Phylogeny, pangenomics, and predicted functional diversity of maize rhizosphere Pseudomonas

Wie alle mehrzelligen Organismen auf diesem Planeten, sind Pflanzen Holobionten. Meistens sind ihre unterirdischen Gewebe im Boden, ein mikrobenreicher Lebensraum bereits an sich, verankert. Aus diesem immensen Reservoir mikrobieller Vielfalt erwirbt die Pflanze eine wesentliche Gemeinschaft von Bakterien, Archaeen, Pilzen und mikroskopischen Eukaryoten, die ihr Wurzelmikrobiom, auch Rhizosphäre genannt, bilden. Diese Form der Lebensgemeinschaft existiert bereits seit Hunderten von Millionen Jahren; sie umfasst ein komplexes Nahrungsnetz mit dem Wirt als Nährstoffquelle und den Mikroben als Konkurrenten um Ressourcen und Vermittler zwischen dem Wirt und der Umwelt. Die wesentlichen Interaktionen werden häufig durch abiotische Faktoren wie Feuchtigkeit, Temperatur, pH-Wert und die Verfügbarkeit anorganischer Mineralien beeinflusst. Diese Symbioseformen reichen von Mutualismus bis Parasitismus, wobei die überwiegende Mehrheit der Mikrobenarten in einer kommensalen Beziehung mit der Pflanze lebt. Um den genetischen Mechanismus der Auswahl bestimmter Bakterientaxa durch die Pflanze näher zu untersuchen, wurde eine Studie wurde eine Studie durchgeführt, um ein Profil dieser Gemeinschaften in Mais zu erstellen und festzustellen, welche Gattungen oder Arten von Bakterien vererbbar zu sein scheinen. Anhand der 16s rRNA Sequenzierung mehrerer tausend Maisrhizosphären zeigte sich, dass einige Taxa vererbbar zu sein schienen, interessanterweise gab es eine auffällige zeitlich begrenzte Zunahme der Gattung Pseudomonas-Abundanz in fast allen Proben. Bei diesm Phänomen handelte es sich weder um eine Kontamination der Proben noch um Sequenzierungsartefakte. Diese Abundanz konnte auf der Gattungsebene der Mikroben nicht mit ihrer Phylogenie oder ihrerer Funktionen in Verbindung gebracht werden, da Pseudomonas äußerst divers und artenreich ist, wobei die Arten von Nützlingen bis Pathogenen reichen. Die Ziele dieser Arbeit umfasst die Identifizierung die Arten dieser blühenden Pseudomonas, die Ermittlung ihrer phylogenetischen Verwandtschaft und die Durchführung von In-silico-Vorhersagen ihres funktionellen Potenzials auf der Grundlage ihres jeweiligen Geninhalts. Darüber hinaus soll mittels metagenomischer Sequenzierung die Genome der Rhizosphären-endemischen Pseudomonas-Stämme zusammengesetzt werden und andere Phyla zu charackterisieren, die in dieser Umgebung vorkommen und von denen bekannt ist, dass sie mit Pseudomonas interagieren. Durch die Shotgun-Sequenzierung des Metagenomes jeder Rhizosphäre wurde eine Auflösung auf Artniveau für alle bakteriellen und eukaryotischen Taxa erreicht. Dabei zeigte sich, dass die Pseudomonas-Population tatsächlich aus 394 verschiedenen Arten mit einem hohen Grad an phylogenetischer Verwandtschaft bestand. Die am häufigsten vorkommenden Arten waren P. brassicacearum, P. frederiksbergensis E und P. silesiensis, wobei der Anteil der einzelnen Arten je nach Feld erheblich variierte. Ein Schwellenwert für die relative Häufigkeit von Pseudomonas wurde für die biologische Relevanz festgelegt, und aus repräsentativen Genomen jeder Art wurde eine Phylogenie auf der Grundlage von Kerngenen mit einer einfachen Kopie erstellt. Auf diese Weise wurden monophyletische Gruppen und Untergruppen identifiziert, benannt auf Grundlage Literatur beschriebener Stämme. Kategorisiert wurden diese Gruppen als Fluorescens-Linie oder Nicht-Fluorescens-Linie, wobei erstere die Rhizosphäre sowohl in Bezug auf die Anzahl der Arten als auch deren kombinierte relative Häufigkeit dominierte. Eine Pan-Genomanalyse dieser Pseudomonas-Arten ergab, dass phylogenetische Gruppenzugehörigkeit auf der Grundlage ganzer Genome mittels Beta-Diversitätsmetriken, wie die Bray-Curtis-Dissimilarität, unterschieden werden können. Phänotypische Vorhersagen deuten darauf hin, dass Gruppen der Fluorescens-Linie gewisse Kohlenhydrate wie Arabinose, Trehalose und Maltose bevorzugt verwerten, während häufig vorkommende Arten dieser Linie offenbar vermehrt Gene für die Stickstoffreduktion aufweisen. Der Gehalt an Metall- und antimikrobiellen Resistenzgenen war über alle phylogenetischen Gruppen hinweg konserviert, wohingegen der Gehalt an Virulenzgenen den größten Unterschied zwischen beiden Linien und Untergruppen ausmachte. Im Gegensatz zum Resistom war der Gehalt an Sekundärstoffwechsel-/Biosynthese-Geneclustern bei den einzelnen Arten sehr unterschiedlich, wobei die überwiegende Mehrheit dieser Gencluster in weniger als zehn Genomen vorkam. Bei der geringen Anzahl, die zwischen den Gruppen übereinstimmte, handelte es sich größtenteils um Beta-Lakton-Antibiotika und Bakteriozine. Diese Ergebnisse zeigen, dass sowohl Kern- als auch akzessorische Gene zur Unterscheidung zwischen Pseudomonas der Fluorescens-Linie unabhängig von der Taxonomie verwendet werden können. Das Resistom ist zwischen den Gruppen sehr konserviert, wobei die Sekundärmetaboliten weitgehend einzigartig für die einzelnen Arten sind. Dies lässt vermuten, dass Pseudomonas in der Rhizosphäre unter dem Druck stehen, eine konsistente Abwehr aufrechtzuerhalten, die spezifische Antibiotika- und Multidrug-Efflux-Operons umfasst, während sie gleichzeitig neue offensive Sekundärmetaboliten entwickeln oder erwerben, um die Wettbewerbsfähigkeit zwischen eng verwandten Arten zu erhalten.Plants, like all multicellular organisms on this planet, exist as a holobiont. Their underground tissues are often anchored in soil, which in itself is a very microbe-rich habitat. From this vast reservoir of microbial diversity the plant acquires an essential community of bacteria, archaea, fungi, and microscopic eukaryotes that comprises their root microbiome, or rhizosphere. This relationship has existed for hundreds of millions of years; it involves a complex food web with the host as a source of nutrients and the microbes as both competitors for resources and intermediaries between the host and the environment. Essential interactions are often modulated by abiotic factors such as moisture, temperature, pH, and inorganic mineral availability. The symbioses formed run the gamut from mutualistic to parasitic, with the vast majority of microbial species existing in a commensal relationship with the plant. To better understand the genetic mechanism by which the plant selects for certain bacterial taxa a study was conducted to profile these communities in maize, and to determine which genera or species of bacteria appeared to be heritable. 16S rRNA sequencing of several thousand maize rhizospheres revealed a possible heritability of some taxa and a striking period of increased abundance of the genera Pseudomonas. This phenomena could not be explained as contamination or as a sequencing artifact. At genus level it was impossible to relate phylogeny or function to this abundance phenotype due to Pseudomonas being highly diverse and containing thousands of individual species, which range from beneficial to pathogenic. The aims of this work are first to identify these blooming Pseudomonas at species level, next to ascertain their phylogenetic relationships, then to perform in silico predictions based on gene content to infer the functional potential of these taxa. Furthermore, to use metagenomic sequencing to assemble the genomes of the Pseudomonas strains endemic to these rhizospheres, as well as profile other phyla that are present within this environment and are known to interact with Pseudomonas. By whole-genome shotgun sequencing of each rhizosphere, species level resolution was achieved for all bacterial and eukaryotic taxa. This revealed the Pseudomonas population consisted of 394 species with a high degree of phylogenetic relatedness. The most abundant of these were P. brassicacearum, P. frederiksbergensis E, and P. silesiensis, with the proportions of each varying significantly by field. A threshold for biological relevance in Pseudomonas relative abundance was set and representative genomes for each species were used to construct a phylogeny based on single copy core genes. With this, monophyletic groups were identified along with subgroups named based on literature type strains. These groups were categorized as belonging to either the fluorescens lineage or non-fluorescens lineage, with the former dominating the rhizosphere in both number of species and their combined relative abundance. A pan-genome analysis of these Pseudomonas species revealed that beta diversity metrics such as Bray-Curtis dissimilarity can distinguish phylogenetic group membership based on whole genomes. Phenotype predictions indicated that fluorescens lineage groups are more likely to utilize certain carbohydrates such as arabinose, trehalose, and maltose, while high abundance species of this lineage appear to be enriched in genes related to nitrogen reduction. Antimicrobial and metal resistance gene content appears to be highly conserved across all phylogenetic groups, with virulence gene content being the most discriminatory between both groups and subgroups. Unlike the resistome, secondary metabolite/biosynthetic gene cluster content was highly unique between individual species, with the vast majority of these gene clusters appearing in fewer than ten genomes. The scant number that were consistent between groups were largely β-lactone antibiotics and bacteriocins. These results indicate both core and accessory genes can be utilized in discriminating between fluorescens lineage Pseudomonas independent of taxonomy. The resistome is highly conserved between groups but secondary metabolites are largely unique to individual species. This suggests rhizosphere Pseudomonas may be under pressure to maintain consistent defenses involving specific antibiotic and multidrug efflux operons, while concurrently evolving or acquiring novel offensive secondary metabolites to maintain competitiveness between closely related species

Market Conditions and Political Forces: Charter School Restarts in Washington, DC

Charter schools provide public education choices to educational consumers, school-aged children and their families. As independently run and publicly funded schools of choice, charter schools straddle the line between government and private enterprise and are held accountable by a combination of market mechanisms and bureaucratic accountability. Schools that fail to satisfy public standards or consumers may close, causing disruption to students and families. Recently, some charter school closures have resulted in charter restarts, the acquisition of the assets of a closed school by a new, proven or promising school operator serving substantially the same student population. This qualitative case study examines eight charter school closures and five charter school restarts in Washington, DC between 2013 and 2016. The study aims to answer three exploratory research questions: Why are some schools restarted and others closed outright? Who decides which charter schools are closed and which are restarted? How do they make these decisions? The study finds that numerous actors are involved in decisions about charter school restarts, including the boards of closing schools, the authorizer, other government entities, and various private actors. Communities and families, however, lack proactive roles in the decision-making process. Decisions are made based on a varied combination of market and political forces, though there is often more of an illusion of process than an actual one. The study also finds that market factors, a complex set of political interactions and conditions, including varying levels of social capital among actors, and issues of race are all at work in determining why some schools close and others restart

Census of the Local Universe (CLU) Narrow-Band Survey I: Galaxy Catalogs from Preliminary Fields

We present the Census of the Local Universe (CLU) narrow-band survey to search for emission-line (\ha) galaxies. CLU-\ha~has imaged $\approx$3$\pi$ of the sky (26,470~deg$^2$) with 4 narrow-band filters that probe a distance out to 200~Mpc. We have obtained spectroscopic follow-up for galaxy candidates in 14 preliminary fields (101.6~deg$^2$) to characterize the limits and completeness of the survey. In these preliminary fields, CLU can identify emission lines down to an \ha~flux limit of $10^{-14}$~$\rm{erg~s^{-1}~cm^{-2}}$ at 90\% completeness, and recovers 83\% (67\%) of the \ha~flux from catalogued galaxies in our search volume at the $\Sigma$=2.5 ($\Sigma$=5) color excess levels. The contamination from galaxies with no emission lines is 61\% (12\%) for $\Sigma$=2.5 ($\Sigma$=5). Also, in the regions of overlap between our preliminary fields and previous emission-line surveys, we recover the majority of the galaxies found in previous surveys and identify an additional $\approx$300 galaxies. In total, we find 90 galaxies with no previous distance information, several of which are interesting objects: 7 blue compact dwarfs, 1 green pea, and a Seyfert galaxy; we also identified a known planetary nebula. These objects show that the CLU-\ha~survey can be a discovery machine for objects in our own Galaxy and extreme galaxies out to intermediate redshifts. However, the majority of the CLU-\ha~galaxies identified in this work show properties consistent with normal star-forming galaxies. CLU-\ha~galaxies with new redshifts will be added to existing galaxy catalogs to focus the search for the electromagnetic counterpart to gravitational wave events.Comment: 28 pages, 22 figures, 4 tables (Accepted to ApJ

Myo/Nog cell regulation of bone morphogenetic protein signaling in the blastocyst is essential for normal morphogenesis and striated muscle lineage specification

AbstractCells that express MyoD mRNA, the G8 antigen and the bone morphogenetic protein (BMP) inhibitor noggin (Nog) are present in the epiblast before gastrulation. Ablation of “Myo/Nog” cells in the blastocyst results in an expansion of canonical BMP signaling and prevents the expression of noggin and follistatin before and after the onset of gastrulation. Once eliminated in the epiblast, they are neither replaced nor compensated for as development progresses. Older embryos lacking Myo/Nog cells exhibit severe axial malformations. Although Wnts and Sonic hedgehog are expressed in ablated embryos, skeletal muscle progenitors expressing Pax3 are missing in the somites. Pax3+ cells do emerge adjacent to Wnt3a+ cells in vitro; however, few undergo skeletal myogenesis. Ablation of Myo/Nog cells also results in ectopically placed cardiac progenitors and cardiomyocytes in the somites. Reintroduction of Myo/Nog cells into the epiblast of ablated embryos restores normal patterns of BMP signaling, morphogenesis and skeletal myogenesis, and inhibits the expression of cardiac markers in the somites. This study demonstrates that Myo/Nog cells are essential regulators of BMP signaling in the early epiblast and are indispensable for normal morphogenesis and striated muscle lineage specification

Identification of microorganisms by a rapid PCR panel from positive blood cultures leads to faster optimal antimicrobial therapy - a before-after study

BACKGROUND The BioFire® FilmArray® Blood Culture Identification Panel 1 (BF-FA-BCIP) detects microorganisms with high accuracy in positive blood cultures (BC) - a key step in the management of patients with suspected bacteraemia. We aimed to compare the time to optimal antimicrobial therapy (OAT) for the BF-FA-BCIP vs. standard culture-based identification. METHODS In this retrospective single-centre study with a before-after design, 386 positive BC cases with identification by BF-FA-BCIP were compared to 414 controls with culture-based identification. The primary endpoint was the time from BC sampling to OAT. Secondary endpoints were time to effective therapy, length of stay, (re-)admission to ICU, in-hospital and 30-day mortality. Outcomes were assessed using Cox proportional hazard models and logistic regressions. RESULTS Baseline characteristics of included adult inpatients were comparable. Main sources of bacteraemia were urinary tract and intra-abdominal infection (19.2% vs. 22.0% and 16.8% vs. 15.7%, for cases and controls, respectively). Median (95%CI) time to OAT was 25.5 (21.0-31.2) hours with BF-FA-BCIP compared to 45.7 (37.7-51.4) hours with culture-based identification. We observed no significant difference for secondary outcomes. CONCLUSIONS Rapid microorganism identification by BF-FA-BCIP was associated with a median 20-h earlier initiation of OAT in patients with positive BC. No impact on length of stay and mortality was noted. TRIAL REGISTRATION Clinicaltrials.gov, NCT04156633, registered on November 5, 2019

Radial Star Formation Histories in 32 Nearby Galaxies

The spatially resolved star formation histories are studied for 32 normal star-forming galaxies drawn from the the Spitzer Extended Disk Galaxy Exploration Science survey. At surface brightness sensitivities fainter than 28 mag arcsec$^{-2}$, the new optical photometry is deep enough to complement archival ultraviolet and infrared imaging and to explore the properties of the emission well beyond the traditional optical extents of these nearby galaxies. Fits to the spectral energy distributions using a delayed star formation history model indicate a subtle but interesting average radial trend for the spiral galaxies: the inner stellar systems decrease in age with increasing radius, consistent with inside-out disk formation, but the trend reverses in the outermost regions with the stellar age nearly as old as the innermost stars. These results suggest an old stellar outer disk population formed through radial migration and/or the cumulative history of minor mergers and accretions of satellite dwarf galaxies. The subset of S0 galaxies studied here show the opposite trend compared to what is inferred for spirals: characteristic stellar ages that are increasingly older with radius for the inner portions of the galaxies, and increasingly younger stellar ages for the outer portions. This result suggests that either S0 galaxies are not well modeled by a delayed-$\tau$ model, and/or that S0 galaxies have a more complicated formation history than spiral galaxies.Comment: Accepted for publication in the Astronomical Journal. arXiv admin note: text overlap with arXiv:1511.0328

Using [C II] 158 μm Emission from Isolated ISM Phases as a Star Formation Rate Indicator

The brightest observed emission line in many star-forming galaxies is the [C II] 158 μm line, making it detectable up to z ~ 7. In order to better understand and quantify the [C II] emission as a tracer of star formation, the theoretical ratio between the [N II] 205 μm emission and the [C II] 158 μm emission has been employed to empirically determine the fraction of [C II] emission that originates from the ionized and neutral phases of the interstellar medium (ISM). Sub-kiloparsec measurements of the [C II] 158 μm and [N II] 205 μm lines in nearby galaxies have recently become available as part of the Key Insights in Nearby Galaxies: a Far Infrared Survey with Herschel (KINGFISH) and Beyond the Peak programs. With the information from these two far-infrared lines along with the multi-wavelength suite of KINGFISH data, a calibration of the [C II] emission line as a star formation rate (SFR) indicator and a better understanding of the [C II] deficit are pursued. [C II] emission is also compared to polycyclic aromatic hydrocarbon (PAH) emission in these regions to compare photoelectric heating from PAH molecules to cooling by [C II] in the neutral and ionized phases of the ISM. We find that the [C II] emission originating in the neutral phase of the ISM does not exhibit a deficit with respect to the infrared luminosity and is therefore preferred over the [C II] emission originating in the ionized phase of the ISM as an SFR indicator for the normal star-forming galaxies included in this sample

PHANGS-JWST: Data-processing Pipeline and First Full Public Data Release

The exquisite angular resolution and sensitivity of JWST are opening a new window for our understanding of the Universe. In nearby galaxies, JWST observations are revolutionizing our understanding of the first phases of star formation and the dusty interstellar medium. Nineteen local galaxies spanning a range of properties and morphologies across the star-forming main sequence have been observed as part of the PHANGS-JWST Cycle 1 Treasury program at spatial scales of ∼5–50 pc. Here, we describe pjpipe, an image-processing pipeline developed for the PHANGS-JWST program that wraps around and extends the official JWST pipeline. We release this pipeline to the community as it contains a number of tools generally useful for JWST NIRCam and MIRI observations. Particularly for extended sources, pjpipe products provide significant improvements over mosaics from the MAST archive in terms of removing instrumental noise in NIRCam data, background flux matching, and calibration of relative and absolute astrometry. We show that slightly smoothing F2100W MIRI data to 0.″9 (degrading the resolution by about 30%) reduces the noise by a factor of ≈3. We also present the first public release (DR1.1.0) of the pjpipe processed eight-band 2–21 μm imaging for all 19 galaxies in the PHANGS-JWST Cycle 1 Treasury program. An additional 55 galaxies will soon follow from a new PHANGS-JWST Cycle 2 Treasury program

Calibrating mid-infrared emission as a tracer of obscured star formation on HII-region scales in the era of JWST

Measurements of the star formation activity on cloud scales are fundamental to uncovering the physics of the molecular cloud, star formation, and stellar feedback cycle in galaxies. Infrared (IR) emission from small dust grains and polycyclic aromatic hydrocarbons (PAHs) are widely used to trace the obscured component of star formation. However, the relation between these emission features and dust attenuation is complicated by the combined effects of dust heating from old stellar populations and an uncertain dust geometry with respect to heating sources. We use images obtained with NIRCam and MIRI as part of the PHANGS--JWST survey to calibrate dust emission at 21$\rm \mu m$, and the emission in the PAH-tracing bands at 3.3, 7.7, 10, and 11.3$\rm \mu m$ as tracers of obscured star formation. We analyse $\sim$ 20000 optically selected HII regions across 19 nearby star-forming galaxies, and benchmark their IR emission against dust attenuation measured from the Balmer decrement. We model the extinction-corrected H$\alpha$ flux as the sum of the observed H$\alpha$ emission and a term proportional to the IR emission, with $a_{IR}$ as the proportionality coefficient. A constant $a_{IR}$ leads to extinction-corrected H$\alpha$ estimates which agree with those obtained with the Balmer decrement with a scatter of $\sim$ 0.1 dex for all bands considered. Among these bands, 21$\rm \mu m$ emission is demonstrated to be the best tracer of dust attenuation. The PAH-tracing bands underestimate the correction for bright HII regions, since in these environments the ratio of PAH-tracing bands to 21$\rm \mu m$ decreases, signalling destruction of the PAH molecules. For fainter HII regions all bands suffer from an increasing contamination from the diffuse infrared background.Comment: accepted for publication in A&

PHANGS-ML: Dissecting Multiphase Gas and Dust in Nearby Galaxies Using Machine Learning

The PHANGS survey uses Atacama Large Millimeter/submillimeter Array, Hubble Space Telescope, Very Large Telescope, and JWST to obtain an unprecedented high-resolution view of nearby galaxies, covering millions of spatially independent regions. The high dimensionality of such a diverse multiwavelength data set makes it challenging to identify new trends, particularly when they connect observables from different wavelengths. Here, we use unsupervised machine-learning algorithms to mine this information-rich data set to identify novel patterns. We focus on three of the PHANGS-JWST galaxies, for which we extract properties pertaining to their stellar populations; warm ionized and cold molecular gas; and polycyclic aromatic hydrocarbons (PAHs), as measured over 150 pc scale regions. We show that we can divide the regions into groups with distinct multiphase gas and PAH properties. In the process, we identify previously unknown galaxy-wide correlations between PAH band and optical line ratios and use our identified groups to interpret them. The correlations we measure can be naturally explained in a scenario where the PAHs and the ionized gas are exposed to different parts of the same radiation field that varies spatially across the galaxies. This scenario has several implications for nearby galaxies: (i) The uniform PAH ionized fraction on 150 pc scales suggests significant self-regulation in the interstellar medium, (ii) the PAH 11.3/7.7 μm band ratio may be used to constrain the shape of the non-ionizing far-ultraviolet to optical part of the radiation field, and (iii) the varying radiation field affects line ratios that are commonly used as PAH size diagnostics. Neglecting this effect leads to incorrect or biased PAH sizes