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Soil aggregates are important drivers of soil productivity. However, the relative importance of soil abiotic and biotic agents in driving aggregate formation and stabilization remain largely unexplored, especially in coastal mudflat saline soils. We amended saline soil with sewage sludge at rates of 0, 30, 75, and 150 t ha−1 to investigate the effects of sewage sludge on the particle size distribution and stability of soil aggregate and the underlying mechanisms induced by soil environmental factors and fungal community. Results revealed that the sewage sludge amendment significantly (p < 0.05) increased the proportion of macroaggregates with sizes larger than 0.25 mm (R0.25) and enhanced aggregate stability. Moreover, alleviation of saline‐alkali stress and nutrient (C, N, and P) deficiency conditions were significantly (p < 0.05) observed in sewage sludge‐amended soils. Additionally, restructured fungal communities in amended soils harbored significantly (p < 0.05) distinguishable structures and core and unique microbiomes. Particularly, fungal species belonging to Moterella significantly (p < 0.05) enriched in sludge reclaimed soils. Results derived from the random forest (RF) model accompanied by linear regression analysis revealed that soil pH, soil organic carbon, and fungal structural diversity were significantly (p < 0.05) related to aggregate composition (R0.25) and stability (geometric average diameter, GMD). Furthermore, fungal consortia composed of 20 closely interconnected operational taxonomic units (OTUs) affiliated with Ascomycota, Basidiomycota, and Zygomycota explained 28.36% and 49.88% variance of R0.25 and GMD, respectively. Overall, our results revealed the effect of sewage sludge on soil aggregation improvement in coastal areas and highlighted the respective importance of soil chemical properties and fungal microbiome in predicting aggregation status. [ABSTRACT FROM AUTHOR]

Changes in the water regime are among the crucial factors controlling soil carbon dynamics. However, at the aggregate scale, the microbial mechanisms that regulate soil respiration under flooding and drying conditions are obscure. In this research, we investigated how the shift from flooding to drying changes the microbial respiration of soil aggregates by affecting microbial community composition and their co-occurrence patterns. Soils collected from a riparian zone of the Three Gorges Reservoir, China, were subjected to a wet-and-dry incubation experiment. Our data illustrated that the shift from flooding to drying substantially enhanced soil respiration for all sizes of aggregate fractions. Moreover, soil respiration declined with aggregate size in both flooding and drying treatments. The keystone taxa in bacterial networks were found to be Acidobacteriales, Gemmatimonadales, Anaerolineales, and Cytophagales during the flooding treatment, and Rhizobiales, Gemmatimonadales, Sphingomonadales, and Solirubrobacterales during the drying treatment. For fungal networks, Hypocreales and Agaricalesin were the keystone taxa in the flooding and drying treatments, respectively. Furthermore, the shift from flooding to drying enhanced the microbial respiration of soil aggregates by changing keystone taxa. Notably, fungal community composition and network properties dominated the changes in the microbial respiration of soil aggregates during the shift from flooding to drying. Thus, our study highlighted that the shift from flooding to drying changes keystone taxa, hence increasing aggregate-scale soil respiration. [ABSTRACT FROM AUTHOR]

The bed of fluvial ecosystems plays a major role in global biogeochemical cycles. All fluvial sediments migrate and although responses of aquatic organisms to such movements have been recorded there is no theoretical framework on how the frequency of sediment movement affects streambed ecology and biogeochemistry. We here developed a theoretical framework describing how the moving‐resting frequencies of fine‐grained sediments constrain streambed communities across spatial scales. Specifically, we suggest that the most drastic impact on benthic and hyporheic communities will exist when ecological and biogeochemical processes are at the same temporal scale as the sediment moving‐resting frequency. Moreover, we propose that the simultaneous occurrence of streambed patches differing in morphodynamics should be considered as an important driver of metacommunity dynamics. We surmise that the frequency of patch transition will add new dimensions to the understanding of biogeochemical cycling and metacommunities from micro‐habitat to segment scales. This theoretical framework is important for fluvial ecosystems with frequent sediment movement, yet it could be applied to any other dynamic habitat. This article is categorized under:Water and Life > Nature of Freshwater Ecosystems [ABSTRACT FROM AUTHOR]

Current state-of-the-art infection and antimicrobial resistance (AMR) diagnostics are based on culture-based methods with a detection time of 48–96 h. Therefore, it is essential to develop novel methods that can do real-time diagnoses. Here, we demonstrate that the complimentary use of label-free optical assay with whole-genome sequencing (WGS) can enable rapid diagnosis of infection and AMR. Our assay is based on microscopy methods exploiting label-free, highly sensitive quantitative phase microscopy (QPM) followed by deep convolutional neural networks-based classification. The workflow was benchmarked on 21 clinical isolates from four WHO priority pathogens that were antibiotic susceptibility tested, and their AMR profile was determined by WGS. The proposed optical assay was in good agreement with the WGS characterization. Accurate classification based on the gram staining (100% recall for gram-negative and 83.4% for grampositive), species (98.6%), and resistant/susceptible type (96.4%), as well as at the individual strain level (100% sensitivity in predicting 19 out of the 21 strains, with an overall accuracy of 95.45%). The results from this initial proof-of-concept study demonstrate the potential of the QPM assay as a rapid and first-stage tool for species, strain-level classification, and the presence or absence of AMR, which WGS can follow up for confirmation. Overall, a combined workflow with QPM and WGS complemented with deep learning data analyses could, in the future, be transformative for detecting and identifying pathogens and characterization of the AMR profile and antibiotic susceptibility. [ABSTRACT FROM AUTHOR]

In a healthy physiological state, the mucous membrane of the oral cavity creates a suitable environment for the colonization of Candida spp. yeasts. The aim of the study was to analyze the nanomechanical properties of C. albicans cells derived from the oral cavity of healthy people in a biofilm produced in laboratory conditions. Candida spp. were sampled from the oral cavity of healthy individuals. The process of biofilm formation was analyzed using classic microscopic observation enriched with SEM (scanning electron microscope) and the nanomechanical properties of the cells were assessed with the use of the atomic force microscopy technique (AFM). From all isolated strains in the samples collected of the oral cavity healthy people was detected 79% C. albicans. Other isolated species belonged to the group „non-albicans". The observations of C. albicans carried out in 24-h cultures revealed a tendency of the cells to form a biofilm structure with multilayer cell systems. The diameter of C. albicans cells in this structure was 5.75 µm, and the length of the pseudohyphae was 17.08 µm. The presence of an extracellular substance surrounding the C. albicans cells was detected. The mean value of the adhesion force determined for C. albicans cells was 4.01 nN. Areas with increased hardness (Force Modulation Mode signal; FMM signal) were found mainly in the zones of cells in contact with the glass substrate. The analysis of Candida cells in liquid samples gives satisfactory results, as it prevents unfavorable changes in the cell surface and thus provides more reliable results. The quality of the biofilm is probably related to the nanomechanical properties of C. albicans cells and may consequently contribute to the stability of the biofilm structures and their susceptibility or resistance to antifungal drugs. The presence of Candida spp. especially in companion animals (dogs, cats) poses a risk of their transmission to the human organism. For this reason, it is advisable to undertake additional research to analyze the ability of zoonotic-origin Candida spp. to form biofilms with comparison of the biofilm-formation capacity of species isolated from humans. [ABSTRACT FROM AUTHOR]

Gas flow properties in nanopores are significantly determined by the flow patterns. Slug flow pattern is a potential wateregas two phase flow pattern, in which gas molecules flow in form of gas slugs and water molecules separate gas slugs. Considering water slippage, a portion of water molecules accumulates at the wall with lower mobility, while the remaining water molecules take the shape of a water bridge. Adopting foam apparent viscosity model to represent slug rheological behavior, how water bridge disturbs on gas flow capacity is estimated. The results are compared with the wateregas two phase flow model that assumes annular flow pattern as well as the single gas flow model without the consideration of water. The comparison illustrates that gas molecular movement is significantly hindered by flow space reduction and loss of gas slippage. The impact from water phase of slug flow pattern is more significant than that of annular flow pattern on gas flow capacity. It is discovered that larger nanopores improve gas flow capacity while maintaining bulk water layer thickness and increasing water bridge thickness tend to reduce gas transport ability. A better understanding of the structure and transport of water and gas molecules is conducive to figure out the specific gasewater flow behavior and predict shale gas production. [ABSTRACT FROM AUTHOR]

Thanks to the synthetic biology, the laborious and restrictive procedure for producing a target protein in living microorganisms by biotechnological approaches can now experience a robust, pliant yet efficient alternative. The new system combined with lab-on-chip microfluidic devices and nanotechnology offers a tremendous potential envisioning novel cell-free formats such as DNA brushes, hydrogels, vesicular particles, droplets, as well as solid surfaces. Acting as robust microreactors/microcompartments/minimal cells, the new platforms can be tuned to perform various tasks in a parallel and integrated manner encompassing gene expression, protein synthesis, purification, detection, and finally enabling cell-cell signaling to bring a collective cell behavior, such as directing differentiation process, characteristics of higher order entities, and beyond. In this review, we issue an update on recent cell-free protein synthesis (CFPS) formats. Furthermore, the latest advances and applications of CFPS for synthetic biology and biotechnology are highlighted. In the end, contemporary challenges and future opportunities of CFPS systems are discussed., (© 2019 Wiley Periodicals, Inc.)

Mass spectrometry imaging (MSI) has made the spatio-chemical characterization of a broad range of small-molecule metabolites within biological tissues possible. However, available matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) suffers from severe background interferences in low-mass ranges and inhomogeneous matrix deposition. Thus, surface-assisted LDI-MS (SALDI-MS) has been an attractive alternative for high-sensitivity detection and imaging of small biomolecules. In this study, we construct a new composite substrate, hydrophobic polydopamine (hPDA)-modified TiO2 nanotube (TDNT) coated with plasmonic gold nanoparticle (AuNP-hPDA-TDNT), as a dual-polarity SALDI substrate using an easy and cost-effective fabrication approach. Benefitting from the synergistic effects of TDNT semiconductor and plasmonic PDA modification, this SALDI substrate exhibits superior performance for dual-polarity detection of a vast diversity of small molecules. Highly reduced background interferences, lower detection limits, and spot-to-spot repeatability can be achieved using AuNP-hPDA-TDNT substrates. Due to its unique imprinting performance, various metabolites and lipids can be visualized within jatropha integerrima petals, ginkgo leaves, strawberry fruits, and latent fingerprints. More valuably, the universality of this matrix-free substrate is demonstrated for mapping spatial distribution of lipids within mouse brain tissue sections. Considered together, this AuNP-hPDA-TDNT material is expected to be a promising SALDI substrate in various fields, especially in nanomaterial development and life sciences. [ABSTRACT FROM AUTHOR]

Microfluidic cultivation and single‐cell analysis are inherent parts of modern microbial biotechnology and microbiology. However, implementing biochemical engineering principles based on the kinetics and stoichiometry of growth in microscopic spaces remained unattained. We here present a novel integrated framework that utilizes distinct microfluidic cultivation technologies and single‐cell analytics to make the fundamental math of process‐oriented biochemical engineering applicable at the single‐cell level. A combination of non‐invasive optical cell mass determination with sub‐pg sensitivity, microfluidic perfusion cultivations for establishing physiological steady‐states, and picoliter batch reactors, enabled the quantification of all physiological parameters relevant to approximate a material balance in microfluidic reaction environments. We determined state variables (biomass concentration based on single‐cell dry weight and mass density), biomass synthesis rates, and substrate affinities of cells grown in microfluidic environments. Based on this data, we mathematically derived the specific kinetics of substrate uptake and growth stoichiometry in glucose‐grown Escherichia coli with single‐cell resolution. This framework may initiate microscale material balancing beyond the averaged values obtained from populations as a basis for integrating heterogeneous kinetic and stoichiometric single‐cell data into generalized bioprocess models and descriptions. [ABSTRACT FROM AUTHOR]

Mounting evidence of recent spectromicroscopic insights have revealed that the distribution of mineral‐associated organic matter (OM) at the microscale and nanoscale is organized heterogeneously in patchy and piled‐up arrangements of varying thickness. Spectromicroscopic approaches could show local deterministic features of distinct OM and mineral composition that influence the heterogeneous lateral OM distribution. OM–OM interactions shape vertical and three‐dimensional OM structures with potentially multilayered composition. Conceptualizing mineral‐associated OM as patchy‐distributed and piled‐up has critical implications for our understanding of soil ecosystem functions as it defines their functional properties in compartmentalized regions at the microscale and nanoscale. The concentrated storage of OM associated to only a minor part of mineral surfaces implies that carbon sequestration may be decoupled from a direct limitation by the amount of fine mineral particles while sustaining mineral surface functionality in other parts. At the microscale and nanoscale, differences in altered surface properties, compartmentalized microhabitats, and biotic architectures shape a conceptual understanding where OM storage and other soil functions are driven by spatially resolved interactions. This novel conceptual framework warrants experimental approaches to incorporate the patchy and piled‐up arrangement of OM and upscale potential effects of its heterogeneous arrangement to systematically understand the effectiveness of soil functions. [ABSTRACT FROM AUTHOR]

As soils store more carbon (C) than the Earth's atmosphere and terrestrial biomass together, the balance between soil C uptake in the form of soil organic matter (SOC) and release as CO2 upon its decomposition is a critical determinant in the global C cycle regulating our planet's climate. Although plant litter is the predominant source of C fuelling both soil C build‐up and losses, the issue of how litter chemistry influences this balance remains unresolved.As a contribution to solving that issue, we traced the fate of C during near‐complete decomposition of 13C‐labelled leaf and root litters from 12 plant species in a coarse‐textured soil. We separated the soil organic carbon into mineral‐associated organic matter (MAOM) and particulate organic matter (POM) pools, and investigated how 14 litter chemical traits affected novel SOC formation and native SOC mineralization (i.e. the priming effect) in these soil fractions.We observed an overall net increase in SOC due to the addition of litter, which was stronger for root than for leaf litters. The presumed stable MAOM‐C pool underwent both substantial stabilization and mineralization, whereas the presumably less stable POM‐C pool showed substantial stabilization and reduced mineralization. Overall, the initial increase in soil C mineralization was fully counterbalanced by a later decrease in native soil C mineralization. POM‐C formation as well as MAOM‐C formation and mineralization were positively related to the initial litter lignin concentration and negatively to that of the nitrogen leachates, whereas the opposite was observed for POM‐C mineralization.Synthesis. Our results highlight the importance of litter chemical traits for SOC formation, and stabilization, destabilization and mineralization. In our coarse‐textured soil, the amount of MAOM‐C did not change despite large C fluxes through this pool. The litter chemical traits that drove these processes differed from those frequently reported for fine‐textured soils far from mineral‐associated C saturation. To account for these discrepancies, we propose an integrative perspective in which litter quality and soil texture interactively control soil C fluxes by modulating several SOC stabilization and destabilization mechanisms. Irrespective, our results open new critical perspectives for managing soil C pools globally. [ABSTRACT FROM AUTHOR]

The phenomenon of bioconvective transport through the manipulation of motile microorganisms is considered a promising process control technique in several biological processes and microdevices. Inducing convective transport in self-propelling microbes could be tailored to improve mixing, reaction propensity, and concentration transport within the media. This paper examined the combined effect of magnetic and rotational fields on the argumentation of bioconvective transport in the nanofluid-mediated plasma flow. A detailed analysis of the transport and dynamics of reactive forces during bioconvection in a rotary disc-like microchannel is presented. The physics of the problem was described by coupled nonlinear ordinary differential equations, which were numerically computed using the spectral relaxation scheme of the spectral homotopy analysis method. It was observed that the imposition of a magnetic field constituted viscous drag in the plasma-nanofluid media, which consequently increases the thermophoretic parameter in the bioconvective flow. It was ascertained that coupled magnetic and rotational effects significantly augmented the motility of microorganisms and translated to growth in momentum and concentration fields which is noticeable in the generation of stretching effect on the bacterium-containing plasma-nanofluid flow. The findings of this study could provide an essential basis for the design of bioreactors, centrifugal microfluidics technologies, and microdevices for use in a broad spectrum of biotechnology. [ABSTRACT FROM AUTHOR]

Soil aggregates provide spatially heterogeneous microhabitats that support the coexistence of soil microbes. However, there remains a lack of detailed assessment of the mechanism underlying aggregate-microbiome formation and impact on soil function. Here, the microbial assemblages within four different aggregate sizes and their correlation with microbial activities related to nutrient cycling were studied in rice fields in Southern China. The results show that deterministic and stochastic processes govern bacterial and fungal assemblages in agricultural soil, respectively. The contribution of determinism to bacterial assemblage improved as aggregate size decreased. In contrast, the importance of stochasticity to fungal assemblage was higher in macroaggregates (>0.25 mm in diameter) than in microaggregates (<0.25 mm). The association between microbial assemblages and nutrient cycling was aggregate-specific. Compared with microaggregates, the impacts of bacterial and fungal assemblages on carbon, nitrogen, and phosphorus cycling within macroaggregates were more easily regulated by soil properties (i.e., soil organic carbon and total phosphorus). Additionally, soil nutrient cycling was positively correlated with deterministic bacterial assemblage but negatively correlated with stochastic fungal assemblage in microaggregates, implying that bacterial community may accelerate soil functions when deterministic selection increases. Overall, our study illustrates the ecological mechanisms underlying the association between microbial assemblages and soil functions in aggregates and highlights that the assembly of aggregate microbes should be explicitly considered for revealing the ecological interactions between agricultural soil and microbial communities. [ABSTRACT FROM AUTHOR]

Soil aggregate composition is an important factor that affects soil organic carbon (SOC) content. Earthworms can greatly affect soil aggregate composition. However, the effects of earthworms' activities on SOC content in soil aggregates and the stability of these compounds was not clear. To reveal the mechanism of earthworms impacts on soil carbon stock, different earthworms densities were set in soil columns planted with clovers (Trifolium repens L.). We then analyzed the relationship that earthworms had with soil physicochemical properties and clover plant growth. Earthworms increased the large (17.5%–35.6%) and medium aggregate content (0.6%–9.79%) and decreased the microaggregates content (19.8%–29%) of the surface soil. Soil aggregates in medium density treatment were more stable than those in others. Both the mean mass diameter and geometric mean diameter of soil aggregates increased with the densities of earthworms. The average SOC content in large‐, medium‐, and microaggregates were 5.5, 4.2, and 4.2 g kg−1 respectively in soils seeded with earthworms. There was a significant correlation between soil organic carbon content and macroaggregate organic carbon content (R2 = 0.623, p < 0.05). The root characteristic values (root length, surface area, diameter, and biomass) of earthworm‐treated clover‐planted soils were higher than those of control. Clover root indices were positively correlated with the soil organic carbon content and soil aggregates. Earthworms altered the soil aggregate content and enhanced soil organic carbon storage, and thus promoted the development of vegetation roots. This study provides scientific support for a deeper understanding of the mechanisms of earthworms in soil carbon storage. [ABSTRACT FROM AUTHOR]

Anthropogenic activities have a critical influence on climate change that directly or indirectly impacts plant and microbial diversity on our planet. Due to climate change, there is an increase in the intensity and frequency of extreme environmental events such as temperature rise, drought, and precipitation. The increase in greenhouse gas emissions such as CO2, CH4, NOx, water vapor, increase in global temperature, and change in rainfall patterns have impacted soil--plant-microbe interactions, which poses a serious threat to food security. Microbes in the soil play an essential role in plants' resilience to abiotic and biotic stressors. The soil microbial communities are sensitive and responsive to these stressors. Therefore, a systemic approach to climate adaptation will be needed which acknowledges the multidimensional nature of plant-microbe-environment interactions. In the last two scores of years, there has been an enhancement in the understanding of plant's response to microbes at physiological, biochemical, and molecular levels due to the availability of techniques and tools. This review highlights some of the critical factors influencing plant-microbe interactions under stress. The association and response of microbe and plants as a result of several stresses such as temperature, salinity, metal toxicity, and greenhouse gases are also depicted. New tools to study the molecular complexity of these interactions, such as genomic and sequencing approaches, which provide researchers greater accuracy, reproducibility, and flexibility for exploring plant-microbe--environment interactions under a changing climate, are also discussed in the review, which will be helpful in the development of resistant crops/plants in present and future. [ABSTRACT FROM AUTHOR]

The Black Queen hypothesis describes the evolutionary strategy to lose costly functions in favour of improving growth efficiency. This results in mutants (cheaters) becoming obligately dependent upon a provider (black queen) to produce a necessary resource. Previous analyses demonstrate black queens and cheaters reach a state of equilibrium in pair-wise systems. However, in complex communities, accumulation of cheaters likely poses a serious burden on shared resources. This should result in a Tragedy of the Commons (ToC), whereby over-utilisation of public resources risks making them growth-limiting. With a collection of differential equations, microbial communities composed of twenty prokaryote 'species' either from rhizosphere, characterised by abundant carbon and energy sources, or bulk soil, with limited carbon and energy supply, were simulated. Functional trait groups differed based on combinations of cellulase and amino acid production, growth and resource uptake. Randomly generated communities were thus composed of species that acted as cellulolytic prototrophic black queens, groups that were either cellulolytic or prototrophic, or non-cellulolytic auxotrophic cheaters. Groups could evolve to lose functions over time. Biomass production and biodiversity were tracked in 8,000 Monte Carlo simulations over 500 generations. Bulk soil favoured oligotrophic co-operative communities where biodiversity was positively associated with growth. Rhizosphere favoured copiotrophic cheaters. The most successful functional group across both environments was neither black queens nor cheaters, but those that balanced providing an essential growth-limiting function at a relatively low maintenance cost. Accumulation of loss of function mutants in bulk soil risked resulting in loss of cumulative growth by ToC, while cumulative growth increased in the rhizosphere. In the bulk soil, oligotrophic adaptations assisted species in avoiding extinction. This demonstrated that loss of function by mutation is a successful evolutionary strategy in host-associated and/or resource-rich environments, but poses a risk to communities that must co-operate with each other for mutual co-existence. It was concluded that microbial communities must follow different evolutionary and community assembly strategies in bulk soil versus rhizosphere, with bulk soil communities more dependent on traits that promote co-operative interactions between microbial species. [ABSTRACT FROM AUTHOR]

To understand the ambient ionization mass spectrometry (AIMS) technology and its application in tobacco chemistry, the research progress of AIMS technology based on electrospray, plasma and laser ionization techniques were reviewed, and the representative and widely used AIMS techniques were introduced in detail. The applications of AIMS technology in tobacco chemistry in recent ten years were summarized. The future directions of AIMS technology in tobacco chemistry were prospected. [ABSTRACT FROM AUTHOR]

Soil structure plays an integral role in regulating the physical, chemical, and biological functioning of soil systems and is essential for maintaining agricultural productivity. Many studies have investigated soil structure formation and stability. However, the underlying mechanisms behind its formation are still often unclear, including how soil microorganisms regulate this process via the aggregation of soil particles. In this review, we seek to summarise current information regarding how microorganisms influence aggregation and explore whether the application of molecular genetic techniques has potential to increase our understanding in this important area. Specifically, we review current information regarding the exact nature and role of microbially produced soil binding agents (extracellular polymeric substances, glomalin, hydrophobins and chaplins) and how different soil microorganisms (bacteria, archaea, fungi, protists) regulate and influence the production of these substances. Molecular genetic techniques have the capacity to provide new information regarding the genetic make‐up of the soil microbial biomass, which could potentially be related to their function in soil and role in the aggregation of soil particles. However, more work is required to identify the key functional genes important for studying aggregation processes. Techniques better able to study the fine scale distribution of microorganisms and microbial products are also required to fully understand microbial interactions and functioning on a scale relevant to aggregation. Future developments in this area may offer an opportunity to improve our understanding of, and potentially manipulate, soil aggregation for the benefit of soil functioning and environments. [ABSTRACT FROM AUTHOR]

The physical and chemical changes that accompany permafrost thaw directly influence the microbial communities that mediate the decomposition of formerly frozen organic matter, leading to uncertainty in permafrost–climate feedbacks. Although changes to microbial metabolism and community structure are documented following thaw, the generality of post‐thaw assembly patterns across permafrost soils of the world remains uncertain, limiting our ability to predict biogeochemistry and microbial community responses to climate change. Based on our review of the Arctic microbiome, permafrost microbiology, and community ecology, we propose that Assembly Theory provides a framework to better understand thaw‐mediated microbiome changes and the implications for community function and climate feedbacks. This framework posits that the prevalence of deterministic or stochastic processes indicates whether the community is well‐suited to thrive in changing environmental conditions. We predict that on a short timescale and following high‐disturbance thaw (e.g., thermokarst), stochasticity dominates post‐thaw microbiome assembly, suggesting that functional predictions will be aided by detailed information about the microbiome. At a longer timescale and lower‐intensity disturbance (e.g., active layer deepening), deterministic processes likely dominate, making environmental parameters sufficient for predicting function. We propose that the contribution of stochastic and deterministic processes to post‐thaw microbiome assembly depends on the characteristics of the thaw disturbance, as well as characteristics of the microbial community, such as the ecological and phylogenetic breadth of functional guilds, their functional redundancy, and biotic interactions. These propagate across space and time, potentially providing a means for predicting the microbial forcing of greenhouse gas feedbacks to global climate change. [ABSTRACT FROM AUTHOR]

The continuous pursuit of designing an ideal infection imaging agent is a crucial and ongoing endeavor in the field of biomedical research. Duramycin, an antimicrobial peptide exerts its antimicrobial action on bacteria by specific recognition of phosphatidylethanolamine (PE) moiety present on most bacterial membranes, particularly Escherichia coli (E. coli). E. coli membranes contain more than 60% PE. Therefore, duramycin is an attractive candidate for the formulation of probes for in situ visualization of E. coli driven focal infections. The aim of the present study is to develop 99m Tc labeled duramycin as a single-photon emission computed tomography (SPECT)-based agent to image such infections. Duramycin was successfully conjugated with a bifunctional chelator, hydrazinonicotinamide (HYNIC). PE specificity of HYNIC-duramycin was confirmed by a dye release assay on PE-containing model membranes. Radiolabeling of HYNIC-duramycin with 99m Tc was performed with consistently high radiochemical yield (>90%) and radiochemical purity (>90%). [ 99m Tc]Tc-HYNIC-duramycin retained its specificity for E. coli, in vitro. SPECT and biodistribution studies showed that the tracer could specifically identify E. coli driven infection at 3 h post injection. While 99m Tc-labeled duramycin is employed for monitoring early response to cancer therapy and cardiotoxicity, the current studies have confirmed, for the first time, the potential of utilizing 99m Tc labeled duramycin as an imaging agent for detecting bacteria. Its application in imaging PE-positive bacteria represents a novel and promising advancement., (© 2023 Wiley Periodicals LLC.)

Soil protists, the major predator of bacteria and fungi, shape the taxonomic and functional structure of soil microbiome via trophic regulation. However, how trophic interactions between protists and their prey influence microbially mediated soil organic carbon turnover remains largely unknown. Here, we investigated the protistan communities and microbial trophic interactions across different aggregates-size fractions in agricultural soil with long-term fertilization regimes. Our results showed that aggregate sizes significantly influenced the protistan community and microbial hierarchical interactions. Bacterivores were the predominant protistan functional group and were more abundant in macroaggregates and silt + clay than in microaggregates, while omnivores showed an opposite distribution pattern. Furthermore, partial least square path modeling revealed positive impacts of omnivores on the C-decomposition genes and soil organic matter (SOM) contents, while bacterivores displayed negative impacts. Microbial trophic interactions were intensive in macroaggregates and silt + clay but were restricted in microaggregates, as indicated by the intensity of protistan-bacterial associations and network complexity and connectivity. Cercozoan taxa were consistently identified as the keystone species in SOM degradation-related ecological clusters in macroaggregates and silt + clay, indicating the critical roles of protists in SOM degradation by regulating bacterial and fungal taxa. Chemical fertilization had a positive effect on soil C sequestration through suppressing SOM degradation-related ecological clusters in macroaggregate and silt + clay. Conversely, the associations between the trophic interactions and SOM contents were decoupled in microaggregates, suggesting limited microbial contributions to SOM turnovers. Our study demonstrates the importance of protists-driven trophic interactions on soil C cycling in agricultural ecosystems., (© 2023 John Wiley & Sons Ltd.)

The excessive usage of nitrogen (N) fertilizers can accelerate the tendency of global climate change. Biological N fixation by diazotrophs contributes substantially to N input and is a viable solution to sustainable agriculture via reducing inorganic N fertilization. However, how manure application influences the abundance, community structure and assembly process of diazotrophs in soil aggregates is not fully understood. Here, we investigated the effect of manure amendment on diazotrophic communities in soil aggregates of an arable soil. Manure application increased soil aggregation, crop yield and the abundance of nifH genes. The abundance of nifH genes increased with aggregate sizes, indicating that diazotrophs prefer to live in larger aggregates. The abundance of nifH genes in large macroaggregates, rather than in microaggregates and silt and clay, was positively associated with plant biomass and crop yield. Both manure application and aggregate size did not alter the Shannon diversity of diazotrophs but significantly changed the diazotrophic community structure. The variation of diazotrophic community structure explained by manure application was greater than that by aggregate size. Manure application promoted the relative abundance of Firmicutes but reduced that of a-Proteobacteria. Stochastic processes played a dominant role in the assembly of diazotrophs in the control treatment. Low-rate manure (9Mg ha-1) application, rather than medium-rate (18Mg ha-1) and high-rate (27Mg ha-1) manure, significantly increased the relative importance of deterministic processes in diazotrophic community assembly. Taken together, our findings demonstrated that long-term manure application increased nifH gene abundance and altered the community structure and assembly process of diazotrophs in soil aggregates, which advanced our understanding of the ecophysiology and functionality of diazotrophs in acidic Ultisols. [ABSTRACT FROM AUTHOR]

Soil, a potential reservoir of antibiotic resistance genes (ARGs), is inhabited by numerous microorganisms. Many microorganisms in soil are embedded within a self-produced matrix of extracellular polymeric substances to form supracellular structures, i.e., biofilms. Representing the predominant microbial lifestyle in soil, soil biofilms are considered hot spots of horizontal gene transfer. Herein, we discuss the distribution, transfer, and fate of ARGs in the soil environment at macro- and micro-scales. Applications of microfluidic platforms, with an advantage of mimicking complex soil environments and permitting the study of microbial behaviors at a micro-scale, coupled with high-throughput sequencing and other innovative platforms, to study soil biofilms and transfer of ARGs are also discussed. This review aims to highlight the neglected role of soil biofilms in the spread of ARGs to expand the current limited knowledge about ARGs in the soil microenvironment. [ABSTRACT FROM AUTHOR]

Diffusiophoresis refers to the movement of colloidal particles in the presence of a concentration gradient of a solute and enables directed motion of colloidal particles in geometries that are inaccessible, such as dead-end pores, without imposing an external field. Previous experimental reports on dead-end pore geometries show that, even in the absence of mean flow, colloidal particles moving through diffusiophoresis exhibit significant dispersion. Existing models of diffusiophoresis are not able to predict the dispersion and thus the comparison between the experiments and the models is largely qualitative. To address these quantitative differences between the experiments and models, we derive an effective one-dimensional equation, similar to a Taylor dispersion analysis, that accounts for the dispersion created by diffusioosmotic flow from the channel sidewalls. We derive the effective dispersion coefficient and validate our results by comparing them with direct numerical simulations. We also compare our model with experiments and obtain quantitative agreement for a wide range of colloidal particle sizes. Our analysis reveals two important conclusions. First, in the absence of mean flow, dispersion is driven by the flow created by diffusioosmotic wall slip such that spreading can be reduced by decreasing the channel wall diffusioosmotic mobility. Second, the model can explain the spreading of colloids in a dead-end pore for a wide range of particle sizes. We note that, while the analysis presented here focuses on a dead-end pore geometry with no mean flow, our theoretical framework is general and can be adapted to other geometries and other background flows. [ABSTRACT FROM AUTHOR]

Competition of different species or cell types for limited space is relevant in a variety of biological processes such as biofilm development, tissue morphogenesis and tumor growth. Predicting the outcome for non-adversarial competition of such growing active matter is non-trivial, as it depends on how processes like growth, proliferation and the degradation of cellular matter are regulated in confinement; regulation that happens even in the absence of competition to achieve the dynamic steady state known as homeostasis. Here, we show that passive by-products of the processes maintaining homeostasis can significantly alter fitness. Even for purely pressure-regulated growth and exclusively mechanical interactions, this enables cell types with lower homeostatic pressure to outcompete those with higher homeostatic pressure. We reveal that interfaces play a critical role for this specific kind of competition: there, growing matter with a higher proportion of active cells can better exploit local growth opportunities that continuously arise as the active processes keep the system out of mechanical equilibrium. We elucidate this effect in a theoretical toy model and test it in an agent-based computational model that includes finite-time mechanical persistence of dead cells and thereby decouples the density of growing cells from the homeostatic pressure. Our results suggest that self-organization of cellular aggregates into active and passive matter can be decisive for competition outcomes and that optimizing the proportion of growing (active) cells can be as important to survival as sensitivity to mechanical cues. [ABSTRACT FROM AUTHOR]

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ATP-sensitive potassium channels (KATP channels) play pivotal roles in excitable cells and link cellular metabolism with membrane excitability. The action potential converts electricity into dynamics by ion channel-mediated ion exchange to generate systole, involved in every heartbeat. Activation of the KATP channel repolarizes the membrane potential and decreases early afterdepolarization (EAD)-mediated arrhythmias. KATP channels in cardiomyocytes have less function under physiological conditions but they open during severe and prolonged anoxia due to a reduced ATP/ADP ratio, lessening cellular excitability and thus preventing action potential generation and cell contraction. Small active molecules activate and enhance the opening of the KATP channel, which induces the repolarization of the membrane and decreases the occurrence of malignant arrhythmia. Accumulated evidence indicates that mutation of KATP channels deteriorates the regulatory roles in mutation-related diseases. However, patients with mutations in KATP channels still have no efficient treatment. Hence, in this study, we describe the role of KATP channels and subunits in angiocardiopathy, summarize the mutations of the KATP channels and the functional regulation of small active molecules in KATP channels, elucidate the potential mechanisms of mutant KATP channels and provide insight into clinical therapeutic strategies. [ABSTRACT FROM AUTHOR]

Bacteria in natural environments and infections are often found in cell aggregates suspended in polymer-rich solutions, and aggregation can promote bacterial survival and stress resistance. One aggregation mechanism, called depletion aggregation, is driven by physical forces between bacteria and high concentrations of polymers in the environment rather than bacterial activity per se. As such, bacteria aggregated by the depletion mechanism will disperse when polymer concentrations fall unless other adhesion mechanisms supervene. Here we investigated whether the depletion mechanism can actuate the aggregating effects of Pseudomonas aeruginosa exopolysaccharides for suspended (i.e. not surface attached) bacteria, and how depletion affects bacterial inter-species interactions. We found that cells overexpressing the exopolysaccharides Pel and Psl remained aggregated after short periods of depletion aggregation whereas wild-type and mucoid P. aeruginosa did not. In co-culture, depletion aggregation had contrasting effects on P. aeruginosa's interactions with coccus- and rod-shaped bacteria. Depletion caused S. aureus (cocci) and P. aeruginosa (rods) to segregate from each other and S. aureus to resist secreted P. aeruginosa antimicrobial factors resulting in species co-existence. In contrast, depletion aggregation caused P. aeruginosa and Burkholderia sp. (both rods) to intermix, enhancing type VI secretion inhibition of Burkholderia by P. aeruginosa , leading to P. aeruginosa dominance. These results show that in addition to being a primary cause of aggregation in polymer-rich suspensions, physical forces inherent to the depletion mechanism can promote aggregation by some self-produced exopolysaccharides and determine species distribution and composition of bacterial communities. [ABSTRACT FROM AUTHOR]

Below‐ground microbial communities drive some of Earth's largest biogeochemical fluxes, yet they represent a major source of uncertainty in global biogeochemical models. This review synthesizes recent advances in trait‐based soil carbon modelling in order to identify how empirical observations of microbial traits can inform the next generation of soil carbon models.We identify four key perspectives from which trait‐based models have investigated the role of microbes in soil carbon fluxes, ranging from the largest to the smallest scales of biological organization: (i) Earth system models, which have recently begun to incorporate microbial traits at a global scale; (ii) ecosystem models, which relate microbial carbon cycling to other trophic levels and element cycles; (iii) models from community ecology, which link theories of species diversity to ecosystem cycles; and (iv) models of fine‐scale physiology, which mechanistically represent traits at the individual level.Highlighting the contributions of diverse trait‐based modelling approaches, we caution that this diversity makes it challenging to link perspectives at different scales. The meaning of a trait depends both on the structure of the model in which it occurs and on the scale treated by the model. Thus, reapplying a fine‐scale trait at a broader scale may make incorrect predictions, an issue we illustrate quantitatively using model simulations.With these challenges in mind, we highlight several ways to synthesize the scales of microbial biogeochemical modelling: (i) quantitatively, using mathematical scaling techniques, (ii) empirically, by applying experiments to test relationships between scales and (iii) conceptually, by identifying key traits and processes across scales.Taking full advantage of trait‐based modelling, ecologists will thus be able to incorporate multiple perspectives to better predict carbon cycling in a changing world. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

The problem of parameter identification appears in many physical applications. A parameter of particular interest in cancer treatment is permeability, which modulates the fluidic streamlines in the tumor microenvironment. Most of the existing permeability identification techniques are invasive and not feasible to identify the permeability with minimal interference with the porous structure in their working conditions. In this paper, a theoretical framework utilizing partial differential equation (PDE)-constrained optimization strategies is established to identify a spatially distributed permeability of a porous structure from its modulated external velocity field measured around the structure. In particular, the flow around and through the porous media are governed by the steady-state Navierâ€"Stokesâ€"Darcy model. The performance of our approach is validated via numerical and experimental tests for the permeability of a 3D printed porous surrogate in a micro-fluidic chip based on the sampled optical velocity measurement. Both numerical and experimental results show a high precision of the permeability estimation. [ABSTRACT FROM AUTHOR]

Microbial communities of soil aggregate-size fractions were explored with molecular and networking assays for topsoil samples from a clayey rice paddy under long-term fertilization treatments. The treatments included no fertilizer (NF) as control, chemical fertilizer only (CF), chemical fertilizer with swine manure (CFM), and chemical fertilizer with rice straw return (CFS). Following a wet-sieving protocol, water-stable aggregates were separated into size fractions of large macroaggregates (L-MacA, >2,000 μm), macroaggregates (MacA, 2,000–250 μm), microaggregates (MicA, 250–53 μm), fine microaggregates (F-MicA, 53–2 μm), and fine clay (F-Clay, <2 μm). Mass proportion was 32.3–38.2% for F-MicA, 23.0–31.5% for MacA, 19.0–23.1% for MicA, 9.1–12.0% for L-MacA, and 4.9–7.5% for F-Clay, respectively. The proportion of MacA was increased, but F-Clay was reduced by fertilization, whereas the mean weight diameter was increased by 8.0–16.2% from 534.8 μm under NF to 621.5 μm under CFM. Fertilization affected bacterial 16S rRNA and fungal 18S rRNA gene abundance in F-MicA and F-Clay but not in aggregates in size larger than 53 μm. However, bacterial and fungal community α-diversities and community structures were quite more divergent among the fertilization treatments in all size fractions. Organic carbon and gene abundance of bacteria and fungi were enriched in both L-MacA and MacA but depleted in F-Clay, whereas microbial Shannon diversity was rarely changed by fraction size under the four treatments. L-MacA and MacA contained more bacteria of r-strategists and copiotrophs, whereas F-MicA and F-Clay were demonstrated with a higher abundance of K-strategists and oligotrophs. Guilds of parasitic and litter saprotrophic fungi were enriched in F-MicA but depleted in L-MacA. Furthermore, most of bacterial and fungal operational taxonomic units were strongly interacted in L-MacA and MacA rather than in MicA and F-Clay. Thus, MacA acted as micro-hotspots enriched with functional and networked microbial communities, which were enhanced with organic/inorganic fertilization in the rice paddy. [ABSTRACT FROM AUTHOR]

Understanding mechanisms shaping distributions and interactions of soil microbes is essential for determining their impact on large scale ecosystem services, such as carbon sequestration, climate regulation, waste decomposition, and nutrient cycling. As the functional unit of soil ecosystems, we focus our attention on the spatial structure of soil macroaggregates. Emulating this complex physico-chemical environment as a patchy habitat landscape we investigate on-chip the effect of changing the connectivity features of this landscape as Escherichia coli forms a metapopulation. We analyze the distributions of E. coli occupancy using Taylor's law, an empirical law in ecology which asserts that the fluctuations in populations is a power law function of the mean. We provide experimental evidence that bacterial metapopulations in patchy habitat landscapes on microchips follow this law. Furthermore, we find that increased variance of patch-corridor connectivity leads to a qualitative transition in the fluctuation scaling. We discuss these results in the context of the spatial ecology of microbes in soil. [ABSTRACT FROM AUTHOR]

Soils and crops are particularly vulnerable to climate change and environmental stresses. In many agrosystems, soil biodiversity and ecosystem services provided by soils are under threat from a range of natural and human drivers. Agricultural soils are often subject to agronomic practices that disrupt soil trophic networks and make soils less productive in the long term. In this scenario, sustainable soil use aimed at improving plant/root status, growth and development plays a crucial role for enhancing the biological capacity of agricultural soils. This commentary paper is divided into the following four main sections: (i) the contentious nature of soil organic matter; (ii) soil biological quality/fertility; (iii) soil classification; and, (iv) which agricultural practices can be defined as sustainable? The published literature was analyzed within a holistic framework, with agrosystems considered as living systems where soil, vegetation, fauna and microorganisms co‐evolve and are reciprocally influenced. Ultimately, this article will suggest a better stewardship of agricultural soils as a natural capital. [ABSTRACT FROM AUTHOR]

The rapid development of nanoscience and nanoengineering provides new perspectives on the composition of food materials, and has great potential for food biology research and applications. The use of nanoparticle additives and the discovery of endogenous nanoparticles in food make it important to elucidate in vivo safety of nanomaterials. Nanoparticles will spontaneously adsorb proteins during transporting in blood and a protein corona can be formed on the nanoparticle surface inside the human body. Protein corona affects the physicochemical properties of nanoparticles and the structure and function of proteins, which in turn affects a series of biological reactions. This article reviewed basic information about protein corona of food‐related nanoparticles, elucidated the influence of protein corona on nanoparticles properties and protein structure and function, and discussed the effect of protein corona on nanoparticles in vivo. The effects of protein corona on nanoparticles transport, cellular uptake, cytotoxicity, and immune response were reviewed, and the reasons for these effects were also discussed. Finally, future research perspectives for food protein corona were proposed. Protein corona gives food nanoparticles a new identity, which makes proteins bound to nanoparticles undergo structural transformations that affect their recognition by receptors in vivo. It can have positive or negative impacts on cellular uptake and toxicity of nanoparticles and even trigger immune responses. Understanding the effects of protein corona have potential in evaluating the fate of the food‐related nanoparticles, providing physicochemical and biological information about the interaction between proteins and foodborne nanoparticles. The review article will help to evaluate the safety of protein coronas formed on nanoparticles in food, and may provide fundamental information for understanding and controlling nanotoxicity. [ABSTRACT FROM AUTHOR]

Antimicrobial resistant (AMR) infections are a leading health threat globally. Previous literature has underscored the farm-to-fork continuum as a potential focal point for the emergence and spread of AMR. In the present study, date (Phoenix dactylifera L.) seed oil was investigated for its chemical composition and antimicrobial activity against common foodborne pathogens including Escherichia coli O157:H7, Salmonella enteritidis, Salmonella typhimurium, Listeria monocytogenes, and Staphylococcus aureus in vitro, and in ultra-high-temperature (UHT) milk as a food model at storage temperatures of 37 °C (24 h) and 10 °C (7 days). GC-MS analysis of the seed oil revealed 20 compounds, with octadecane (52.2-55.4%) as the major constituent, and the fatty acid analysis revealed 17 fatty acids, with oleic acid (42.3-43.1%) as the main constituent, followed by lauric acid (19.8-20.3%). The antimicrobial activity of date seed oil was determined using the microdilution method. A significant inhibition against gram-negative bacteria was noted in microbiological media and UHT milk, with a log reduction ranging from 4.3 to 6.7 (at 37 °C/24 h) and 5.7 to 7.2 (at 10 °C/7 days), respectively, at oil concentrations ranging between 10 and 15 µl/ml. The oil showed a similar significant inhibitory effect against St. aureus in the microbiological media (2.0-6.0 log reduction), whereas the inhibitory effect against L. monocytogenes was not statistically significant, with a maximum log reduction of 0.64 achieved at a concentration of 10 µl/ml. AFM imaging of the bacteria showed that oil treatment led to morphological changes in the bacteria including the formation of distorted shapes, surface blebs, indentations, stiffness, and swelling. Present findings suggest that date seed oil can be a promising by-product with potential antimicrobial activity and a food preservative., (© 2023. Springer Nature Limited.)

Recent mechanistic studies have indicated that at subwavelength post diameters and selected aspect ratios nanopost arrays (NAPA) exhibit ion yield resonances (Walker, B. N., Stolee, J. A., Pickel, D. L., Retterer, S. T., and Vertes, A. J. Phys. Chem. C 2010, 114, 4835−4840). In this contribution we explore the analytical utility of these optimized structures as matrix-free platforms for laser desorption ionization mass spectrometry (LDI-MS). Using NAPA, we show that high ionization efficiencies enable the detection of ultratrace amounts of analytes (e.g., 800 zmol of verapamil) with a dynamic range spanning up to 4 orders of magnitude. Due to the clean nanofabrication process and the lack of matrix material, minimal background interferences are present in the low-mass range. We demonstrate that LDI from NAPA ionizes a broad class of small molecules including pharmaceuticals, natural products, metabolites, and explosives. Quantitation of resveratrol in red wine samples shows that the analysis of targeted analytes in complex mixtures is feasible with minimal sample preparation using NAPA-based LDI. We also describe how multiple metabolite species can be directly detected in single yeast cells deposited on the NAPA chip. Twenty-four metabolites, or 4% of the yeast metabolome, were identified in the single-cell spectra. [ABSTRACT FROM AUTHOR]

Wetlands are the largest natural source of terrestrial CH4 emissions. Afforestation can enhance soil CH4 oxidation and decrease methanogenesis, yet the driving mechanisms leading to these effects remain unclear. We analyzed the structures of communities of methanogenic and methanotrophic microbes, quantification of mcr A and pmo A genes, the soil microbial metagenome, soil properties and CH4 fluxes in afforested and non-afforested areas in the marshland of the Yangtze River. Compared to the non-afforested land use types, net CH4 emission decreased from bare land, natural vegetation and 5-year forest plantation and transitioned to net CH4 sinks in the 10- and 20-year forest plantations. Both abundances of mcr A and pmo A genes decreased significantly with increasing plantation age. By combining random forest analysis and structural equation modeling, our results provide evidence for an important role of the abundance of functional genes related to methane production in explaining the net CH4 flux in this ecosystem. The structures of methanogenic and methanotrophic microbial communities were of lower importance as explanatory factors than functional genes in terms of in situ CH4 flux. We also found a substantial interaction between functional genes and soil properties in the control of CH4 flux, particularly soil particle size. Our study provides empirical evidence that microbial community function has more explanatory power than taxonomic microbial community structure with respect to in situ CH4 fluxes. This suggests that focusing on gene abundances obtained, e.g., through metagenomics or quantitative/digital PCR could be more effective than community profiling in predicting CH4 fluxes, and such data should be considered for ecosystem modeling. [ABSTRACT FROM AUTHOR]

The world is rapidly changing, the resources are getting depleted, and the demand for newer technologies and products is increasing. To keep up with these new advances, highly efficient catalytic routes need to be taken to be sustainable and ensure a drawn-out existence of resources for future generations. Catalysis turns out to be a significantly important field of application when it comes to the era of nanoscience, where all devices and technologies are becoming smaller and smaller in size with improved properties. When deeming the usability of a catalyst, it is of paramount importance to have a good understanding of their properties and their synergistic effect on the other reagents in the reaction. Over the last decade, the field of nanocatalysis has grown rapidly, both in homogeneous and heterogeneous catalysis. Given that nanoparticles have a high surface-to-volume ratio when compared to bulk materials, they are appealing as catalysts. Catalysts accelerate and boost thousands of different chemical reactions on a daily basis, forming the foundation of the multibillion-dollar chemical industry worldwide, a pathway leading to green chemistry, and a novel, yet crucial, environmental protection technology. As a result, in this review, the use of nanocatalysts and the application of their special features in the renewable energy, hydrocarbon processing, and fine chemical synthesis sector was explored. A detailed explanation of the working mechanism of these nanocatalysts, starting from how they are synthesized to the effect of modification of their surface, has been put together. We have tried to collect all the current progresses in these three sectors to the best of our abilities. Furthermore, it is anticipated that this paper would be useful for future researchers and academicians wishing to contribute toward this subject of interest. [ABSTRACT FROM AUTHOR]

Maintaining or recovering soil health is becoming a goal of many policies carried out at national, continental and global scales to promote global health. This viewpoint is aimed at stressing the relevance of a holistic approach to soil health assessment and monitoring, which is not only related to soil functional biodiversity but also considers the genetic horizons of the soil profile and not just the topsoil. We highlight that soil health has different connotations depending on the environmental setting and may show high spatial and temporal dynamics. Although the biological activity is often concentrated in the surficial horizon, we report increasing evidence that deep soil horizons host relevant biological communities, which are regulated by soil conditions that are usually different from those present in the topsoil. The processes responsible for the formation of surface and subsurface soil genetic horizons produce soil features that select the presence of organisms. The natural self‐organization of soil features is at the basis of the soil classification systems and of their ability to differentiate soil taxa and appreciate pedodiversity. Examples are reported of surface and deep soil genetic horizons as an important interpretative tool of soil functional biodiversity and soil health. Therefore, the assessing and monitoring of soil health should not be carried out at fixed depth, but according to soil genetic horizons. We conclude that the loss of the natural self‐organization of genetic horizons is a form of soil health degradation. [ABSTRACT FROM AUTHOR]

Including information about soil microbial communities into global decomposition models is critical for predicting and understanding how ecosystem functions may shift in response to global change. Here we combined a standardised litter bag method for estimating decomposition rates, the Tea Bag Index (TBI), with high-throughput sequencing of the microbial communities colonising the plant litter in the bags. Together with students of the Federal College for Viticulture and Fruit Growing, Klosterneuburg, Austria, acting as citizen scientists, we used this approach to investigate the diversity of prokaryotes and fungi-colonising recalcitrant (rooibos) and labile (green tea) plant litter buried in three different soil types and during four seasons with the aim of (i) comparing litter decomposition (decomposition rates (k) and stabilisation factors (S)) between soil types and seasons, (ii) comparing the microbial communities colonising labile and recalcitrant plant litter between soil types and seasons, and (iii) correlating microbial diversity and taxa relative abundance patterns of colonisers with litter decomposition rates (k) and stabilisation factors (S). Stabilisation factor (S), but not decomposition rate (k), correlated with the season and was significantly lower in the summer, indicating a decomposition of a larger fraction of the organic material during the warm months. This finding highlights the necessity to include colder seasons in the efforts of determining decomposition dynamics in order to quantify nutrient cycling in soils accurately. With our approach, we further showed selective colonisation of plant litter by fungal and prokaryotic taxa sourced from the soil. The community structures of these microbial colonisers differed most profoundly between summer and winter, and selective enrichment of microbial orders on either rooibos or green tea hinted at indicator taxa specialised for the primary degradation of recalcitrant or labile organic matter, respectively. Our results collectively demonstrate the importance of analysing decomposition dynamics over multiple seasons and further testify to the potential of the microbiome-resolved TBI to identify the active component of the microbial community associated with litter decomposition. This work demonstrates the power of the microbiome-resolved TBI to give a holistic description of the litter decomposition process in soils. [ABSTRACT FROM AUTHOR]

Numerous examples of microbial phase-separated biomolecular condensates have now been identified following advances in fluorescence imaging and single molecule microscopy technologies. The structure, function, and potential applications of these microbial condensates are currently receiving a great deal of attention. By neatly compartmentalizing proteins and their interactors in membrane-less organizations while maintaining free communication between these macromolecules and the external environment, microbial cells are able to achieve enhanced metabolic efficiency. Typically, these condensates also possess the ability to rapidly adapt to internal and external changes. The biological functions of several phase-separated condensates in small bacterial cells show evolutionary convergence with the biological functions of their eukaryotic paralogs. Artificial microbial membrane-less organelles are being constructed with application prospects in biocatalysis, biosynthesis, and biomedicine. In this review, we provide an overview of currently known biomolecular condensates driven by liquid-liquid phase separation (LLPS) in microbial cells, and we elaborate on their biogenesis mechanisms and biological functions. Additionally, we highlight the major challenges and future research prospects in studying microbial LLPS. [ABSTRACT FROM AUTHOR]

There are medical treatment vulnerabilities in longer-duration space missions present in the current International Space Station crew health care system with risks, arising from spaceflight-accelerated pharmaceutical degradation and resupply lag times. Bioregenerative life support systems may be a way to close this risk gap by leveraging in situ resource utilization (ISRU) to perform pharmaceutical synthesis and purification. Recent literature has begun to consider biological ISRU using microbes and plants as the basis for pharmaceutical life support technologies. However, there has not yet been a rigorous analysis of the processing and quality systems required to implement biologically produced pharmaceuticals for human medical treatment. In this work, we use the equivalent system mass (ESM) metric to evaluate pharmaceutical purification processing strategies for longer-duration space exploration missions. Monoclonal antibodies, representing a diverse therapeutic platform capable of treating multiple space-relevant disease states, were selected as the target products for this analysis. We investigate the ESM resource costs (mass, volume, power, cooling, and crew time) of an affinity-based capture step for monoclonal antibody purification as a test case within a manned Mars mission architecture. We compare six technologies (three biotic capture methods and three abiotic capture methods), optimize scheduling to minimize ESM for each technology, and perform scenario analysis to consider a range of input stream compositions and pharmaceutical demand. We also compare the base case ESM to scenarios of alternative mission configuration, equipment models, and technology reusability. Throughout the analyses, we identify key areas for development of pharmaceutical life support technology and improvement of the ESM framework for assessment of bioregenerative life support technologies. [ABSTRACT FROM AUTHOR]

In this paper, a cell-based smoothed finite element method using the arbitrary n -sided polygonal element (CS-FEM-Poly) is developed to solve fluid mechanics problems. A stabilization method, characteristic-based split coupled with stabilized pressure gradient projection (CBS/SPGP), is employed to deal with numerical oscillations for CS-FEM-Poly. We validate CS-FEM-Poly and test its numerical behaviors using triangular, quadrilateral and polygonal elements on four typical numerical examples. Numerical results show that the CS-FEM-Poly based on CBS/SPGP produces well-agreed solutions with the exact solutions of benchmarks, and gives desirable convergence rate as compared with FEM. In the backward-facing step flow example, the numerical robustness for concave elements is manifested for CS-FEM-Poly. The proposed CS-FEM-Poly exhibits the remarkable potential for polygonal mesh or glued polygonal elements in the hybrid mesh to solve incompressible flows. [ABSTRACT FROM AUTHOR]

Sorghum/sorghum–sudangrass hybrids (SSgH) have been used as a cover crop to improve soil health by adding soil organic matter, enhancing microbial activities, and suppressing soilborne pathogens in various cropping systems. A series of SSgH were screened for (1) allelopathic suppression and (2) improvement of soil edaphic factors and soil microbial profile against plantparasitic nematode (PPNs). The allelopathic potential of SSgH against PPNs is hypothesized to vary by variety and age. In two greenhouse bioassays, ‘NX-D-610 sorghum and the ‘Latte’ SSgH amendment provided the most suppressive allelopathic effect against the female formation of Meloidogyne incognita on mustard green seedlings when using 1-, 2-, or 3-month-old SSgH tissue, though most varieties showed a decrease in allelopathic effect as SSgH mature. A field trial was conducted where seven SSgH varieties were grown for 2.5 months and terminated using a flail mower, and eggplant was planted in a no-till system. Multivariate analysis of measured parameters revealed that increase in soil moisture, microbial biomass, respiration rate, nematode enrichment index, and sorghum biomass were negatively related to the initial abundance of PPNs and the root-gall index at 5 months after planting eggplant in a no-till system. These results suggested that improvement of soil health by SSgH could lead to suppression of PPN infection. [ABSTRACT FROM AUTHOR]

Packaging is an often overlooked component in microfluidic devices for biomedical implant applications. Robust and reliable connectors to interface microscale and macroscale features are especially critical for chronic implant applications. Existing microfluidic packaging methods are incompatible with emerging polymeric materials designed to enhance device integration with the surrounding tissue. A microfluidic connector scheme was developed to promote compatibility with novel materials and implant applications. The connectors and an adhesive wax were printed on a scaffold via additive manufacturing processes. The low-temperature packaging process entailed bonding the connector to a polymer nanocomposite-based intracortical microfluidic probe using an adhesive wax. The robustness of the packaging was assessed by measuring the tensile and shear bond strengths of the connector-adhesive wax-polymer film interface. After soak testing for 4 weeks, the bond strength continued to exceed the force required to infuse fluids through the microfluidic channel. Further, the shear bond strength exceeded typical probe insertion forces by at least ten-fold. These results support the use of the connector and thermal bonding method as a viable option for chronic implant applications. [ABSTRACT FROM AUTHOR]

Plasmonic nanostructures are successfully demonstrated in solar cells due to their broad spectra-selective resonance in the range of ultraviolet to near-infrared, and thus light absorption can be mostly improved and power conversion efficiency (PCE) further. Here, we demonstrate plasmonic dye-sensitized solar cells (DSSCs) using collapsible Au nanofingers to build photoanode to enhance light absorption. In this plasmonic DSSCs, by balancing local field enhancement due to gap-plasmon resonance and dye fluorescence quenching, the optimal gap size in collapsed Au/Al2O3/Au nanofingers is designed by twice the Al2O3 thickness and then deposited a TiO2 layer as photoanode. The results show that the PCE of DSSCs is mostly improved as compared to DSSCs with photoanode of Au/Al2O3/TiO2 films, which can be ascribed to the coupled local field enhancement within the sub-nanometer gaps. In addition, fluorescence of dyes on plasmonic nanofingers is nearly 10 times higher than plain Au/Al2O3/TiO2 films, which further proves the dye absorption enhancement. These plasmonic nanofingers enable the precise engineering of gap-plasmon modes and can be scaled up to wafer scale with low cost by the nanoimprint lithography technique, which suggests the feasibility of applying our result in constructing the photoanode for other types of solar cells. [ABSTRACT FROM AUTHOR]

Variations in cell wall composition and biomechanical properties can contribute to the cellular plasticity required during complex processes such as polarized growth and elongation in microbial cells. This study utilizes atomic force microscopy (AFM) to map the cell surface topography of fission yeast, Schizosaccharomyces pombe, at the pole regions and to characterize the biophysical properties within these regions under physiological, hydrated conditions. High‐resolution images acquired from AFM topographic scanning reveal decreased surface roughness at the cell poles. Force extension curves acquired by nanoindentation probing with AFM cantilever tips under low applied force revealed increased cell wall deformation and decreased cellular stiffness (cellular spring constant) at cell poles (17 ± 4 mN/m) relative to the main body of the cell that is not undergoing growth and expansion (44 ± 10 mN/m). These findings suggest that the increased deformation and decreased stiffness at regions of polarized growth at fission yeast cell poles provide the plasticity necessary for cellular extension. This study provides a direct biophysical characterization of the S. pombe cell surface by AFM, and it provides a foundation for future investigation of how the surface topography and local nanomechanical properties vary during different cellular processes. Take away: AFM was utilized to provide high‐resolution surface topography mapping of S. pombe cell surface.Cell poles had decreased cellular stiffness, increased cell wall deformation, and decreased surface rougness compared to the cell body. [ABSTRACT FROM AUTHOR]

Continuous cropping negatively affects soil fertility, physicochemical properties and the microbial community structure. However, the effects of long-term chili monoculture on the dominant microbial community assembly are not known. In this study, the impact of long-term chili monoculture on the correlation between the dominant microbial community and soil environmental variables was assessed. The results indicated that increasing duration of chili monoculture generated significant changes in soil nutrients, soil aggregates and soil enzymes: nutrient contents increased overall, mechanically stable macroaggregates increased and microaggregates decreased, water-stable macroaggregates and microaggregates decreased, β-glucosidase decreased nonlinearly, and nitrate reductase and alkaline phosphatase activities showed a nonlinear increase. Moreover, an increasing number of years of chili monoculture also affected the structure of the dominant microbiota, with substantial changes in the relative abundances of 11 bacterial and fungal genera. The drivers of the dominant microbial community assembly in rhizosphere soil were soil moisture, abiotic nitrogen, pH and salt. Long-term chili monoculture alters environmental variables affecting the dominant microbial community in rhizosphere soil. [ABSTRACT FROM AUTHOR]