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The metabolic activity of soil microbiomes has a central role in global nutrient cycles. Understanding how soil metabolic activity responds to climate-driven environmental perturbations is a key challenge. However, the ecological, spatial and chemical complexity of soils impedes understanding how these communities respond to perturbations. Here we address this complexity by combining dynamic measurements of respiratory nitrate metabolism with modelling to reveal functional regimes that define soil responses to environmental change. Measurements across more than 1,500 soil microcosms subjected to pH perturbations reveal regimes in which distinct mechanisms govern metabolite dynamics. A minimal model with two parameters, biomass activity and growth-limiting nutrient availability, predicts nitrate utilization dynamics across soils and pH perturbations. Parameter shifts under perturbation reveal three functional regimes, each linked to distinct mechanisms: (1) an acidic regime marked by cell death and suppressed metabolism; (2) a nutrient-limited regime in which dominant taxa exploit matrix-released nutrients; and (3) a resurgent growth regime driven by exponential growth of rare taxa in nutrient-rich conditions. We validated these model-derived mechanisms with nutrient measurements, amendment experiments, sequencing and isolate studies. Additional experiments and meta-analyses suggest that functional regimes are widespread in pH-perturbed soils. 

Abstract The metabolic activity of soil microbiomes plays a central role in carbon and nitrogen cycling. Given the changing climate, it is important to understand how the metabolism of natural communities responds to environmental change. However, the ecological, spatial, and chemical complexity of soils makes understanding the mechanisms governing the response of these communities to perturbations challenging. Here, we overcome this complexity by using dynamic measurements of metabolism in microcosms and modeling to reveal regimes where a few key mechanisms govern the response of soils to environmental change. We sample soils along a natural pH gradient, construct >1500 microcosms to perturb the pH, and quantify the dynamics of respiratory nitrate utilization, a key process in the nitrogen cycle. Despite the complexity of the soil microbiome, a minimal mathematical model with two variables, the quantity of active biomass in the community and the availability of a growth-limiting nutrient, quantifies observed nitrate utilization dynamics across soils and pH perturbations. Across environmental perturbations, changes in these two variables give rise to three functional regimes each with qualitatively distinct dynamics of nitrate utilization over time: a regime where acidic perturbations induce cell death that limits metabolic activity, a nutrientlimiting regime where nitrate uptake is performed by dominant taxa that utilize nutrients released from the soil matrix, and a resurgent growth regime in basic conditions, where excess nutrients enable growth of initially rare taxa. The underlying mechanism of each regime is predicted by our interpretable model and tested via amendment experiments, nutrient measurements, and sequencing. Further, our data suggest that the long-term history of environmental variation in the wild influences the transitions between functional regimes. Therefore, quantitative measurements and a mathematical model reveal the existence of qualitative regimes that capture the mechanisms and dynamics of a community responding to environmental change. 

ABSTRACT The intricate three-dimensional (3D) structures of multicellular organisms emerge through genetically encoded spatio-temporal patterns of mechanical stress. Cell atlases of gene expression during embryogenesis are now available for many organisms, but connecting these to the mechanical drivers of embryonic shape requires physical models of multicellular tissues that identify the relevant mechanical and geometric constraints, and an ability to measure mechanical stresses at single-cell resolution over time. Here we report significant steps towardsboththese goals. We describe a new mathematical theory for the mechanics of 3D multicellular aggregates involving the quasi-static balance of cellular pressures, surface tensions, and line tensions. Our theory yields a quantitatively accurate low-dimensional description for the time-varying geometric dynamics of 3D multicellular aggregates and, through the solution of a mechanical inverse problem, an image-based strategy for constructing spatio-temporal maps of the mechanical stresses driving morphogenesis in 3D. Using synthetic image data, we confirm the accuracy and robustness of our geometric and mechanical approaches. We then apply these approaches to segmented light sheet data, representing cellular membranes with isotropic resolution, to construct a 3D mechanical atlas for ascidian gastrulation. The atlas captures a surprisingly accurate low-dimensional description of ascidian gastrulation, revealing the adiabatic nature of the underlying mechanical dynamics. Mapping the inferred forces onto the invariant embryonic lineage reveals a rich correspondence between dynamically evolving cell states, patterns of cell division, and local regulation of cellular pressure and contractile stress. Thus, our mechanical atlas reveals a new view of ascidian gastrulation in which lineage-specific control over a complex heterogenous pattern of cellular pressure and contractile stress, integrated globally, governs the emergent dynamics of ascidian gastrulation. 

Ionic liquid mixed with poly(methyl methacrylate)-grafted nanoparticle aggregates at low particle concentrations was shown to exhibit different dynamics and ionic conductivity than that of pure ionic liquid in our previous studies. In this work, we report on the quasi-elastic neutron scattering results on ionic liquid containing polymer-grafted nanoparticles at the higher particle concentration. The diffusivity of imidazolium (HMIM + ) cations of 1-hexyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (HMIM-TFSI) in the presence of poly(methyl methacrylate)-grafted iron oxide nanoparticles and the ionic conductivity of solutions were discussed through the confinement. Analysis of the elastic incoherent structure factor suggested the confinement radius decreased with the addition of grafted particles in HMIM-TFSI/solvent mixture, indicating the confinement that is induced by the high concentration of grafted particles, shrinks the HMIM-TFSI restricted volume. We further conjecture that this enhanced diffusivity occurs as a result of the local ordering of cations within aggregates of poly(methyl methacrylate)-grafted particles. 

Named Data Networking (NDN) secures network communications by requiring all data packets to be signed upon production. This requirement makes usable and efficient NDN certificate issuance and revocation essential for NDN operations. In this paper, we first investigate and clarify core concepts related to NDN certificate revocation, then proceed with the design of CertRevoke, an NDN certificate revocation framework. CertRevoke utilizes naming conventions and trust schema to ensure certificate owners and issuers legitimately produce in-network cacheable records for revoked certificates. We evaluate the security properties and performance of CertRevoke through case studies. Our results show that deploying CertRevoke in an operational NDN network is feasible.