Genomic lineages of Rhizobium etli revealed by the extent of nucleotide polymorphisms and low recombination

<p>Abstract</p> <p>Background</p> <p>Most of the DNA variations found in bacterial species are in the form of single nucleotide polymorphisms (SNPs), but there is some debate regarding how much of this variation comes from mutation versus recombination. The nitrogen-fixing symbiotic bacteria <it>Rhizobium etli </it>is highly variable in both genomic structure and gene content. However, no previous report has provided a detailed genomic analysis of this variation at nucleotide level or the role of recombination in generating diversity in this bacterium. Here, we compared draft genomic sequences versus complete genomic sequences to obtain reliable measures of genetic diversity and then estimated the role of recombination in the generation of genomic diversity among <it>Rhizobium etli</it>.</p> <p>Results</p> <p>We identified high levels of DNA polymorphism in <it>R. etli</it>, and found that there was an average divergence of 4% to 6% among the tested strain pairs. DNA recombination events were estimated to affect 3% to 10% of the genomic sample analyzed. In most instances, the nucleotide diversity (π) was greater in DNA segments with recombinant events than in non-recombinant segments. However, this degree of recombination was not sufficiently large to disrupt the congruence of the phylogenetic trees, and further evaluation of recombination in strains quartets indicated that the recombination levels in this species are proportionally low.</p> <p>Conclusion</p> <p>Our data suggest that <it>R. etli </it>is a species composed of separated lineages with low homologous recombination among the strains. Horizontal gene transfer, particularly via the symbiotic plasmid characteristic of this species, seems to play an important role in diversity but the lineages maintain their evolutionary cohesiveness.</p

Spatial patterns in phage-Rhizobium coevolutionary interactions across regions of common bean domestication

Bacteriophages play significant roles in the composition, diversity, and evolution of bacterial communities. Despite their importance, it remains unclear how phage diversity and phage-host interactions are spatially structured. Local adaptation may play a key role. Nitrogen-fixing symbiotic bacteria, known as rhizobia, have been shown to locally adapt to domesticated common bean at its Mesoamerican and Andean sites of origin. This may affect phage-rhizobium interactions. However, knowledge about the diversity and coevolution of phages with their respective Rhizobium populations is lacking. Here, through the study of four phage-Rhizobium communities in Mexico and Argentina, we show that both phage and host diversity is spatially structured. Cross-infection experiments demonstrated that phage infection rates were higher overall in sympatric rhizobia than in allopatric rhizobia except for one Argentinean community, indicating phage local adaptation and host maladaptation. Phage-host interactions were shaped by the genetic identity and geographic origin of both the phage and the host. The phages ranged from specialists to generalists, revealing a nested network of interactions. Our results suggest a key role of local adaptation to resident host bacterial communities in shaping the phage genetic and phenotypic composition, following a similar spatial pattern of diversity and coevolution to that in the host.Fil: Van Cauwenberghe, Jannick. University of California at Berkeley; Estados Unidos. Universidad Nacional Autónoma de México; MéxicoFil: Santamaría, Rosa I.. Universidad Nacional Autónoma de México; MéxicoFil: Bustos, Patricia. Universidad Nacional Autónoma de México; MéxicoFil: Juárez, Soledad. Universidad Nacional Autónoma de México; MéxicoFil: Ducci, Maria Antonella. Universidad Nacional de Salta; Argentina. Instituto Nacional de Tecnología Agropecuaria; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta; ArgentinaFil: Figueroa Fleming, Trinidad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta; Argentina. Universidad Nacional de Salta; ArgentinaFil: Etcheverry, Angela Virginia. Universidad Nacional de Salta; ArgentinaFil: González, Víctor. Universidad Nacional Autónoma de México; Méxic

Analizando el sesgo implícito de género en Óptica y Fotónica en la etapa predoctoral en España

Gender biases play a very significant role in areas related to science, technology, engineering, and mathematics (STEM). The association of gender with certain attributes, behaviors or professions leads to a lower proportion of women in STEM. In the field of Optics and Photonics, we can identify a gender disparity between technical or bio-clinical approaches within the same area when examining the authorship of the defended thesis. In this work, we quantify the impact of implicit gender bias in the Ph.D. programs related to Optics and Photonics in Spain. Here we present an exhaustive study about the UNESCO descriptors of the theses defended within 2015-2020 through the open-access repository TESEO, where all the doctoral theses of Spanish universities are compiled. The doctorate program of each thesis is considered and classified into a technical or bio-clinical category. With this classification, we quantify the number of male and female authors within each category, and the results show up a clear unbalance in most of the evaluated descriptors: men are more likely to choose technical doctorate programs, while women are mostly present in clinical or biological programs. This difference is seen even in descriptors where both genders are equally represented. On one side, women’s underrepresentation is higher in “Physics”, “Astronomy and Astrophysics”, “Earth and Space Sciences”, and “Technological Sciences”. Oppositely, the areas of “Chemistry”, “Life Sciences”, and “Medical Sciences” show a greater gender-balanced distribution for most of the descriptors.Los prejuicios de género desempeñan un papel muy importante en áreas relacionadas con la ciencia, la tecnología, la ingeniería y las matemáticas (STEM). La asociación del género con determinados atributos, comportamientos o profesiones conduce a una menor proporción de mujeres en STEM. En el campo de la Óptica y la Fotónica, podemos identificar una disparidad de género entre enfoques técnicos o bioclínicos dentro de la misma área al examinar la autoría de la tesis defendida. En este trabajo, cuantificamos el impacto del sesgo implícito de género en los programas de doctorado relacionados con la Óptica y Fotónica en España. Aquí presentamos un estudio exhaustivo sobre los descriptores UNESCO de las tesis defendidas en el periodo 2015-2020 a través del repositorio de acceso abierto TESEO, donde se recopilan todas las tesis doctorales de las universidades españolas. Se considera el programa de doctorado de cada tesis y se clasifica en una categoría técnica o bioclínica. Con esta clasificación, cuantificamos el número de autores y autoras dentro de cada categoría, y los resultados muestran un claro desequilibrio en la mayoría de los descriptores evaluados: los hombres son más propensos a elegir programas de doctorado técnicos, mientras que las mujeres están mayoritariamente presentes en programas clínicos o biológicos. Esta diferencia se observa incluso en los descriptores en los que ambos sexos están representados por igual. Por un lado, la infrarrepresentación femenina es mayor en "Física", "Astronomía y Astrofísica", "Ciencias de la Tierra y del Espacio" y "Ciencias Tecnológicas". Por el contrario, las áreas de "Química", "Ciencias de la Vida" y "Ciencias Médicas" muestran una distribución más equilibrada entre hombres y mujeres en la mayoría de los descriptores

Comparative assessment of satellite- and drone-based vegetation indices to predict arthropod biomass in shrub-steppes

Arthropod biomass is a key element in ecosystem functionality and a basic food item for many species. It must be estimated through traditional costly field sampling, normally at just a few sampling points. Arthropod biomass and plant productivity should be narrowly related because a large majority of arthropods are herbivorous, and others depend on these. Quantifying plant productivity with satellite or aerial vehicle imagery is an easy and fast procedure already tested and implemented in agriculture and field ecology. However, the capability of satellite or aerial vehicle imagery for quantifying arthropod biomass and its relationship with plant productivity has been scarcely addressed. Here, we used unmanned aerial vehicle (UAV) and satellite Sentinel-2 (S2) imagery to establish a relationship between plant productivity and arthropod biomass estimated through ground-truth field sampling in shrub steppes. We UAV-sampled seven plots of 47.6–72.3 ha at a 4-cm pixel resolution, subsequently downscaling spatial resolution to 50 cm resolution. In parallel, we used S2 imagery from the same and other dates and locations at 10-m spatial resolution. We related several vegetation indices (VIs) with arthropod biomass (epigeous, coprophagous, and four functional consumer groups: predatory, detritivore, phytophagous, and diverse) estimated at 41–48 sampling stations for UAV flying plots and in 67–79 sampling stations for S2. VIs derived from UAV were consistently and positively related to all arthropod biomass groups. Three out of seven and six out of seven S2-derived VIs were positively related to epigeous and coprophagous arthropod biomass, respectively. The blue normalized difference VI (BNDVI) and enhanced normalized difference VI (ENDVI) showed consistent and positive relationships with arthropod biomass, regardless of the arthropod group or spatial resolution. Our results showed that UAV and S2-VI imagery data may be viable and cost-efficient alternatives for quantifying arthropod biomass at large scales in shrub steppes. The relationship between VI and arthropod biomass is probably habitat-dependent, so future research should address this relationship and include several habitats to validate VIs as proxies of arthropod biomassBBVA Foundation, BBVA Dron Ricoti project; European Commission, Grant/ Award Number: LIFE15-NAT-ES-000802; REMEDINAL-3 from CAM; European Comission, Grant/Award Number: LIFE20-NAT-ES-00013

Sensitivity Studies for Third-Generation Gravitational Wave Observatories

Advanced gravitational wave detectors, currently under construction, are expected to directly observe gravitational wave signals of astrophysical origin. The Einstein Telescope, a third-generation gravitational wave detector, has been proposed in order to fully open up the emerging field of gravitational wave astronomy. In this article we describe sensitivity models for the Einstein Telescope and investigate potential limits imposed by fundamental noise sources. A special focus is set on evaluating the frequency band below 10Hz where a complex mixture of seismic, gravity gradient, suspension thermal and radiation pressure noise dominates. We develop the most accurate sensitivity model, referred to as ET-D, for a third-generation detector so far, including the most relevant fundamental noise contributions.Comment: 13 pages, 7 picture

Scientific Objectives of Einstein Telescope

The advanced interferometer network will herald a new era in observational astronomy. There is a very strong science case to go beyond the advanced detector network and build detectors that operate in a frequency range from 1 Hz-10 kHz, with sensitivity a factor ten better in amplitude. Such detectors will be able to probe a range of topics in nuclear physics, astronomy, cosmology and fundamental physics, providing insights into many unsolved problems in these areas.Comment: 18 pages, 4 figures, Plenary talk given at Amaldi Meeting, July 201

Sensitivity to Gravitational Waves from Compact Binary Coalescences Achieved during LIGO's Fifth and Virgo's First Science Run

We summarize the sensitivity achieved by the LIGO and Virgo gravitational wave detectors for compact binary coalescence (CBC) searches during LIGO's fifth science run and Virgo's first science run. We present noise spectral density curves for each of the four detectors that operated during these science runs which are representative of the typical performance achieved by the detectors for CBC searches. These spectra are intended for release to the public as a summary of detector performance for CBC searches during these science runs.Comment: 12 pages, 5 figure

Implementation and testing of the first prompt search for gravitational wave transients with electromagnetic counterparts

Aims. A transient astrophysical event observed in both gravitational wave (GW) and electromagnetic (EM) channels would yield rich scientific rewards. A first program initiating EM follow-ups to possible transient GW events has been developed and exercised by the LIGO and Virgo community in association with several partners. In this paper, we describe and evaluate the methods used to promptly identify and localize GW event candidates and to request images of targeted sky locations. Methods. During two observing periods (Dec 17 2009 to Jan 8 2010 and Sep 2 to Oct 20 2010), a low-latency analysis pipeline was used to identify GW event candidates and to reconstruct maps of possible sky locations. A catalog of nearby galaxies and Milky Way globular clusters was used to select the most promising sky positions to be imaged, and this directional information was delivered to EM observatories with time lags of about thirty minutes. A Monte Carlo simulation has been used to evaluate the low-latency GW pipeline's ability to reconstruct source positions correctly. Results. For signals near the detection threshold, our low-latency algorithms often localized simulated GW burst signals to tens of square degrees, while neutron star/neutron star inspirals and neutron star/black hole inspirals were localized to a few hundred square degrees. Localization precision improves for moderately stronger signals. The correct sky location of signals well above threshold and originating from nearby galaxies may be observed with ~50% or better probability with a few pointings of wide-field telescopes.Comment: 17 pages. This version (v2) includes two tables and 1 section not included in v1. Accepted for publication in Astronomy & Astrophysic

Swift follow-up observations of candidate gravitational-wave transient events

We present the first multi-wavelength follow-up observations of two candidate gravitational-wave (GW) transient events recorded by LIGO and Virgo in their 2009-2010 science run. The events were selected with low latency by the network of GW detectors and their candidate sky locations were observed by the Swift observatory. Image transient detection was used to analyze the collected electromagnetic data, which were found to be consistent with background. Off-line analysis of the GW data alone has also established that the selected GW events show no evidence of an astrophysical origin; one of them is consistent with background and the other one was a test, part of a "blind injection challenge". With this work we demonstrate the feasibility of rapid follow-ups of GW transients and establish the sensitivity improvement joint electromagnetic and GW observations could bring. This is a first step toward an electromagnetic follow-up program in the regime of routine detections with the advanced GW instruments expected within this decade. In that regime multi-wavelength observations will play a significant role in completing the astrophysical identification of GW sources. We present the methods and results from this first combined analysis and discuss its implications in terms of sensitivity for the present and future instruments.Comment: Submitted for publication 2012 May 25, accepted 2012 October 25, published 2012 November 21, in ApJS, 203, 28 ( http://stacks.iop.org/0067-0049/203/28 ); 14 pages, 3 figures, 6 tables; LIGO-P1100038; Science summary at http://www.ligo.org/science/Publication-S6LVSwift/index.php ; Public access area to figures, tables at https://dcc.ligo.org/cgi-bin/DocDB/ShowDocument?docid=p110003

Search for Gravitational Waves from Low Mass Compact Binary Coalescence in LIGO's Sixth Science Run and Virgo's Science Runs 2 and 3

We report on a search for gravitational waves from coalescing compact binaries using LIGO and Virgo observations between July 7, 2009 and October 20, 2010. We searched for signals from binaries with total mass between 2 and 25 solar masses; this includes binary neutron stars, binary black holes, and binaries consisting of a black hole and neutron star. The detectors were sensitive to systems up to 40 Mpc distant for binary neutron stars, and further for higher mass systems. No gravitational-wave signals were detected. We report upper limits on the rate of compact binary coalescence as a function of total mass, including the results from previous LIGO and Virgo observations. The cumulative 90%-confidence rate upper limits of the binary coalescence of binary neutron star, neutron star- black hole and binary black hole systems are 1.3 x 10^{-4}, 3.1 x 10^{-5} and 6.4 x 10^{-6} Mpc^{-3}yr^{-1}, respectively. These upper limits are up to a factor 1.4 lower than previously derived limits. We also report on results from a blind injection challenge.Comment: 11 pages, 5 figures. For a repository of data used in the publication, go to: . Also see the announcement for this paper on ligo.org at: <http://www.ligo.org/science/Publication-S6CBCLowMass/index.php