Contribution of soil bacteria to the atmosphere across biomes

Artículo escrito por un elevado número de autores, solo se referencian el que aparece en primer lugar, los autores pertenecientes a la UAM y el nombre del grupo de colaboración, si lo hubiereThe dispersion of microorganisms through the atmosphere is a continual and essential process that underpins biogeography and ecosystem development and function. Despite the ubiquity of atmospheric microorganisms globally, specific knowledge of the determinants of atmospheric microbial diversity at any given location remains unresolved. Here we describe bacterial diversity in the atmospheric boundary layer and underlying soil at twelve globally distributed locations encompassing all major biomes, and characterise the contribution of local and distant soils to the observed atmospheric community. Across biomes the diversity of bacteria in the atmosphere was negatively correlated with mean annual precipitation but positively correlated to mean annual temperature. We identified distinct non-randomly assembled atmosphere and soil communities from each location, and some broad trends persisted across biomes including the enrichment of desiccation and UV tolerant taxa in the atmospheric community. Source tracking revealed that local soils were more influential than distant soil sources in determining observed diversity in the atmosphere, with more emissive semi-arid and arid biomes contributing most to signatures from distant soil. Our findings highlight complexities in the atmospheric microbiota that are relevant to understanding regional and global ecosystem connectivityThis work was supported by the Singapore Ministry of Education and Yale-NUS College, grant number R-607-265-331-12

Analysis by RNA-seq of transcriptomic changes elicited by heat shock in Leishmania major

Besides their medical relevance, Leishmania is an adequate model for studying post-transcriptional mechanisms of gene expression. In this microorganism, mRNA degradation/stabilization mechanisms together with translational control and post-translational modifications of proteins are the major drivers of gene expression. Leishmania parasites develop as promastigotes in sandflies and as amastigotes in mammalians, and during host transmission, the parasite experiences a sudden temperature increase. Here, changes in the transcriptome of Leishmania major promastigotes after a moderate heat shock were analysed by RNA-seq. Several of the up-regulated transcripts code for heat shock proteins, other for proteins previously reported to be amastigote-specific and many for hypothetical proteins. Many of the transcripts experiencing a decrease in their steady-state levels code for transporters, proteins involved in RNA metabolism or translational factors. In addition, putative long noncoding RNAs were identified among the differentially expressed transcripts. Finally, temperature-dependent changes in the selection of the spliced leader addition sites were inferred from the RNA-seq data, and particular cases were further validated by RT-PCR and Northern blotting. This study provides new insights into the post-transcriptional mechanisms by which Leishmania modulate gene expressionThis work was supported by grants (to B.A. and J.M.R.) from Ministerio de Economía, Industria y Competitividad, project number SAF2017-86965-R (co-funded with FEDER funds), and by the Network of Tropical Diseases Research RICET (RD16/0027/0008), co-funded with FEDER funds. The CBMSO receives institutional grants from the Fundación Ramón Areces and from the Fundación Banco de Santande

Estudio comparativo del splicing alternativo del gen NCR3 en diferentes especies de mamíferos y sus posibles implicaciones funcionales

Tesis doctoral inédita. Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 13-12-2013Alternative splicing (AS) is a major source of transcriptome and proteome diversity in higher eukaryotes allowing the generation of several structurally and functionally distinct mRNAs and protein isoforms from a single gene. Differential AS variants expression has been implicated in tissue and cellular differentiation, which in an evolutionary context could account for the phenotypic divergence of mammals that share a common repertoire of genes. On the other hand, the miss-regulation of AS is one of the mayor sources of human disease. However, there are not many detailed comparative analyses showing the alternative splice forms generated from particular genes among different organisms. The work presented here is a deep study of the splice variants expressed by the “Natural Cytotoxicity Receptor 3” (NCR3) gene and its comparative analysis among 13 mammals. NCR3 is a member of the NCR family, which represents the major NK cells triggering receptors. It has been involved in the recognition and killing of tumoral and infected cells, and in the maturation of dendritic cells. By using a combination of nested RT-PCR and RNA-seq analysis, it was possible to detect the expression of several NCR3 transcripts in all the analysed mammalian species, except in Mus musculus, where NCR3 is a pseudogen. It was observed an increase in the number of coding variants in primates, mainly by the internal splicing of exon 2 and the presence of exons 4II and 4III, which are only expressed in higher primates (Hominoidea). In contrast, the diversity of non-coding variants is similar among all analysed species, although there are some conserved ones, which could have a potential regulatory role. The nine human splice variants, six coding and three non-coding, were only detected at high expression levels in immune-related tissues, being the coding A, B y C the most abundant ones. The predicted human protein isoforms are potential transmembrane type I receptors, which extracellular domains are predicted to be Immunoglobulin type V (IgV) or type C (IgC). The interaction of these potential NCR3 extracellular domains with the ligand B7-H6 was analysed using flow citometry assays. Firstly, they were over-expressed in insect cells finding that defective glycosylation avoids binding. In a second approach, it was used a mammalian system detecting only specific binding of IgV domain to B7H6, indicating that B7H6 is not a ligand for IgC containing isoforms. In conclusion, all the presented data suggest a potential role of AS in the NCR3 functions and immune system regulation and evolution

Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake

© 2015 John Wiley & Sons Ltd. RNA viruses exist as complex mixtures of genotypes, known as quasispecies, where the evolution potential resides in the whole community of related genotypes. Quasispecies structure and dynamics have been studied in detail for virus infecting animals and plants but remain unexplored for those infecting micro-organisms in environmental samples. We report the first metagenomic study of RNA viruses in an Antarctic lake (Lake Limnopolar, Livingston Island). Similar to low-latitude aquatic environments, this lake harbours an RNA virome dominated by positive single-strand RNA viruses from the order Picornavirales probably infecting micro-organisms. Antarctic picorna-like virus 1 (APLV1), one of the most abundant viruses in the lake, does not incorporate any mutation in the consensus sequence from 2006 to 2010 and shows stable quasispecies with low-complexity indexes. By contrast, APLV2-APLV3 are detected in the lake water exclusively in summer samples and are major constituents of surrounding cyanobacterial mats. Their quasispecies exhibit low complexity in cyanobacterial mat, but their run-off-mediated transfer to the lake results in a remarkable increase of complexity that may reflect the convergence of different viral quasispecies from the catchment area or replication in a more diverse host community. This is the first example of viral quasispecies from natural aquatic ecosystems and points to ecological connectivity as a modulating factor of quasispecies complexity.Spanish Polar Programme and the Spanish Ministry of Economy and Competitiveness (CTM2008-05134-E/ANT and CTM2009-08644-E).Peer Reviewe

Leishmania mitochondrial genomes: Maxicircle structure and heterogeneity of minicircles

The mitochondrial DNA (mtDNA), which is present in almost all eukaryotic organisms, is a useful marker for phylogenetic studies due to its relative high conservation and its inheritance manner. In Leishmania and other trypanosomatids, the mtDNA (also referred to as kinetoplast DNA or kDNA) is composed of thousands of minicircles and a few maxicircles, catenated together into a complex network. Maxicircles are functionally similar to other eukaryotic mtDNAs, whereas minicircles are involved in RNA editing of some maxicircle-encoded transcripts. Next-generation sequencing (NGS) is increasingly used for assembling nuclear genomes and, currently, a large number of genomic sequences are available. However, most of the time, the mitochondrial genome is ignored in the genome assembly processes. The aim of this study was to develop a pipeline to assemble Leishmania minicircles and maxicircle DNA molecules, exploiting the raw data generated in the NGS projects. As a result, the maxicircle molecules and the plethora of minicircle classes for Leishmania major, Leishmania infantum and Leishmania braziliensis have been characterized. We have observed that whereas the heterogeneity of minicircle sequences existing in a single cell hampers their use for Leishmania typing and classification, maxicircles emerge as an extremely robust genetic marker for taxonomic studies within the clade of kinetoplastidsThis work was supported by grants (to B.A. and J.M.R.) from Proyecto del Ministerio de Economía, Industria y Competitividad SAF2017-86965-R, and by the Network of Tropical Diseases Research RICET (RD16/0027/0008); both grants are co-funded with FEDER funds. The CBMSO receives institutional grants from the Fundación Ramón Areces and from the Fundación Banco de Santande

Simulation and comparative analysis of waste in concrete slabs

Construction sector generates significant amounts of waste that affects the environment and obsturcts a sustainable development. The horizontal structure (slabs and roofs) is one of the building elements, by its functional requirement (geometry and layout) and volume, who uses more raw material for its constitution (potential generators of waste) On the other hand, the choice of the system to use, is typically based on criteria such as the ease of construction, the economy availability or the tecnological feasibility; so, from a sustainable perspective, the generation of waste has not been considered or evaluated. This work compares and analyzes four different common elements used in slabs and the possible generation of waste produced for the construction and eventual demolition of them, in order to provide a new weighiting criterion in the choice.Peer ReviewedPostprint (published version

Simulation and comparative analysis of waste in concrete slabs

Construction sector generates significant amounts of waste that affects the environment and obstructs a sustainable development. The horizontal structure (slabs and roofs) is one of the building elements, by its functional requirement (geometry and layout) and volume, who uses more raw material for its constitution (potential generators of waste) On the other hand, the choice of the system to use, is typically based on criteria such as the ease of construction, the economy availability or the technological feasibility; so, from a sustainable perspective, the generation of waste has not been considered or evaluated. This work compares and analyzes four different common elements used in slabs and the possible generation of waste produced for the construction and eventual demolition of them, in order to provide a new weighting criterion in the choice.Peer ReviewedPostprint (published version

Monitoring of airborne biological particles in outdoor atmosphere. Part 2: Metagenomics applied to urban environments

The air we breathe contains microscopic biological particles such as viruses, bacteria, fungi and pollen, some of them with relevant clinic importance. These organisms and/or their propagules have been traditionally studied by different disciplines and diverse methodologies like culture and microscopy. These techniques require time, expertise and also have some important biases. As a consequence, our knowledge on the total diversity and the relationships between the different biological entities present in the air is far from being complete. Currently, metagenomics and next-generation sequencing (NGS) may resolve this shortage of information and have been recently applied to metropolitan areas. Although the procedures and methods are not totally standardized yet, the first studies from urban air samples confirm the previous results obtained by culture and microscopy regarding abundance and variation of these biological particles. However, DNA-sequence analyses call into question some preceding ideas and also provide new interesting insights into diversity and their spatial distribution inside the cities. Here, we review the procedures, results and perspectives of the recent works that apply NGS to study the main biological particles present in the air of urban environments. [Int Microbiol 19(2): 69-80 (2016)]Keywords: airborne biological particles · metagenomics · next-generation sequencing (NGS) · air biomonitoring · urban aerobiolog

Monitoring of the airborne biological particles in outdoor atmosphere. Part 1: Importance, variability and ratios

The first part of this review (“Monitoring of airborne biological particles in outdoor atmosphere. Part 1: Importance, variability and ratios”) describes the current knowledge on the major biological particles present in the air regarding their global distribution, concentrations, ratios and influence of meteorological factors in an attempt to provide a framework for monitoring their biodiversity and variability in such a singular environment as the atmosphere. Viruses, bacteria, fungi, pollen and fragments thereof are the most abundant microscopic biological particles in the air outdoors. Some of them can cause allergy and severe diseases in humans, other animals and plants, with the subsequent economic impact. Despite the harsh conditions, they can be found from land and sea surfaces to beyond the troposphere and have been proposed to play a role also in weather conditions and climate change by acting as nucleation particles and inducing water vapour condensation. In regards to their global distribution, marine environments act mostly as a source for bacteria while continents additionally provide fungal and pollen elements. Within terrestrial environments, their abundances and diversity seem to be influenced by the land-use type (rural, urban, coastal) and their particularities. Temporal variability has been observed for all these organisms, mostly triggered by global changes in temperature, relative humidity, et cetera. Local fluctuations in meteorological factors may also result in pronounced changes in the airbiota. Although biological particles can be transported several hundreds of meters from the original source, and even intercontinentally, the time and final distance travelled are strongly influenced by factors such as wind speed and direction. [Int Microbiol 2016; 19(1):1-1 3]Keywords: airborne biological particles · airbiota · bioaerosols · meteorological factors · air-genome ratio

Variability of the Pr77 sequence of L1Tc retrotransposon among six T. cruzi strains belonging to different discrete typing units (DTUs)

All trypanosomatid genomes are colonized by non-LTR retrotransposons which exhibit a highly conserved 77-nt sequence at their 5′ ends, known as the Pr77-hallmark (Pr77). The wide distribution of Pr77 is expected to be related to the gene regulation processes in these organisms as it has promoter and HDV-like ribozyme activities at the DNA and RNA levels, respectively. The identification of Pr77 hallmark-bearing retrotransposons and the study of the associations of mobile elements with relevant genes have been analyzed in the genomes of six strains of Trypanosoma cruzi belonging to different discrete typing units (DTUs) and with different geographical origins and host/vectors. The genomes have been sequenced, assembled and annotated. BUSCO analyses indicated a good quality for the assemblies that were used in comparative analyses. The results show differences among the six genomes in the copy number of genes related to virulence processes, the abundance of retrotransposons bearing the Pr77 sequence and the presence of the Pr77 hallmarks not associated with retroelements. The analyses also show frequent associations of Pr77-bearing retrotransposons and single Pr77 hallmarks with genes coding for trans-sialidases, RHS, MASP or hypothetical proteins, showing variable proportion depending on the type of retroelement, gene class and parasite strain. These differences in the genomic distribution of active retroelements and other Pr77-containing elements have shaped the genome architecture of these six strains and might be contributing to the phenotypic variability existing among the