Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Seyler, L. M., Trembath-Reichert, E., Tully, B. J., & Huber, J. A. Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community. Isme Journal, (2020), doi:10.1038/s41396-020-00843-4.The oceanic crustal aquifer is one of the largest habitable volumes on Earth, and it harbors a reservoir of microbial life that influences global-scale biogeochemical cycles. Here, we use time series metagenomic and metatranscriptomic data from a low-temperature, ridge flank environment representative of the majority of global hydrothermal fluid circulation in the ocean to reconstruct microbial metabolic potential, transcript abundance, and community dynamics. We also present metagenome-assembled genomes from recently collected fluids that are furthest removed from drilling disturbances. Our results suggest that the microbial community in the North Pond aquifer plays an important role in the oxidation of organic carbon within the crust. This community is motile and metabolically flexible, with the ability to use both autotrophic and organotrophic pathways, as well as function under low oxygen conditions by using alternative electron acceptors such as nitrate and thiosulfate. Anaerobic processes are most abundant in subseafloor horizons deepest in the aquifer, furthest from connectivity with the deep ocean, and there was little overlap in the active microbial populations between sampling horizons. This work highlights the heterogeneity of microbial life in the subseafloor aquifer and provides new insights into biogeochemical cycling in ocean crust.The Gordon and Betty Moore Foundation sponsored most of the observatory components at North Pond through grant GBMF1609. This work was supported by NSF OCE-1062006, OCE-1745589 and OCE-1635208 to J.A.H. E.T.R. was supported by a NASA Postdoctoral Fellowship with the NASA Astrobiology Institute and a L’Oréal USA For Women in Science Fellowship. The Center for Dark Energy Biosphere Investigations (C-DEBI OCE-0939564) also supported the participation of J.A.H. and B.T. This is C-DEBI contribution number 548

Microbial populations are shaped by dispersal and recombination in a low biomass subseafloor habitat

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Anderson, R., Graham, E., Huber, J., & Tully, B. Microbial populations are shaped by dispersal and recombination in a low biomass subseafloor habitat. MBio, 13(4), (2022): e0035422, https://doi.org/10.1128/mbio.00354-22.The subseafloor is a vast habitat that supports microorganisms that have a global scale impact on geochemical cycles. Many of the endemic microbial communities inhabiting the subseafloor consist of small populations under growth-limited conditions. For small populations, stochastic evolutionary events can have large impacts on intraspecific population dynamics and allele frequencies. These conditions are fundamentally different from those experienced by most microorganisms in surface environments, and it is unknown how small population sizes and growth-limiting conditions influence evolution and population structure in the subsurface. Using a 2-year, high-resolution environmental time series, we examine the dynamics of microbial populations from cold, oxic crustal fluids collected from the subseafloor site North Pond, located near the mid-Atlantic ridge. Our results reveal rapid shifts in overall abundance, allele frequency, and strain abundance across the time points observed, with evidence for homologous recombination between coexisting lineages. We show that the subseafloor aquifer is a dynamic habitat that hosts microbial metapopulations that disperse frequently through the crustal fluids, enabling gene flow and recombination between microbial populations. The dynamism and stochasticity of microbial population dynamics in North Pond suggest that these forces are important drivers in the evolution of microbial populations in the vast subseafloor habitat.This work was supported by NSF OCE-1062006, OCE-1745589, and OCE-1635208 to J.A.H. The Gordon and Betty Moore Foundation sponsored observatory components at North Pond through grant GBMF1609. The Center for Dark Energy Biosphere Investigations (C-DEBI) (OCE-0939564) supported J.A.H. and B.J.T. This is C-DEBI contribution 598

Combinar la escuela con trabajo a tiempo parcial. Resultados empíricos de Alemania

En el presente artículo se pretende esbozar el estado actual de las investigaciones sobre el empleo a tiempo parcial de estudiantes escolares. Los datos con respecto a Alemania se derivan de la encuesta AID:A con una población de estudiantes de entre 13 y 17 años (N = 2,763). Puesto que el motivo principal por el que los jóvenes deciden trabajar mientras estudian es ganar dinero, se han incluido en este estudio datos sobre su situación económica con y sin trabajo. Aproximadamente un tercio de los estudiantes trabajan. Éstos intervienen simultáneamente en distintos mundos (la escuela, la familia, los grupos de iguales, la cultura juvenil, el ambiente laboral). La proporción de jóvenes escolares que trabajan aumenta notablemente con la edad. Este hecho no afecta a sus compromisos voluntarios ni al rendimiento escolar. Los alumnos de familias con rentas más bajas trabajan con más frecuencia, pero obtienen menos ingresos que los alumnos de familias de rentas más altas. En términos generales, los empleos a tiempo parcial permiten a los jóvenes tener un mayor margen de maniobra en su presupuesto. Esto a su vez facilita su participación en una cultura juvenil basada en el consumo. Este artículo finaliza con una reflexión sobre los déficits en la investigación y lanza un debate sobre el desarrollo previsto en el mercado de trabajo a tiempo parcial.En aquest article es pretén esbossar l'estat actual de les investigacions sobre l'ocupació a temps parcial d'estudiants escolars. Les dades respecte d'Alemanya es deriven de l'enquesta AID:A amb una població d'estudiants d'entre 13 i 17 anys (N = 2,763). Atès que el motiu principal pel qual els joves decideixen treballar mentre estudien és guanyar diners, s'han inclòs en aquest estudi dades sobre la seva situació econòmica amb o sense feina.Aproximadament un terç dels estudiants treballen. Aquests intervenen simultàniament en diferents mons (l'escola, la família, els grups d'iguals, la cultura juvenil, l'ambient laboral). La proporció de joves escolars que treballen augmenta notablement amb l'edat. Aquest fet no afecta els seus compromisos voluntaris ni el rendiment escolar. Els alumnes de famílies amb rendes més baixes treballen amb més freqüència, però obtenen menys ingressos que els alumnes de famílies de rendes més altes. En termes generals, les feines a temps parcial permeten als joves tenir un marge de maniobra més gran en el seu pressupost. Això alhora facilita la seva participació en una cultura juvenil basada en el consum. Aquest article acaba amb una reflexió sobre els dèficits en la investigació i llança un debat sobre el desenvolupament previst en el mercat de treball a temps parcial.This article begins by outlining the current state of research into the issue of part-time work taken by secondary school students. The findings for Germany are based on a childhood and youth survey (AID:A). The survey population comprises school students aged 13 to 17 (N = 2,763). As young people's primary motive for taking a job while at school is to earn income, their financial position with and without jobs is included in the study. About one third of the students have jobs. Thus young people operate simultaneously in parallel worlds (school, family, peer group, youth culture, work environment). The proportion of school students with jobs increases markedly with age. No detriment to voluntary commitments or school achievement results from having a job. Students from lower-income households take jobs more frequently, but earn less income from them than do students from higher-income households. In broad terms, part-time jobs provide appreciable additional freedom of manoeuvre in young people's budgets. This in turn facilitates participation in consumption-based youth culture. The article ends with a reflection on research deficits and a discussion of anticipated developments in the part-time labour market

De Novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a aariable genomic landscape

Hypersaline systems near salt saturation levels represent an extreme environment, in which organisms grow and survive near the limits of life. One of the abundant members of the microbial communities in hypersaline systems is the square archaeon, Haloquadratum walsbyi. Utilizing a short-read metagenome from Lake Tyrrell, a hypersaline ecosystem in Victoria, Australia, we performed a comparative genomic analysis of H. walsbyi to better understand the extent of variation between strains/subspecies. Results revealed that previously isolated strains/subspecies do not fully describe the complete repertoire of the genomic landscape present in H. walsbyi. Rearrangements, insertions, and deletions were observed for the Lake Tyrrell derived Haloquadratum genomes and were supported by environmental de novo sequences, including shifts in the dominant genomic landscape of the two most abundant strains. Analysis pertaining to halomucins indicated that homologs for this large protein are not a feature common for all species of Haloquadratum. Further, we analyzed ATP-binding cassette transporters (ABC-type transporters) for evidence of niche partitioning between different strains/subspecies. We were able to identify unique and variable transporter subunits from all five genomes analyzed and the de novo environmental sequences, suggesting that differences in nutrient and carbon source acquisition may play a role in maintaining distinct strains/subspecies.Funding for this was provided by the National Science Foundation (NSF) MCB Award no. 0626526 to J. Banfield, E. Allen, and K. Heidelberg

Prospects for the Study of Evolution in the Deep Biosphere

Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times, and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in population genetics may be applicable to microbial genomes (Martiny et al., 2006; Manhes and Velicer, 2011). Microbial biogeography and adaptation has been examined in many different environments. Here we argue that the deep biosphere is a unique environment for the study of evolution and list specific factors that can be considered and where the studies may be performed. This publication is the result of the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) theme team on Evolution (www.darkenergybiosphere.org)

The Tully-Fisher Relation as a Measure of Luminosity Evolution: A Low Redshift Baseline for Evolving Galaxies

We use optical rotation curves to investigate the R-band Tully-Fisher properties of a sample of 90 spiral galaxies in close pairs. The galaxies follow the Tully-Fisher relation remarkably well, with the exception of eight distinct 3-sigma outliers. Although most of the outliers show signs of recent star formation, gasdynamical effects are probably the dominant cause of their anomalous Tully-Fisher properties. Four outliers with small emission line widths have very centrally concentrated line emission and truncated rotation curves; the central emission indicates recent gas infall after a close galaxy-galaxy pass. These four galaxies may be local counterparts to compact, blue galaxies at intermediate redshift. The remaining galaxies have a negligible offset from the reference Tully-Fisher relation, but a shallower slope (2.6-sigma significance) and a 25% larger scatter. We characterize the non-outlier sample with measures of distortion and star formation to search for third parameter dependence in the residuals of the TF relation. Severe kinematic distortion is the only significant predictor of TF residuals; this distortion is not, however, responsible for the slope difference from the reference distribution. Because the outliers are easily removed by sigma clipping, we conclude that even in the presence of some tidal distortion, detection of moderate luminosity evolution should be possible with high-redshift samples the size of this 90-galaxy study. (Abridged.)Comment: LaTeX document, 55 pages including 18 figures, to appear in A

A Multivariable Approach Using Magnetic Resonance Imaging to Avoid a Protocol-based Prostate Biopsy in Men on Active Surveillance for Prostate Cancer-Data from the International Multicenter Prospective PRIAS Study

Publisher Copyright: Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.BACKGROUND: There is ongoing discussion whether a multivariable approach including magnetic resonance imaging (MRI) can safely prevent unnecessary protocol-advised repeat biopsy during active surveillance (AS). OBJECTIVE: To determine predictors for grade group (GG) reclassification in patients undergoing an MRI-informed prostate biopsy (MRI-Bx) during AS and to evaluate whether a confirmatory biopsy can be omitted in patients diagnosed with upfront MRI. DESIGN, SETTING, AND PARTICIPANTS: The Prostate cancer Research International: Active Surveillance (PRIAS) study is a multicenter prospective study of patients on AS (www.prias-project.org). We selected all patients undergoing MRI-Bx (targeted ± systematic biopsy) during AS. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: A time-dependent Cox regression analysis was used to determine the predictors of GG progression/reclassification in patients undergoing MRI-Bx. A sensitivity analysis and a multivariable logistic regression analysis were also performed. RESULTS AND LIMITATIONS: A total of 1185 patients underwent 1488 MRI-Bx sessions. The time-dependent Cox regression analysis showed that age (per 10 yr, hazard ratio [HR] 0.84 [95% confidence interval {CI} 0.71-0.99]), MRI outcome (Prostate Imaging Reporting and Data System [PIRADS] 3 vs negative HR 2.46 [95% CI 1.56-3.88], PIRADS 4 vs negative HR 3.39 [95% CI 2.28-5.05], and PIRADS 5 vs negative HR 4.95 [95% CI 3.25-7.56]), prostate-specific antigen (PSA) density (per 0.1 ng/ml cm3, HR 1.20 [95% CI 1.12-1.30]), and percentage positive cores on the last systematic biopsy (per 10%, HR 1.16 [95% CI 1.10-1.23]) were significant predictors of GG reclassification. Of the patients with negative MRI and a PSA density of <0.15 ng/ml cm3 (n = 315), 3% were reclassified to GG ≥2 and 0.6% to GG ≥3. At the confirmatory biopsy, reclassification to GG ≥2 and ≥3 was observed in 23% and 7% of the patients diagnosed without upfront MRI and in 19% and 6% of the patients diagnosed with upfront MRI, respectively. The multivariable analysis showed no significant difference in upgrading at the confirmatory biopsy between patients diagnosed with or without upfront MRI. CONCLUSIONS: Age, MRI outcome, PSA density, and percentage positive cores are significant predictors of reclassification at an MRI-informed biopsy. Patients with negative MRI and a PSA density of <0.15 ng/ml cm3 can safely omit a protocol-based prostate biopsy, whereas in other patients, a multivariable approach is advised. Being diagnosed with upfront MRI appears not to significantly affect reclassification risk; hence, a confirmatory MRI-Bx cannot totally be omitted yet. PATIENT SUMMARY: A protocol-based prostate biopsy while on active surveillance can be omitted in patients with negative magnetic resonance imaging (MRI) and prostate-specific antigen density <0.15 ng/ml cm3. A confirmatory biopsy cannot simply be omitted in all patients diagnosed with upfront MRI.Peer reviewe

The Disk and Dark Halo Mass of the Barred Galaxy NGC 4123. I. Observations

The non-circular streaming motions in barred galaxies are sensitive to the mass of the bar and can be used to lift the degeneracy between disk and dark matter halo encountered when fitting axisymmetric rotation curves of disk galaxies. In this paper, we present photometric and kinematic observations of NGC 4123, a barred galaxy of modest size (V_rot = 130 km/sec, L = 0.7 L_*), which reveal strong non-circular motions. The bar has straight dust lanes and an inner Lindblad resonance. The disk of NGC 4123 has no sign of truncation out to 10 scale lengths, and star-forming regions are found well outside R_25. A Fabry-Perot H-alpha velocity field shows velocity jumps of >100 km/sec at the location of the dust lanes within the bar, indicating shocks in the gas flow. VLA observations yield the velocity field of the H I disk. Axisymmetric mass models yield good fits to the rotation curve outside the bar regionfor disk I-band M/L of 2.25 or less, and dark halos with either isothermal or power-law profiles can fit the data well. In a companion paper, we model the full 2-D velocity field, including non-circular motions, to determine the stellar M/L and the mass of the dark halo.Comment: accepted by ApJ, 16 pages, 9 figures (1 color), uses emulateapj.sty, onecolfloat.st

High-Mass X-ray Binaries and the Spiral Structure of the Host Galaxy

We investigate the manifestation of the spiral structure in the distribution of high-mass X-ray binaries (HMXBs) over the host galaxy. We construct the simple kinematic model. It shows that the HMXBs should be displaced relative to the spiral structure observed in such traditional star formation rate indicators as the Halpha and FIR emissions because of their finite lifetimes. Using Chandra observations of M51, we have studied the distribution of X-ray sources relative to the spiral arms of this galaxy observed in Halpha. Based on K-band data and background source number counts, we have separated the contributions from high-mass and low-mass X-ray binaries and active galactic nuclei. In agreement with model predictions, the distribution of HMXBs is wider than that of bright HII regions concentrated in the region of ongoing star formation. However, the statistical significance of this result is low, as is the significance of the concentration of the total population of X-ray sources to the spiral arms. We also predict the distribution of HMXBs in our Galaxy in Galactic longitude. The distribution depends on the mean HMXB age and can differ significantly from the distributions of such young objects as ultracompact HII regions.Comment: 18 pages, 6 figures; Astronomy Letters, Vol. 33, No. 5, 2007, pp. 299-30