Glycyl Radical Enzyme-Associated Microcompartments: Redox-Replete Bacterial Organelles

An increasing number of microbes are being identified that organize catabolic pathways within self-assembling proteinaceous structures known as bacterial microcompartments (BMCs). Most BMCs are characterized by their singular substrate specificity and commonly employ B12-dependent radical mechanisms. In contrast, a less-well-known BMC type utilizes the B12-independent radical chemistry of glycyl radical enzymes (GREs). Unlike B12-dependent enzymes, GREs require an activating enzyme (AE) as well as an external source of electrons to generate an adenosyl radical and form their catalytic glycyl radical. Organisms encoding these glycyl radical enzyme-associated microcompartments (GRMs) confront the challenge of coordinating the activation and maintenance of their GREs with the assembly of a multienzyme core that is encapsulated in a protein shell. The GRMs appear to enlist redox proteins to either generate reductants internally or facilitate the transfer of electrons from the cytosol across the shell. Despite this relative complexity, GRMs are one of the most widespread types of BMC, with distinct subtypes to catabolize different substrates. Moreover, they are encoded by many prominent gut-associated and pathogenic bacteria. In this review, we will focus on the diversity, function, and physiological importance of GRMs, with particular attention given to their associated and enigmatic redox proteins.

Systems-Level Analysis of Oxygen Exposure in Zymomonas mobilis: Implications for Isoprenoid Production

Zymomonas mobilis is an aerotolerant anaerobe and prolific ethanologen with attractive characteristics for industrial bioproduct generation. However, there is currently insufficient knowledge of the impact that environmental factors have on flux through industrially relevant biosynthetic pathways. Here, we examined the effect of oxygen exposure on metabolism and gene expression in Z. mobilis by combining targeted metabolomics, mRNA sequencing, and shotgun proteomics. We found that exposure to oxygen profoundly influenced metabolism, inducing both transient metabolic bottlenecks and long-term metabolic remodeling. In particular, oxygen induced a severe but temporary metabolic bottleneck in the methyl erythritol 4-phosphate pathway for isoprenoid biosynthesis caused by oxidative damage to the iron-sulfur cofactors of the final two enzymes in the pathway. This bottleneck was resolved with minimal changes in expression of isoprenoid biosynthetic enzymes. Instead, it was associated with pronounced upregulation of enzymes related to iron-sulfur cluster maintenance and biogenesis (i.e., flavodoxin reductase and the suf operon). We also detected major changes in glucose utilization in the presence of oxygen. Specifically, we observed increased gluconate production following exposure to oxygen, accounting for 18% of glucose uptake. Our results suggest that under aerobic conditions, electrons derived from the oxidation of glucose to gluconate are diverted to the electron transport chain, where they can minimize oxidative damage by reducing reactive oxygen species such as H2O2. This model is supported by the simultaneous upregulation of three membrane-bound dehydrogenases, cytochrome c peroxidase, and a cytochrome bd oxidase following exposure to oxygen. IMPORTANCE Microbially generated biofuels and bioproducts have the potential to provide a more environmentally sustainable alternative to fossil-fuel-derived products. In particular, isoprenoids, a diverse class of natural products, are chemically suitable for use as high-grade transport fuels and other commodity molecules. However, metabolic engineering for increased production of isoprenoids and other bioproducts is limited by an incomplete understanding of factors that control flux through biosynthetic pathways. Here, we examined the native regulation of the isoprenoid biosynthetic pathway in the biofuel producer Zymomonas mobilis. We leveraged oxygen exposure as a means to perturb carbon flux, allowing us to observe the formation and resolution of a metabolic bottleneck in the pathway. Our multi-omics analysis of this perturbation enabled us to identify key auxiliary enzymes whose expression correlates with increased production of isoprenoid precursors, which we propose as potential targets for future metabolic engineering.

Micron-gap spacers with ultrahigh thermal resistance and mechanical robustness for direct energy conversion

In thermionic energy converters, the absolute efficiency can be increased up to 40% if space-charge losses are eliminated by using a sub-10-µm gap between the electrodes. One practical way to achieve such small gaps over large device areas is to use a stiff and thermally insulating spacer between the two electrodes. We report on the design, fabrication and characterization of thin-film alumina-based spacers that provided robust 3-8 μm gaps between planar substrates and had effective thermal conductivities less than those of aerogels. The spacers were fabricated on silicon molds and, after release, could be manually transferred onto any substrate. In large-scale compression testing, they sustained compressive stresses of 0.4-4 MPa without fracture. Experimentally, the thermal conductance was 10-30 mWcm^-2K^-1 and, surprisingly, independent of film thickness (100-800 nm) and spacer height. To explain this independence, we developed a model that includes the pressure-dependent conductance of locally distributed asperities and sparse contact points throughout the spacer structure, indicating that only 0.1-0.5% of the spacer-electrode interface was conducting heat. Our spacers show remarkable functionality over multiple length scales, providing insulating micrometer gaps over centimeter areas using nanoscale films. These innovations can be applied to other technologies requiring high thermal resistance in small spaces, such as thermophotovoltaic converters, insulation for spacecraft and cryogenic devices.

Emergent Subpopulation Behavior Uncovered with a Community Dynamic Metabolic Model of Escherichia coli Diauxic Growth

Microbes have adapted to greatly variable environments in order to survive both short-term perturbations and permanent changes. A classical and yet still actively studied example of adaptation to dynamic environments is the diauxic shift of Escherichia coli, in which cells grow on glucose until its exhaustion and then transition to using previously secreted acetate. Here we tested different hypotheses concerning the nature of this transition by using dynamic metabolic modeling. To reach this goal, we developed an open source modeling framework integrating dynamic models (ordinary differential equation systems) with structural models (metabolic networks) which can take into account the behavior of multiple subpopulations and smooth flux transitions between time points. We used this framework to model the diauxic shift, first with a single E. coli model whose metabolic state represents the overall population average and then with a community of two subpopulations, each growing exclusively on one carbon source (glucose or acetate). After introduction of an environment-dependent transition function that determined the balance between subpopulations, our model generated predictions that are in strong agreement with published data. Our results thus support recent experimental evidence that diauxie, rather than a coordinated metabolic shift, would be the emergent pattern of individual cells differentiating for optimal growth on different substrates. This work offers a new perspective on the use of dynamic metabolic modeling to investigate population heterogeneity dynamics. The proposed approach can easily be applied to other biological systems composed of metabolically distinct, interconverting subpopulations and could be extended to include single-cell-level stochasticity. IMPORTANCE Escherichia coli diauxie is a fundamental example of metabolic adaptation, a phenomenon that is not yet completely understood. Further insight into this process can be achieved by integrating experimental and computational modeling methods. We present a dynamic metabolic modeling approach that captures diauxie as an emergent property of subpopulation dynamics in E. coli monocultures. Without fine-tuning the parameters of the E. coli core metabolic model, we achieved good agreement with published data. Our results suggest that single-organism metabolic models can only approximate the average metabolic state of a population, therefore offering a new perspective on the use of such modeling approaches. The open source modeling framework that we provide can be applied to model general subpopulation systems in more-complex environments and can be extended to include single-cell-level stochasticity.

A Novel Sparse Compositional Technique Reveals Microbial Perturbations

The central aims of many host or environmental microbiome studies are to elucidate factors associated with microbial community compositions and to relate microbial features to outcomes. However, these aims are often complicated by difficulties stemming from high-dimensionality, non-normality, sparsity, and the compositional nature of microbiome data sets. A key tool in microbiome analysis is beta diversity, defined by the distances between microbial samples. Many different distance metrics have been proposed, all with varying discriminatory power on data with differing characteristics. Here, we propose a compositional beta diversity metric rooted in a centered log-ratio transformation and matrix completion called robust Aitchison PCA. We demonstrate the benefits of compositional transformations upstream of beta diversity calculations through simulations. Additionally, we demonstrate improved effect size, classification accuracy, and robustness to sequencing depth over the current methods on several decreased sample subsets of real microbiome data sets. Finally, we highlight the ability of this new beta diversity metric to retain the feature loadings linked to sample ordinations revealing salient intercommunity niche feature importance. IMPORTANCE By accounting for the sparse compositional nature of microbiome data sets, robust Aitchison PCA can yield high discriminatory power and salient feature ranking between microbial niches. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/DEICODE; additionally, a QIIME 2 plugin is provided to perform this analysis at https://library.qiime2.org/plugins/deicode/.

An electrochemical thermal transistor

The ability to actively regulate heat flow at the nanoscale could be a game changer for applications in thermal management and energy harvesting. Such a breakthrough could also enable the control of heat flow using thermal circuits, in a manner analogous to electronic circuits. Here we demonstrate switchable thermal transistors with an order of magnitude thermal on/off ratio, based on reversible electrochemical lithium intercalation in MoS2 thin films. We use spatially-resolved time-domain thermoreflectance to map the lithium ion distribution during device operation, and atomic force microscopy to show that the lithiated state correlates with increased thickness and surface roughness. First principles calculations reveal that the thermal conductance modulation is due to phonon scattering by lithium rattler modes, c-axis strain, and stacking disorder. This study lays the foundation for electrochemically-driven nanoscale thermal regulators, and establishes thermal metrology as a useful probe of spatio-temporal intercalant dynamics in nanomaterials.

Mycobacterial DnaB helicase intein as oxidative stress sensor

Inteins are widespread self-splicing protein elements emerging as potential post-translational environmental sensors. Here, we describe two inteins within one protein, the Mycobacterium smegmatis replicative helicase DnaB. These inteins, DnaBi1 and DnaBi2, have homology to inteins in pathogens, splice with vastly varied rates, and are differentially responsive to environmental stressors. Whereas DnaBi1 splicing is reversibly inhibited by oxidative and nitrosative insults, DnaBi2 is not. Using a reporter that measures splicing in a native intein-containing organism and western blotting, we show that H2O2 inhibits DnaBi1 splicing in M. smegmatis. Intriguingly, upon oxidation, the catalytic cysteine of DnaBi1 forms an intramolecular disulfide bond. We report a crystal structure of the class 3 DnaBi1 intein at 1.95 Å, supporting our findings and providing insight into this splicing mechanism. We propose that this cysteine toggle allows DnaBi1 to sense stress, pausing replication to maintain genome integrity, and then allowing splicing immediately when permissive conditions return.

Anisotropic Dirac Fermions in BaMnBi2 and BaZnBi2

We investigate the electronic structure of BaMnBi2 and BaZnBi2 using angle-resolved photoemission spectroscopy and first-principles calculations. Although they share similar structural properties, we show that their electronic structure exhibit dramatic differences. A strong anisotropic Dirac dispersion is revealed in BaMnBi2 with a decreased asymmetry factor compared with other members of AMnBi2 (A = alkali earth or rare earth elements) family. In addition to the Dirac cones, multiple bands crossing the Fermi energy give rise to a complex Fermi surface topology for BaZnBi2. We further show that the strength of hybridization between Bi-p and Mn-d/Zn-s states is the main driver of the differences in electronic structure for these two related compounds.

Relativistic and resonant effects in the ionization of heavy atoms by ultra-intense hard X-rays

An accurate description of the interaction of intense hard X-ray pulses with heavy atoms, which is crucial for many applications of free-electron lasers, represents a hitherto unresolved challenge for theory because of the enormous number of electronic configurations and relativistic effects, which need to be taken into account. Here we report results on multiple ionization of xenon atoms by ultra-intense (about 1019 W/cm2) femtosecond X-ray pulses at photon energies from 5.5 to 8.3 keV and present a theoretical model capable of reproducing the experimental data in the entire energy range. Our analysis shows that the interplay of resonant and relativistic effects results in strongly structured charge state distributions, which reflect resonant positions of relativistically shifted electronic levels of highly charged ions created during the X-ray pulse. The theoretical approach described here provides a basis for accurate modeling of radiation damage in hard X-ray imaging experiments on targets with high-Z constituents.

Physical descriptor for the Gibbs energy of inorganic crystalline solids and temperature-dependent materials chemistry

The Gibbs energy, G, determines the equilibrium conditions of chemical reactions and materials stability. Despite this fundamental and ubiquitous role, G has been tabulated for only a small fraction of known inorganic compounds, impeding a comprehensive perspective on the effects of temperature and composition on materials stability and synthesizability. Here, we use the SISSO (sure independence screening and sparsifying operator) approach to identify a simple and accurate descriptor to predict G for stoichiometric inorganic compounds with ~50 meV atom-1 (~1 kcal mol-1) resolution, and with minimal computational cost, for temperatures ranging from 300-1800 K. We then apply this descriptor to ~30,000 known materials curated from the Inorganic Crystal Structure Database (ICSD). Using the resulting predicted thermochemical data, we generate thousands of temperature-dependent phase diagrams to provide insights into the effects of temperature and composition on materials synthesizability and stability and to establish the temperature-dependent scale of metastability for inorganic compounds.

Calibration of Multi-Parameter Models of Avascular Tumor Growth Using Time Resolved Microscopy Data

Two of the central challenges of using mathematical models for predicting the spatiotemporal development of tumors is the lack of appropriate data to calibrate the parameters of the model, and quantitative characterization of the uncertainties in both the experimental data and the modeling process itself. We present a sequence of experiments, with increasing complexity, designed to systematically calibrate the rates of apoptosis, proliferation, and necrosis, as well as mobility, within a phase-field tumor growth model. The in vitro experiments characterize the proliferation and death of human liver carcinoma cells under different initial cell concentrations, nutrient availabilities, and treatment conditions. A Bayesian framework is employed to quantify the uncertainties in model parameters. The average difference between the calibration and the data, across all time points is between 11.54% and 14.04% for the apoptosis experiments, 7.33% and 23.30% for the proliferation experiments, and 8.12% and 31.55% for the necrosis experiments. The results indicate the proposed experiment-computational approach is generalizable and appropriate for step-by-step calibration of multi-parameter models, yielding accurate estimations of model parameters related to rates of proliferation, apoptosis, and necrosis.

Systemic signaling contributes to the unfolded protein response of the plant endoplasmic reticulum

The unfolded protein response (UPR) of the endoplasmic reticulum constitutes a conserved and essential cytoprotective pathway designed to survive biotic and abiotic stresses that alter the proteostasis of the endoplasmic reticulum. The UPR is typically considered cell-autonomous and it is yet unclear whether it can also act systemically through non-cell autonomous signaling. We have addressed this question using a genetic approach coupled with micro-grafting and a suite of molecular reporters in the model plant species Arabidopsis thaliana. We show that the UPR has a non-cell autonomous component, and we demonstrate that this is partially mediated by the intercellular movement of the UPR transcription factor bZIP60 facilitating systemic UPR signaling. Therefore, in multicellular eukaryotes such as plants, non-cell autonomous UPR signaling relies on the systemic movement of at least a UPR transcriptional modulator.

Deep neural networks for accurate predictions of crystal stability

Predicting the stability of crystals is one of the central problems in materials science. Today, density functional theory (DFT) calculations remain comparatively expensive and scale poorly with system size. Here we show that deep neural networks utilizing just two descriptors-the Pauling electronegativity and ionic radii-can predict the DFT formation energies of C3A2D3O12 garnets and ABO3 perovskites with low mean absolute errors (MAEs) of 7-10 meV atom-1 and 20-34 meV atom-1, respectively, well within the limits of DFT accuracy. Further extension to mixed garnets and perovskites with little loss in accuracy can be achieved using a binary encoding scheme, addressing a critical gap in the extension of machine-learning models from fixed stoichiometry crystals to infinite universe of mixed-species crystals. Finally, we demonstrate the potential of these models to rapidly transverse vast chemical spaces to accurately identify stable compositions, accelerating the discovery of novel materials with potentially superior properties.

Efficient generation of neutral and charged biexcitons in encapsulated WSe2 monolayers

Higher-order correlated excitonic states arise from the mutual interactions of excitons, which generally requires a significant exciton density and therefore high excitation levels. Here, we report the emergence of two biexcitons species, one neutral and one charged, in monolayer tungsten diselenide under moderate continuous-wave excitation. The efficient formation of biexcitons is facilitated by the long lifetime of the dark exciton state associated with a spin-forbidden transition, as well as improved sample quality from encapsulation between hexagonal boron nitride layers. From studies of the polarization and magnetic field dependence of the neutral biexciton, we conclude that this species is composed of a bright and a dark excitons residing in opposite valleys in momentum space. Our observations demonstrate that the distinctive features associated with biexciton states can be accessed at low light intensities and excitation densities.

Low temperature synthesis of NbC/C nano-composites as visible light photoactive catalyst

A facile carbothermal route was adopted to obtain niobium carbide nanoparticles (NPs) embedded in carbon network from Nb2O5 to study photocatalytic behavior. Optimization of synthesis parameters to obtain single phase NbC NPs has been successfully done. The phase identification, morphology and nature of carbon were determined with the help of X-ray diffraction, transmission electron microscopy (TEM) and Raman spectroscopy. X-ray photoelectron spectroscopy (XPS) suggested the presence of multiple oxidation states of Nb associated to NbC and NbCxOy centers on the surface of NPs. Due to the presence of NbCxOy on the surface of NPs, absorption under visible region of EM spectrum has been observed by UV-visible spectroscopy. Different organic dyes (RhB, MB and MO) were used to study the effect of holding time on the photocatalytic performance of as-synthesized samples. RhB dye was found to be the most sensitive organic molecule among all the considered dyes and degraded 78% in 120 min.

X-ray Fluorescence Nanotomography of Single Bacteria with a Sub-15 nm Beam

X-ray Fluorescence (XRF) microscopy is a growing approach for imaging the trace element concentration, distribution, and speciation in biological cells at the nanoscale. Moreover, three-dimensional nanotomography provides the added advantage of imaging subcellular structure and chemical identity in three dimensions without the need for staining or sectioning of cells. To date, technical challenges in X-ray optics, sample preparation, and detection sensitivity have limited the use of XRF nanotomography in this area. Here, XRF nanotomography was used to image the elemental distribution in individual E. coli bacterial cells using a sub-15 nm beam at the Hard X-ray Nanoprobe beamline (HXN, 3-ID) at NSLS-II. These measurements were simultaneously combined with ptychography to image structural components of the cells. The cells were embedded in small (3-20 µm) sodium chloride crystals, which provided a non-aqueous matrix to retain the three-dimensional structure of the E. coli while collecting data at room temperature. Results showed a generally uniform distribution of calcium in the cells, but an inhomogeneous zinc distribution, most notably with concentrated regions of zinc at the polar ends of the cells. This work demonstrates that simultaneous two-dimensional ptychography and XRF nanotomography can be performed with a sub-15 nm beam size on unfrozen biological cells to co-localize elemental distribution and nanostructure simultaneously.

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

Rapidly thawing permafrost harbors ∼30 to 50% of global soil carbon, and the fate of this carbon remains unknown. Microorganisms will play a central role in its fate, and their viruses could modulate that impact via induced mortality and metabolic controls. Because of the challenges of recovering viruses from soils, little is known about soil viruses or their role(s) in microbial biogeochemical cycling. Here, we describe 53 viral populations (viral operational taxonomic units [vOTUs]) recovered from seven quantitatively derived (i.e., not multiple-displacement-amplified) viral-particle metagenomes (viromes) along a permafrost thaw gradient at the Stordalen Mire field site in northern Sweden. Only 15% of these vOTUs had genetic similarity to publicly available viruses in the RefSeq database, and ∼30% of the genes could be annotated, supporting the concept of soils as reservoirs of substantial undescribed viral genetic diversity. The vOTUs exhibited distinct ecology, with different distributions along the thaw gradient habitats, and a shift from soil-virus-like assemblages in the dry palsas to aquatic-virus-like assemblages in the inundated fen. Seventeen vOTUs were linked to microbial hosts (in silico), implicating viruses in infecting abundant microbial lineages from Acidobacteria, Verrucomicrobia, and Deltaproteobacteria, including those encoding key biogeochemical functions such as organic matter degradation. Thirty auxiliary metabolic genes (AMGs) were identified and suggested virus-mediated modulation of central carbon metabolism, soil organic matter degradation, polysaccharide binding, and regulation of sporulation. Together, these findings suggest that these soil viruses have distinct ecology, impact host-mediated biogeochemistry, and likely impact ecosystem function in the rapidly changing Arctic. IMPORTANCE This work is part of a 10-year project to examine thawing permafrost peatlands and is the first virome-particle-based approach to characterize viruses in these systems. This method yielded >2-fold-more viral populations (vOTUs) per gigabase of metagenome than vOTUs derived from bulk-soil metagenomes from the same site (J. B. Emerson, S. Roux, J. R. Brum, B. Bolduc, et al., Nat Microbiol 3:870-880, 2018, https://doi.org/10.1038/s41564-018-0190-y). We compared the ecology of the recovered vOTUs along a permafrost thaw gradient and found (i) habitat specificity, (ii) a shift in viral community identity from soil-like to aquatic-like viruses, (iii) infection of dominant microbial hosts, and (iv) carriage of host metabolic genes. These vOTUs can impact ecosystem carbon processing via top-down (inferred from lysing dominant microbial hosts) and bottom-up (inferred from carriage of auxiliary metabolic genes) controls. This work serves as a foundation which future studies can build upon to increase our understanding of the soil virosphere and how viruses affect soil ecosystem services.

Observation of topologically protected states at crystalline phase boundaries in single-layer WSe2

Transition metal dichalcogenide materials are unique in the wide variety of structural and electronic phases they exhibit in the two-dimensional limit. Here we show how such polymorphic flexibility can be used to achieve topological states at highly ordered phase boundaries in a new quantum spin Hall insulator (QSHI), 1T'-WSe2. We observe edge states at the crystallographically aligned interface between a quantum spin Hall insulating domain of 1T'-WSe2 and a semiconducting domain of 1H-WSe2 in contiguous single layers. The QSHI nature of single-layer 1T'-WSe2 is verified using angle-resolved photoemission spectroscopy to determine band inversion around a 120 meV energy gap, as well as scanning tunneling spectroscopy to directly image edge-state formation. Using this edge-state geometry we confirm the predicted penetration depth of one-dimensional interface states into the two-dimensional bulk of a QSHI for a well-specified crystallographic direction. These interfaces create opportunities for testing predictions of the microscopic behavior of topologically protected boundary states.

Contiguous US summer maximum temperature and heat stress trends in CRU and NOAA Climate Division data plus comparisons to reanalyses

Warming is a major climate change concern, but the impact of high maximum temperatures depends upon the air's moisture content. Trends in maximum summertime temperature, moisture, and heat index are tracked over three time periods: 1900-2011, 1950-2011, and 1979-2011; these trends differ notably from annual temperature trends. Trends are emphasized from two CRU datasets (CRUTS3.25 and CRUTS4.01) and two reanalyses (ERA-20C and 20CRv2). Maximum temperature trends tend towards warming that is stronger over the Great Lakes, the interior western and the northeastern contiguous United States. A warming hole in the Midwest generally decreases in size and magnitude when heat stress trends are calculated because the region has increasing moisture. CRU and nearly all reanalyses find cooling in the northern high plains that is not found in NOAA Climate Division trends. These NOAA trends are captured better by CRUTS401. Moistening in the northeast amplifies the heat stress there. Elsewhere the moisture trends are less clear. Drying over northern Texas (after 1996) in CRUTS401 translates into decreasing heat stress there (less so in CRUTS325). Though other reanalyses are not intended for long-term trends, MERRA-2 and ERA-Interim match observed trends better than other reanalyses.

Magnetostatic twists in room-temperature skyrmions explored by nitrogen-vacancy center spin texture reconstruction

Magnetic skyrmions are two-dimensional non-collinear spin textures characterized by an integer topological number. Room-temperature skyrmions were recently found in magnetic multilayer stacks, where their stability was largely attributed to the interfacial Dzyaloshinskii-Moriya interaction. The strength of this interaction and its role in stabilizing the skyrmions is not yet well understood, and imaging of the full spin structure is needed to address this question. Here, we use a nitrogen-vacancy centre in diamond to measure a map of magnetic fields produced by a skyrmion in a magnetic multilayer under ambient conditions. We compute the manifold of candidate spin structures and select the physically meaningful solution. We find a Néel-type skyrmion whose chirality is not left-handed, contrary to preceding reports. We propose skyrmion tube-like structures whose chirality rotates through the film thickness. We show that NV magnetometry, combined with our analysis method, provides a unique tool to investigate this previously inaccessible phenomenon.

Distribution and Diversity of Rhodopsin-Producing Microbes in the Chesapeake Bay

Although sunlight is an abundant source of energy in surface environments, less than 0.5% of the available photons are captured by (bacterio)chlorophyll-dependent photosynthesis in plants and bacteria. Metagenomic data indicate that 30 to 60% of the bacterial genomes in some environments encode rhodopsins, retinal-based photosystems found in heterotrophs, suggesting that sunlight may provide energy for more life than previously suspected. However, quantitative data on the number of cells that produce rhodopsins in environmental systems are limited. Here, we use total internal reflection fluorescence microscopy to show that the number of free-living microbes that produce rhodopsins increases along the salinity gradient in the Chesapeake Bay. We correlate this functional data with environmental data to show that rhodopsin abundance is positively correlated with salinity and with indicators of active heterotrophy during the day. Metagenomic and metatranscriptomic data suggest that the microbial rhodopsins in the low-salinity samples are primarily found in Actinobacteria and Bacteroidetes, while those in the high-salinity samples are associated with SAR-11 type AlphaproteobacteriaIMPORTANCE Microbial rhodopsins are common light-activated ion pumps in heterotrophs, and previous work has proposed that heterotrophic microbes use them to conserve energy when organic carbon is limiting. If this hypothesis is correct, rhodopsin-producing cells should be most abundant where nutrients are most limited. Our results indicate that in the Chesapeake Bay, rhodopsin gene abundance is correlated with salinity, and functional rhodopsin production is correlated with nitrate, bacterial production, and chlorophyll a We propose that in this environment, where carbon and nitrogen are likely not limiting, heterotrophs do not need to use rhodopsins to supplement ATP synthesis. Rather, the light-generated proton motive force in nutrient-rich environments could be used to power energy-dependent membrane-associated processes, such as active transport of organic carbon and cofactors, enabling these organisms to more efficiently utilize exudates from primary producers.

Understanding crystallization pathways leading to manganese oxide polymorph formation

Hydrothermal synthesis is challenging in metal oxide systems with diverse polymorphism, as reaction products are often sensitive to subtle variations in synthesis parameters. This sensitivity is rooted in the non-equilibrium nature of low-temperature crystallization, where competition between different metastable phases can lead to complex multistage crystallization pathways. Here, we propose an ab initio framework to predict how particle size and solution composition influence polymorph stability during nucleation and growth. We validate this framework using in situ X-ray scattering, by monitoring how the hydrothermal synthesis of MnO2 proceeds through different crystallization pathways under varying solution potassium ion concentrations ([K+] = 0, 0.2, and 0.33 M). We find that our computed size-dependent phase diagrams qualitatively capture which metastable polymorphs appear, the order of their appearance, and their relative lifetimes. Our combined computational and experimental approach offers a rational and systematic paradigm for the aqueous synthesis of target metal oxides.

Discovery of ZrCoBi based half Heuslers with high thermoelectric conversion efficiency

Thermoelectric materials are capable of converting waste heat into electricity. The dimensionless figure-of-merit (ZT), as the critical measure for the material's thermoelectric performance, plays a decisive role in the energy conversion efficiency. Half-Heusler materials, as one of the most promising candidates for thermoelectric power generation, have relatively low ZTs compared to other material systems. Here we report the discovery of p-type ZrCoBi-based half-Heuslers with a record-high ZT of ∼1.42 at 973 K and a high thermoelectric conversion efficiency of ∼9% at the temperature difference of ∼500 K. Such an outstanding thermoelectric performance originates from its unique band structure offering a high band degeneracy (Nv) of 10 in conjunction with a low thermal conductivity benefiting from the low mean sound velocity (vm ∼2800 m s-1). Our work demonstrates that ZrCoBi-based half-Heuslers are promising candidates for high-temperature thermoelectric power generation.

Physiological Effect of XoxG(4) on Lanthanide-Dependent Methanotrophy

A recent surprising discovery of the activity of rare earth metals (lanthanides) as enzyme cofactors as well as transcriptional regulators has overturned the traditional assumption of biological inertia of these metals. However, so far, examples of such activities have been limited to alcohol dehydrogenases. Here we describe the physiological effects of a mutation in xoxG, a gene encoding a novel cytochrome, XoxG(4), and compare these to the effects of mutation in XoxF, a lanthanide-dependent methanol dehydrogenase, at the enzyme activity level and also at the community function level, using Methylomonas sp. strain LW13 as a model organism. Through comparative phenotypic characterization, we establish XoxG as the second protein directly involved in lanthanide-dependent metabolism, likely as a dedicated electron acceptor from XoxF. However, mutation in XoxG caused a phenotype that was dramatically different from the phenotype of the mutant in XoxF, suggesting a secondary function for this cytochrome, in metabolism of methane. We also purify XoxG(4) and demonstrate that this protein is a true cytochrome c, based on the typical absorption spectra, and we demonstrate that XoxG can be directly reduced by a purified XoxF, supporting one of its proposed physiological functions. Overall, our data continue to suggest the complex nature of the interplay between the calcium-dependent and lanthanide-dependent alcohol oxidation systems, while they also suggest that addressing the roles of these alternative systems is essential at the enzyme and community function level, in addition to the gene transcription level.IMPORTANCE The lanthanide-dependent biochemistry of living organisms remains a barely tapped area of knowledge. So far, only a handful of lanthanide-dependent alcohol dehydrogenases have been described, and their regulation by lanthanides has been demonstrated at the transcription level. Little information is available regarding the concentrations of lanthanides that could support sufficient enzymatic activities to support specific metabolisms, and so far, no other redox proteins involved in lanthanide-dependent methanotrophy have been demonstrated. The research presented here provides enzyme activity-level data on lanthanide-dependent methanotrophy in a model methanotroph. Additionally, we identify a second protein important for lanthanide-dependent metabolism in this organism, XoxG(4), a novel cytochrome. XoxG(4) appears to have multiple functions in methanotrophy, one function as an electron acceptor from XoxF and another function remaining unknown. On the basis of the dramatic phenotype of the XoxG(4) mutant, this function must be crucial for methanotrophy.

Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline

The dinitrogenase reductase gene (nifH) is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. The developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. Based on our primer evaluation, we recommend the Ando primer set be used with a modified annealing temperature of 58°C, as this approach captured the largest diversity of nifH templates, including paralog cluster IV/V sequences. To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. In addition, we employed an empirical model to derive optimal operational taxonomic unit (OTU) cutoffs for the nifH gene at the species, genus, and family levels. A comprehensive workflow script named TaxADivA (TAXonomy Assignment and DIVersity Assessment) is provided to ease processing and analysis of nifH amplicons. Our approach is then validated through characterization of diazotroph communities across environmental gradients in beach sands impacted by the Deepwater Horizon oil spill in the Gulf of Mexico, in a peat moss-dominated wetland, and in various plant compartments of a sugarcane field.IMPORTANCE Nitrogen availability often limits ecosystem productivity, and nitrogen fixation, exclusive to prokaryotes, comprises a major source of nitrogen input that sustains food webs. The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. Diazotroph diversity and community composition are linked to ecosystem functioning, and our results advance the phylogenetic characterization of diazotroph communities by providing empirically derived nifH similarity cutoffs for species, genus, and family levels. The utility of our pipeline is validated for diazotroph communities in a variety of ecosystems, including contaminated beach sands, peatland ecosystems, living plant tissues, and rhizosphere soil.

Divergence in Gene Regulation Contributes to Sympatric Speciation of Shewanella baltica Strains

Niche partitioning and sequence evolution drive genomic and phenotypic divergence, which ultimately leads to bacterial diversification. This study investigated the genomic composition of two Shewanella baltica clades previously identified through multilocus sequencing typing and recovered from the redox transition zone in the central Baltic Sea. Comparative genomic analysis revealed significantly higher interclade than intraclade genomic dissimilarity and that a subset of genes present in clade A were associated with potential adaptation to respiration of sulfur compounds present in the redox transition zone. The transcriptomic divergence between two representative strains of clades A and D, OS185 and OS195, was also characterized and revealed marked regulatory differences. We found that both the transcriptional divergence of shared genes and expression of strain-specific genes led to differences in regulatory patterns between strains that correlate with environmental redox niches. For instance, under anoxic conditions of respiratory nitrate ammonification, OS185-the strain isolated from a nitrate-rich environment-upregulated nearly twice the number of shared genes upregulated by OS195-the strain isolated from an H2S-containing anoxic environment. Conversely, OS195 showed stronger induction of strain-specific genes, especially those associated with sulfur compound respiration, under thiosulfate-reducing conditions. A positive association between the level of transcriptional divergence and the level of sequence divergence for shared genes was also noted. Our results provide further support for the hypothesis that genomic changes impacting transcriptional regulation play an important role in the diversification of ecologically distinct populations.IMPORTANCE This study examined potential mechanisms through which co-occurring Shewanella baltica strains diversified to form ecologically distinct populations. At the time of isolation, the strains studied composed the major fraction of culturable nitrate-reducing communities in the Baltica Sea. Analysis of genomic content of 13 S. baltica strains from two clades representing different ecotypes demonstrated that one clade specifically possesses a number of genes that could favor successful adaptation to respire sulfur compounds in the portion of the water column from which these strains were isolated. In addition, transcriptional profiling of fully sequenced strains representative of these two clades, OS185 and OS195, under oxygen-, nitrate-, and thiosulfate-respiring conditions demonstrated that the strains exhibit relatively similar transcriptional responses during aerobic growth but more-distinct transcriptional responses under nitrate- and thiosulfate-respiring conditions. Results from this study provide insights into how genomic and gene regulatory diversification together impacted the redox specialization of the S. baltica strains.

Broadband achromatic dielectric metalenses

Metasurfaces offer a unique platform to precisely control optical wavefronts and enable the realization of flat lenses, or metalenses, which have the potential to substantially reduce the size and complexity of imaging systems and to realize new imaging modalities. However, it is a major challenge to create achromatic metalenses that produce a single focal length over a broad wavelength range because of the difficulty in simultaneously engineering phase profiles at distinct wavelengths on a single metasurface. For practical applications, there is a further challenge to create broadband achromatic metalenses that work in the transmission mode for incident light waves with any arbitrary polarization state. We developed a design methodology and created libraries of meta-units-building blocks of metasurfaces-with complex cross-sectional geometries to provide diverse phase dispersions (phase as a function of wavelength), which is crucial for creating broadband achromatic metalenses. We elucidated the fundamental limitations of achromatic metalens performance by deriving mathematical equations that govern the tradeoffs between phase dispersion and achievable lens parameters, including the lens diameter, numerical aperture (NA), and bandwidth of achromatic operation. We experimentally demonstrated several dielectric achromatic metalenses reaching the fundamental limitations. These metalenses work in the transmission mode with polarization-independent focusing efficiencies up to 50% and continuously provide a near-constant focal length over λ = 1200-1650 nm. These unprecedented properties represent a major advance compared to the state of the art and a major step toward practical implementations of metalenses.