A Generalized Spatial Measure for Resilience of Microbial Systems

The emergent property of resilience is the ability of a system to return to an original state after a disturbance. Resilience may be used as an early warning system for significant or irreversible community transition; that is, a community with diminishing or low resilience may be close to catastrophic shift in function or an irreversible collapse. Typically, resilience is quantified using recovery time, which may be difficult or impossible to directly measure in microbial systems. A recent study in the literature showed that under certain conditions, a set of spatial-based metrics termed recovery length, can be correlated to recovery time, and thus may be a reasonable alternative measure of resilience. However, this spatial metric of resilience is limited to use for step-change perturbations. Building upon the concept of recovery length, we propose a more general form of the spatial metric of resilience that can be applied to any shape of perturbation profiles (for example, either sharp or smooth gradients). We termed this new spatial measure “perturbation-adjusted spatial metric of resilience” (PASMORE). We demonstrate the applicability of the proposed metric using a mathematical model of a microbial mat

Integrating Ecological and Engineering Concepts of Resilience in Microbial Communities

Many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. We argue that the disconnect largely results from the wide variance in microbial community complexity, which range from compositionally simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems that undergo both recoverable and unrecoverable transitions, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the two concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community\u27s functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities and suggest that state changes in response to environmental variation may be a key mechanism driving functional resilience in microbial communities

Spatiotemporal Metabolic Network Models Reveal Complex Autotroph-Heterotroph Biofilm Interactions Governed by Photon Incidences

Autotroph-heterotroph interactions are ubiquitous in natural environment and play a key role in controlling various essential ecosystem functions, such as production and utilization of organic matter, cycling of nitrogen, sulfur, and other chemical elements. Understanding how these biofilm metabolic interactions are constrained in space and time remains challenging because fully predictive models designed for this purpose are currently limited. Toward filling this gap, here we developed community metabolic network models for two autotroph-heterotroph biofilm consortia (termed UCC-A and UCC-O), which share a suite of common heterotrophic members but have a single distinct photoautotrophic cyanobacterium (Phormidesmis priestleyi str. ANA and Phormidium sp. OSCR) that provides organic carbon and nitrogen sources to support the growth of heterotrophic partners. After determining model parameters by data fitting using the spatiotemporal distributions of microbial abundances, we comparatively analyzed the resulting biofilm models to examine any fundamental differences in microbial interactions between the two consortia under the variation of key environmental variables: CO2 and photon levels. The UCC-A model predicted generally expected responses, i.e., the autotroph population increased in response to elevated levels of CO2 and photon, followed by increase in the heterotroph population. In contrast, the UCC-O model showed somewhat complicated dynamics, e.g., higher photon incidence rates resulted in the increase in autotroph population but decrease in heterotroph population due to the lowered provision of glucose from the autotroph. A further analysis showed that species coexistence was governed by the photon incidences rather than the carbon availability for UCC-O, which was the opposite for UCC-A

Quantum Chemistry Calculations for Metabolomics

A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials (“standards”), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for “standards-free” identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials (“standards”), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for “standards-free” identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples

SLIM Ultrahigh Resolution Ion Mobility Spectrometry Separations of Isotopologues and Isotopomers Reveal Mobility Shifts due to Mass Distribution Changes

We report on separations of ion isotopologues and isotopomers using ultrahigh-resolution traveling wave-based Structures for Lossless Ion Manipulations with serpentine ultralong path and extended routing ion mobility spectrometry coupled to mass spectrometry (SLIM SUPER IMS-MS). Mobility separations of ions from the naturally occurring ion isotopic envelopes (e.g., [M], [M+1], [M+2], ... ions) showed the first and second isotopic peaks (i.e., [M+1] and [M+2]) for various tetraalkylammonium ions could be resolved from their respective monoisotopic ion peak ([M]) after SLIM SUPER IMS with resolving powers of ∼400–600. Similar separations were obtained for other compounds (e.g., tetrapeptide ions). Greater separation was obtained using argon versus helium drift gas, as expected from the greater reduced mass contribution to ion mobility described by the Mason–Schamp relationship. To more directly explore the role of isotopic substitutions, we studied a mixture of specific isotopically substituted (15N, 13C, and 2H) protonated arginine isotopologues. While the separations in nitrogen were primarily due to their reduced mass differences, similar to the naturally occurring isotopologues, their separations in helium, where higher resolving powers could also be achieved, revealed distinct additional relative mobility shifts. These shifts appeared correlated, after correction for the reduced mass contribution, with changes in the ion center of mass due to the different locations of heavy atom substitutions. The origin of these apparent mass distribution-induced mobility shifts was then further explored using a mixture of Iodoacetyl Tandem Mass Tag (iodoTMT) isotopomers (i.e., each having the same exact mass, but with different isotopic substitution sites). Again, the observed mobility shifts appeared correlated with changes in the ion center of mass leading to multiple monoisotopic mobilities being observed for some isotopomers (up to a ∼0.04% difference in mobility). These mobility shifts thus appear to reflect details of the ion structure, derived from the changes due to ion rotation impacting collision frequency or momentum transfer, and highlight the potential for new approaches for ion structural characterization

Advancing microbial sciences by individual-based modelling

Remarkable technological advances have revealed ever more properties and behaviours of individual microorganisms, but the novel data generated by these techniques have not yet been fully exploited. In this Opinion article, we explain how individual-based models (IBMs) can be constructed based on the findings of such techniques and how they help to explore competitive and cooperative microbial interactions. Furthermore, we describe how IBMs have provided insights into self-organized spatial patterns from biofilms to the oceans of the world, phage-CRISPR dynamics and other emergent phenomena. Finally, we discuss how combining individual-based observations with IBMs can advance our understanding at both the individual and population levels, leading to the new approach of microbial individual-based ecology (μIBE)

Optimizing colormaps with consideration for color vision deficiency to enable accurate interpretation of scientific data

Color vision deficiency (CVD) affects more than 4% of the population and leads to a different visual perception of colors. Though this has been known for decades, colormaps with many colors across the visual spectra are often used to represent data, leading to the potential for misinterpretation or difficulty with interpretation by someone with this deficiency. Until the creation of the module presented here, there were no colormaps mathematically optimized for CVD using modern color appearance models. While there have been some attempts to make aesthetically pleasing or subjectively tolerable colormaps for those with CVD, our goal was to make optimized colormaps for the most accurate perception of scientific data by as many viewers as possible. We developed a Python module, cmaputil, to create CVD-optimized colormaps, which imports colormaps and modifies them to be perceptually uniform in CVD-safe colorspace while linearizing and maximizing the brightness range. The module is made available to the science community to enable others to easily create their own CVD-optimized colormaps. Here, we present an example CVD-optimized colormap created with this module that is optimized for viewing by those without a CVD as well as those with red-green colorblindness. This colormap, cividis, enables nearly-identical visual-data interpretation to both groups, is perceptually uniform in hue and brightness, and increases in brightness linearly