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Bacillus subtilis EA-CB0575 genome reveals clues for plant growth promotion and potential for sustainable agriculture
(Springer, 2020-01-01) Franco-Sierra, N.D.; Posada, L.F.; Santa-María, G.; Romero-Tabarez, M.; Villegas-Escobar, V.; Álvarez, J.C.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Bacillus subtilis is a remarkably diverse bacterial species that displays many ecological functions. Given its genomic diversity, the strain Bacillus subtilis EA-CB0575, isolated from the rhizosphere of a banana plant, was sequenced and assembled to determine the genomic potential associated with its plant growth promotion potential. The genome was sequenced by Illumina technology and assembled using Velvet 1.2.10, resulting in a whole genome of 4.09 Mb with 4332 genes. Genes involved in the production of indoles, siderophores, lipopeptides, volatile compounds, phytase, bacilibactin, and nitrogenase were predicted by gene annotation or by metabolic pathway prediction by RAST. These potential traits were determined using in vitro biochemical tests, finding that B. subtilis EA-CB0575 produces two families of lipopeptides (surfactin and fengycin), solubilizes phosphate, fixes nitrogen, and produces indole and siderophores compounds. Finally, strain EA-CB0575 increased 34.60% the total dry weight (TDW) of tomato plants with respect to non-inoculated plants at greenhouse level. These results suggest that the identification of strain-specific genes and predicted metabolic pathways might explain the strain potential to promote plant growth by several mechanisms of action, accelerating the development of plant biostimulants for sustainable agricultural. © 2020, Springer-Verlag GmbH Germany, part of Springer Nature.
Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC)
(BioMed Central Ltd., 2018-01-17) Molano, E.P.L.; Cabrera, O.G.; Jose, J.; do Nascimento, L.C.; Carazzolle, M.F.; Teixeira, P.J.P.L.; Alvarez, J.C.; Tiburcio, R.A.; Tokimatu Filho, P.M.; de Lima, G.M.A.; Guido, R.V.C.; Corrêa, T.L.R.; Leme, A.F.P.; Mieczkowski, P.; Pereira, G.A.G.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Background: The Ceratocystis genus harbors a large number of phytopathogenic fungi that cause xylem parenchyma degradation and vascular destruction on a broad range of economically important plants. Ceratocystis cacaofunesta is a necrotrophic fungus responsible for lethal wilt disease in cacao. The aim of this work is to analyze the genome of C. cacaofunesta through a comparative approach with genomes of other Sordariomycetes in order to better understand the molecular basis of pathogenicity in the Ceratocystis genus. Results: We present an analysis of the C. cacaofunesta genome focusing on secreted proteins that might constitute pathogenicity factors. Comparative genome analyses among five Ceratocystidaceae species and 23 other Sordariomycetes fungi showed a strong reduction in gene content of the Ceratocystis genus. However, some gene families displayed a remarkable expansion, in particular, the Phosphatidylinositol specific phospholipases-C (PI-PLC) family. Also, evolutionary rate calculations suggest that the evolution process of this family was guided by positive selection. Interestingly, among the 82 PI-PLCs genes identified in the C. cacaofunesta genome, 70 genes encoding extracellular PI-PLCs are grouped in eight small scaffolds surrounded by transposon fragments and scars that could be involved in the rapid evolution of the PI-PLC family. Experimental secretome using LC-MS/MS validated 24% (86 proteins) of the total predicted secretome (342 proteins), including four PI-PLCs and other important pathogenicity factors. Conclusion: Analysis of the Ceratocystis cacaofunesta genome provides evidence that PI-PLCs may play a role in pathogenicity. Subsequent functional studies will be aimed at evaluating this hypothesis. The observed genetic arsenals, together with the analysis of the PI-PLC family shown in this work, reveal significant differences in the Ceratocystis genome compared to the classical vascular fungi, Verticillium and Fusarium. Altogether, our analyses provide new insights into the evolution and the molecular basis of plant pathogenicity. © 2018 The Author(s).
Colombia's cyberinfrastructure for biodiversity: Building data infrastructure in emerging countries to foster socioeconomic growth
(Wiley Open Access, 2019-12-22) De Vega, Jose J.; Davey, Robert P.; Duitama, Jorge; Escobar, Dairo; Cristancho, Marco A.; Etherington, Graham J.; Minotto, Alice; Pineda J.D.; Correa Alvarez J; Camargo, Anyela V.; Haerty, Wilfried; Mallarino, Juan P.; Barreto, Emiliano; Fuentes, Narcis; Di, Federica; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Science and innovation are not a luxury but a prerequisite for social and economic development (Annan, 2003).
Complete mitogenome of the biocontroller fungus Purpureocillium sp. (Ascomycota, Ophiocordycipitaceae, Hypocreales)
(Taylor and Francis Ltd., 2018-01-01) Cardona N.L.; Franco-Sierra N.D.; Correa Alvarez J.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
The strain Purpureocillium sp. UdeA0106 is an antagonist of nematodes, fungi, and garden symphylans from crops with high economic importance in Colombia (Salazar 2013; Salazar et al. 2014; Cardona et al. 2014; Gallego et al. 2014) and is being studied to be proposed as new species. It was included on the 1000 fungal genomes project to elucidate its phylogenetic relationships with other fungi. Purpureocillium’s mitogenome has 23,495 bp of circular size. It contains 15 protein-coding genes without duplications (PCGs), corresponding to the 60% of its total length, 23 transfer genes (7.6% tRNA), two of them duplicated (trnR and trnM), and two ribosomal genes (17.6% rRNA) and a GC content of 28.44%. A phylogenetic tree was proposed using their 14 PCGs mitochondrial genes and was compared with other fungi of the Subphylum Pezizomycotina. Phylogenetics relationships showed UdeA0106 to be close to P. chlamydosporia and M. anisopliae forming a cluster with other fungal biocontrol agents and separated the strain of plant pathogenic fungi. © 2018, © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
Construction of probe of the plant growth-promoting bacteria Bacillus subtilis useful for fluorescence in situ hybridization
(Elsevier, 2016-09-01) Posada, L.F.; Alvarez, J.C.; Hu, C.-H.; de-Bashan, L.E.; Bashan, Y.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Strains of Bacillus subtilis are plant growth-promoting bacteria (PGPB) of many crops and are used as inoculants. PGPB colonization is an important trait for success of a PGPB on plants. A specific probe, based on the 16 s rRNA of Bacillus subtilis, was designed and evaluated to distinguishing, by fluorescence in situ hybridization (FISH), between this species and the closely related Bacillus amyloliquefaciens. The selected target for the probe was between nucleotides 465 and 483 of the gene, where three different nucleotides can be identified. The designed probe successfully hybridized with several strains of Bacillus subtilis, but failed to hybridize not only with B. amyloliquefaciens, but also with other strains such as Bacillus altitudinis, Bacillus cereus, Bacillus gibsonii, Bacillus megaterium, Bacillus pumilus; and with the external phylogenetic strains Azospirillum brasilense Cd, Micrococcus sp. and Paenibacillus sp. The results showed the specificity of this molecular probe for B. subtilis. (C) 2016 Elsevier B.V. All rights reserved.
DIRECT in vitro REGENERATION OF CASTOR BEAN PLANTS (Ricinus communis) USING EPICOTYLS
(Univ Feder Uberlandia, 2019-03-15) D.F. Villanueva-Mejía; Álvarez, J.C.; Gil, Alejandro; Restrepo, Martha Catalina; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
regeneration protocol for castor bean plant (Ricinus communis) was successfully developed using epicotyl sections obtained from in vitro seedlings.
Directional Landscapes: Using Parametric Loudspeakers for Sound Reproduction in Art
(Taylor and Francis Ltd., 2017-01-01) Alunno, M.; Yarce Botero, A.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
As new technologies appear, the expressive palette of creators broadens. Parametric loudspeakers are one of such new technologies that makes it possible to direct sound as though it were a light beam. Since their debut in the market, they have thus far received little attention from part of the artistic world. Some peculiarities concerning the sound reproduction might explain why musicians in particular are hesitating to use an otherwise highly attractive acoustic innovation. Due to such peculiarities, a proper use of parametric loudspeakers in art must start with investigating a whole array of different topics (i.e. non-linear acoustics and ultrasonic transducers) in order to understand how this technology works and utilize it at its best. The result of our project is ultimately a sound installation that makes use of directional sound to ruminate on issues concerning sound perception and the responsible use of our sound environment. © 2016 Informa UK Limited, trading as Taylor & Francis Group.
DNA sequencing reveals unexpected Recent diversity and an ancient dichotomy in the American marsupial genus Marmosops (Didelphidae: Thylamyini)
(Oxford University Press, 2016-04-01) Diaz-Nieto, Juan F.; Jansa, Sharon A.; Voss, Robert S.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Dynamics of species composition of small non-volant mammals from the northern Cordillera Central of Colombia
(De Gruyter, 2015-11-01) Díaz-Nieto, J.F.; Sanchez, Camilo; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
On the basis of our recent fieldwork and historical records, we document the diversity of small non-volant mammals in the northern end of Cordillera Central of Colombia, an important region in the context of vertebrate biodiversity.
Early Miocene CO2 estimates from a Neotropical fossil leaf assemblage exceed 400 ppm
(Wiley-Blackwell Publishing Ltd, 2018-11-01) Londoño L.; Royer D.L.; Jaramillo C.; Escobar J.; Foster D.A.; Cárdenas-Rozo A.L.; Wood A.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Premise of the Study: The global climate during the early Miocene was warmer than the present and preceded the even warmer middle Miocene climatic optimum. The paleo-CO2 records for this interval suggest paradoxically low concentrations (<450 ppm) that are difficult to reconcile with a warmer-than-present global climate. Methods: In this study, we use a leaf gas-exchange model to estimate CO2 concentrations using stomatal characteristics of fossil leaves from a late early Miocene Neotropical assemblage from Panama that we date to 18.01 ± 0.17 Ma via 238U/206Pb zircon geochronology. We first validated the model for Neotropical environments by estimating CO2 from canopy leaves of 21 extant species in a natural Panamanian forest and from leaves of seven Neotropical species in greenhouse experiments at 400 and 700 ppm. Key Results: The results showed that the most probable combined CO2 estimate from the natural forests and 400 ppm experiments is 475 ppm, and for the 700 ppm experiments is 665 ppm. CO2 estimates from the five fossil species exhibit bimodality, with two species most consistent with a low mode (528 ppm) and three with a high mode (912 ppm). Conclusions: Despite uncertainties, it is very likely (at >95% confidence) that CO2 during the late early Miocene exceeded 400 ppm. These results revise upwards the likely CO2 concentration at this time, more in keeping with a CO2-forced greenhouse climate. © 2018 Botanical Society of America
Efficient direct shoot organogenesis and genetic stability in micropropagated sacha inchi (Plukenetia volubilis L.)
(BioMed Central Ltd., 2020-09-03) Restrepo-Osorio C.; Gil-Correal A.; Chamorro-Gutiérrez L.; Ramírez-Ríos V.; Álvarez J.C.; Villanueva-Mejía D.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Objective: It is necessary to improve biotech platforms based on in vitro cell tissue culture to support sacha inchi (Plukenetia volubilis L.) research programs and draw on the nutritional value of the high polyunsaturated fatty acid content of its oilseed. Here, we developed a rapid and efficient method for induction and direct in vitro shoot development for this species. Results: Shoots were generated from hypocotyl explants. The highest organogenic response was obtained in woody plant medium supplemented with 1 mg/L thidiazuron and 0.5 mg/L zeatin supplemented with L-glutamine, adenine hemisulfate, and L-arginine. Shoots obtained using this medium were transferred and subcultivated with different concentrations of indole-3-butyric acid and 1-naphthylacetic acid for rooting. For the first time, a histological analysis was performed supporting direct organogenic development in this species. The plantlets obtained were transferred ex vitro with a survival percentage of 80%. The genetic stability of the plants recovered was confirmed by randomly amplified polymorphic DNA analysis. All results indicate that it would be possible to stimulate direct shoot formation from hypocotyls to support the sustainable use of this species. © 2020 The Author(s).
Enhanced molecular visualization of root colonization and growth promotion by Bacillus subtilis EA-CB0575 in different growth systems
(Elsevier GmbH, 2018-01-01) Posada, L.F.; Álvarez, J.C.; Romero-Tabarez, M.; de-Bashan, L.; Villegas-Escobar, V.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Bacillus subtilis EA-CB0575 is a plant growth-promoting bacterium (PGPB) associated with banana and tomato crops. Root colonization is an important trait for PGPB microorganisms and potentiates the bacterial effect related to the mechanisms of plant growth promotion. Therefore, detection of bacterial colonization of roots in different culture systems is important in the study of plant–microorganism interactions. In this study, fluorescent in situ hybridization (FISH) and catalyzed reporter deposition–FISH (CARD–FISH) were evaluated to determine the colonization ability of B. subtilis EA-CB0575 on banana and tomato roots planted on solid and liquid Murashige and Skoog medium (MS(S) and MS(L), respectively) and in soil for tomato plants. Results showed B. subtilis colonization 0–30 days post inoculation for banana and tomato plants in different culture systems with differential distribution of bacterial cells along tomato and banana roots. FISH and CARD–FISH methodologies were both successful in detecting B. subtilis colonies, but CARD–FISH proved to be superior due to its enhanced fluorescence signal. The presence of bacteria correlated with the promotion of plant growth in both plant species, providing clues to relate rhizospheric colonization with improvement in plant growth. FISH and CARD–FISH analysis results suggested the presence of native microbiota on the roots of in vitro banana plants, but not on those of tomato plants. © 2018 Elsevier GmbH
An Entropy-Based Graph Construction Method for Representing and Clustering Biological Data
(SPRINGER, 2019-10-01) Ariza-Jiménez L.; Pinel N.; Villa L.F.; Quintero O.L.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Unsupervised learning methods are commonly used to perform the non-trivial task of uncovering structure in biological data. However, conventional approaches rely on methods that make assumptions about data distribution and reduce the dimensionality of the input data. Here we propose the incorporation of entropy related measures into the process of constructing graph-based representations for biological datasets in order to uncover their inner structure. Experimental results demonstrated the potential of the proposed entropy-based graph data representation to cope with biological applications related to unsupervised learning problems, such as metagenomic binning and neuronal spike sorting, in which it is necessary to organize data into unknown and meaningful groups. © 2020, Springer Nature Switzerland AG.
Extracted information quality, a comparative study in high and low dimensions
(Inderscience Enterprises Ltd., 2020-12-11) Ariza-Jimenez L.; Villa, LF; Pinel N.; Lucia Quintero M, O.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Forecasting PM10 and PM2.5 in the Aburrá Valley (Medellín, Colombia) via EnKF based data assimilation
(Elsevier Ltd., 2020-07-10) Quintero, O.; López, S.; Yarce, A.; Pinel, N.; Segers, Arjo; Heemink, A.W; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
How integrative taxonomy can save a species from extinction: The supposedly extinct mouse opossum Cryptonanus ignitus (Diaz, Flores and Barquez, 2000) is a synonym of the living C. chacoensis (Tate, 1931)
(Elsevier BV, 2019-01-01) Teta P.; Díaz-Nieto J.F.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
We reviewed the taxonomic status of the “extinct” mouse opossum Cryptonanus ignitus (Diaz, Flores and Barquez, 2000). This species is only known from the type, an adult male collected in the province of Jujuy, northwestern Argentina, in 1962. Based on both qualitative and quantitative external and cranial traits and the analysis of DNA sequences extracted from the 57-year-old type skin, we confirm the suggestion of previous researchers that C. ignitus is an elderly example of the living species C. chacoensis (Tate, 1931). Most of the supposedly diagnostic morphological traits of C. ignitus (e.g., zygomatic arches unusually wide and robust, postorbital process of the jugal massively developed, prominent temporal scars) are age-correlated in didelphids and were observed in other adult specimens of C. chacoensis. The clay coloration of the ventral pelage of C. ignitus, which allegedly sets apart this species from other congeners, is here reported for new examples of C. chacoensis from other localities. Our results suggest the need to carefully evaluate the taxonomic status of other species supposed to have become extinct in recent times in mainland South America. © 2019 Deutsche Gesellschaft für Säugetierkunde
Identification of Fusarium cf . verticillioides as The Causal Agent of Pokka Boheng Disease in Sugarcane in the Department of Antioquia, Colombia
(Fondo Editorial Universidad EAFIT, 2018-11-01) Franco, Nicolas David; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Identification of Fusarium cf. Verticillioides as The Causal Agent of Pokka Boheng Disease in Sugarcane in the Department of Antioquia, Colombia
(Fondo Editorial Universidad EAFIT, 2018-07-01) Correa, Javier; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
(BioMed Central Ltd., 2016-12-16) Narayanasamy, S.; Jarosz, Y.; Muller, E.E.L.; Heintz-Buschart, A.; Herold, M.; Kaysen, A.; Laczny, C.C.; Pinel, N.; May, P.; Wilmes, P.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning, as well as genomic signature-based visualizations. The IMP-based data integration strategy enhances data usage, output volume, and output quality as demonstrated using relevant use-cases. Finally, IMP is encapsulated within a user-friendly implementation using Python and Docker. IMP is available at http://r3lab.uni.lu/web/imp/ (MIT license).
Implementation of a Non-InvasiveBioprospecting Protocol for Isolation ofLactobacillusfrom Feces of Hens UnderForaging Conditions
(Fondo Editorial Universidad EAFIT, 2018-07-01) Correa, Javier; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación

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