Randomized lasso links microbial taxa with aquatic functional groups inferred from flow cytometry

High-nucleic-acid (HNA) and low-nucleic-acid (LNA) bacteria are two operational groups identified by flow cytometry (FCM) in aquatic systems. A number of reports have shown that HNA cell density correlates strongly with heterotrophic production, while LNA cell density does not. However, which taxa are specifically associated with these groups, and by extension, productivity has remained elusive. Here, we addressed this knowledge gap by using a machine learning-based variable selection approach that integrated FCM and 16S rRNA gene sequencing data collected from 14 freshwater lakes spanning a broad range in physicochemical conditions. There was a strong association between bacterial heterotrophic production and HNA absolute cell abundances (R-2 = 0.65), but not with the more abundant LNA cells. This solidifies findings, mainly from marine systems, that HNA and LNA bacteria could be considered separate functional groups, the former contributing a disproportionately large share of carbon cycling. Taxa selected by the models could predict HNA and LNA absolute cell abundances at all taxonomic levels. Selected operational taxonomic units (OTUs) ranged from low to high relative abundance and were mostly lake system specific (89.5% to 99.2%). A subset of selected OTUs was associated with both LNA and HNA groups (12.5% to 33.3%), suggesting either phenotypic plasticity or within-OTU genetic and physiological heterogeneity. These findings may lead to the identification of system-specific putative ecological indicators for heterotrophic productivity. Generally, our approach allows for the association of OTUs with specific functional groups in diverse ecosystems in order to improve our understanding of (microbial) biodiversity-ecosystem functioning relationships. IMPORTANCE A major goal in microbial ecology is to understand how microbial community structure influences ecosystem functioning. Various methods to directly associate bacterial taxa to functional groups in the environment are being developed. In this study, we applied machine learning methods to relate taxonomic data obtained from marker gene surveys to functional groups identified by flow cytometry. This allowed us to identify the taxa that are associated with heterotrophic productivity in freshwater lakes and indicated that the key contributors were highly system specific, regularly rare members of the community, and that some could possibly switch between being low and high contributors. Our approach provides a promising framework to identify taxa that contribute to ecosystem functioning and can be further developed to explore microbial contributions beyond heterotrophic production

Microhabitats are associated with diversity-productivity relationships in freshwater bacterial communities

Eukaryotic communities commonly display a positive relationship between biodiversity and ecosystem function (BEF) but the results have been mixed when assessed in bacterial communities. Habitat heterogeneity, a factor in eukaryotic BEFs, may explain these variable observations but it has not been thoroughly evaluated in bacterial communities. Here, we examined the impact of habitat on the relationship between diversity assessed based on the (phylogenetic) Hill diversity metrics and heterotrophic productivity. We sampled co-occurring free-living (more homogenous) and particle-associated (more heterogeneous) bacterial habitats in a freshwater, estuarine lake over three seasons: spring, summer and fall. There was a strong, positive, linear relationship between particle-associated bacterial richness and heterotrophic productivity that strengthened when considering dominant taxa. There were no observable BEF trends in free-living bacterial communities for any diversity metric. Biodiversity, richness and Inverse Simpson's index, were the best predictors of particle-associated production whereas pH was the best predictor of free-living production. Our findings show that heterotrophic productivity is positively correlated with the effective number of taxa and that BEF relationships are associated with microhabitats. These results add to the understanding of the highly distinct contributions to diversity and functioning contributed by bacteria in free-living and particle-associated habitats

Multiple sulfur isotope signatures of sulfite and thiosulfate reduction by the model dissimilatory sulfate-reducer, Desulfovibrio alaskensis str. G20

Dissimilatory sulfate reduction serves as a key metabolic carbon remineralization process in anoxic marine environments. Sulfate reducing microorganisms can impart a wide range in mass-dependent sulfur isotopic fractionation. As such, the presence and relative activity of these organisms is identifiable from geological materials. By extension, sulfur isotope records are used to infer the redox balance of marine sedimentary environments, and the oxidation state of Earth's oceans and atmosphere. However, recent work suggests that our understanding of microbial sulfate reduction (MSRs) may be missing complexity associated with the presence and role of key chemical intermediates in the reductive process. This study provides a test of proposed metabolic models of sulfate reduction by growing an axenic culture of the well-studied MSRs, Desulfovibrio alaskensis strain G20, under electron donor limited conditions on the terminal electron acceptors sulfate, sulfite or thiosulfate, and tracking the multiple S isotopic consequences of each condition set. The dissimilatory reduction of thiosulfate and sulfite produce unique minor isotope effects, as compared to the reduction of sulfate. Further, these experiments reveal a complex biochemistry associated with sulfite reduction. That is, under high sulfite concentrations, sulfur is shuttled to an intermediate pool of thiosulfate. Site-specific isotope fractionation (within thiosulfate) is very large (34ε ~ 30‰) while terminal product sulfide carries only a small fractionation from the initial sulfite (34ε < 10‰): a signature similar in magnitude to sulfate and thiosulfate reduction. Together these findings show that microbial sulfate reduction (MSR) is highly sensitive to the concentration of environmentally important sulfur-cycle intermediates (sulfite and thiosulfate), especially when thiosulfate and the large site-specific isotope effects are involved

Resummation in nonlinear equation for high energy factorizable gluon density and its extension to include coherence

Motivated by forthcoming p-Pb experiments at Large Hadron Collider which require both knowledge of gluon densities accounting for saturation and for processes at a wide range of $p_t$ we study basic momentum space evolution equations of high energy QCD factorization. Solutions of those equations might be used to form a set of gluon densities to calculate observables in generalized high energy factorization. Moreover in order to provide a framework for predictions for exclusive final states in p-Pb scattering with high $p_t$ we rewrite the equation for the high energy factorizable gluon density in a resummed form, similarly to what has been done in \cite{Kutak:2011fu} for the BK equation. The resummed equation is then extended to account for colour coherence. This introduces an external scale to the evolution of the gluon density, and therefore makes it applicable in studies of final states.Comment: 14 pages, appendix added, accepted for publication in JHE

Early life stress determines the effects of glucocorticoids and stress on hippocampal function:Electrophysiological and behavioral evidence respectively

Exposure to early-life adversity may program brain function to prepare individuals for adaptation to matching environmental contexts. In this study we tested this hypothesis in more detail by examining the effects of early-life stress - induced by raising offspring with limited nesting and bedding material from postnatal days 2-9 - in various behavioral tasks and on synaptic function in adult mice. Early-life stress impaired adult performance in the hippocampal dependent low-arousing object-in-context recognition memory task. This effect was absent when animals were exposed to a single stressor before training. Early-life stress did not alter high-arousing context and auditory fear conditioning. Early-life stress-induced behavioral modifications were not associated with alterations in the dendritic architecture of hippocampal CA1 pyramidal neurons or principal neurons of the basolateral amygdala. However, early-life stress reduced the ratio of NMDA to AMPA receptor-mediated excitatory postsynaptic currents and glutamate release probability specifically in hippocampal CA1 neurons, but not in the basolateral amygdala. These ex vivo effects in the hippocampus were abolished by acute glucocorticoid treatment. Our findings support that early-life stress can hamper object-in-context learning via pre- and post synaptic mechanisms that affect hippocampal function but these effects are counteracted by acute stress or elevated glucocorticoid levels. (C) 2018 Published by Elsevier Ltd

Weak lensing, dark matter and dark energy

Weak gravitational lensing is rapidly becoming one of the principal probes of dark matter and dark energy in the universe. In this brief review we outline how weak lensing helps determine the structure of dark matter halos, measure the expansion rate of the universe, and distinguish between modified gravity and dark energy explanations for the acceleration of the universe. We also discuss requirements on the control of systematic errors so that the systematics do not appreciably degrade the power of weak lensing as a cosmological probe.Comment: Invited review article for the GRG special issue on gravitational lensing (P. Jetzer, Y. Mellier and V. Perlick Eds.). V3: subsection on three-point function and some references added. Matches the published versio

Cumulant expansion for studying damped quantum solitons

The quantum statistics of damped optical solitons is studied using cumulant-expansion techniques. The effect of absorption is described in terms of ordinary Markovian relaxation theory, by coupling the optical field to a continuum of reservoir modes. After introduction of local bosonic field operators and spatial discretization pseudo-Fokker-Planck equations for multidimensional s-parameterized phase-space functions are derived. These partial differential equations are equivalent to an infinite set of ordinary differential equations for the cumulants of the phase-space functions. Introducing an appropriate truncation condition, the resulting finite set of cumulant evolution equations can be solved numerically. Solutions are presented in Gaussian approximation and the quantum noise is calculated, with special emphasis on squeezing and the recently measured spectral photon-number correlations [Spaelter et al., Phys. Rev. Lett. 81, 786 (1998)].Comment: 17 pages, 13 figures, revtex, psfig, multicols, published in Phys.Rev.

Stochastic Theory of Relativistic Particles Moving in a Quantum Field: II. Scalar Abraham-Lorentz-Dirac-Langevin Equation, Radiation Reaction and Vacuum Fluctuations

We apply the open systems concept and the influence functional formalism introduced in Paper I to establish a stochastic theory of relativistic moving spinless particles in a quantum scalar field. The stochastic regime resting between the quantum and semi-classical captures the statistical mechanical attributes of the full theory. Applying the particle-centric world-line quantization formulation to the quantum field theory of scalar QED we derive a time-dependent (scalar) Abraham-Lorentz-Dirac (ALD) equation and show that it is the correct semiclassical limit for nonlinear particle-field systems without the need of making the dipole or non-relativistic approximations. Progressing to the stochastic regime, we derive multiparticle ALD-Langevin equations for nonlinearly coupled particle-field systems. With these equations we show how to address time-dependent dissipation/noise/renormalization in the semiclassical and stochastic limits of QED. We clarify the the relation of radiation reaction, quantum dissipation and vacuum fluctuations and the role that initial conditions may play in producing non-Lorentz invariant noise. We emphasize the fundamental role of decoherence in reaching the semiclassical limit, which also suggests the correct way to think about the issues of runaway solutions and preacceleration from the presence of third derivative terms in the ALD equation. We show that the semiclassical self-consistent solutions obtained in this way are ``paradox'' and pathology free both technically and conceptually. This self-consistent treatment serves as a new platform for investigations into problems related to relativistic moving charges.Comment: RevTex; 20 pages, 3 figures, Replaced version has corrected typos, slightly modified derivation, improved discussion including new section with comparisons to related work, and expanded reference