of "horchata." METHODS: Interviews were made to 185 vendors at 31 traditional markets in Loja province. Bunches of medicinal plants were purchased to identify the species and to prepare voucher specimens. Culturally important medicinal plants species were established with the Fidelity Level (FL) index. Agreement among vendors on the therapeutic use of medicinal plants was measured with the Factor of Informant Consensus (FIC) index. A cluster analysis was made to determine the groups of medicinal plants sold by market vendors to prepare the "horchata" drink. RESULTS: In Loja province, the "horchata" drink is consumed for its therapeutic uses. This study registered 33 families with 58 genera and 71 medicinal plant species, 50 of which are herbs and three are endemic to the Andean highlands of Ecuador. The FL index (46.1-96.3) determined 20 culturally important medicinal plant species. The highest FIC value (1.00) among vendors corresponds to four plant species employed each for a different therapeutic use. The cluster analysis identified a core group of 16 plant species which are essential to the drink and which likely interact to provide wellbeing. CONCLUSIONS: The "horchata" is a heritage drink in Loja province. The 71 medicinal plants species registered for this drink is the largest number reported to date, and they have a total of 32 therapeutic uses. The combined results of the FL and FIC indices, the cluster analysis, and the field observations reveal an agreement among vendors on 16 medicinal plant species and their therapeutic use. This core group of plants requires bioactivity and bioassays analyses to determine biomedicine benefits that would be based on their pharmacological properties.

Mapping evolutionary process: a multi-taxa approach to conservation prioritization.

Human-induced land use changes are causing extensive habitat fragmentation. As a result, many species are not able to shift their ranges in response to climate change and will likely need to adapt in situ to changing climate conditions. Consequently, a prudent strategy to maintain the ability of populations to adapt is to focus conservation efforts on areas where levels of intraspecific variation are high. By doing so, the potential for an evolutionary response to environmental change is maximized. Here, we use modeling approaches in conjunction with environmental variables to model species distributions and patterns of genetic and morphological variation in seven Ecuadorian amphibian, bird, and mammal species. We then used reserve selection software to prioritize areas for conservation based on intraspecific variation or species-level diversity. Reserves selected using species richness and complementarity showed little overlap with those based on genetic and morphological variation. Priority areas for intraspecific variation were mainly located along the slopes of the Andes and were largely concordant among species, but were not well represented in existing reserves. Our results imply that in order to maximize representation of intraspecific variation in reserves, genetic and morphological variation should be included in conservation prioritization.

Morphological variation in the short-tailed fruit bat (Carollia) in Ecuador, with comments on the practical and philosophical aspects of boundaries among species.

The mechanisms for the morphological delimitation of species in Carollia remain poorly understood. This is the first study to assess variation in size and shape from strictly geometric terms. Both factors are assessed by statistical perspectives of distribution, overlap and relative distances. Despite its overlap, the size of the skull seems to be the most influential character for the discrimination of species, with shape playing a much smaller role. The smallest species seems to be the most distinct in shape, not only in terms of distance among centroids in morphometric space, but also in the overall trend and direction of variation. Contrary to previous studies, sexual dimorphism is not given by size but by distinct shapes of the skull. Characters such as the shape of the maxilla, previously described qualitatively as discrete with sharp boundaries, appear to be truly continuous with fuzzy borders among species. Because morphometric space is a gamut of continuous variation and overlap, the taxonomic error rate for size characters seems to be substantial for the medium-sized species (Carollia brevicauda Schinz, 1821), with approximately 30-40% of individuals erroneously assigned to a different species after a jackknifed discriminant function. This taxonomic error is higher for shape characters. Morphological, systematic and ecological consequences of the observed patterns of shape and size variation are commented within the context of previously proposed arguments and hypotheses.