Ya tenemos disponibles sus calificaciones de la materia. Pueden pasar con Valeria para la firma de sus actas y conmigo (en Biomédicas) para quien guste recoger sus trabajos.
Monday, June 1, 2015
Thursday, May 14, 2015
Trabajo Semestral
El trabajo semestral consistirá en un trabajo de revisión o de análisis de datos relacionados a los temas del programa, original y creativo, en formato de un artículo de revista científica. La extensión máxima del escrito son 15 páginas incluyendo figuras y bibliografía.
La fecha de entrega del trabajo final será el Viernes 22 de Mayo 2015. Los trabajos los estaré recibiendo en el Insituto de Investigaciones Biomédicas, Nueva sede, edificio C, laboratorio 110.
La fecha de entrega del trabajo final será el Viernes 22 de Mayo 2015. Los trabajos los estaré recibiendo en el Insituto de Investigaciones Biomédicas, Nueva sede, edificio C, laboratorio 110.
Wednesday, May 13, 2015
Lectura 13 Mayo 2015
Complex Ecological Interactions in the Coffee Agroecosystem
Ivette Perfecto, John Vandermeer and Stacy M. Philpott
Coffee agroecosystems have become iconic in the study of how agriculture can contribute to the conservation of biodiversity and how biodiversity can deliver ecosystem services to agriculture. However, coffee farms are also excellent model systems for ecological research. Throughout the tropics coffee farms are cultivated using varying numbers and diversity of shade trees, representing a gradient of diversity and complexity, ranging from forest-like “shade coffee” to intensified shadeless “sun coffee.” Here we synthesize ecological research in the coffee agroecosystem focusing on four topics that have received considerable recent attention: (a) trophic interactions (especially vertebrates and ants as predators), (b) trait-mediated indirect interactions, (c) competition and community assembly (mainly birds and ants), and (d ) spatial constraints on interactions.
Ivette Perfecto, John Vandermeer and Stacy M. Philpott
Coffee agroecosystems have become iconic in the study of how agriculture can contribute to the conservation of biodiversity and how biodiversity can deliver ecosystem services to agriculture. However, coffee farms are also excellent model systems for ecological research. Throughout the tropics coffee farms are cultivated using varying numbers and diversity of shade trees, representing a gradient of diversity and complexity, ranging from forest-like “shade coffee” to intensified shadeless “sun coffee.” Here we synthesize ecological research in the coffee agroecosystem focusing on four topics that have received considerable recent attention: (a) trophic interactions (especially vertebrates and ants as predators), (b) trait-mediated indirect interactions, (c) competition and community assembly (mainly birds and ants), and (d ) spatial constraints on interactions.
Wednesday, May 6, 2015
Lectura 2 - 11 Mayo 2015
Mutualistic Interactions and Biological Invasions
Anna Traveset and David M. Richardson
Mutualisms structure ecosystems and mediate their functioning. They also enhance invasions of many alien species. Invasions disrupt native mutualisms, often leading to population declines, reduced biodiversity, and altered ecosystem functioning. Focusing on three main types of mutualisms (pollination, seed dispersal, and plant-microbial symbioses) and drawing on examples from different ecosystems and from species- and community-level studies, we review the key mechanisms whereby such positive interactions mediate invasions and are in turn influenced by invasions. High interaction generalization is “the norm” in most systems, allowing alien species to infiltrate recipient communities. We identify traits that influence invasiveness (e.g., selfing capacity in plants, animal behavioral traits) or invasibility (e.g., partner choice in mycorrhizas/rhizobia) through mutualistic interactions. Mutualistic disruptions due to invasions are pervasive, and subsequent cascading effects are also widespread. Ecological networks provide a useful framework for predicting tipping points for community collapse in response to invasions and other synergistic drivers of global change.
Anna Traveset and David M. Richardson
Mutualisms structure ecosystems and mediate their functioning. They also enhance invasions of many alien species. Invasions disrupt native mutualisms, often leading to population declines, reduced biodiversity, and altered ecosystem functioning. Focusing on three main types of mutualisms (pollination, seed dispersal, and plant-microbial symbioses) and drawing on examples from different ecosystems and from species- and community-level studies, we review the key mechanisms whereby such positive interactions mediate invasions and are in turn influenced by invasions. High interaction generalization is “the norm” in most systems, allowing alien species to infiltrate recipient communities. We identify traits that influence invasiveness (e.g., selfing capacity in plants, animal behavioral traits) or invasibility (e.g., partner choice in mycorrhizas/rhizobia) through mutualistic interactions. Mutualistic disruptions due to invasions are pervasive, and subsequent cascading effects are also widespread. Ecological networks provide a useful framework for predicting tipping points for community collapse in response to invasions and other synergistic drivers of global change.
Lectura 1 - 11 Mayo 2015
Solar-Powered Sea Slugs. Mollusc/Algal Chloroplast Symbiosis
Mary E. Rumpho, Elizabeth J. Summer, and James R. Manhart
Solar-powered “leaves that crawl”? This description of photosynthetic sea slugs (adapted from Bill Rudman [www.austmus.gov.au/seaslugs/solarpow. htm] and Robert Trench [1975]) aptly describes the symbiotic association that occurs between certain molluscan sea slugs and algal chloroplasts. Faced with life without a protective shell in a predatory environment, some sea slugs evolved a protective mechanism dependent largely upon camouflage provided by symbiont plastids (Fig. 1). Sea slugs in the opisthobranch order of Gastropods, Ascoglossa (! Sacoglossa), have taken this one step further. They feed by slicing or puncturing siphonaceous algal cells and sucking out the cell contents. All of the contents, including the algal nucleus, are discarded except for the chloroplasts, which are engulfed phagocytotically into the digestive cells (see micrographs in Fig. 2, A and B). By distributing the “photosynthetic factories” throughout their extensively branched digestive system just one cell layer beneath the epidermis, the sea slugs not only blend into the green algal bed (Fig. 1C), but also capture light energy to fuel photoautotrophic CO2 fixation.
Mary E. Rumpho, Elizabeth J. Summer, and James R. Manhart
Solar-powered “leaves that crawl”? This description of photosynthetic sea slugs (adapted from Bill Rudman [www.austmus.gov.au/seaslugs/solarpow. htm] and Robert Trench [1975]) aptly describes the symbiotic association that occurs between certain molluscan sea slugs and algal chloroplasts. Faced with life without a protective shell in a predatory environment, some sea slugs evolved a protective mechanism dependent largely upon camouflage provided by symbiont plastids (Fig. 1). Sea slugs in the opisthobranch order of Gastropods, Ascoglossa (! Sacoglossa), have taken this one step further. They feed by slicing or puncturing siphonaceous algal cells and sucking out the cell contents. All of the contents, including the algal nucleus, are discarded except for the chloroplasts, which are engulfed phagocytotically into the digestive cells (see micrographs in Fig. 2, A and B). By distributing the “photosynthetic factories” throughout their extensively branched digestive system just one cell layer beneath the epidermis, the sea slugs not only blend into the green algal bed (Fig. 1C), but also capture light energy to fuel photoautotrophic CO2 fixation.
Monday, May 4, 2015
Lectura 06 Mayo 2015
Geographic isolation trumps coevolution as a driver of yucca and yucca moth diversification
David M. Althoff, Kari A. Segraves, Christopher I. Smith, James Leebens-Mack and Olle Pellmyr
Coevolution is thought to be especially important in diversification of obligate mutualistic interactions such as the one between yuccas and pollinating yucca moths. We took a three-step approach to examine if plant and pollinator speciation events were likely driven by coevolution. First, we tested whether there has been co-speciation between yuccas and pollinator yucca moths in the genus Tegeticula (Prodoxidae). Second, we tested whether co-speciation also occurred between yuccas and commensalistic yucca moths in the genus Prodoxus (Prodoxidae) in which reciprocal evolutionary change is unlikely. Finally, we examined the current range distributions of yuccas in relationship to pollinator speciation events to determine if plant and moth speciation events likely occurred in sympatry or allopatry. Co-speciation analyses of yuccas with their coexisting Tegeticula pollinator and commensalistic Prodoxus lineages demonstratedphylogenetic congruence between both groups of moths and yuccas, even though moth lineages differ in the type of interaction with yuccas. Furthermore, Yucca species within a lineage occur primarily in allopatry rather than sympatry. We conclude that biogeographic factors are the overriding force in plant and pollinator moth speciation and significant phylogenetic congruence between the moth and plant lineages is likely due to shared biogeography rather than coevolution.
David M. Althoff, Kari A. Segraves, Christopher I. Smith, James Leebens-Mack and Olle Pellmyr
Coevolution is thought to be especially important in diversification of obligate mutualistic interactions such as the one between yuccas and pollinating yucca moths. We took a three-step approach to examine if plant and pollinator speciation events were likely driven by coevolution. First, we tested whether there has been co-speciation between yuccas and pollinator yucca moths in the genus Tegeticula (Prodoxidae). Second, we tested whether co-speciation also occurred between yuccas and commensalistic yucca moths in the genus Prodoxus (Prodoxidae) in which reciprocal evolutionary change is unlikely. Finally, we examined the current range distributions of yuccas in relationship to pollinator speciation events to determine if plant and moth speciation events likely occurred in sympatry or allopatry. Co-speciation analyses of yuccas with their coexisting Tegeticula pollinator and commensalistic Prodoxus lineages demonstratedphylogenetic congruence between both groups of moths and yuccas, even though moth lineages differ in the type of interaction with yuccas. Furthermore, Yucca species within a lineage occur primarily in allopatry rather than sympatry. We conclude that biogeographic factors are the overriding force in plant and pollinator moth speciation and significant phylogenetic congruence between the moth and plant lineages is likely due to shared biogeography rather than coevolution.
Wednesday, April 29, 2015
Lectura 04 Mayo 2015
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
Itai Sharon, Michael J. Morowitz, Brian C. Thomas, Elizabeth K. Costello, David A. Relman, and Jillian F. Banfield,
The gastrointestinal microbiome undergoes shifts in species and strain abundances, yet dynamics involving closely related microorganisms remain largely unknown because most methods cannot resolve them. We developed new metagenomic methods and utilized them to track species and strain level variations in microbial communities in 11 fecal samples collected from a premature infant during the first month of life. Ninety six percent of the sequencing reads were assembled into scaffolds of >500 bp in length that could be assigned to organisms at the strain level. Six essentially complete (~99%) and two near-complete genomes were assembled for bacteria that comprised as little as 1% of the community, as well as nine partial genomes of bacteria representing as little as 0.05%. In addition, three viral genomes were assembled and assigned to their hosts. The relative abundance of three Staphylococcus epidermidis strains, as well as three phages that infect them, changed dramatically over time. Genes possibly related to these shifts include those for resistance to antibiotics, heavy metals, and phage. At the species level, we observed the decline of an early-colonizing Propionibacterium acnes strain similar to SK137 and the proliferation of novel Propionibacterium and Peptoniphilus species late in colonization. The Propionibacterium species differed in their ability to metabolize carbon compounds such as inositol and sialic acid, indicating that shifts in species composition likely impact the metabolic potential of the community.
Itai Sharon, Michael J. Morowitz, Brian C. Thomas, Elizabeth K. Costello, David A. Relman, and Jillian F. Banfield,
The gastrointestinal microbiome undergoes shifts in species and strain abundances, yet dynamics involving closely related microorganisms remain largely unknown because most methods cannot resolve them. We developed new metagenomic methods and utilized them to track species and strain level variations in microbial communities in 11 fecal samples collected from a premature infant during the first month of life. Ninety six percent of the sequencing reads were assembled into scaffolds of >500 bp in length that could be assigned to organisms at the strain level. Six essentially complete (~99%) and two near-complete genomes were assembled for bacteria that comprised as little as 1% of the community, as well as nine partial genomes of bacteria representing as little as 0.05%. In addition, three viral genomes were assembled and assigned to their hosts. The relative abundance of three Staphylococcus epidermidis strains, as well as three phages that infect them, changed dramatically over time. Genes possibly related to these shifts include those for resistance to antibiotics, heavy metals, and phage. At the species level, we observed the decline of an early-colonizing Propionibacterium acnes strain similar to SK137 and the proliferation of novel Propionibacterium and Peptoniphilus species late in colonization. The Propionibacterium species differed in their ability to metabolize carbon compounds such as inositol and sialic acid, indicating that shifts in species composition likely impact the metabolic potential of the community.
Monday, April 27, 2015
Lectura 29 Abril 2015
Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity
Ashley Shade, Stuart E. Jones, J. Gregory Caporaso, Jo Handelsman, Rob Knight, Noah Fierer, Jack A. Gilbert
Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT made up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amounts of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified “one-hit wonder” CRT that were observed at only one time point. Using a case study from a temperate lake, we gained additional insights into the ecology of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amount to microbial community dynamics than is apparent from their low proportional abundances. This observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time.
Ashley Shade, Stuart E. Jones, J. Gregory Caporaso, Jo Handelsman, Rob Knight, Noah Fierer, Jack A. Gilbert
Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT made up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amounts of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified “one-hit wonder” CRT that were observed at only one time point. Using a case study from a temperate lake, we gained additional insights into the ecology of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amount to microbial community dynamics than is apparent from their low proportional abundances. This observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time.
Sunday, April 26, 2015
Lectura 27 Abril 2015
The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
Douglas B. Rusch, Aaron L. Halpern, Granger Sutton, Karla B. Heidelberg, Shannon Williamson, Shibu Yooseph, Dongying Wu, Jonathan A. Eisen, Jeff M. Hoffman, Karin Remington, Karen Beeson, Bao Tran, Hamilton Smith, Holly Baden-Tillson, Clare Stewart, Joyce Thorpe, Jason Freeman, Cynthia Andrews-Pfannkoch, Joseph E. Venter, Kelvin Li, Saul Kravitz, John F. Heidelberg, Terry Utterback, Yu-Hui Rogers, Luisa I. Falco´n, Valeria Souza, Germa´n Bonilla-Rosso, Luis E. Eguiarte, David M. Karl, Shubha Sathyendranath, Trevor Platt, Eldredge Bermingham, Victor Gallardo, Giselle Tamayo-Castillo, Michael R. Ferrari, Robert L. Strausberg, Kenneth Nealson, Robert Friedman, Marvin Frazier, J. Craig Venter
The world’s oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed ‘‘fragment recruitment,’’ addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed ‘‘extreme assembly,’’ made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS.
Douglas B. Rusch, Aaron L. Halpern, Granger Sutton, Karla B. Heidelberg, Shannon Williamson, Shibu Yooseph, Dongying Wu, Jonathan A. Eisen, Jeff M. Hoffman, Karin Remington, Karen Beeson, Bao Tran, Hamilton Smith, Holly Baden-Tillson, Clare Stewart, Joyce Thorpe, Jason Freeman, Cynthia Andrews-Pfannkoch, Joseph E. Venter, Kelvin Li, Saul Kravitz, John F. Heidelberg, Terry Utterback, Yu-Hui Rogers, Luisa I. Falco´n, Valeria Souza, Germa´n Bonilla-Rosso, Luis E. Eguiarte, David M. Karl, Shubha Sathyendranath, Trevor Platt, Eldredge Bermingham, Victor Gallardo, Giselle Tamayo-Castillo, Michael R. Ferrari, Robert L. Strausberg, Kenneth Nealson, Robert Friedman, Marvin Frazier, J. Craig Venter
The world’s oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed ‘‘fragment recruitment,’’ addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed ‘‘extreme assembly,’’ made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS.
Monday, April 20, 2015
Lectura 22 Abril 2015
Bacterial biogeography of the human digestive tract
Jennifer C. Stearns, Michael D. J. Lynch1, Dilani B. Senadheera, Howard C. Tenenbaum, Michael B. Goldberg, Dennis G. Cvitkovitch, Kenneth Croitoru, Gabriel Moreno-Hagelsieb & Josh D. Neufeld
We present bacterial biogeography as sampled from the human gastrointestinal tract of four healthy subjects. This study generated .32 million paired-end sequences of bacterial 16S rRNA genes (V3 region) representing .95,000 unique operational taxonomic units (OTUs; 97% similarity clusters), with .99% Good’s coverage for all samples. The highest OTU richness and phylogenetic diversity was found in the mouth samples. The microbial communities of multiple biopsy sites within the colon were highly similar within individuals and largely distinct from those in stool. Within an individual, OTU overlap among broad site definitions (mouth, stomach/duodenum, colon and stool) ranged from 32–110 OTUs, 25 of which were common to all individuals and included OTUs affiliated with Faecalibacterium prasnitzii and the TM7 phylum. This first comprehensive characterization of the abundant and rare microflora found along the healthy human digestive tract represents essential groundwork to investigate further how the human microbiome relates to health and disease.
Jennifer C. Stearns, Michael D. J. Lynch1, Dilani B. Senadheera, Howard C. Tenenbaum, Michael B. Goldberg, Dennis G. Cvitkovitch, Kenneth Croitoru, Gabriel Moreno-Hagelsieb & Josh D. Neufeld
We present bacterial biogeography as sampled from the human gastrointestinal tract of four healthy subjects. This study generated .32 million paired-end sequences of bacterial 16S rRNA genes (V3 region) representing .95,000 unique operational taxonomic units (OTUs; 97% similarity clusters), with .99% Good’s coverage for all samples. The highest OTU richness and phylogenetic diversity was found in the mouth samples. The microbial communities of multiple biopsy sites within the colon were highly similar within individuals and largely distinct from those in stool. Within an individual, OTU overlap among broad site definitions (mouth, stomach/duodenum, colon and stool) ranged from 32–110 OTUs, 25 of which were common to all individuals and included OTUs affiliated with Faecalibacterium prasnitzii and the TM7 phylum. This first comprehensive characterization of the abundant and rare microflora found along the healthy human digestive tract represents essential groundwork to investigate further how the human microbiome relates to health and disease.
Friday, April 17, 2015
Cambio de lectura
Habrá un cambio en las fechas de lecturas intercanbiando de fechas las lecturas del 22 y 29 de Abril, quedando de la siguiente manera:
Miércoles 22 de Abril
Stearns et al. 2011 - Bacterial biogeography of the human digestive tract
Miércoles 29 de Abril
Shade et al. 2014 - Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity.
Miércoles 22 de Abril
Stearns et al. 2011 - Bacterial biogeography of the human digestive tract
Miércoles 29 de Abril
Shade et al. 2014 - Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity.
Lectura 20 Abril 2015
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium
Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.
The Human Microbiome Project Consortium
Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.
Tuesday, April 14, 2015
Lectura 15 Abril 2015
The Neolithic revolution of bacterial genomes
Alex Mira, Ravindra Pushker and Francisco Rodríguez-Valera
Current human activities undoubtedly impact natural ecosystems. However, the influence of Homo sapiens on living organisms must have also occurred in the past. Certain genomic characteristics of prokaryotes can be used to study the impact of ancient human activities on microorganisms. By analyzing DNA sequence similarity features of transposable elements, dramatic genomic changes have been identified in bacteria that are associated with large and stable human communities, agriculture and animal domestication: three features unequivocally linked to the Neolithic revolution. It is hypothesized that bacteria specialized in human-associated niches underwent an intense transformation after the social and demographic changes that took place with the first Neolithic settlements. These genomic changes are absent in related species that are not specialized in humans.
Alex Mira, Ravindra Pushker and Francisco Rodríguez-Valera
Current human activities undoubtedly impact natural ecosystems. However, the influence of Homo sapiens on living organisms must have also occurred in the past. Certain genomic characteristics of prokaryotes can be used to study the impact of ancient human activities on microorganisms. By analyzing DNA sequence similarity features of transposable elements, dramatic genomic changes have been identified in bacteria that are associated with large and stable human communities, agriculture and animal domestication: three features unequivocally linked to the Neolithic revolution. It is hypothesized that bacteria specialized in human-associated niches underwent an intense transformation after the social and demographic changes that took place with the first Neolithic settlements. These genomic changes are absent in related species that are not specialized in humans.
Saturday, April 11, 2015
Lectura 13 Abril 2015
The Tiniest Tiny Genomes
Nancy A. Moran and Gordon M. Bennett
Starting in 2006, surprisingly tiny genomes have been discovered from numerous bacterial symbionts of insect hosts. Despite their size, each retains some genes that enable provisioning of limiting nutrients or other capabilities required by hosts. Genome sequence analyses show that genome reduction is an ongoing process, resulting in a continuum of sizes, with the smallest genome currently known at 112 kilobases. Genome reduction is typical in host-restricted symbionts and pathogens, but the tiniest genomes are restricted to symbionts required by hosts and restricted to specialized host cells, resulting from long coevolution with hosts. Genes are lost in all functional categories, but core genes for central informational processes, including genes encoding ribosomal proteins, are mostly retained, whereas genes underlying production of cell envelope components are especially depleted. Thus, these entities retain cell-like properties but are heavily dependent on coadaptation of hosts, which continuously evolve to support the symbionts upon which they depend.
Nancy A. Moran and Gordon M. Bennett
Starting in 2006, surprisingly tiny genomes have been discovered from numerous bacterial symbionts of insect hosts. Despite their size, each retains some genes that enable provisioning of limiting nutrients or other capabilities required by hosts. Genome sequence analyses show that genome reduction is an ongoing process, resulting in a continuum of sizes, with the smallest genome currently known at 112 kilobases. Genome reduction is typical in host-restricted symbionts and pathogens, but the tiniest genomes are restricted to symbionts required by hosts and restricted to specialized host cells, resulting from long coevolution with hosts. Genes are lost in all functional categories, but core genes for central informational processes, including genes encoding ribosomal proteins, are mostly retained, whereas genes underlying production of cell envelope components are especially depleted. Thus, these entities retain cell-like properties but are heavily dependent on coadaptation of hosts, which continuously evolve to support the symbionts upon which they depend.
Tuesday, April 7, 2015
Lectura 08 Abril 2015
Defining the core Arabidopsis thaliana root microbiome
Derek S. Lundberg, Sarah L. Lebeis, Sur Herrera Paredes, Scott Yourstone, Jase Gehring, Stephanie Malfatti, Julien Tremblay, Anna Engelbrektson,VictorKunin, Tijana Glavina del Rio, Robert C. Edgar, Thilo Eickhorst, Ruth E. Ley, Philip Hugenholtz, Susannah Green Tringe & Jeffery L. Dangl
Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surroundingthe root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation. Colonization of the root occurs despite a sophisticated plant immune system, suggesting finely tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. Here we report the pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophytic compartmentmicrobiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils and in rhizosphere and endophytic compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophytic compartments fromboth soils feature overlapping, low-complexity communities that are markedly enriched in Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stage and genotype. Our rigorous definition of an endophytic compartment microbiome should facilitate controlled dissection of plant–microbe interactions derived from complex soil communities.
Derek S. Lundberg, Sarah L. Lebeis, Sur Herrera Paredes, Scott Yourstone, Jase Gehring, Stephanie Malfatti, Julien Tremblay, Anna Engelbrektson,VictorKunin, Tijana Glavina del Rio, Robert C. Edgar, Thilo Eickhorst, Ruth E. Ley, Philip Hugenholtz, Susannah Green Tringe & Jeffery L. Dangl
Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surroundingthe root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation. Colonization of the root occurs despite a sophisticated plant immune system, suggesting finely tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. Here we report the pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophytic compartmentmicrobiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils and in rhizosphere and endophytic compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophytic compartments fromboth soils feature overlapping, low-complexity communities that are markedly enriched in Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stage and genotype. Our rigorous definition of an endophytic compartment microbiome should facilitate controlled dissection of plant–microbe interactions derived from complex soil communities.
Sunday, April 5, 2015
Lectura 06 Abril 2015
Bacterial-Fungal Interactions: Hyphens between Agricultural, Clinical,Environmental, and Food Microbiologists
P. Frey-Klett, P. Burlinson, A. Deveau, M. Barret, M. Tarkka, and A. Sarniguet
P. Frey-Klett, P. Burlinson, A. Deveau, M. Barret, M. Tarkka, and A. Sarniguet
Tuesday, March 24, 2015
Lectura 25 Marzo 2015
Lifestyle of Vibrio cholerae foster gene transfers
Melanie Blokesh
Waterborne Vibrio cholerae bacteria cause cholera, a pandemic during the last 50 years across Asia, Africa, and Latin America. Although most infected individuals do not develop severe symptoms, some become violently ill with severe diarrhea, vomiting, and cramps, and the loss of body fluids, if untreated, can lead to shock and death. V. cholerae, which is primarily encountered in estuaries, rivers, and coastal waters in its environmental reservoir, is found not only in a free-living state but also associated with phytoplankton and zooplankton (Fig. 1). Because factors such as increasing temperatures, the El Niño phenomenon, and heavy rainfalls and floods can raise the abundance of phytoplankton and zooplankton, and, along with them, cholera bacteria, changing climatic conditions could well drive the re-emergence of cholera.
Melanie Blokesh
Waterborne Vibrio cholerae bacteria cause cholera, a pandemic during the last 50 years across Asia, Africa, and Latin America. Although most infected individuals do not develop severe symptoms, some become violently ill with severe diarrhea, vomiting, and cramps, and the loss of body fluids, if untreated, can lead to shock and death. V. cholerae, which is primarily encountered in estuaries, rivers, and coastal waters in its environmental reservoir, is found not only in a free-living state but also associated with phytoplankton and zooplankton (Fig. 1). Because factors such as increasing temperatures, the El Niño phenomenon, and heavy rainfalls and floods can raise the abundance of phytoplankton and zooplankton, and, along with them, cholera bacteria, changing climatic conditions could well drive the re-emergence of cholera.
Thursday, March 19, 2015
Lectura 23 Marzo 2015
Horizontal gene transfer in evolution: facts and challenges
Luis Boto
The contribution of horizontal gene transfer to evolution has been controversial since it was suggested to be a force driving evolution in the microbial world. In this paper, I review the current standpoint on horizontal gene transfer in evolutionary thinking and discuss how important horizontal gene transfer is in evolution in the broad sense, and particularly in prokaryotic evolution. I review recent literature, asking, first, which processes are involved in the evolutionary success of transferred genes and, secondly, about the extent of horizontal gene transfer towards different evolutionary times. Moreover, I discuss the feasibility of reconstructing ancient phylogenetic relationships in the face of horizontal gene transfer. Finally, I discuss how horizontal gene transfer fits in the current neo-Darwinian evolutionary paradigm and conclude there is a need for a new evolutionary paradigm that includes horizontal gene transfer as well as other mechanisms in the explanation of evolution.
Luis Boto
The contribution of horizontal gene transfer to evolution has been controversial since it was suggested to be a force driving evolution in the microbial world. In this paper, I review the current standpoint on horizontal gene transfer in evolutionary thinking and discuss how important horizontal gene transfer is in evolution in the broad sense, and particularly in prokaryotic evolution. I review recent literature, asking, first, which processes are involved in the evolutionary success of transferred genes and, secondly, about the extent of horizontal gene transfer towards different evolutionary times. Moreover, I discuss the feasibility of reconstructing ancient phylogenetic relationships in the face of horizontal gene transfer. Finally, I discuss how horizontal gene transfer fits in the current neo-Darwinian evolutionary paradigm and conclude there is a need for a new evolutionary paradigm that includes horizontal gene transfer as well as other mechanisms in the explanation of evolution.
Monday, March 16, 2015
Lectura 2 - 18 Marzo 2015
Chemical warfare between microbes promotes biodiversity
Tamás L. Czárán, Rolf F. Hoekstra and Ludo Pagie
Evolutionary processes generating biodiversity and ecological mechanisms maintaining biodiversity seem to be diverse themselves. Conventional explanations of biodiversity such as niche differentiation, density-dependent predation pressure, or habitat heterogeneity seem satisfactory to explain diversity in communities of macrobial organisms such as higher plants and animals. For a long time the often high diversity among microscopic organisms in seemingly uniform environments, the famous ‘‘paradox of the plankton,’’ has been difficult to understand. The biodiversity in bacterial communities has been shown to be sometimes orders of magnitudes higher than the diversity of known macrobial systems. Based on a spatially explicit game theoretical model with multiply cyclic dominance structures, we suggest that antibiotic interactions within microbial communities may be very effective in maintaining diversity.
Tamás L. Czárán, Rolf F. Hoekstra and Ludo Pagie
Evolutionary processes generating biodiversity and ecological mechanisms maintaining biodiversity seem to be diverse themselves. Conventional explanations of biodiversity such as niche differentiation, density-dependent predation pressure, or habitat heterogeneity seem satisfactory to explain diversity in communities of macrobial organisms such as higher plants and animals. For a long time the often high diversity among microscopic organisms in seemingly uniform environments, the famous ‘‘paradox of the plankton,’’ has been difficult to understand. The biodiversity in bacterial communities has been shown to be sometimes orders of magnitudes higher than the diversity of known macrobial systems. Based on a spatially explicit game theoretical model with multiply cyclic dominance structures, we suggest that antibiotic interactions within microbial communities may be very effective in maintaining diversity.
Lectura 1 - 18 Marzo 2015
Evolution of species interactions in a biofilm community
Susse Kirkelund Hansen, Paul B. Rainey, Janus A. J. Haagensen & Søren Molin
Biofilms are spatially structured communities of microbes whose function is dependent on a complex web of symbiotic interactions. Localized interactions within these assemblages are predicted to affect the coexistence of the component species, community structure6 and function, but there have been few explicit empirical analyses of the evolution of interactions. Here we show, with the use of a two-species community, that selection in a spatially structured environment leads to the evolution of an exploitative interaction. Simple mutations in the genome of one species caused it to adapt to the presence of the other, forming an intimate and specialized association. The derived community was more stable and more productive than the ancestral community. Our results show that evolution in a spatially structured environment can stabilize interactions between species, provoke marked changes in their symbiotic nature and affect community function.
Susse Kirkelund Hansen, Paul B. Rainey, Janus A. J. Haagensen & Søren Molin
Biofilms are spatially structured communities of microbes whose function is dependent on a complex web of symbiotic interactions. Localized interactions within these assemblages are predicted to affect the coexistence of the component species, community structure6 and function, but there have been few explicit empirical analyses of the evolution of interactions. Here we show, with the use of a two-species community, that selection in a spatially structured environment leads to the evolution of an exploitative interaction. Simple mutations in the genome of one species caused it to adapt to the presence of the other, forming an intimate and specialized association. The derived community was more stable and more productive than the ancestral community. Our results show that evolution in a spatially structured environment can stabilize interactions between species, provoke marked changes in their symbiotic nature and affect community function.
Sunday, March 8, 2015
Lectura 11 Marzo 2015
The Social Lives of Microbes
Stuart A.West, Stephen P. Diggle, Angus Buckling, Andy Gardner and Ashleigh S. Griffin
Our understanding of the social lives of microbes has been revolutionized over the past 20 years. It used to be assumed that bacteria and other microorganisms lived relatively independent unicellular lives, without the cooperative behaviors that have provoked so much interest in mammals, birds, and insects. However, a rapidly expanding body of research has completely overturned this idea, showing that microbes indulge in a variety of social behaviors involving complex systems of cooperation, communication, and synchronization. Work in this area has already provided some elegant experimental tests of social evolutionary theory, demonstrating the importance of factors such as relatedness, kin discrimination, competition between relatives, and enforcement of cooperation. Our aim here is to review these social behaviors, emphasizing the unique opportunities they offer for testing existing evolutionary theory as well as highlighting the novel theoretical problems that they pose.
Stuart A.West, Stephen P. Diggle, Angus Buckling, Andy Gardner and Ashleigh S. Griffin
Our understanding of the social lives of microbes has been revolutionized over the past 20 years. It used to be assumed that bacteria and other microorganisms lived relatively independent unicellular lives, without the cooperative behaviors that have provoked so much interest in mammals, birds, and insects. However, a rapidly expanding body of research has completely overturned this idea, showing that microbes indulge in a variety of social behaviors involving complex systems of cooperation, communication, and synchronization. Work in this area has already provided some elegant experimental tests of social evolutionary theory, demonstrating the importance of factors such as relatedness, kin discrimination, competition between relatives, and enforcement of cooperation. Our aim here is to review these social behaviors, emphasizing the unique opportunities they offer for testing existing evolutionary theory as well as highlighting the novel theoretical problems that they pose.
Lectura 09 Marzo 2015
The Genotypic View of Social Interactions in Microbial Communities
Sara Mitri and Kevin Richard Foster
Dense and diverse microbial communities are found in many environments. Disentangling the social interactions between strains and species is central to understanding microbes and how they respond to perturbations. However, the study of social evolution in microbes tends to focus on single species. Here, we broaden this perspective and review evolutionary and ecological theory relevant to microbial interactions across all phylogenetic scales. Despite increased complexity, we reduce the theory to a simple null model that we call the genotypic view. This states that cooperation will occur when cells are surrounded by identical genotypes at the loci that drive interactions, with genetic identity coming from recent clonal growth or horizontal gene transfer (HGT). In contrast, because cooperation is only expected to evolve between different genotypes under restrictive ecological conditions, different genotypes will typically compete. Competition between two genotypes includes mutual harm but, importantly, also many interactions that are beneficial to one of the two genotypes, such as predation. The literature offers support for the genotypic view with relatively few examples of cooperation between genotypes. However, the study of microbial interactions is still at an early stage.Weoutline the logic andmethods that help to better evaluate our perspective and move us toward rationally engineering microbial communities to our own advantage
Sara Mitri and Kevin Richard Foster
Dense and diverse microbial communities are found in many environments. Disentangling the social interactions between strains and species is central to understanding microbes and how they respond to perturbations. However, the study of social evolution in microbes tends to focus on single species. Here, we broaden this perspective and review evolutionary and ecological theory relevant to microbial interactions across all phylogenetic scales. Despite increased complexity, we reduce the theory to a simple null model that we call the genotypic view. This states that cooperation will occur when cells are surrounded by identical genotypes at the loci that drive interactions, with genetic identity coming from recent clonal growth or horizontal gene transfer (HGT). In contrast, because cooperation is only expected to evolve between different genotypes under restrictive ecological conditions, different genotypes will typically compete. Competition between two genotypes includes mutual harm but, importantly, also many interactions that are beneficial to one of the two genotypes, such as predation. The literature offers support for the genotypic view with relatively few examples of cooperation between genotypes. However, the study of microbial interactions is still at an early stage.Weoutline the logic andmethods that help to better evaluate our perspective and move us toward rationally engineering microbial communities to our own advantage
Thursday, February 26, 2015
Taller R
Ya se encuentran en la carpeta del curso tanto el tutoral de R de lo que se vio en la clase con Jonás, como el set de datos para que puedan practicar lo visto.
Friday, February 20, 2015
Lectura 23 Febrero 2015
The nested assembly of plant–animal mutualistic networks
Jordi Bascompte, Pedro Jordano, Carlos J. Melián, and Jens M. Olesen
Most studies of plant–animal mutualisms involve a small number of species. There is almost no information on the structural organization of species-rich mutualistic networks despite its potential importance for the maintenance of diversity. Here we analyze 52 mutualistic networks and show that they are highly nested; that is, the more specialist species interact only with proper subsets of those species interacting with the more generalists. This assembly pattern generates highly asymmetrical interactions and organizes the community cohesively around a central core of interactions. Thus, mutualistic networks are neither randomly assembled nor organized in compartments arising from tight, parallel specialization. Furthermore, nestedness increases with the complexity (number of interactions) of the network: for a given number of species, communities with more interactions are significantly more nested. Our results indicate a nonrandom pattern of community organization that may be relevant for our understanding of the organization and persistence of biodiversity.
Jordi Bascompte, Pedro Jordano, Carlos J. Melián, and Jens M. Olesen
Most studies of plant–animal mutualisms involve a small number of species. There is almost no information on the structural organization of species-rich mutualistic networks despite its potential importance for the maintenance of diversity. Here we analyze 52 mutualistic networks and show that they are highly nested; that is, the more specialist species interact only with proper subsets of those species interacting with the more generalists. This assembly pattern generates highly asymmetrical interactions and organizes the community cohesively around a central core of interactions. Thus, mutualistic networks are neither randomly assembled nor organized in compartments arising from tight, parallel specialization. Furthermore, nestedness increases with the complexity (number of interactions) of the network: for a given number of species, communities with more interactions are significantly more nested. Our results indicate a nonrandom pattern of community organization that may be relevant for our understanding of the organization and persistence of biodiversity.
Monday, February 16, 2015
Febrero 2015
Local dispersal promotes biodiversity in a real-life game of rock–paper–scissors
Benjamin Kerr, Margaret A. Riley, Marcus W. Feldman and Brendan J. M. Bohannan
One of the central aims of ecology is to identify mechanisms that maintain biodiversity. Numerous theoretical models have shown that competing species can coexist if ecological processes such as dispersal, movement, and interaction occur over small spatial scales. In particular, this may be the case for nontransitive communities, that is, those without strict competitive hierarchies. The classic non-transitive system involves a community of three competing species satisfying a relationship similar to the children’s game rock–paper–scissors, where rock crushes scissors, scissors cuts paper, and paper covers rock. Such relationships have been demonstrated in several natural systems. Some models predict that local interaction and dispersal are sufficient to ensure coexistence of all three species in such a community, whereas diversity is lost when ecological processes occur over larger scales. Here, we test these predictions empirically using a non-transitive model community containing three populations of Escherichia coli. We find that diversity is rapidly lost in our experimental community when dispersal and interaction occur over relatively large spatial scales, whereas all populations coexist when ecological processes are localized.
Benjamin Kerr, Margaret A. Riley, Marcus W. Feldman and Brendan J. M. Bohannan
One of the central aims of ecology is to identify mechanisms that maintain biodiversity. Numerous theoretical models have shown that competing species can coexist if ecological processes such as dispersal, movement, and interaction occur over small spatial scales. In particular, this may be the case for nontransitive communities, that is, those without strict competitive hierarchies. The classic non-transitive system involves a community of three competing species satisfying a relationship similar to the children’s game rock–paper–scissors, where rock crushes scissors, scissors cuts paper, and paper covers rock. Such relationships have been demonstrated in several natural systems. Some models predict that local interaction and dispersal are sufficient to ensure coexistence of all three species in such a community, whereas diversity is lost when ecological processes occur over larger scales. Here, we test these predictions empirically using a non-transitive model community containing three populations of Escherichia coli. We find that diversity is rapidly lost in our experimental community when dispersal and interaction occur over relatively large spatial scales, whereas all populations coexist when ecological processes are localized.
Lectura 3 - 18 Febrero 2015
Chemical warfare from an ecological perspective
Richard E. Lenski and Margaret A. Riley
Chemical weapons are recent acquisitions in humankind’s ever-growing arsenal of destruction. But bacteria and fungi have been practicing chemical warfare for a very long time. Among the numerous and structurally diverse antimicrobial agents that microbes produce are penicillin by the mold Penicillium notatum, many important antibiotics by streptomycetes, a wide range of bacteriocins by Escherichia coli and most other bacteria (including the food preservative, nisin, by Lactococcus lactis), and killer toxins by the yeast Saccharomyces cerevisiae.
Richard E. Lenski and Margaret A. Riley
Chemical weapons are recent acquisitions in humankind’s ever-growing arsenal of destruction. But bacteria and fungi have been practicing chemical warfare for a very long time. Among the numerous and structurally diverse antimicrobial agents that microbes produce are penicillin by the mold Penicillium notatum, many important antibiotics by streptomycetes, a wide range of bacteriocins by Escherichia coli and most other bacteria (including the food preservative, nisin, by Lactococcus lactis), and killer toxins by the yeast Saccharomyces cerevisiae.
Lectura 2 - 18 Febrero
Red Queen Hypothesis
Paul N. Pearson
It has long been debated to what extent evolution is driven by environmental change and to what extent it is driven by competitive interactions between species. A simple model that encapsulates the competitive aspect of coevolution was proposed by Leigh Van Valen in 1973 and termed the Red Queen hypothesis. Like all good scientific models, it had the effect of simplifying the issues and focusing the debate, and hence it has become an influential part of evolutionary theory.
Paul N. Pearson
It has long been debated to what extent evolution is driven by environmental change and to what extent it is driven by competitive interactions between species. A simple model that encapsulates the competitive aspect of coevolution was proposed by Leigh Van Valen in 1973 and termed the Red Queen hypothesis. Like all good scientific models, it had the effect of simplifying the issues and focusing the debate, and hence it has become an influential part of evolutionary theory.
Thursday, February 12, 2015
Lectura 18 Febrero
The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss
J. Jeffrey Morris, Richard E. Lenski and Erik R. Zinser
Reductive genomic evolution, driven by genetic drift, is common in endosymbiotic bacteria. Genome reduction is less common in free-living organisms, but it has occurred in the numerically dominant open-ocean bacterioplankton Prochlorococcus and “Candidatus Pelagibacter,” and in these cases the reduction appears to be driven by natural selection rather than drift. Gene loss in free-living organisms may leave them dependent on cooccurring microbes for lost metabolic functions. We present the Black Queen Hypothesis (BQH), a novel theory of reductive evolution that explains how selection leads to such dependencies; its name refers to the queen of spades in the game Hearts, where the usual strategy is to avoid taking this card. Gene loss can provide a selective advantage by conserving an organism’s limiting resources, provided the gene’s function is dispensable. Many vital genetic functions are leaky, thereby unavoidably producing public goods that are available to the entire community. Such leaky functions are thus dispensable for individuals, provided they are not lost entirely from the community. The BQH predicts that the loss of a costly, leaky function is selectively favored at the individual level and will proceed until the production of public goods is just sufficient to support the equilibrium community; at that point, the benefit of any further loss would be offset by the cost. Evolution in accordance with the BQH thus generates “beneficiaries” of reduced genomic content that are dependent on leaky “helpers,” and it may explain the observed nonuniversality of prototrophy, stress resistance, and other cellular functions in the microbial world.
J. Jeffrey Morris, Richard E. Lenski and Erik R. Zinser
Reductive genomic evolution, driven by genetic drift, is common in endosymbiotic bacteria. Genome reduction is less common in free-living organisms, but it has occurred in the numerically dominant open-ocean bacterioplankton Prochlorococcus and “Candidatus Pelagibacter,” and in these cases the reduction appears to be driven by natural selection rather than drift. Gene loss in free-living organisms may leave them dependent on cooccurring microbes for lost metabolic functions. We present the Black Queen Hypothesis (BQH), a novel theory of reductive evolution that explains how selection leads to such dependencies; its name refers to the queen of spades in the game Hearts, where the usual strategy is to avoid taking this card. Gene loss can provide a selective advantage by conserving an organism’s limiting resources, provided the gene’s function is dispensable. Many vital genetic functions are leaky, thereby unavoidably producing public goods that are available to the entire community. Such leaky functions are thus dispensable for individuals, provided they are not lost entirely from the community. The BQH predicts that the loss of a costly, leaky function is selectively favored at the individual level and will proceed until the production of public goods is just sufficient to support the equilibrium community; at that point, the benefit of any further loss would be offset by the cost. Evolution in accordance with the BQH thus generates “beneficiaries” of reduced genomic content that are dependent on leaky “helpers,” and it may explain the observed nonuniversality of prototrophy, stress resistance, and other cellular functions in the microbial world.
Thursday, February 5, 2015
Lectura 11 Febrero
Evolution of microbial markets
Gijsbert D. A. Werner, Joan E. Strassmann, Aniek B. F. Ivens, Daniel J. P. Engelmoer, Erik Verbruggen, David C. Queller, Ronald Noë, Nancy Collins Johnson, Peter Hammerstein, and E. Toby Kiers
Biological market theory has been used successfully to explain cooperative behavior in many animal species. Microbes also engage in cooperative behaviors, both with hosts and other microbes, that can be described in economic terms. However, a market approach is not traditionally used to analyze these interactions. Here, we extend the biological market framework to ask whether this theory is of use to evolutionary biologists studying microbes. We consider six economic strategies used by microbes to optimize their success in markets. We argue that an economic market framework is a useful tool to generate specific and interesting predictions about microbial interactions, including the evolution of partner discrimination, hoarding strategies, specialized versus diversified mutualistic services, and the role of spatial structures, such as flocks and consortia. There is untapped potential for studying the evolutionary dynamics of microbial systems. Market theory can help structure this potential by characterizing strategic investment of microbes across a diversity of conditions.
Gijsbert D. A. Werner, Joan E. Strassmann, Aniek B. F. Ivens, Daniel J. P. Engelmoer, Erik Verbruggen, David C. Queller, Ronald Noë, Nancy Collins Johnson, Peter Hammerstein, and E. Toby Kiers
Biological market theory has been used successfully to explain cooperative behavior in many animal species. Microbes also engage in cooperative behaviors, both with hosts and other microbes, that can be described in economic terms. However, a market approach is not traditionally used to analyze these interactions. Here, we extend the biological market framework to ask whether this theory is of use to evolutionary biologists studying microbes. We consider six economic strategies used by microbes to optimize their success in markets. We argue that an economic market framework is a useful tool to generate specific and interesting predictions about microbial interactions, including the evolution of partner discrimination, hoarding strategies, specialized versus diversified mutualistic services, and the role of spatial structures, such as flocks and consortia. There is untapped potential for studying the evolutionary dynamics of microbial systems. Market theory can help structure this potential by characterizing strategic investment of microbes across a diversity of conditions.
Lectura 09 Febrero
Microbial interactions: from networks to models
Karoline Faust and Jeroen RaesMetagenomics and 16S pyrosequencing have enabled the study of ecosystem structure and dynamics to great depth and accuracy. Co-occurrence and correlation patterns found in these data sets are increasingly used for the prediction of species interactions in environments ranging from the oceans to the human microbiome. In addition, parallelized co-culture assays and combinatorial labelling experiments allow high-throughput discovery of cooperative and competitive relationships between species.
Friday, January 30, 2015
Lectura 04 Febrero
What Ecologists Can Tell Virologists
John J. Dennehy
Ecology as a science evolved from natural history, the observational study of the interactions of plants and animals with each other and their environments. As natural history matured, it became increasingly quantitative, experimental, and taxonomically broad. Focus diversified beyond the Eukarya to include the hidden world of microbial life. Microbes, particularly viruses, were shown to exist in unfathomable numbers, affecting every living organism. Slowly viruses came to be viewed in an ecological context rather than as abstract, disease-causing agents. This shift is exemplified by an increasing tendency to refer to viruses as living organisms instead of inert particles. In recent years, researchers have recognized the critical contributions of viruses to fundamental ecological processes such as biogeochemical cycling, competition, community structuring, and horizontal gene transfer.
John J. Dennehy
Ecology as a science evolved from natural history, the observational study of the interactions of plants and animals with each other and their environments. As natural history matured, it became increasingly quantitative, experimental, and taxonomically broad. Focus diversified beyond the Eukarya to include the hidden world of microbial life. Microbes, particularly viruses, were shown to exist in unfathomable numbers, affecting every living organism. Slowly viruses came to be viewed in an ecological context rather than as abstract, disease-causing agents. This shift is exemplified by an increasing tendency to refer to viruses as living organisms instead of inert particles. In recent years, researchers have recognized the critical contributions of viruses to fundamental ecological processes such as biogeochemical cycling, competition, community structuring, and horizontal gene transfer.
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