Microbial carbon use efficiency promotes global soil carbon storage.

Soils store more carbon than other terrestrial ecosystems1,2. How soil organic carbon (SOC) forms and persists remains uncertain1,3, which makes it challenging to understand how it will respond to climatic change3,4. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss5-7. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways4,6,8-11, microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes12,13. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved7,14,15. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.

Accelerating the design of pili-enabled living materials using an integrative technological workflow.

Bacteria can be programmed to create engineered living materials (ELMs) with self-healing and evolvable functionalities. However, further development of ELMs is greatly hampered by the lack of engineerable nonpathogenic chassis and corresponding programmable endogenous biopolymers. Here, we describe a technological workflow for facilitating ELMs design by rationally integrating bioinformatics, structural biology and synthetic biology technologies. We first develop bioinformatics software, termed Bacteria Biopolymer Sniffer (BBSniffer), that allows fast mining of biopolymers and biopolymer-producing bacteria of interest. As a proof-of-principle study, using existing pathogenic pilus as input, we identify the covalently linked pili (CLP) biosynthetic gene cluster in the industrial workhorse Corynebacterium glutamicum. Genetic manipulation and structural characterization reveal the molecular mechanism of the CLP assembly, ultimately enabling a type of programmable pili for ELM design. Finally, engineering of the CLP-enabled living materials transforms cellulosic biomass into lycopene by coupling the extracellular and intracellular bioconversion ability.

KINASE-INDUCIBLE DOMAIN INTERACTING 8 regulates helical pod morphology in Medicago truncatula.

Leguminosae exhibits a wide diversity of legume forms with varying degrees of spiral morphologies, serving as an ideal clade for studying the growth and development of spiral organs. While soybean (Glycine max) develops straight pods, the pod of the model legume Medicago truncatula is a helix structure. Despite the fascinating structures and intensive description of the pods in legumes, little is known regarding the genetic mechanism underlying the highly varied spirality of the legume pods. In this study, we found that KINASE-INDUCIBLE DOMAIN INTERACTING 8 (MtKIX8) plays a key role in regulating the pod structure and spirality in M. truncatula. Unlike the coiled and barrel-shaped helix pods of the wild type, the pods of the mtkix8 mutant are loose and deformed and lose the topologic structure as observed in the wild-type pods. In the pods of the mtkix8 mutant, the cells proliferate more actively and overly expand, particularly in the ventral suture, resulting in uncoordinated growth along the dorsal and ventral sutures of pods. The core cell cycle genes CYCLIN D3s are upregulated in the mtkix8 pods, leading to the prolonged growth of the ventral suture region of the pods. Our study revealed the key role of MtKIX8 in regulating seed pod development in M. truncatula and demonstrates a genetic regulatory model underlying the establishment of the helical pod in legumes.

Engineered Living Materials For Sustainability.

Recent advances in synthetic biology and materials science have given rise to a new form of materials, namely engineered living materials (ELMs), which are composed of living matter or cell communities embedded in self-regenerating matrices of their own or artificial scaffolds. Like natural materials such as bone, wood, and skin, ELMs, which possess the functional capabilities of living organisms, can grow, self-organize, and self-repair when needed. They also spontaneously perform programmed biological functions upon sensing external cues. Currently, ELMs show promise for green energy production, bioremediation, disease treatment, and fabricating advanced smart materials. This review first introduces the dynamic features of natural living systems and their potential for developing novel materials. We then summarize the recent research progress on living materials and emerging design strategies from both synthetic biology and materials science perspectives. Finally, we discuss the positive impacts of living materials on promoting sustainability and key future research directions.

CAVE: a cloud-based platform for analysis and visualization of metabolic pathways.

Flux balance analysis (FBA) is an important method for calculating optimal pathways to produce industrially important chemicals in genome-scale metabolic models (GEMs). However, for biologists, the requirement of coding skills poses a significant obstacle to using FBA for pathway analysis and engineering target identification. Additionally, a time-consuming manual drawing process is often needed to illustrate the mass flow in an FBA-calculated pathway, making it challenging to detect errors or discover interesting metabolic features. To solve this problem, we developed CAVE, a cloud-based platform for the integrated calculation, visualization, examination and correction of metabolic pathways. CAVE can analyze and visualize pathways for over 100 published GEMs or user-uploaded GEMs, allowing for quicker examination and identification of special metabolic features in a particular GEM. Additionally, CAVE offers model modification functions, such as gene/reaction removal or addition, making it easy for users to correct errors found in pathway analysis and obtain more reliable pathways. With a focus on the design and analysis of optimal pathways for biochemicals, CAVE complements existing visualization tools based on manually drawn global maps and can be applied to a broader range of organisms for rational metabolic engineering. CAVE is available at https://cave.biodesign.ac.cn/.

Climatic and biotic factors influencing regional declines and recovery of tropical forest biomass from the 2015/16 El Niño.

The 2015/16 El Niño brought severe drought and record-breaking temperatures in the tropics. Here, using satellite-based L-band microwave vegetation optical depth, we mapped changes of above-ground biomass (AGB) during the drought and in subsequent years up to 2019. Over more than 60% of drought-affected intact forests, AGB reduced during the drought, except in the wettest part of the central Amazon, where it declined 1 y later. By the end of 2019, only 40% of AGB reduced intact forests had fully recovered to the predrought level. Using random-forest models, we found that the magnitude of AGB losses during the drought was mainly associated with regionally distinct patterns of soil water deficits and soil clay content. For the AGB recovery, we found strong influences of AGB losses during the drought and of [Formula: see text]. [Formula: see text] is a parameter related to canopy structure and is defined as the ratio of two relative height (RH) metrics of Geoscience Laser Altimeter System (GLAS) waveform data-RH25 (25% energy return height) and RH100 (100% energy return height; i.e., top canopy height). A high [Formula: see text] may reflect forests with a tall understory, thick and closed canopy, and/or without degradation. Such forests with a high [Formula: see text] ([Formula: see text] ≥ 0.3) appear to have a stronger capacity to recover than low-[Formula: see text] ones. Our results highlight the importance of forest structure when predicting the consequences of future drought stress in the tropics.

High Ambipolar Mobility and Long-Range Carrier Transport in Violet Phosphorus Nanosheet.

Carrier transport capacity with high mobility and long-range diffusion length holds particular significance for the advancement of modern optoelectronic devices. Herein, we have unveiled the carrier dynamics and transport properties of a pristine violet phosphorus (VP) nanosheet by a transient absorption microscopy. Under the excitation (2.41 eV) above the exciton band, two photoinduced absorption peaks with the energy difference of approximately 520 meV emerge within a broadband transient absorption background which originates from the prompt generation of free carriers and the concomitant formation of excitons (lifetime of 467.21 ps). This observation is consistent with the established band-edge model of VP. Intriguingly, we have determined the ambipolar diffusion coefficient and mobility of VP to be approximately 47.32 cm2·s-1 and 1798 cm2·V-1·s-1, respectively, which further indicate a long-range carrier transport of approximately 2.10 µm. This work unveils the significant carrier transport capacity of VP, highlighting its potential for future optoelectronic and excitonic applications.

Safety, tolerability, and pharmacokinetics of HRS9432(A) injection in healthy Chinese subjects: a phase-I randomized, double-blind, dose escalation, placebo-controlled study.

HRS9432(A) is a long-acting echinocandin antifungal medication primarily used to treat invasive fungal infections, particularly invasive candidiasis. The safety, tolerability, and pharmacokinetic characteristics of HRS9432(A) injection were investigated in a randomized, double-blind, placebo-controlled, single- and multiple-ascending-dose Phase I study involving 56 healthy adult subjects. Doses ranging from 200 to 1200 mg were administered. Safety was continually monitored, including adverse events, clinical laboratory examinations, vital signs, 12-lead electrocardiograms, and physical examinations, while the pharmacokinetic profile within the body was evaluated. The results indicated that concentrations of HRS9432 peaked immediately after infusion, demonstrating essentially linear pharmacokinetic characteristics within the dosage range of 200-1,200 mg. It exhibited a low clearance rate and an extended half-life, with a clearance of approximately 0.2 L/h, a volume of distribution of around 40 L, and a half-life of approximately 140h following a single dose. The accumulation index for AUC0-τ after multiple doses ranged from 1.41 to 1.75. No severe adverse events occurred during the study, and the severity of all adverse events was mild or moderate. Therefore, the intravenous administration of HRS9432(A) in healthy Chinese adult subjects, either as multiple infusions of 200 to 600 mg (once a week, four doses) or as a single infusion of 900-1,200 mg, demonstrated overall good safety and tolerability. The pharmacokinetic exhibited essentially linear characteristics in the body, supporting a weekly dosing frequency for clinical applications and providing additional options for the treatment or prevention of invasive fungal infections. CLINICAL TRIALS: This study is registered with the International Clinical Trials Registry Platform as ChiCTR2300073525.

Enhanced MALDI-2 Sensitivity with Reflecting Post-Ionization Laser for High-Resolution MS Imaging Combined with Real-Time Microscope Imaging.

Laser-induced matrix-assisted laser desorption/ionization post-ionization (MALDI-2) could improve the MALDI sensitivity of biological metabolites by over 1 order of magnitude. Herein, we demonstrate that MALDI-2 sensitivity can be further enhanced with reflecting post-ionization laser that multiplies the intersection times between laser and MALDI plume. This method, which we named MALDI-2+, typically brought over 2 times sensitivity improvement from conventional MALDI-2. Advancing in sensitivity thereby prompted us to pursue higher mass spectrometry imaging (MSI) spatial resolution. A dedicated T-shaped ion guide was designed to allow perpendicular incidence of ablation laser in reflection geometry MALDI. Although 8-10 µm pixel was used in MALDI imaging due to the limited precision of the motorized stage, the laser spot diameter could be down to 2.5 µm for potentially higher spatial resolution. In addition, this ion source enabled real-time and high-quality microscope imaging from backward of the sample plate. Beneficially, we were able to monitor the actual laser spot condition in real time as well as obtain high-resolution microscopic sample images that inherently register with MSI images. All of these benefits have been demonstrated by analyzing standard samples and imaging of cells. We believe that the enhancement in sensitivity, spatial resolution, and microscope capacity of our design could facilitate spatial omics studies.

Mycorrhizal type and tree diversity affect foliar elemental pools and stoichiometry.

Species-specific differences in nutrient acquisition strategies allow for complementary use of resources among plants in mixtures, which may be further shaped by mycorrhizal associations. However, empirical evidence of this potential role of mycorrhizae is scarce, particularly for tree communities. We investigated the impact of tree species richness and mycorrhizal types, arbuscular mycorrhizal fungi (AM) and ectomycorrhizal fungi (EM), on above- and belowground carbon (C), nitrogen (N), and phosphorus (P) dynamics. Soil and soil microbial biomass elemental dynamics showed weak responses to tree species richness and none to mycorrhizal type. However, foliar elemental concentrations, stoichiometry, and pools were significantly affected by both treatments. Tree species richness increased foliar C and P pools but not N pools. Additive partitioning analyses showed that net biodiversity effects of foliar C, N, P pools in EM tree communities were driven by selection effects, but in mixtures of both mycorrhizal types by complementarity effects. Furthermore, increased tree species richness reduced soil nitrate availability, over 2 yr. Our results indicate that positive effects of tree diversity on aboveground nutrient storage are mediated by complementary mycorrhizal strategies and highlight the importance of using mixtures composed of tree species with different types of mycorrhizae to achieve more multifunctional afforestation.

Mycorrhizal associations modify tree diversity-productivity relationships across experimental tree plantations.

Decades of studies have demonstrated links between biodiversity and ecosystem functioning, yet the generality of the relationships and the underlying mechanisms remain unclear, especially for forest ecosystems. Using 11 tree-diversity experiments, we tested tree species richness-community productivity relationships and the role of arbuscular (AM) or ectomycorrhizal (ECM) fungal-associated tree species in these relationships. Tree species richness had a positive effect on community productivity across experiments, modified by the diversity of tree mycorrhizal associations. In communities with both AM and ECM trees, species richness showed positive effects on community productivity, which could have resulted from complementarity between AM and ECM trees. Moreover, both AM and ECM trees were more productive in mixed communities with both AM and ECM trees than in communities assembled by their own mycorrhizal type of trees. In communities containing only ECM trees, species richness had a significant positive effect on productivity, whereas species richness did not show any significant effects on productivity in communities containing only AM trees. Our study provides novel explanations for variations in diversity-productivity relationships by suggesting that tree-mycorrhiza interactions can shape productivity in mixed-species forest ecosystems.

Plant diversity and community age stabilize ecosystem multifunctionality.

It is well known that biodiversity positively affects ecosystem functioning, leading to enhanced ecosystem stability. However, this knowledge is mainly based on analyses using single ecosystem functions, while studies focusing on the stability of ecosystem multifunctionality (EMF) are rare. Taking advantage of a long-term grassland biodiversity experiment, we studied the effect of plant diversity (1-60 species) on EMF over 5 years, its temporal stability, as well as multifunctional resistance and resilience to a 2-year drought event. Using split-plot treatments, we further tested whether a shared history of plants and soil influences the studied relationships. We calculated EMF based on functions related to plants and higher-trophic levels. Plant diversity enhanced EMF in all studied years, and this effect strengthened over the study period. Moreover, plant diversity increased the temporal stability of EMF and fostered resistance to reoccurring drought events. Old plant communities with shared plant and soil history showed a stronger plant diversity-multifunctionality relationship and higher temporal stability of EMF than younger communities without shared histories. Our results highlight the importance of old and biodiverse plant communities for EMF and its stability to extreme climate events in a world increasingly threatened by global change.

Convergence in simulating global soil organic carbon by structurally different models after data assimilation.

Current biogeochemical models produce carbon-climate feedback projections with large uncertainties, often attributed to their structural differences when simulating soil organic carbon (SOC) dynamics worldwide. However, choices of model parameter values that quantify the strength and represent properties of different soil carbon cycle processes could also contribute to model simulation uncertainties. Here, we demonstrate the critical role of using common observational data in reducing model uncertainty in estimates of global SOC storage. Two structurally different models featuring distinctive carbon pools, decomposition kinetics, and carbon transfer pathways simulate opposite global SOC distributions with their customary parameter values yet converge to similar results after being informed by the same global SOC database using a data assimilation approach. The converged spatial SOC simulations result from similar simulations in key model components such as carbon transfer efficiency, baseline decomposition rate, and environmental effects on carbon fluxes by these two models after data assimilation. Moreover, data assimilation results suggest equally effective simulations of SOC using models following either first-order or Michaelis-Menten kinetics at the global scale. Nevertheless, a wider range of data with high-quality control and assurance are needed to further constrain SOC dynamics simulations and reduce unconstrained parameters. New sets of data, such as microbial genomics-function relationships, may also suggest novel structures to account for in future model development. Overall, our results highlight the importance of observational data in informing model development and constraining model predictions.

Pervasive soil phosphorus losses in terrestrial ecosystems in China.

Future phosphorus (P) shortages could seriously affect terrestrial productivity and food security. We investigated the changes in topsoil available P (AP) and total P (TP) in China's forests, grasslands, paddy fields, and upland croplands during the 1980s-2010s based on substantial repeated soil P measurements (63,220 samples in the 1980s, 2000s, and 2010s) and machine learning techniques. Between the 1980s and 2010s, total soil AP stock increased with a small but significant rate of 0.13 kg P ha-1 year-1 , but total soil TP stock declined substantially (4.5 kg P ha-1 year-1 ) in the four ecosystems. We quantified the P budgets of soil-plant systems by harmonizing P fluxes from various sources for this period. Matching trends of soil contents over the decades with P budgets and fluxes, we found that the P-surplus in cultivated soils (especially in upland croplands) might be overestimated due to the great soil TP pool compared to fertilization and the substantial soil P losses through plant uptake and water erosion that offset the P additions. Our findings of P-deficit in China raise the alarm on the sustainability of future biomass production (especially in forests), highlight the urgency of P recycling in croplands, and emphasize the critical role of country-level basic data in guiding sound policies to tackle the global P crises.

Development and validation of a rapid five-minute nucleic acid extraction method for respiratory viruses.

BACKGROUND: The rapid transmission and high pathogenicity of respiratory viruses significantly impact the health of both children and adults. Extracting and detecting their nucleic acid is crucial for disease prevention and treatment strategies. However, current extraction methods are laborious and time-consuming and show significant variations in nucleic acid content and purity among different kits, affecting detection sensitivity and efficiency. Our aim is to develop a novel method that reduces extraction time, simplifies operational steps, and ensures high-quality acquisition of respiratory viral nucleic acid. METHODS: We extracted respiratory syncytial virus (RSV) nucleic acid using reagents with different components and analyzed cycle threshold (Ct) values via quantitative real-time polymerase chain reaction (qRT-PCR) to optimize and validate the novel lysis and washing solution. The performance of this method was compared against magnetic bead, spin column, and precipitation methods for extracting nucleic acid from various respiratory viruses. The clinical utility of this method was confirmed by comparing it to the standard magnetic bead method for extracting clinical specimens of influenza A virus (IAV). RESULTS: The solution, composed of equal parts glycerin and ethanol (50% each), offers an innovative washing approach that achieved comparable efficacy to conventional methods in a single abbreviated cycle. When combined with our A Plus lysis solution, our novel five-minute nucleic acid extraction (FME) method for respiratory viruses yielded superior RNA concentrations and purity compared to traditional methods. FME, when used with a universal automatic nucleic acid extractor, demonstrated similar efficiency as various conventional methods in analyzing diverse concentrations of respiratory viruses. In detecting respiratory specimens from 525 patients suspected of IAV infection, the FME method showed an equivalent detection rate to the standard magnetic bead method, with a total coincidence rate of 95.43% and a kappa statistic of 0.901 (P < 0.001). CONCLUSIONS: The FME developed in this study enables the rapid and efficient extraction of nucleic acid from respiratory samples, laying a crucial foundation for the implementation of expedited molecular diagnosis.

P(NMe2)3-Mediated Regioselective N-Alkylation of 2-Pyridones via Direct Deoxygenation of α-Keto Esters.

A practical and regioselective direct N-alkylation of 2-pyridones is enabled by use of α-keto esters in the P(NMe2)3-mediated deoxygenation process. The reaction proceeds under mild conditions to produce N-alkylated 2-pyridones with high selectivity and generality, and the protocol is shown to be applicable for the scale-up synthesis, which makes it promising for practical applications.

Efficient Synthesis of Cyanohydrin Esters: P(NMe2)3 Mediated Direct Deoxygenation of Acyl Cyanides with Carboxylic Acids.

An efficient synthesis of cyanohydrin esters via a P(NMe2)3 mediated direct deoxygenation process has been exploited, circumventing the release or transformation of the CN─ anion during the reaction. This approach possesses a broad scope and acts as a powerful supplement for the construction of diverse cyanohydrin esters. It offers advantages such as mild conditions, straightforward operations, and excellent scalability, affirming the feasibility and versatility of this approach and highlighting its potential in practical synthesis.

Climate-dependent plant responses to earthworms in two land-use types.

Plant nutrient uptake and productivity are driven by a multitude of factors that have been modified by human activities, like climate change and the activity of decomposers. However, interactive effects of climate change and key decomposer groups like earthworms have rarely been studied. In a field microcosm experiment, we investigated the effects of a mean future climate scenario with warming (+ 0.50 °C to + 0.62 °C) and altered precipitation (+ 10% in spring and autumn, - 20% in summer) and earthworms (anecic-two Lumbricus terrestris, endogeic-four Allolobophora chlorotica and both together within 10 cm diameter tubes) on plant biomass and stoichiometry in two land-use types (intensively used meadow and conventional farming). We found little evidence for earthworm effects on aboveground biomass. However, future climate increased above- (+40.9%) and belowground biomass (+44.7%) of grass communities, which was mainly driven by production of the dominant Festulolium species during non-summer drought periods, but decreased the aboveground biomass (- 36.9%) of winter wheat. Projected climate change and earthworms interactively affected the N content and C:N ratio of grasses. Earthworms enhanced the N content (+1.2%) thereby decreasing the C:N ratio (- 4.1%) in grasses, but only under ambient climate conditions. The future climate treatment generally decreased the N content of grasses (aboveground: - 1.1%, belowground: - 0.15%) and winter wheat (- 0.14%), resulting in an increase in C:N ratio of grasses (aboveground: + 4.2%, belowground: +6.3%) and wheat (+5.9%). Our results suggest that climate change diminishes the positive effects of earthworms on plant nutrient uptakes due to soil water deficit, especially during summer drought.

MS2/GmAMS1 encodes a bHLH transcription factor important for tapetum degeneration in soybean.

KEY MESSAGE: GmAMS1 is the only functional AMS and works with GmTDF1-1 and GmMS3 to orchestrate the tapetum degeneration in soybean. Heterosis could significantly increase the production of major crops as well as soybean [Glycine max (L.) Merr.]. Stable male-sterile/female-fertile mutants including ms2 are useful resources to apply in soybean hybrid production. Here, we identified the detailed mutated sites of two classic mutants ms2 (Eldorado) and ms2 (Ames) in MS2/GmAMS1 via the high-throughput sequencing method. Subsequently, we verified that GmAMS1, a bHLH transcription factor, is the only functional AMS member in soybean through the complementary experiment in Arabidopsis; and elucidated the dysfunction of its homolog GmAMS2 is caused by the premature stop codon in the gene's coding sequence. Further qRT-PCR analysis and protein-protein interaction assays indicated GmAMS1 is required for expressing downstream members in the putative DYT1-TDF1-AMS-MYB80/MYB103/MS188-MS1 cascade module, and might regulate the upstream members in a feedback mechanism. GmAMS1 could interact with GmTDF1-1 and GmMS3 via different region, which contributes to dissect the mechanism in the tapetum degeneration process. Additionally, as a core member in the conserved cascade module controlling the tapetum development and degeneration, AMS is conservatively present in all land plant lineages, implying that AMS-mediated signaling pathway has been established before land plants diverged, which provides further insight into the tapetal evolution.