Back to the future of soil metagenomics

Direct extraction and characterization of microbial community DNA through PCR amplicon surveys and metagenomics has revolutionized the study of environmental microbiology and microbial ecology. In particular, metagenomic analysis of nucleic acids provides direct access to the genomes of the “uncultivated majority.” Accelerated by advances in sequencing technology, microbiologists have discovered more novel phyla, classes, genera, and genes from microorganisms in the first decade and a half of the twenty-first century than since these “many very little living animalcules” were first discovered by van Leeuwenhoek. The unsurpassed diversity of soils promises continued exploration of a range of industrial, agricultural, and environmental functions. The ability to explore soil microbial communities with increasing capacity offers the highest promise for answering many outstanding who, what, where, when, why, and with whom questions such as: Which microorganisms are linked to which soil habitats? How do microbial abundances change with changing edaphic conditions? How do microbial assemblages interact and influence one another synergistically or antagonistically? What is the full extent of soil microbial diversity, both functionally and phylogenetically? What are the dynamics of microbial communities in space and time? How sensitive are microbial communities to a changing climate? What is the role of horizontal gene transfer in the stability of microbial communities? Do highly diverse microbial communities confer resistance and resilience in soils?La lista completa de autores que integran el documento puede consultarse en el archivo.Facultad de Ciencias Exacta

Back to the future of soil metagenomics

Direct extraction and characterization of microbial community DNA through PCR amplicon surveys and metagenomics has revolutionized the study of environmental microbiology and microbial ecology. In particular, metagenomic analysis of nucleic acids provides direct access to the genomes of the “uncultivated majority.” Accelerated by advances in sequencing technology, microbiologists have discovered more novel phyla, classes, genera, and genes from microorganisms in the first decade and a half of the twenty-first century than since these “many very little living animalcules” were first discovered by van Leeuwenhoek. The unsurpassed diversity of soils promises continued exploration of a range of industrial, agricultural, and environmental functions. The ability to explore soil microbial communities with increasing capacity offers the highest promise for answering many outstanding who, what, where, when, why, and with whom questions such as: Which microorganisms are linked to which soil habitats? How do microbial abundances change with changing edaphic conditions? How do microbial assemblages interact and influence one another synergistically or antagonistically? What is the full extent of soil microbial diversity, both functionally and phylogenetically? What are the dynamics of microbial communities in space and time? How sensitive are microbial communities to a changing climate? What is the role of horizontal gene transfer in the stability of microbial communities? Do highly diverse microbial communities confer resistance and resilience in soils?La lista completa de autores que integran el documento puede consultarse en el archivo.Facultad de Ciencias Exacta

Back to the future of soil metagenomics

Direct extraction and characterization of microbial community DNA through PCR amplicon surveys and metagenomics has revolutionized the study of environmental microbiology and microbial ecology. In particular, metagenomic analysis of nucleic acids provides direct access to the genomes of the “uncultivated majority.” Accelerated by advances in sequencing technology, microbiologists have discovered more novel phyla, classes, genera, and genes from microorganisms in the first decade and a half of the twenty-first century than since these “many very little living animalcules” were first discovered by van Leeuwenhoek. The unsurpassed diversity of soils promises continued exploration of a range of industrial, agricultural, and environmental functions. The ability to explore soil microbial communities with increasing capacity offers the highest promise for answering many outstanding who, what, where, when, why, and with whom questions such as: Which microorganisms are linked to which soil habitats? How do microbial abundances change with changing edaphic conditions? How do microbial assemblages interact and influence one another synergistically or antagonistically? What is the full extent of soil microbial diversity, both functionally and phylogenetically? What are the dynamics of microbial communities in space and time? How sensitive are microbial communities to a changing climate? What is the role of horizontal gene transfer in the stability of microbial communities? Do highly diverse microbial communities confer resistance and resilience in soils?La lista completa de autores que integran el documento puede consultarse en el archivo.Facultad de Ciencias Exacta

The Plasmid Mobilome of the Model Plant-Symbiont Sinorhizobium meliloti: Coming up with New Questions and Answers

Rhizobia are Gram-negative Alpha- andBetaproteobacteria living in the underground that have theability to associate with legumes for the establishment ofnitrogen-fixing symbioses.Sinorhizobium melilotiinparticular—the symbiont ofMedicago,Melilotus, andTrigonellaspp.—has for the past decades served as a model organism forinvestigating, at the molecular level, the biology, biochemistry,and genetics of a free-living and symbiotic soil bacterium ofagricultural relevance. To date, the genomes of seven differentS. melilotistrains have been fully sequenced and annotated,and several other draft genomic sequences are also available(http://www.ncbi.nlm.nih.gov/genome/genomes/1004).The vast amount of plasmid DNA thatS. melilotifrequently bears(up to 45% of its total genome), the conjugative ability of some ofthose plasmids, and the extent of the plasmid diversity hasprovided researchers with an extraordinary system to investigatefunctional and structural plasmid molecular biology within theevolutionary context surrounding a plant-associated modelbacterium. Current evidence indicates that the plasmidmobilome inS. melilotiis composed of replicons varying greatlyin size and having diverse conjugative systems and propertiesalong with different evolutionary stabilities and biological roles.While plasmids carrying symbiotic functions (pSyms) are knownto have high structural stability (approaching that ofchromosomes), the remaining plasmid mobilome (referred to asthe non-pSym,functionally cryptic,oraccessorycompartment)has been shown to possess remarkable diversity and to be highlyactive in conjugation. In light of the modern genomic andcurrent biochemical data on the plasmids ofS. meliloti,the current article revises their main structural components,their transfer and regulatory mechanisms, and their potentialas vehicles in shaping the evolution of the rhizobial genome.Fil: Lagares, Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Sanjuán Pinilla, Juan. Consejo Superior de Investigaciones Científicas. Estación Experimental del Zaidín; EspañaFil: Pistorio, Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentin

Disruption of dTDP-rhamnose biosynthesis modifies lipopolysaccharide core, exopolysaccharide production, and root colonization in Azospirillum brasilense

The interaction between Azospirillum brasilense and plants is not fully understood, although several bacterial surface components like exopolysaccharides (EPS), flagella, and capsular polysaccharides are required for attachment and colonization. While in other plant-bacteria associations (Rhizobium-legume, Pseudomonas-potato), lipopolysaccharides (LPS) play a key role in the establishment of an effective association, their role in the root colonization by Azospirillum had not been determined. In this study, we isolated a Tn5 mutant of A. brasilense Cd (EJ1) with an apparently modified LPS core structure, non-mucoid colony morphology, increased EPS production, and affected in maize root colonization. A 3790-bp region revealed the presence of three complete open reading frames designated rmlC, rmlB and rmlD. The beginning of a fourth open reading frame was found and designated rmlA. These genes are organized in a cluster which shows homology to the cluster involved in the synthesis of dTDP-rhamnose in other bacteria. Additionally, the analysis of the monosaccharide composition of LPSs showed a diminution of rhamnose compared to the wild-type strain.Facultad de Ciencias ExactasInstituto de Biotecnologia y Biologia Molecula

Disruption of dTDP-rhamnose biosynthesis modifies lipopolysaccharide core, exopolysaccharide production, and root colonization in Azospirillum brasilense

The interaction between Azospirillum brasilense and plants is not fully understood, although several bacterial surface components like exopolysaccharides (EPS), flagella, and capsular polysaccharides are required for attachment and colonization. While in other plant-bacteria associations (Rhizobium-legume, Pseudomonas-potato), lipopolysaccharides (LPS) play a key role in the establishment of an effective association, their role in the root colonization by Azospirillum had not been determined. In this study, we isolated a Tn5 mutant of A. brasilense Cd (EJ1) with an apparently modified LPS core structure, non-mucoid colony morphology, increased EPS production, and affected in maize root colonization. A 3790-bp region revealed the presence of three complete open reading frames designated rmlC, rmlB and rmlD. The beginning of a fourth open reading frame was found and designated rmlA. These genes are organized in a cluster which shows homology to the cluster involved in the synthesis of dTDP-rhamnose in other bacteria. Additionally, the analysis of the monosaccharide composition of LPSs showed a diminution of rhamnose compared to the wild-type strain.Facultad de Ciencias ExactasInstituto de Biotecnologia y Biologia Molecula

Back to the future of soil metagenomics

Direct extraction and characterization of microbial community DNA through PCR amplicon surveys and metagenomics has revolutionized the study of environmental microbiology and microbial ecology. In particular, metagenomic analysis of nucleic acids provides direct access to the genomes of the “uncultivated majority.” Accelerated by advances in sequencing technology, microbiologists have discovered more novel phyla, classes, genera, and genes from microorganisms in the first decade and a half of the twenty-first century than since these “many very little living animalcules” were first discovered by van Leeuwenhoek. The unsurpassed diversity of soils promises continued exploration of a range of industrial, agricultural, and environmental functions. The ability to explore soil microbial communities with increasing capacity offers the highest promise for answering many outstanding who, what, where, when, why, and with whom questions such as: Which microorganisms are linked to which soil habitats? How do microbial abundances change with changing edaphic conditions? How do microbial assemblages interact and influence one another synergistically or antagonistically? What is the full extent of soil microbial diversity, both functionally and phylogenetically? What are the dynamics of microbial communities in space and time? How sensitive are microbial communities to a changing climate? What is the role of horizontal gene transfer in the stability of microbial communities? Do highly diverse microbial communities confer resistance and resilience in soils?La lista completa de autores que integran el documento puede consultarse en el archivo.Facultad de Ciencias Exacta

Carreras: Especialización en Bioinformática

Dentro de la oferta académica del Postgrado de la Facultad de Informática UNLP se encuentra la Especialización en BioInformática, que se desarrolla a partir de 2023 en conjunto con la Facultad de Ciencias Exactas de la UNLP. La Especialización en Bioinformática está dirigida a egresados universitarios de carreras afines a las Ciencias Biológicas, Informática, Ingeniería, y Ciencias Exactas en general. Tiene por objetivo integrar conocimientos para formar egresados con capacidad de resolver problemas en temas de Bioinformática, a partir de sólidos fundamentos de las ciencias biológicas e informáticas, utilizando los métodos y herramientas que ofrece la tecnología actual.Facultad de Informátic

Rapid preparation of affinity-purified lipopolysaccharide samples for electrophoretic analysis

Lipopolysaccharides (LPS) are the major components of the outer membrane of gram-negative bacteria. These surface molecules are relevant both for the outer membrane stability and for the interaction of the bacteria with other organisms and with the environment (18). Extensive literature is available concerning LPS physiology in different symbiotic (parasitic) and pathogenic host-bacterial interaction systems (5,20). Physiological, biochemical and chemical approaches to study LPS functions commonly require LPS extraction and purification. In the literature, LPS have been prepared by a number of different cell disruption procedures. Protocols for LPS isolation include organic solvent extractions followed by exhaustive dialysis or evaporation steps, and their modifications (11,22).Facultad de Ciencias Exacta

Adsorption of Rhizobium meliloti to alfalfa roots: dependence on divalent cations and pH

Adsorption of Rhizobium meliloti L5-30 in low numbers to alfalfa (Medicago sativa L.) roots was dependent on the presence of divalent cations, and required neutral pH. Adsorption was proportional to Ca and/or Mg concentrations up to 1.5 mM. Ca was not substituted by Sr, Ba or Mn. Adsorption was abolished and viability decreased at pH≤6. When lowering pH, higher Ca concentrations were required to attain similar adsorption levels, indicating a marked interactive effect between Ca and H ions. Pretreatment of the roots with Ca and low pH did not affect subsequent adsorption of the bacteria. However, Ca pretreatment ofR. meliloti sustained further adsorption at low Ca levels and low pH substantially affected their ability to adsorb. Low pH appears to affect the stability of binding causing desorption of the previously bound bacteria. The presence of saturating concentrations of heterologousR. leguminosarum bv.trifolii A118, did not prevent the expression of divalent cations and pH requirements, as well as their interaction. Our results suggest that rhizobial binding to the root surface already shows the Ca and pH dependence of alfalfa nodulation, which was generally associated to some event prior to rhizobial penetration of root hairs.Facultad de Ciencias Exacta