Ectomycorrhizal fungi and past high CO2 atmospheres enhance mineral weathering through increased below-ground carbon-energy fluxes

Field studies indicate an intensification of mineral weathering with advancement from arbuscular mycorrhizal (AM) to later-evolving ectomycorrhizal (EM) fungal partners of gymnosperm and angiosperm trees. We test the hypothesis that this intensification is driven by increasing photosynthate carbon allocation to mycorrhizal mycelial networks using 14CO2-tracer experiments with representative tree–fungus mycorrhizal partnerships. Trees were grown in either a simulated past CO2 atmosphere (1500 ppm)—under which EM fungi evolved—or near-current CO2 (450 ppm). We report a direct linkage between photosynthate-energy fluxes from trees to EM and AM mycorrhizal mycelium and rates of calcium silicate weathering. Calcium dissolution rates halved for both AM and EM trees as CO2 fell from 1500 to 450 ppm, but silicate weathering by AM trees at high CO2 approached rates for EM trees at near-current CO2. Our findings provide mechanistic insights into the involvement of EM-associating forest trees in strengthening biological feedbacks on the geochemical carbon cycle that regulate atmospheric CO2 over millions of years

An accurate calculation of the nucleon axial charge with lattice QCD

We report on a lattice QCD calculation of the nucleon axial charge, $g_A$, using M\"{o}bius Domain-Wall fermions solved on the dynamical $N_f=2+1+1$ HISQ ensembles after they are smeared using the gradient-flow algorithm. The calculation is performed with three pion masses, $m_\pi\sim\{310,220,130\}$ MeV. Three lattice spacings ($a\sim\{0.15,0.12,0.09\}$ fm) are used with the heaviest pion mass, while the coarsest two spacings are used on the middle pion mass and only the coarsest spacing is used with the near physical pion mass. On the $m_\pi\sim220$ MeV, $a\sim0.12$ fm point, a dedicated volume study is performed with $m_\pi L \sim \{3.22,4.29,5.36\}$. Using a new strategy motivated by the Feynman-Hellmann Theorem, we achieve a precise determination of $g_A$ with relatively low statistics, and demonstrable control over the excited state, continuum, infinite volume and chiral extrapolation systematic uncertainties, the latter of which remains the dominant uncertainty. Our final determination at 2.6\% total uncertainty is $g_A = 1.278(21)(26)$, with the first uncertainty including statistical and systematic uncertainties from fitting and the second including model selection systematics related to the chiral and continuum extrapolation. The largest reduction of the second uncertainty will come from a greater number of pion mass points as well as more precise lattice QCD results near the physical pion mass.Comment: 17 pages + 11 pages of references and appendices. 15 figures. Interested readers can download the Python analysis scripts and an hdf5 data file at https://github.com/callat-qcd/project_gA_v

Characterization of an electron conduit between bacteria and the extracellular environment

A number of species of Gram-negative bacteria can use insoluble minerals of Fe(III) and Mn(IV) as extracellular respiratory electron acceptors. In some species of Shewanella, deca-heme electron transfer proteins lie at the extracellular face of the outer membrane (OM), where they can interact with insoluble substrates. To reduce extracellular substrates, these redox proteins must be charged by the inner membrane/periplasmic electron transfer system. Here, we present a spectro-potentiometric characterization of a trans-OM icosa-heme complex, MtrCAB, and demonstrate its capacity to move electrons across a lipid bilayer after incorporation into proteoliposomes. We also show that a stable MtrAB subcomplex can assemble in the absence of MtrC; an MtrBC subcomplex is not assembled in the absence of MtrA; and MtrA is only associated to the membrane in cells when MtrB is present. We propose a model for the modular organization of the MtrCAB complex in which MtrC is an extracellular element that mediates electron transfer to extracellular substrates and MtrB is a trans-OM spanning ß-barrel protein that serves as a sheath, within which MtrA and MtrC exchange electrons. We have identified the MtrAB module in a range of bacterial phyla, suggesting that it is widely used in electron exchange with the extracellular environment

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.

Inflammatory bowel diseases, which include Crohn's disease and ulcerative colitis, affect several million individuals worldwide. Crohn's disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (up to 24 time points each; in total 2,965 stool, biopsy, and blood specimens). Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. We demonstrate a characteristic increase in facultative anaerobes at the expense of obligate anaerobes, as well as molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. The study's infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi'omics Database ( http://ibdmdb.org ), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases

Designing a suite of measurements to understand the critical zone

Many scientists have begun to refer to the earth surface environment from the upper canopy to the depths of bedrock as the critical zone (CZ). Identification of the CZ as an integral object worthy of study implicitly posits that the study of the whole earth surface will provide benefits that do not arise when studying the individual parts. To study the CZ, however, requires prioritizing among the measurements that can be made – and we do not generally agree on the priorities. Currently, the Susquehanna Shale Hills Critical Zone Observatory (SSHCZO) is expanding from a small original focus area (0.08 km2 , Shale Hills catchment), to a larger watershed (164 km2 , Shavers Creek watershed) and is grappling with the prioritization. This effort is an expansion from a monolithologic first-order forested catchment to a watershed that encompasses several lithologies (shale, sandstone, limestone) and land use types (forest, agriculture). The goal of the project remains the same: to understand water, energy, gas, solute, and sediment (WEGSS) fluxes that are occurring today in the context of the record of those fluxes over geologic time as recorded in soil profiles, the sedimentary record, and landscape morphology. Given the small size of the Shale Hills catchment, the original design incorporated measurement of as many parameters as possible at high temporal and spatial density. In the larger Shavers Creek watershed, however, we must focus the measurements. We describe a strategy of data collection and modeling based on a geomorphological and land use framework that builds on the hillslope as the basic unit. Interpolation and extrapolation beyond specific sites relies on geophysical surveying, remote sensing, geomorphic analysis, the study of natural integrators such as streams, groundwaters or air, and application of a suite of CZ models. We hypothesize that measurements of a few important variables at strategic locations within a geomorphological framework will allow development of predictive models of CZ behavior. In turn, the measurements and models will reveal how the larger watershed will respond to perturbations both now and into the future

Scale setting the M\"obius Domain Wall Fermion on gradient-flowed HISQ action using the omega baryon mass and the gradient-flow scales t0t_0 and w0w_0

We report on a sub-percent scale determination using the omega baryon mass and gradient-flow methods. The calculations are performed on 22 ensembles of $N_f=2+1+1$ highly improved, rooted staggered sea-quark configurations generated by the MILC and CalLat Collaborations. The valence quark action used is M\"obius Domain-Wall fermions solved on these configurations after a gradient-flow smearing is applied with a flowtime of $t_{\rm gf}=1$ in lattice units. The ensembles span four lattice spacings in the range $0.06 \lesssim a \lesssim 0.15$ fm, six pion masses in the range $130 \lesssim m_\pi \lesssim 400$ MeV and multiple lattice volumes. On each ensemble, the gradient-flow scales $t_0/a^2$ and $w_0/a$ and the omega baryon mass $a m_\Omega$ are computed. The dimensionless product of these quantities is then extrapolated to the continuum and infinite volume limits and interpolated to the physical light, strange and charm quark mass point in the isospin limit, resulting in the determination of $\sqrt{t_0}=0.1422(14)$ fm and $w_0 = 0.1709(11)$ fm with all sources of statistical and systematic uncertainty accounted for. The dominant uncertainty in this result is the stochastic uncertainty, providing a clear path for a few-per-mille uncertainty, as recently obtained by the Budapest-Marseille-Wuppertal Collaboration.Comment: v3: Published version; v2: Added determination of t_0 as well as w_0; v1: 13 pages plus appendices. The correlation function data, mass results and analysis code accompanying this publication can be found at this github repository: https://github.com/callat-qcd/project_scale_setting_mdwf_his