Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal (2019), doi:10.1038/s41396-019-0373-4.The benthos in estuarine environments often experiences periods of regularly occurring hypoxic and anoxic conditions, dramatically impacting biogeochemical cycles. How oxygen depletion affects the growth of specific uncultivated microbial populations within these diverse benthic communities, however, remains poorly understood. Here, we applied H218O quantitative stable isotope probing (qSIP) in order to quantify the growth of diverse, uncultured bacterial populations in response to low oxygen concentrations in estuarine sediments. Over the course of 7- and 28-day incubations with redox conditions spanning from hypoxia to euxinia (sulfidic), 18O labeling of bacterial populations exhibited different patterns consistent with micro-aerophilic, anaerobic, facultative anaerobic, and aerotolerant anaerobic growth. 18O-labeled populations displaying anaerobic growth had a significantly non-random phylogenetic distribution, exhibited by numerous clades currently lacking cultured representatives within the Planctomycetes, Actinobacteria, Latescibacteria, Verrucomicrobia, and Acidobacteria. Genes encoding the beta-subunit of the dissimilatory sulfate reductase (dsrB) became 18O labeled only during euxinic conditions. Sequencing of these 18O-labeled dsrB genes showed that Acidobacteria were the dominant group of growing sulfate-reducing bacteria, highlighting their importance for sulfur cycling in estuarine sediments. Our findings provide the first experimental constraints on the redox conditions underlying increased growth in several groups of “microbial dark matter”, validating hypotheses put forth by earlier metagenomic studies.This work was supported by a grant OR 417/1-1 from the Deutsche Forschungsgemeinschaft, and a Junior Researcher Fund grant from LMU Munich to WDO. This work was performed in part, through the Master’s Program in Geobiology and Paleontology (MGAP) at LMU Munich

Transcriptional down-regulation of ccr5 in a subset of HIV+ controllers and their family members.

HIV +Elite and Viremic controllers (EC/VCs) are able to control virus infection, perhaps because of host genetic determinants. We identified 16% (21 of 131) EC/VCs with CD4 +T cells with resistance specific to R5-tropic HIV, reversed after introduction of ccr5. R5 resistance was not observed in macrophages and depended upon the method of T cell activation. CD4 +T cells of these EC/VCs had lower ccr2 and ccr5 RNA levels, reduced CCR2 and CCR5 cell-surface expression, and decreased levels of secreted chemokines. T cells had no changes in chemokine receptor mRNA half-life but instead had lower levels of active transcription of ccr2 and ccr5, despite having more accessible chromatin by ATAC-seq. Other nearby genes were also down-regulated, over a region of ~500 kb on chromosome 3p21. This same R5 resistance phenotype was observed in family members of an index VC, also associated with ccr2/ccr5 down-regulation, suggesting that the phenotype is heritable

Linking Uncultivated Microbial Populations and Benthic Carbon Turnover by Using Quantitative Stable Isotope Probing

Benthic environments harbor highly diverse and complex microbial communities that control carbon fluxes, but the role of specific uncultivated microbial groups in organic matter turnover is poorly understood. In this study, quantitative DNA stable isotope probing (DNA-qSIP) was used for the first time to link uncultivated populations of bacteria and archaea to carbon turnover in lacustrine surface sediments. After 1-week incubations in the dark with [C-13]bicarbonate, DNA-qSIP showed that ammoniaoxidizing archaea (AOA) were the dominant active chemolithoautotrophs involved in the production of new organic matter. Natural C-13-labeled organic matter was then obtained by incubating sediments in the dark for 2.5 months with [C-13] bicarbonate, followed by extraction and concentration of high-molecular-weight (HMW) (> 50-kDa) organic matter. qSIP showed that the labeled organic matter was turned over within 1 week by 823 microbial populations (operational taxonomic units [OTUs]) affiliated primarily with heterotrophic Proteobacteria, Chloroflexi, Verrucomicrobia, and Bacteroidetes. However, several OTUs affiliated with the candidate microbial taxa Latescibacteria, Omnitrophica, Aminicentantes, Cloacimonates, AC1, Bathyarchaeota, and Woesearchaeota, groups known only from genomic signatures, also contributed to biomass turnover. Of these 823 labeled OTUs, 52% (primarily affiliated with Proteobacteria) also became labeled in 1-week incubations with [C-13] bicarbonate, indicating that they turned over carbon faster than OTUs that were labeled only in incubations with C-13-labeled HMW organic matter. These taxa consisted primarily of uncultivated populations within the Firmicutes, Bacteroidetes, Verrucomicrobia, and Chloroflexi, highlighting their ecological importance. Our study helps define the role of several poorly understood, uncultivated microbial groups in the turnover of benthic carbon derived from "dark" primary production. IMPORTANCE Little is known about the ecological role of uncultivated microbial populations in carbon turnover in benthic environments. To better understand this, we used quantitative stable isotope probing (qSIP) to quantify the abundance of diverse, specific groups of uncultivated bacteria and archaea involved in autotrophy and heterotrophy in a benthic lacustrine habitat. Our results provide quantitative evidence for active heterotrophic and autotrophic metabolism of several poorly understood microbial groups, thus demonstrating their relevance for carbon turnover in benthic settings. Archaeal ammonia oxidizers were significant drivers of in situ "dark" primary production supporting the growth of heterotrophic bacteria. These findings expand our understanding of the microbial populations within benthic food webs and the role of uncultivated microbes in benthic carbon turnover

Quantum Particles Constrained on Cylindrical Surfaces with Non-constant Diameter

We present a theoretical formulation of the one-electron problem constrained on the surface of a cylindrical tubule with varying diameter. Because of the cylindrical symmetry, we may reduce the problem to a one-dimensional equation for each angular momentum quantum number $m$ along the cylindrical axis. The geometrical properties of the surface determine the electronic structures through the geometry dependent term in the equation. Magnetic fields parallel to the axis can readily be incorporated. Our formulation is applied to simple examples such as the catenoid and the sinusoidal tubules. The existence of bound states as well as the band structures, which are induced geometrically, for these surfaces are shown. To show that the electronic structures can be altered significantly by applying a magnetic field, Aharonov-Bohm effects in these examples are demonstrated.Comment: 7 pages, 7 figures, submitted to J. Phys. Soc. Jp

Statistical Theory for Incoherent Light Propagation in Nonlinear Media

A novel statistical approach based on the Wigner transform is proposed for the description of partially incoherent optical wave dynamics in nonlinear media. An evolution equation for the Wigner transform is derived from a nonlinear Schrodinger equation with arbitrary nonlinearity. It is shown that random phase fluctuations of an incoherent plane wave lead to a Landau-like damping effect, which can stabilize the modulational instability. In the limit of the geometrical optics approximation, incoherent, localized, and stationary wave-fields are shown to exist for a wide class of nonlinear media.Comment: 4 pages, REVTeX4. Submitted to Physical Review E. Revised manuscrip

Schubert calculus of Richardson varieties stable under spherical Levi subgroups

We observe that the expansion in the basis of Schubert cycles for $H^*(G/B)$ of the class of a Richardson variety stable under a spherical Levi subgroup is described by a theorem of Brion. Using this observation, along with a combinatorial model of the poset of certain symmetric subgroup orbit closures, we give positive combinatorial descriptions of certain Schubert structure constants on the full flag variety in type $A$. Namely, we describe $c_{u,v}^w$ when $u$ and $v$ are inverse to Grassmannian permutations with unique descents at $p$ and $q$, respectively. We offer some conjectures for similar rules in types $B$ and $D$, associated to Richardson varieties stable under spherical Levi subgroups of SO(2n+1,\C) and SO(2n,\C), respectively.Comment: Section 4 significantly shortened, and other minor changes made as suggested by referees. Final version, to appear in Journal of Algebraic Combinatoric

Extracorporeal life support in pediatric cardiac dysfunction

<p>Abstract</p> <p>Background</p> <p>Low cardiac output (LCO) after corrective surgery remains a serious complication in pediatric congenital heart diseases (CHD). In the case of refractory LCO, extra corporeal life support (ECLS) extra corporeal membrane oxygenation (ECMO) or ventricle assist devices (VAD) is the final therapeutic option. In the present study we have reviewed the outcomes of pediatric patients after corrective surgery necessitating ECLS and compared outcomes with pediatric patients necessitating ECLS because of dilatated cardiomyopathy (DCM).</p> <p>Methods</p> <p>A retrospective single-centre cohort study was evaluated in pediatric patients, between 1991 and 2008, that required ECLS. A total of 48 patients received ECLS, of which 23 were male and 25 female. The indications for ECLS included CHD in 32 patients and DCM in 16 patients.</p> <p>Results</p> <p>The mean age was 1.2 ± 3.9 years for CHD patients and 10.4 ± 5.8 years for DCM patients. Twenty-six patients received ECMO and 22 patients received VAD. A total of 15 patients out of 48 survived, 8 were discharged after myocardial recovery and 7 were discharged after successful heart transplantation. The overall mortality in patients with extracorporeal life support was 68%.</p> <p>Conclusion</p> <p>Although the use of ECLS shows a significantly high mortality rate it remains the ultimate chance for children. For better results, ECLS should be initiated in the operating room or shortly thereafter. Bridge to heart transplantation should be considered if there is no improvement in cardiac function to avoid irreversible multiorgan failure (MFO).</p

Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks

Thermodynamic models predict that H2 is energetically favorable for seafloor microbial life, but how H2 affects anabolic processes in seafloor-associated communities is poorly understood. Here, we used quantitative 13C DNA stable isotope probing (qSIP) to quantify the effect of H2 on carbon assimilation by microbial taxa synthesizing 13C-labeled DNA that are associated with partially serpentinized peridotite rocks from the equatorial Mid-Atlantic Ridge. The rock-hosted seafloor community was an order of magnitude more diverse compared to the seawater community directly above the rocks. With added H2, peridotite-associated taxa increased assimilation of 13C-bicarbonate and 13C-acetate into 16S rRNA genes of operational taxonomic units by 146% (±29%) and 55% (±34%), respectively, which correlated with enrichment of H2-oxidizing NiFe-hydrogenases encoded in peridotite-associated metagenomes. The effect of H2 on anabolism was phylogenetically organized, with taxa affiliated with Atribacteria, Nitrospira, and Thaumarchaeota exhibiting the most significant increases in 13C-substrate assimilation in the presence of H2. In SIP incubations with added H2, an order of magnitude higher number of peridotite rock-associated taxa assimilated 13C-bicarbonate, 13C-acetate, and 13C-formate compared to taxa that were not associated with peridotites. Collectively, these findings indicate that the unique geochemical nature of the peridotite-hosted ecosystem has selected for H2-metabolizing, rock-associated taxa that can increase anabolism under high H2 concentrations. Because ultramafic rocks are widespread in slow-, and ultraslow-spreading oceanic lithosphere, continental margins, and subduction zones where H2 is formed in copious amounts, the link between H2 and carbon assimilation demonstrated here may be widespread within these geological settings

Myocardial contractile function in survived neonatal piglets after cardiopulmonary bypass

<p>Abstract</p> <p>Background</p> <p>Hemodynamic function may be depressed in the early postoperative stages after cardiac surgery. The aim of this study was the analysis of the myocardial contractility in neonates after cardiopulmonary bypass (CPB) and mild hypothermia.</p> <p>Methods</p> <p>Three indices of left ventricular myocardial contractile function (dP/dt, (dP/dt)/P, and wall thickening) were studied up to 6 hours after CPB in neonatal piglets (CPB group; n = 4). The contractility data were analysed and then compared to the data of newborn piglets who also underwent median thoracotomy and instrumentation for the same time intervals but without CPB (non-CPB group; n = 3).</p> <p>Results</p> <p>Left ventricular dP/dt_maxand (dP/dt_max)/P remained stable in CPB group, while dP/dt_maxdecreased in non-CPB group 5 hours postoperatively (1761 ± 205 mmHg/s at baseline vs. 1170 ± 205 mmHg/s after 5 h; p < 0.05). However, with regard to dP/dt_maxand (dP/dt_max)/P there were no statistically significant differences between the two groups. Comparably, although myocardial thickening decreased in the non-CPB group the differences between the two groups were not statistically significant.</p> <p>Conclusions</p> <p>The myocardial contractile function in survived neonatal piglets remained stable 6 hours after cardiopulmonary bypass and mild hypothermia probably due to regional hypercontractility.</p