A5022289175- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Air Quality Monitoring and Forecasting
- Atmospheric chemistry and aerosols
- Air Quality and Health Impacts
- Meteorological Phenomena and Simulations
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Atmospheric and Environmental Gas Dynamics
- Gut microbiota and health
- Microbial Metabolic Engineering and Bioproduction
- Protist diversity and phylogeny
- Vehicle emissions and performance
- Soil Moisture and Remote Sensing
- Evolution and Genetic Dynamics
- CRISPR and Genetic Engineering
- Climate variability and models
- Data Visualization and Analytics
- Oceanographic and Atmospheric Processes
- Insect symbiosis and bacterial influences
- Algorithms and Data Compression
- Wind and Air Flow Studies
- Scarabaeidae Beetle Taxonomy and Biogeography
- Complex Network Analysis Techniques
- Atmospheric Ozone and Climate
Universidad EAFIT
2016-2024
Universidad de Medellín
2020
Universidad de Granada
2019
Institute for Systems Biology
2012-2016
Seattle University
2016
Institute of Remote Sensing and Digital Earth
2014
University of Luxembourg
2012-2014
University of Washington
2002-2012
Institut Supérieur de l'Électronique et du Numérique
2011
NASA Astrobiology Institute
2009
Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments now thought to be significant contributors carbon nitrogen cycling. The isolation of Candidatus “ Nitrosopumilus maritimus ” strain SCM1 provided the opportunity for linking its chemolithotrophic physiology with a genomic inventory globally distributed archaea. Here we report 1,645,259-bp closed genome SCM1, revealing highly copper-dependent systems ammonia oxidation electron transport that distinctly different...
Article13 March 2007Open Access Metabolic modeling of a mutualistic microbial community Sergey Stolyar Corresponding Author Department Civil and Environmental Engineering, University Washington, Seattle, WA, USA Search for more papers by this author Steve Van Dien USAPresent address: Genomatica Inc., 5405 Morehouse Drive; San Diego, CA 92121, Kristina Linnea Hillesland Nicolas Pinel Microbiology, Thomas J Lie John A Leigh David Stahl Information 1, Dien1, Hillesland1, Pinel2, Lie2, Leigh2 1...
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 modular pipeline integrated reference-independent coupled metagenomic metatranscriptomic data. IMP incorporates robust read preprocessing, iterative co-assembly, analyses microbial community structure function, automated binning, as well genomic signature-based visualizations. The IMP-based integration strategy enhances usage,...
Tubulins, the protein constituents of microtubule cytoskeleton, are present in all known eukaryotes but have never been found Bacteria or Archaea. Here we report presence two tubulin-like genes [bacterial tubulin a ( btuba ) and bacterial b btubb )] bacteria genus Prosthecobacter (Division Verrucomicrobia). In this study, investigated organization expression these conducted comparative analysis eukaryotic sequences, focusing on their phylogeny 3D structures. The arranged as adjacent loci...
Abstract Microbial communities are complex and dynamic systems that primarily structured according to their members’ ecological niches. To investigate how niche breadth (generalist versus specialist lifestyle strategies) relates success, we develop apply an integrative workflow for the multi-omic analysis of oleaginous mixed microbial from a biological wastewater treatment plant. Time- space-resolved coupled metabolomic taxonomic analyses demonstrate community-wide lipid accumulation...
Significance Nature is full of species that cooperate in mutually beneficial interactions to survive. Some are completely dependent on such relationships. How and why does this specialization evolve? We show as the bacterium Desulfovibrio vulgaris evolved for 1,000 generations conditions forcing cooperation with archaeon Methanococcus maripaludis , it lost a key metabolic trait would be required grow alone most environments. Large subpopulations lacking capacity respire sulfate 13 21...
The article examines municipal solid waste (MSW), specifically organic or food (OW), which constitutes between 42 % and 69 of MSW globally. These wastes contain a high concentration matter, nutrients moisture, with an easily acidified pH. Its management is crucial due to its environmental impact, generating greenhouse gas emissions pollution problems. Anaerobic Digestion (AD) presented as biotechnological solution harness the energy waste. This process, without oxygen, decomposes matter by...
A Gram-negative, flagellated, heterotrophic, catalase-negative, rod-shaped bacterium previously identified as an earthworm symbiont was isolated from nephridia of the Eisenia foetida. Comparisons 16S rRNA gene sequences indicated its relatedness to betaproteobacterial genus Acidovorax and novel isolates shared 92–94 % sequence similarity with recognized species this genus. Gene phylogenies revealed that group symbionts formed a cohesive independent clade. The DNA G+C content 67.0±0.2 mol%....
Hypersaline microbial mat communities have recently been shown to be more diverse than once thought. The variability in community composition of hypersaline mats, both terms spatial and temporal dimensions, is still poorly understood. Because this information essential understanding the complex biotic abiotic interactions within these communities, terminal restriction fragment analysis 16S rRNA gene sequencing were used characterize near-surface a Guerrero Negro, Mexico. Core samples...
The visualization of metagenomic data, especially without prior taxonomic identification reconstructed genomic fragments, is a challenging problem in computational biology. An ideal method should, among others, enable clear distinction congruent groups sequences closely related taxa, be applicable to fragments lengths typically achievable following assembly, and allow the efficient analysis growing amounts community sequence data. Here, we report scalable approach for data that based on...
The use of low air quality networks has been increasing in recent years to study urban pollution dynamics. Here we show the evaluation operational Aburrá Valley’s low-cost network against official monitoring network. results that PM2.5 measurements are very close those observed by Additionally, allows a higher spatial representation concentrations across valley. We integrate observations with chemical transport model Long Term Ozone Simulation-European Operational Smog (LOTOS-EUROS) using...
"Candidatus Microthrix" bacteria are deeply branching filamentous actinobacteria which occur at the water-air interface of biological wastewater treatment plants, where they often responsible for foaming and bulking. Here, we report first draft genome sequence a strain from this genus: Microthrix parvicella" Bio17-1.
While genomic erosion is common among intracellular symbionts, patterns of genome evolution in heritable extracellular endosymbionts remain elusive. We study vertically transmitted (Verminephrobacter, Betaproteobacteria) that form a beneficial, species-specific, and evolutionarily old (60–130 Myr) association with earthworms. assembled draft Verminephrobacter aporrectodeae compared it the genomes eiseniae two nonsymbiotic close relatives (Acidovorax). Similar to V. eiseniae, was not markedly...
Although tractable model organisms are essential to characterize the molecular mechanisms of evolution and adaptation, ecological relevance their behavior is not always clear because certain traits easily lost during long-term laboratory culturing. Here, we demonstrate that despite long tenure in laboratory, retain "ecological memory" complex environmental changes. We have discovered Halobacterium salinarum NRC-1, a halophilic archaeon dominates microbial communities dynamically changing...
ABSTRACT The genome of the unicellular cyanobacterium Thermosynechococcus sp. strain NK55a, isolated from Nakabusa hot spring, Nagano Prefecture, Japan, comprises a single, circular, 2.5-Mb chromosome. is predicted to contain 2,358 protein-encoding genes, including genes for all typical cyanobacterial photosynthetic and metabolic functions. No encoding hydrogenases or nitrogenase were identified.
The genome of Desulfovibrio vulgaris strain DePue, a sulfate-reducing Deltaproteobacterium isolated from heavy metal-impacted lake sediment, was completely sequenced and compared with the type D. Hildenborough. two genomes share high degree relatedness synteny, but harbour distinct prophage signatures past phage encounters. In addition to highly variable contribution, DePue contains cluster open-reading frames not found in Hildenborough coding for production export capsule exopolysaccharide,...
In this work, we present the development of a 4D-Ensemble-Variational (4DEnVar) data assimilation technique to estimate NOx top-down emissions using regional chemical transport model LOTOS-EUROS with NO2 observations from TROPOspheric Monitoring Instrument (TROPOMI). The was performed for domain in northwest South America centered over Colombia, and includes regions Panama, Venezuela Ecuador. 4DEnVar approach, implementation linearized adjoint are avoided by generating an ensemble...
The densest network for measuring air pollutant concentrations in Colombia is Medellin, where most sensors are located the heavily polluted lower parts of valley. Measuring stations higher elevations on mountains surrounding valley not available, which limits our understanding valley’s dynamics and hinders effectiveness data assimilation studies using chemical transport models such as LOTOS-EUROS. To address this gap measurements, we have designed a new low-cost to be installed at altitudes...
Summary A novel sulfate‐reducing bacterium (strain DePue) closely related to Desulfovibrio vulgaris ssp. strain Hildenborough was isolated from the sediment of a heavy‐metal impacted lake using established techniques. Although few physiological differences between strains DePue and were observed, pulse‐field gel electrophoresis (PFGE) revealed significant genome reduction in DePue. Comparative whole‐genome microarray polymerase chain reaction analyses demonstrated that absence genes...
Abstract In this paper, we propose an efficient and practical implementation of the ensemble Kalman filter via shrinkage covariance matrix estimation. Our combines information brought by model realizations, that based on our prior knowledge about dynamical system interest. We perform combination both sources optimal factors. The method exploits rank-deficiency matrices to provide analysis step in EnKF formulations. Localization inflation aspects are discussed, as well. Experimental tests...
The dense microbial communities commonly associated with plants and animals should offer many opportunities for horizontal gene transfer through described mechanisms of DNA exchange including natural transformation (NT). However, studies the significance NT have focused primarily on pathogens. study presented here demonstrates highly efficient by in a common symbiont earthworms. obligate bacterial Verminephrobacter eiseniae is member consortium earthworm Eisenia fetida that transmitted into...
The ear layer, which is a component of rice, crucial to rice monitoring and yield estimation. By adding in the we have extended original coherent microwave scattering model, based on both first-order solution radiation transfer equation Monte Carlo numerical simulation methods, full stage rice. detailed scene generation geometrical description elements are presented. propagation path canopy reduced. Two approximation methods used fit curving by straight cylinders. Ground truth measurements...
This work proposes a robust and non-Gaussian version of the shrinkage-based knowledge-aided EnKF implementation called Ensemble Time Local H ∞ Filter Knowledge-Aided (EnTLHF-KA). The EnTLHF-KA requires target covariance matrix to integrate previously obtained information knowledge directly into data assimilation (DA). proposed method is based on filter its ensemble time-local EnTLHF, using an adaptive inflation factor depending shrinkage estimated matrix. implies theoretical solid background...