MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: Unraveling the sulfur cycle

The increasing number of metagenomic and genomic sequences has dramatically improved our understanding of microbial diversity, yet our ability to infer metabolic capabilities in such datasets remains challenging. We describe the Multigenomic Entropy Based Score pipeline (MEBS), a software platform designed to evaluate, compare, and infer complex metabolic pathways in large "omic" datasets, including entire biogeochemical cycles. MEBS is open source and available through https://github.com/eead-csic-compbio/metagenome Pfam score. To demonstrate its use, we modeled the sulfur cycle by exhaustively curating the molecular and ecological elements involved (compounds, genes, metabolic pathways, and microbial taxa). This information was reduced to a collection of 112 characteristic Pfam protein domains and a list of complete-sequenced sulfur genomes. Using the mathematical framework of relative entropy (H''), we quantitatively measured the enrichment of these domains among sulfur genomes. The entropy of each domain was used both to build up a final score that indicates whether a (meta)genomic sample contains the metabolic machinery of interest and to propose marker domains in metagenomic sequences such as DsrC (PF04358). MEBS was benchmarked with a dataset of 2107 non-redundant microbial genomes from RefSeq and 935 metagenomes from MG-RAST. Its performance, reproducibility, and robustness were evaluated using several approaches, including random sampling, linear regression models, receiver operator characteristic plots, and the area under the curve metric (AUC). Our results support the broad applicability of this algorithm to accurately classify (AUC = 0.985) hard-to-culture genomes (e.g., Candidatus Desulforudis audaxviator), previously characterized ones, and metagenomic environments such as hydrothermal vents, or deep-sea sediment. Our benchmark indicates that an entropy-based score can capture the metabolic machinery of interest and can be used to efficiently classify large genomic and metagenomic datasets, including uncultivated/unexplored taxa

Pollination efficiency of native and invading Africanized bees in the tropical dry forest annual plant, Kallstroemia grandiflora Torr ex Gray

We compared the pollinator effectiveness of native and exotic bees on Kallstroemia grandiflora in a tropical dry forest in Mexico. Although exotic Apis mellifera transfer 2.5 times less pollen grains on a per visit basis, they visited the flowers 2.65 times more frequently than the native bee Trigona nigra. Thus, when all measures of pollinator effectiveness are combined, exotic bees appear to be as efficient pollinators as native bees

Fifteen-year trends of long-term disability and sick leaves in ankylosing spondylitis

Analysis of fine scale genetic structure in continuous populations of outcrossing plant species has traditionally been limited by the availability of sufficient markers. We used a set of 468 SNPs to characterize fine-scale genetic structure within and between two dense stands of the wild ancestor of maize, teosinte (Zea mays ssp. parviglumis). Our analyses confirmed that teosinte is highly outcrossing and showed little population structure over short distances. We found that the two populations were clearly genetically differentiated, although the actual level of differentiation was low. Spatial autocorrelation of relatedness was observed within both sites but was somewhat stronger in one of the populations. Using principal component analysis, we found evidence for significant local differentiation in the population with stronger spatial autocorrelation. This differentiation was associated with pronounced shifts in the first two principal components along the field. These shifts corresponded to changes in allele frequencies, potentially due to local topographical features. There was little evidence for selection at individual loci as a contributing factor to differentiation. Our results demonstrate that significant local differentiation may, but need not, co-occur with spatial autocorrelation of relatedness. The present study represents one of the most detailed analyses of local genetic structure to date and provides a benchmark for future studies dealing with fine scale patterns of genetic diversity in natural plant populations. " 2010 Blackwell Publishing Ltd.",,,,,,"10.1111/j.1365-294X.2010.04559.x",,,"http://hdl.handle.net/20.500.12104/41510","http://www.scopus.com/inward/record.url?eid=2-s2.0-77950292826&partnerID=40&md5=095b598a34a7094c855c5ccf81686a4f",,,,,,"6",,"Molecular Ecology",,"116

Quadrulella texcalense sp. nov. from a Mexican desert: An unexpected new environment for hyalospheniid testate amoebae

Quadrulella (Amoebozoa, Arcellinida, Hyalospheniidae) is a genus of testate amoebae with unmistakable morphology, which secretes characteristic square plates to reinforce the test. They are mainly known from fens and freshwater habitats and have never been documented in deserts. We describe a new species, Quadrulella texcalense, from biological soil crusts in the intertropical desert of Tehuacán (state of Puebla, Mexico). Quadrulella texcalense occurred only at altitudes between 2140 and 2221 m.a.s.l., together with the bryophyte genera Pseudocrossidium, Weissia, Bryum, Didymodon, Neohyophyla and Aloina. The soil was extremely dry (moisture of 1.97–2.6%), which contrasts sharply with previous reports for the Quadrulella genus. Single cell mitochondrial cytochrome oxidase I (COI) barcoding of thirteen isolated cells showed an important morphological variability despite having all the same COI barcode sequence. Quadrulella texcalense was placed in a tree containing other Hyalsopheniidae, including a newly barcoded South African species, Q. elegans. Q. texcalense unambiguously branched within genus Quadrulella in a compact clade but with a long branch, suggesting accelerated evolution due to a transition towards a new environment and/or under-sampling

The relative contribution of fruits and arthropods to the diet of three trogon species (Aves, Trogonidae) in the Brazilian Atlantic Forest

Trogons are pan-tropical forest birds that eat a mix of fruits and arthropods. With direct observations of wild feeding birds, I assessed the relative contribution of fruits and arthropods to the diet of three trogon species (Trogonviridis, T.surrucura, and T.rufus) at Parque Estadual Intervales, southeast Brazil. Fruits and arthropods made the bulk of the food items recorded, with a tendency of frugivory increasing with body mass. The Trogon species differed in the proportion of fruits and arthropods taken, with T.viridis being the most frugivorous species (66% of feeding bouts, n = 47). The relative contribution of fruits and arthropods did not differ between the wet and dry seasons for any species. In the omnivorous gradient, T.viridis is close to the frugivorous extreme, whereas T.surrucura and T.rufus is next to the insectivorous end. Such a distinction may have important consequences for the territoriality and social behavior of these birds.<br>Os surucuás são aves florestais pantropicais que se alimentam de frutos e artrópodes. Com observações diretas de aves forrageando na natureza, estudei a contribuição relativa de frutos e artrópodes para a dieta de três espécies de surucuás (Trogonviridis, T.surrucura, and T.rufus) no Parque Estadual Intervales, sudeste do Brasil. Frutos e artrópodes foram os itens mais registrados, com uma tendência do grau de frugivoria aumentar com o aumento da massa corporal da ave. As três espécies diferiram em relação à proporção de frutos e artrópodes de que se alimentam; T.viridisfoi a espécie mais frugívora (66% dos registros, n = 47). As contribuições relativas de frutos e artrópodes para a dieta não diferiram entre as estações seca e úmida para nenhuma das três espécies. A diferença no grau de frugivoria aqui revelada pode ter conseqüências importantes para a territorialidade e organização social dos surucuás