Large Deletions in the pAtC58 Megaplasmid of Agrobacterium tumefaciens Can Confer Reduced Carriage Cost and Increased Expression of Virulence Genes

The accessory plasmid pAtC58 of the common laboratory strain of Agrobacterium tumefaciens confers numerous catabolic functions and has been proposed to play a role in virulence. Genomic sequencing of evolved laboratory strains of A. tumefaciens revealed the presence of multiple deletion events in the At plasmid, with reductions in plasmid size ranging from 25% to 30% (115–194 kb). Flanking both ends of the sites of these deletions is a short-nucleotide repeat sequence that is in a single copy in the deleted plasmids, characteristic of a phage- or transposon-mediated deletion event. This repeat sequence is widespread throughout the C58 genome, but concentrated on the At plasmid, suggesting its frequency to be nonrandom. In this study, we assess the prevalence of the larger of these deletions in multiple C58 derivatives and characterize its functional significance. We find that in addition to elevating virulence gene expression, this deletion is associated with a significantly reduced carriage cost to the cell. These observations are a clear demonstration of the dynamic nature of the bacterial genome and suggest a mechanism for genetic plasticity of these costly but otherwise stable plasmids. Additionally, this phenomenon could be the basis for some of the dramatic recombination events so ubiquitous within and among megaplasmids

Territory occupancy and breeding success of peregrine falcons Falco peregrinus at various stages of population recovery

Organochlorine pesticides disrupted reproduction and killed many raptorial birds, and contributed to population declines during the 1940s to 1970s. We sought to discern whether and to what extent territory occupancy and breeding success changed from the pesticide era to recent years in a resident population of Peregrine Falcons Falco peregrinus in southern Scotland using long-term (1964–2015) field data and multi-state, multi-season occupancy models. Peregrine territories that were occupied with successful reproduction in one year were much more likely to be occupied and experience reproductive success in the following year, compared with those that were unoccupied or occupied by unsuccessful breeders in the previous year. Probability of territory occupancy differed between territories in the eastern and western parts of the study area, and varied over time. The probability of occupancy of territories that were unoccupied and those that were occupied with successful reproduction during the previous breeding season generally increased over time, whereas the probability of occupancy of territories that were occupied after failed reproduction decreased. The probability of reproductive success (conditional on occupancy) in territories that were occupied during the previous breeding season increased over time. Specifically, for territories that had been successful in the previous year, the probability of occupancy as well as reproductive success increased steadily over time; these probabilities were substantially higher in recent years than earlier, when the population was still exposed to direct or residual effects of organochlorine pesticides. These results are consistent with the hypothesis that progressive reduction, followed by a complete ban, in the use of organochlorine pesticides improved reproductive success of Peregrines in southern Scotland. Differences in the temporal pattern of probability of reproductive success between south-eastern and south-western Scotland suggest that the effect of organochlorine pesticides on Peregrine reproductive success and/or the recovery from pesticide effects varied geographically and was possibly affected by other factors such as persecution

A planet within the debris disk around the pre-main-sequence star AU Microscopii

AU Microscopii (AU Mic) is the second closest pre main sequence star, at a distance of 9.79 parsecs and with an age of 22 million years. AU Mic possesses a relatively rare and spatially resolved3 edge-on debris disk extending from about 35 to 210 astronomical units from the star, and with clumps exhibiting non-Keplerian motion. Detection of newly formed planets around such a star is challenged by the presence of spots, plage, flares and other manifestations of magnetic activity on the star. Here we report observations of a planet transiting AU Mic. The transiting planet, AU Mic b, has an orbital period of 8.46 days, an orbital distance of 0.07 astronomical units, a radius of 0.4 Jupiter radii, and a mass of less than 0.18 Jupiter masses at 3 sigma confidence. Our observations of a planet co-existing with a debris disk offer the opportunity to test the predictions of current models of planet formation and evolution.Comment: Nature, published June 24th [author spelling name fix

Hyperoxemia and excess oxygen use in early acute respiratory distress syndrome : Insights from the LUNG SAFE study

Publisher Copyright: © 2020 The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.Background: Concerns exist regarding the prevalence and impact of unnecessary oxygen use in patients with acute respiratory distress syndrome (ARDS). We examined this issue in patients with ARDS enrolled in the Large observational study to UNderstand the Global impact of Severe Acute respiratory FailurE (LUNG SAFE) study. Methods: In this secondary analysis of the LUNG SAFE study, we wished to determine the prevalence and the outcomes associated with hyperoxemia on day 1, sustained hyperoxemia, and excessive oxygen use in patients with early ARDS. Patients who fulfilled criteria of ARDS on day 1 and day 2 of acute hypoxemic respiratory failure were categorized based on the presence of hyperoxemia (PaO2 > 100 mmHg) on day 1, sustained (i.e., present on day 1 and day 2) hyperoxemia, or excessive oxygen use (FIO2 ≥ 0.60 during hyperoxemia). Results: Of 2005 patients that met the inclusion criteria, 131 (6.5%) were hypoxemic (PaO2 < 55 mmHg), 607 (30%) had hyperoxemia on day 1, and 250 (12%) had sustained hyperoxemia. Excess FIO2 use occurred in 400 (66%) out of 607 patients with hyperoxemia. Excess FIO2 use decreased from day 1 to day 2 of ARDS, with most hyperoxemic patients on day 2 receiving relatively low FIO2. Multivariate analyses found no independent relationship between day 1 hyperoxemia, sustained hyperoxemia, or excess FIO2 use and adverse clinical outcomes. Mortality was 42% in patients with excess FIO2 use, compared to 39% in a propensity-matched sample of normoxemic (PaO2 55-100 mmHg) patients (P = 0.47). Conclusions: Hyperoxemia and excess oxygen use are both prevalent in early ARDS but are most often non-sustained. No relationship was found between hyperoxemia or excessive oxygen use and patient outcome in this cohort. Trial registration: LUNG-SAFE is registered with ClinicalTrials.gov, NCT02010073publishersversionPeer reviewe

Perceptions of Landowners Concerning Conservation, Grazing, Fire, and Eastern Redcedar Management in Tallgrass Prairie

Successful prairie restoration will depend in part on convincing private landowners with agricultural and recreational use goals to implement appropriate rangeland management practices, such as prescribed burning and cattle grazing, to control invasive species and encroachment of woody plants. However, landowners have been slow to adopt appropriate practices in the US Midwest. The purpose of this study was to explore attitudes and behaviors of private landowners toward prescribed burning and moderate stocking as rangeland management tools. A survey was mailed to 193 landowners (response rate 51%) in the Grand River Grasslands region of southern Iowa and northern Missouri. While 68% of landowners viewed grazing as a legitimate land management tool, only half of landowners thought of fire as a legitimate tool. Over 75% of respondents believed that the increase in eastern redcedar and other trees in grasslands was a problem, with 44% considering it a major problem. Although 84% of landowners said that they had taken action to control eastern redcedar, only 25% had participated in a prescribed burn. Income from agriculture and recreational goals were negatively and significantly correlated (–0.252, P = 0.035). While holding recreational goals constant in the analysis, landowners reporting income from agriculture goals as very or extremely important were negatively and significantly associated with reporting environment and grassland factors as very or extremely important. Adoption of prescribed burning by private landowners might be more widespread if proponents focus on the effectiveness of fire for controlling eastern redcedar, which is viewed as a problem by most landowners in the region. Intervention efforts must include landowners with different goals as part of the promotion and educational process. The Rangeland Ecology & Management archives are made available by the Society for Range Management and the University of Arizona Libraries. Contact [email protected] for further information.Migrated from OJS platform August 202

Ecological dynamics and complex interactions of Agrobacterium megaplasmids

As with many pathogenic bacteria, agrobacterial plant pathogens carry most of their virulence functions on a horizontally transmissible genetic element. The tumor-inducing (Ti) plasmid encodes the majority of virulence functions for the crown gall agent Agrobacterium tumefaciens. This includes the vir genes which drive genetic transformation of host cells and the catabolic genes needed to utilize the opines produced by infected plants. The Ti plasmid also encodes, an opine-dependent quorum sensing system that tightly regulates Ti plasmid copy number and its conjugal transfer to other agrobacteria. Many natural agrobacteria are avirulent, lacking the Ti plasmid. The burden of harboring the Ti plasmid depends on the environmental context. Away from diseased hosts, plasmid costs are low but the benefit of the plasmid is also absent. Consequently, plasmidless genotypes are favored. On infected plants the costs of the Ti plasmid can be very high, but balanced by the opine benefits, locally favoring plasmid bearing cells. Cheating derivatives which do not incur virulence costs but can benefit from opines are favored on infected plants and in most other environments, and these are frequently isolated from nature. Many agrobacteria also harbor an At plasmid which can stably coexist with a Ti plasmid. At plasmid genes are less well characterized but in general facilitate metabolic activities in the rhizosphere and bulk soil, such as the ability to breakdown plant exudates. Examination of A. tumefaciens C58, revealed that harboring it’s At plasmid is much more costly than harboring it’s Ti plasmid, but conversely the At plasmid is extremely difficult to cure. The interactions between these co-resident plasmids are complex, and depend on environmental context. However, the presence of a Ti plasmid appears to mitigate At plasmid costs, consistent with the high frequency with which they are found together

Spatiotemporal patterns in an Afrotropical montane forest bird community

Understanding how species richness and diversity patterns vary across time and space is essential for predicting how biodiversity will respond to anthropogenic threats and for effective conservation planning. Tropical montane forests are among the most biodiverse places in the world, yet high rates of endemism and narrow physiological tolerances place tropical montane species among the most vulnerable to anthropogenic impacts. Therefore, it is of the utmost importance to understand how ecological communities are structured along elevational and spatial gradients, particularly in the Afrotropics, which are historically understudied despite their unique climate and rich biodiversity. Here we examine how the Afrotropical montane bird community of Nyungwe National Park in Rwanda is spatially and temporally structured with respect to elevation and geography. We show that despite the absence of geographic barriers, avian communities are spatially structured across the elevational gradient with significant regional differences in both species composition and richness, and that high elevation assemblages are comprised of fewer species compared to lower and middle elevations. We find evidence for overall stability in species richness during this study period (2001–2011) yet differing season-specific trends across the elevational range of the study. Specifically, the high elevation assemblage exhibited a wet season-specific increase in richness, congruent with predicted upslope elevational shifts for low and middle elevation species. Our findings suggest that anthropogenic factors may have different effects on richness patterns depending on elevation and region, and that protected areas large enough to encompass the full range of geographic and elevation gradients are required to effectively conserve Afromontane bird communities

Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by <i>Entamoeba</i> and Subsistence

<div><p>The human gut microbiota is impacted by host nutrition and health status and therefore represents a potentially adaptive phenotype influenced by metabolic and immune constraints. Previous studies contrasting rural populations in developing countries to urban industrialized ones have shown that industrialization is strongly correlated with patterns in human gut microbiota; however, we know little about the relative contribution of factors such as climate, diet, medicine, hygiene practices, host genetics, and parasitism. Here, we focus on fine-scale comparisons of African rural populations in order to (i) contrast the gut microbiota of populations inhabiting similar environments but having different traditional subsistence modes and either shared or distinct genetic ancestry, and (ii) examine the relationship between gut parasites and bacterial communities. Characterizing the fecal microbiota of Pygmy hunter-gatherers as well as Bantu individuals from both farming and fishing populations in Southwest Cameroon, we found that the gut parasite <i>Entamoeba</i> is significantly correlated with microbiome composition and diversity. We show that across populations, colonization by this protozoa can be predicted with 79% accuracy based on the composition of an individual's gut microbiota, and that several of the taxa most important for distinguishing <i>Entamoeba</i> absence or presence are signature taxa for autoimmune disorders. We also found gut communities to vary significantly with subsistence mode, notably with some taxa previously shown to be enriched in other hunter-gatherers groups (in Tanzania and Peru) also discriminating hunter-gatherers from neighboring farming or fishing populations in Cameroon.</p></div

(a) Comparison of alpha diversity for <i>Entamoeba</i> negative (<i>Ent</i>-) and positive (<i>Ent</i>+) individuals using the phylogenetic distance whole tree metric.

<p>(b) Comparison of beta diversity within <i>Ent</i>-, within <i>Ent</i>+, and between <i>Ent</i>- and <i>Ent</i>+ individuals based on unweighted UniFrac distances. P-values are based on Welch’s t-test.</p