A Novel Eukaryotic Denitrification Pathway in Foraminifera

Benthic foraminifera are unicellular eukaryotes inhabiting sediments of aquatic environments. Several species were shown to store and use nitrate for complete denitrification, a unique energy metabolism among eukaryotes. The population of benthic foraminifera reaches high densities in oxygen-depleted marine habitats, where they play a key role in the marine nitrogen cycle. However, the mechanisms of denitrification in foraminifera are still unknown, and the possibility of a contribution of associated bacteria is debated. Here, we present evidence for a novel eukaryotic denitrification pathway that is encoded in foraminiferal genomes. Large-scale genome and transcriptomes analyses reveal the presence of a denitrification pathway in foraminifera species of the genus Globobulimina. This includes the enzymes nitrite reductase (NirK) and nitric oxide reductase (Nor) as well as a wide range of nitrate transporters (Nrt). A phylogenetic reconstruction of the enzymes' evolutionary history uncovers evidence for an ancient acquisition of the foraminiferal denitrification pathway from prokaryotes. We propose a model for denitrification in foraminifera, where a common electron transport chain is used for anaerobic and aerobic respiration. The evolution of hybrid respiration in foraminifera likely contributed to their ecological success, which is well documented in palaeontological records since the Cambrian period

Genomic and Culturomic Analysis of Gut Microbiota Function and Salmonella Enterica Expansion

Enteric bacteria that are resident in the hindgut of mammals are critical in immune development, digestion, and colonization resistance against pathogens. One of the major pathogens that gut commensals provide resistance against is Salmonella enterica, a major foodborne pathogen capable of infecting almost every warm-blooded animal. Given the interplay between pathogens and commensals in the gut lumen, the gut microbiota of pigs was studied by combining two disparate techniques: shotgun metagenomics and high throughput culturomics. Metagenomics readily identifies major taxa present in samples and can give an estimation to total genetic catalogue from an environment. However, many rare or low abundance taxa were retrieved in culture that were not reliably obtained from metagenomics. Major gene pathways recovered from culture isolates were absent from metagenomics. In addition to studying the gut microbiota, two genomics studies were conducted on S. enterica. The first study was to establish and investigate the genomic population structure of a bovine-adapted serovar, S. enterica Dublin. The serovar is a primary pathogen of cattle and can establish carrier states with the pathogen being shed intermittently in the feces and milk. It was observed that the core and ancillary genomes are strongly influence by region of isolation. Virulence and prophage content were homogenous among the geographic clades. However, US genomes yielded multiple antibiotic resistance genes mediated by an IncA/C2 plasmid. Antibiotic resistance was not common in isolates outside of the US. The second S. enterica genome investigation was to identify co-occurrence between metal and antibiotic resistance. Co-occurrence between the genotypes was identified, but is isolated to one clade of S. enterica I 4,[5],12:i:-. However, multiple serovars contain resistance to copper and silver, which may permit the expansion into novel niches as metal use continues to rise in medicine and agriculture

Characterisation of the Carpinus betulus L. Phyllomicrobiome in Urban and Forest Areas

Urban green areas are highly valued by citizens for their contribution to the quality of life in cities. Plants play an important role in mitigating airborne pollutants and are assisted in this role by the metabolic capacities of the millions of microbial cells that colonize leaf surfaces (phyllosphere). Many factors influence phyllosphere microbial community composition and function, but to what extent does airborne pollution in cities impact the composition of microbial communities and their functional degradation genes? Here we describe the characterization of the phyllospheric bacterial communities of Carpinus betulus L. trees (hornbeam) across three locations: the city center of Warsaw (Poland), a forest in a UNESCO World Heritage Site (Białowieża), and a forest in one of the world’s oldest operational oil fields (Bóbrka). C. betulus contained higher particulate matter (PM) concentrations, with higher concentrations of palladium and radon in the PM, on leaves in Warsaw than in the forests. Volatile organic compound (VOC) analyses of sampled air revealed higher concentrations of butanone methyl propanal, butylbenzene, and cyclohexane in Bóbrka than Warsaw and Białowieża, while in Warsaw, xylene and toluene were higher. Shotgun microbiome sequencing uncovered a dominance of Gammaproteobacteria (71%), mainly Pseudomonas spp., Actinobacteria, Alpha- and Betaproteobacteria, and Firmicutes. Community composition and function differed significantly between the forests and Warsaw city center. Statistically more hydrocarbon degradation genes were found in Białowieża compared to Warsaw and Bóbrka, and in vitro tests of diesel degradation and plant growth promotion traits of culturable representatives revealed that Białowieża held the highest number of bacteria with plant beneficial properties and degradation genes. This study provides the first detailed insights into the microbiome of C. betulus and sets the stage for developing to a more integrated understanding of phyllosphere microbiota in cities, and their relationships with human health

Análisis bioinformático de la especificidad de las secuencias de aminoácidos de la LH murina y canina candidatas para inmunocontracepción

Canine overpopulation has increased dramatically in the last decade, a great portion of them do not receive responsible care so it becomes a social problem not only for Ecuador but for the entire world. Given this problem several contraceptive strategies have been designed and tested, such as surgical sterilization, traditional castration and chemical castration. Each one of these methods has advantages and disadvantages; however, in the context of Ecuador they are not available to the entire population...La sobrepoblación canina ha aumentado drásticamente en la última década, dentro de la cual una gran parte no recibe un cuidado responsable, por lo cual se convierte en un problema social no solo para el Ecuador sino para el mundo entero. Ante esta problemática varias estrategias contraceptivas se han diseñado y probado como la esterilización quirúrgica, la castración tradicional y la castración química. Cada de uno de estos métodos tienen ventajas y desventajas, sin embargo, en el contexto del Ecuador estos no son asequibles para toda la población..

Bioinformatics approaches for assessing microbial communities in the surface ocean

Microbes are vital for life on Earth. Within the oceans, they are the major primary producers of oxygen and contribute greatly to the other biogeochemical cycling of the elements which in turn influence the global climate. These microbes can be found inhabiting the oceans throughout the world and they cover over ~70% of the surface of the Earth. Microbes have evolved in different environments in the oceans and in different ways. To gain an understanding of the microbial communities in the surface oceans in the Arctic and Atlantic oceans environmental scientists based at the University of East Anglia, the University of Groningen and Royal Netherlands Institute for Sea Research collected ocean samples from 68 stations along a transect of the Arctic Ocean, North Atlantic Ocean and South Atlantic Ocean. In addition, they recorded environmental data at the time of sampling, such as temperature and salinity. Genomic DNA from filtered samples was sequenced using high-throughput sequencing. This thesis contains a comprehensive analysis of this sequencing data with the aim of understanding the composition and distribution of microbial communities in the surface of the ocean. To this end, we designed bioinformatic pipelines in order to analyse metatranscriptome, 18S and 16S rDNA datasets from the set of stations. In addition, we developed a novel methodology for normalising 18S and 16S rDNA copy numbers. This enabled us to perform additional analyses such as biodiversity, co-occurrence and breakpoint analyses. The breakpoint analysis is the first of this type performed for microbes in the ocean across a temperature gradient. In our results, we observed a greater diversity of 18S and 16S rDNA taxa in the tropical regions of the South Atlantic Ocean, versus the polar regions of the Arctic Ocean. Moreover, in the co-occurrence analysis of the 18S and 16S rDNA datasets, we found two community networks, one positively correlated to temperature and the other negatively. We also performed a breakpoint analysis on our metatranscriptome, 18S and 16S rDNA datasets and found a shift in diversity occurring in the North Atlantic Ocean. In particular, the shift occurs in the temperate region of the North Atlantic Ocean, between the polar Arctic Ocean and tropical South Atlantic Ocean. These results are important because the co-occurrence analysis enables us to hypothesise that different microbial communities have different preferences for temperature. Moreover, as global warming is predicted to raise the temperatures in the ocean, our results could potentially enable forecasts of how climate change will affect these microbial communities using climate models underpinned by genetic information