Continuous monocropping and inappropriate fertilization have contributed to nutrient depletion and soil degradation, limiting peanut productivity in subtropical red soil agroecosystems. Although diversified cropping may help alleviate these constraints, the reasons why it improves peanut productivity remain unclear. In this study, we conducted a long-term field experiment in Jiangxi, China, to compare four cropping systems, assess soil nutrients, peanut productivity, and bacterial communities, and further evaluate the role of key taxa through inoculation assays and structural equation modeling. Results showed that diversified cropping improved peanut growth and yield, with the green manure integrated system performing best overall. Diversified cropping also increased soil organic carbon, total nitrogen, and available phosphorus, while reshaping bacterial communities. Several taxa, including Bradyrhizobium, Mycobacterium, Dormibacter, and Ardenticatena, were positively associated with soil nutrients. Inoculation assays further showed that a synthetic consortium assembled from representative strains affiliated with key taxa produced stronger effects on plant growth than a single-strain inoculation. Structural equation modeling identified key taxa as the factor most strongly associated with crop productivity. These findings suggest that higher peanut productivity under diversified cropping was closely associated with concurrent improvements in soil fertility and the enrichment of key taxa.

(1) Background: Improving nitrogen use efficiency in peanuts is essential for achieving a high yield with reduced nitrogen fertilizer input. This study investigates the role of the fungal endophyte Phomopsis liquidambaris in regulating nitrogen utilization throughout the entire growth cycle of peanuts. (2) Methods: Field pot experiments and a two-year plot trial were conducted. The effects of Ph. liquidambaris colonization on the rhizosphere microbial community, soil nitrogen forms, and peanut physiology were analyzed. (3) Results: Colonization by Ph. liquidambaris significantly suppressed the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the rhizosphere at the seedling stage. This led to a transient decrease in nitrate and an increase in ammonium availability, which enhanced nodulation-related physiological responses. Concurrently, the peanut-specific rhizobium Bradyrhizobium sp. was enriched in the rhizosphere, and the root exudates induced by the fungus further stimulated nodulation activity. These early-stage effects promoted the establishment of peanut-Bradyrhizobium symbiosis. During the mid-to-late growth stages, the fungus positively reshaped the composition of key functional microbial groups (including diazotrophs, AOA, and AOB), thereby increasing rhizosphere nitrogen availability. (4) Conclusions: Under low nitrogen fertilization, inoculation with Ph. liquidambaris maintained yield stability in long-term monocropped peanuts by enhancing early nodulation and late-stage rhizosphere nitrogen availability. This study provides a promising microbe-based strategy to support sustainable legume production with reduced nitrogen fertilizer application.

Plants actively reshape the soil environment through their roots and associated microbes, creating lasting changes known as soil legacies that influence future plant generations via plant-soil feedbacks. While biotic factors such as pathogens and mutualists have received much attention, the chemical legacies, including water-soluble and volatile organic compounds, remain underexplored. These metabolites, produced by plants and soil microbes, modulate microbial communities, nutrient dynamics, and plant defenses, driving positive or negative feedbacks. This opinion article synthesizes recent evidence on soil chemical diversity, their role in legacy formation and persistence, while highlighting analytical challenges and promising applications in agriculture and ecology.

The pig (Sus scrofa) is an important model for evolutionary, comparative, and translational research; however, current functional genomic resources in pigs remain largely limited to one-dimensional genomic annotation and are therefore insufficient for systematically resolving regulatory region-gene relationships, particularly distal ones. Here, we present the Pig Matrix database, a comprehensive 3D regulatory genomics database for pigs, available at https://pigmatrix.kiz.ac.cn/. Built on a standardized experimental framework, Pig Matrix integrates matched multiomics datasets across tissues, developmental stages, and porcine cell lines, including genomic, transcriptomic, epigenomic, and 3D genome information. In total, it contains 16 library types across 7 omics layers and 7,959 processed files from 1,170 libraries. By integrating epigenomic and 3D genome information, Pig Matrix links cis-regulatory elements (CREs) to putative proximal and distal target genes, thereby facilitating interpretation of noncoding variants and genomic signals. This database provides modules for genes, candidate CREs, 3D genome architecture, genome browsing, and single-cell transcriptomics, together with dedicated evolution and comparative resources and user-oriented Genome Annotation and LiftOver tools. A representative use case illustrates how 3D regulatory annotation extends interpretation beyond linear annotation alone, recovering additional candidate genes in domestication-related signals, notably including the classical domestication gene KIT. Pig Matrix also incorporates xenotransplantation-related resources and may support benchmarking of AI models for regulatory genomics. Together, Pig Matrix provides an integrated platform for regulatory interpretation, evolutionary analysis, and comparative genomics in pigs.

Crop rotation serves as a valuable agronomic practice for addressing succession barriers in crops, particularly in tobacco growing. The effect of different previous crops on the microbiology of soils planted with tobacco is an area that deserves further study.This study investigated the chemical properties, microbial community composition, and functional genes related to nutrient cycling in tobacco-planted soils with no preceding crop (CK), garlic (T1), or faba bean (T2) as preceding crops. The results indicated that the T1 treatment significantly decreased the contents of soil organic matter (SOM, 11.32%), total phosphorus (TP, 29.41%), total potassium (TK, 3.33%), and available potassium (AK, 46.88%), whereas the T2 treatment notably increased the content of hydrolyzable nitrogen (HN, 34.88%). Furthermore, the T2 treatment significantly enhanced the diversity of soil bacteria and fungi, particularly the bacterial Shannon index (1.49%) and fungal Chao1 (24.11%) and Shannon (7.73%) indices. In terms of microbial composition, compared to the CK, the T2 treatment enriched the relative abundance of beneficial bacterial genera (e.g., Sphingomonas, Methyloceanibacter, Rhizophagus) and reduced the relative abundance of pathogenic fungi (e.g., Fusarium). Additionally, T2 treatment increased the abundance of functional genes associated with nitrogen, phosphorus, and potassium, thereby promoting the cycling of soil nutrients. Overall, faba bean as a preceding crop was more beneficial for subsequent tobacco cultivation than fallow periods or garlic.

Exploring the impacts of anthropogenic processes on the organic matter (OM) input and phosphorus (P) burial characteristics is essential for describing the carbon (C) cycle and its environmental effects on aquatic ecosystems from multiple perspectives. In this study, the centennial sedimentary P, C, and nitrogen (N) characteristics and terrestrial OM input changes in the upper Yangtze River were reconstructed by 210Pb-dated and positive matrix factorization (PMF) methods, and the key factors were identified. The P accumulation and stock averaged at 2.23 ± 1.08 g P m−2 yr−1 and 0.01–0.07 Mg P ha−1 from 1855 to 2019. Changes in corresponding loads of total organic C (TOC) and N (TN) separately ranged between 0.58 and 1.81 Mg C ha−1 and 0.07–0.29 Mg N ha−1 over the past century. The total sequestration was 4.20 × 105 t of C, 5.51 × 104 t of N, and 1.22 × 104 t of P, respectively, accounting for 33

Gold nanoparticle-based surface-enhanced Raman scattering (SERS) substrates exhibit better chemical stability compared with silver ones, making them suitable for characterizing reaction intermediates in the presence of strong oxidants such as H2O2. However, conventional wet-chemistry-synthesized gold nanoparticles often show strong background signals from organic stabilizers, which could overlap and disturb the SERS signals of reaction intermediates and products. In this work, a low-background corrosion-resistant gold-based SERS substrate was prepared via a facile one-pot method using anionic ligands as stabilizers, achieving the rapid characterization of the reaction process in the presence of H2O2. Anionic ligands (such as I-, SCN-, Br- and S2O32-) were used instead of commonly used surfactants as stabilizers to obtain monodisperse colloidal gold nanoparticles. The obtained gold nanoparticles displayed an ultralow SERS background signal, allowing for precise characterization of trace reaction intermediates. Moreover, the low-background gold substrate exhibited much better corrosion resistance (10 mM H2O2) compared with the low-background silver substrate, enabling sensitive and stable detection of target analytes even under harsh oxidative conditions. Finally, we successfully employed this SERS substrate for the direct detection and monitoring of degradation intermediates of sulfamerazine (SMR) through a UV-H2O2-induced degradation reaction without using any sample treatment. Combination of SERS spectroscopic data with DFT calculations provided a robust framework for elucidating the photodegradation mechanism. Results indicated that the SERS substrate has a robust and broad application prospect in the precise characterization of various reactions under harsh oxidative conditions. Moreover, this work may provide guidance for the synthesis of other colloidal nanoparticles using anionic ligands as universal stabilizers.

Early diagenetic nodules with low permeable and weather-resistant structures are considered to be favorable for biosignature preservation. Numerous nodular structures forming in neutral-to-alkaline and saline diagenetic fluids were previously identified at Gale Crater on Mars, yet their astrobiological significance remains poorly understood. In the Mars-like western Qaidam Basin, China, there are a multitude of carbonate nodules which can be analogous to those found at Gale Crater on Mars in terms of their formation backgrounds and post-depositional processes. In this study, we combine microscopic, spectroscopic, and geochemical methods to characterize the biosignature preservation of the Qaidam nodules. Carbonaceous materials, including an organic annulus inferred to be a fossil spore or algal filament microfossil, are observed in the Qaidam nodules. The total organic carbon contents of the Qaidam nodules are slightly higher than those of the surrounding fluvio-lacustrine deposits, suggesting that early diagenesis of the Qaidam nodules might facilitate the rapid entombment of biomass within magnesium carbonate or aragonite matrixes before complete degradation. The carbonate matrix showing alternating micritic and sparry layers as well as enrichment of 13C could have a physicochemical origin though the possibilities of biomineralization and organomineralization cannot be entirely ruled out. The I-1350/1,600 distribution of carbonaceous materials implies the existence of carbon precursors of various subcellular components or coexisting organisms in pore waters. Organic carbon isotopes indicate the carbon fixation pathways such as the Calvin cycle or the Wood-Ljungdahl pathway utilized by organisms in pore waters. The findings of this study shed light into the taphonomy and detection of biosignatures in terrestrial playa nodules, with potential applications for biosignature exploration on Mars.

Light transmittance is a closely related and inseparable key environmental limiting factor shaping the presence and distribution of macrophytes in aquatic environments. However, little is known about the responses of the morphology and photosynthetic capacity of macrophytes to different light conditions. Here, we conducted a short-term mesocosm experiment with Vallisneria denseserrulata as subjects, exposing them to the light transmittance of 10%, 20%, 30%, 60%, and 100%. Plant growth indicators and photosynthesis-related indicators were monitored during the 28-day experiment. The results showed that V. denseserrulata responded rapidly to changes in the light environment. Under high light transmittance conditions, V. denseserrulata rapidly expanded to obtain more resources. In low light transmittance conditions, V. denseserrulata mainly maintained its growth, rarely forming ramet, and grew longer leaves and larger leaf areas to improve light acquisition ability. There were 158, 47, 192, and 554 differentially expressed genes (DEGs) were identified in the pairwise comparison of 10%VS100%, 20%VS100%, 30%VS100%, and 60%VS100%, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that the DEGs were mainly involved in “pigment biosynthetic” and “photosynthesis”. Furthermore, genes involved in the photosynthesis pathway obtained different expression levels in V. denseserrulata between different treatments. The lower the light transmittance, the higher the expression of genes involved in photosynthesis in V. denseserrulata. Therefore, macrophytes have strong plasticity to maintain growth in stressful environments. Synthesis: V. denseserrulata exhibits strong plasticity in morphology, cytochrome production, and photosynthetic pathway regulation to maintain its growth in low-light environments. However, our results also indicated that the degraded underwater light climate surely results in a decreased macrophyte community. These results help elucidate the degradation process of submerged macrophytes in turbid lakes and guide the restoration of aquatic plants in eutrophic lakes.

Biological nitrogen fixation by free-living bacteria and rhizobial symbiosis with legumes plays a key role in sustainable crop production. Here, we study how different crop combinations influence the interaction between peanut plants and their rhizosphere microbiota via metabolite deposition and functional responses of free-living and symbiotic nitrogen-fixing bacteria. Based on a long-term (8 year) diversified cropping field experiment, we find that peanut co-cultured with maize and oilseed rape lead to specific changes in peanut rhizosphere metabolite profiles and bacterial functions and nodulation. Flavonoids and coumarins accumulate due to the activation of phenylpropanoid biosynthesis pathways in peanuts. These changes enhance the growth and nitrogen fixation activity of free-living bacterial isolates, and root nodulation by symbiotic Bradyrhizobium isolates. Peanut plant root metabolites interact with Bradyrhizobium isolates contributing to initiate nodulation. Our findings demonstrate that tailored intercropping could be used to improve soil nitrogen availability through changes in the rhizosphere microbiome and its functions. Sustainability in agriculture can be improved harnessing biological N2 fixation in legumes. Here, the authors combine different crops with peanut plants finding that maize and oilseed rape are the most successful combinations which have potential to enhance rhizosphere microbiota N2 fixation.

Unraveling the influence of community assembly processes on soil ecosystem functioning presents a major challenge in the field of theoretical ecology, as it has received limited attention. Here, we used a series of long-term experiments spanning over 25 years to explore the assembly processes of bacterial, fungal, protist, and nematode communities using high-throughput sequencing. We characterized the soil microbial functional potential by the abundance of microbial genes associated with carbon, nitrogen, phosphorus, and sulfur cycling using GeoChip-based functional gene profiling, and determined how the assembly processes of organism groups regulate soil microbial functional potential through community diversity and network stability. Our results indicated that balanced fertilization (NPK) treatment improved the stochastic assembly of bacterial, fungal, and protist communities compared to phosphorus-deficient fertilization (NK) treatment. However, there was a nonsignificant increase in the normalized stochasticity ratio of the nematode community in response to fertilization across sites. Our findings emphasized that soil environmental factors influenced the assembly processes of the biotic community, which regulated soil microbial functional potential through dual mechanisms. One mechanism indicated that the high phosphorus levels and low soil nutrient stoichiometry may increase the stochasticity of bacterial, fungal, and protist communities and the determinism of the nematode community under NPK treatment, ultimately enhancing soil microbial functional potential by reinforcing the network stability of the biotic community. The other mechanism indicated that the low phosphorus levels and high soil nutrient stoichiometry may increase the stochastic process of the bacterial community and the determinism of the fungal, protist, and nematode communities under NK treatment, thereby enhancing soil microbial functional potential by improving the β-diversity of the biotic community. Taken together, these results provide valuable insights into the mechanisms underlying the assembly processes of the biotic community that regulate ecosystem functioning.

IMPORTANCE:The hyperarid Dalangtan Playa in the western Qaidam Basin, northwestern China, is a unique terrestrial analog of Mars. Despite the polyextreme environments of this area, habitats below translucent rocks capable of environmental buffering could serve as refuges for microbial life. In this study, the hybrid assembly of Illumina short reads and Nanopore long reads recovered high-quality and high-continuity genomes, allowing for high-accuracy analysis and a deeper understanding of extremophiles in the sheltered soils of the Dalangtan Playa. Our findings reveal self-supporting and metabolically versatile sheltered soil communities adapted to a hyperarid and hypersaline playa, which provides implications for the search for life signals on Mars.

The authors declare no conflict of interest. The final ancestral sequences in FASTA (https://doi.org/10.57760/sciencedb.07853), the multi-genome alignment in HAL (https://doi.org/10.57760/sciencedb.07855) and the ancestral states of all Sscrofa11.1 positions validated by re-sequencing data (https://doi.org/10.57760/sciencedb.07858) are accessible at ScienceDB. Appendix S1 Appendix S2 Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Soil texture, i.e. the fractions of different sized mineral particles, is critical to root growth and an important determinant of the occurrence and distribution of soil microbiota. More recently it was shown that individual plant species and even different cultivars harbor highly distinct rhizosphere associated microbiota, but it is still an open question how soil texture and its influence on root growth feeds back on root microbial assembly.We manipulated soil texture by stepwise additions of quartz sand to an agricultural loam. We grew maize (Zea mays L.) in these soils, measured changes in root traits and sampled bulk soil and rhizosphere to apply amplicon based high-throughput sequencing. We investigated changes in root morphology of maize and the concomitant shift in prokaryote (archaea and bacteria) and protist (Cercozoa and Endomyxa) diversity, community composition and co-occurrence in the maize rhizosphere along the soil texture gradient.A linear relationship between loam fraction and root morphology and a shift in microbial diversity along the soil texture gradient, as well as a stronger selection effect of the rhizosphere in soils with a high sand fraction (and high bulk density) were found. Co-occurrence network analysis revealed high modularity in fine textured soil, demonstrating that bulk density and texture are important factors affecting the recruitment of the core rhizosphere microbiome of maize.

Duckweeds are the most promising non-food feedstock for sustainable bioenergy production. Mixotrophy is the best growth mode compared to photoautotrophy and heterotrophy for biomass and starch accumulation. This work investigated the impacts of light intensities (3,000, 6,000, 9,000, 12,000, 15,000 and 20,000 lux) and exogenous glucose concentrations (5, 10, 15, 20, 30 and 40 g/L) on the biomass and starch accumulation of mixotrophic duckweed. The results showed that increasing light intensity and the initially applied concentration of glucose enhanced both growth and starch content. However, high concentrations of glucose (15–40 g/L) provided higher biomass yield and concurrently greatly inhibited photosynthesis. Moreover, excess carbon was redirected into starch biosynthesis under high glucose. The maximum starch productivity of 655.4 g/m 2 was obtained at 40 g/L of glucose, with maximum starch contents of 72.7% of dry biomass, and biomass yields of 1024.6 g/m 2 . The optimum light intensity for starch accumulation was 20,000 lux, with a maximum starch yield of 236.2 g/m 2 . These results indicated that high organic carbon levels were a robust way for starch production of mixotrophic duckweed. This work provides optimal glucose and light conditions for mixotrophic duckweed biomass production as a sustainable feedstock for bioenergy.

• The abundance of N-cycling genes differently responded to NPK application. • Chemical NPK application greatly altered the N-cycling microbial community structure. • Soil acidification was the main driver for the variation in the N-cycling microbial community. • Manure addition was beneficial for stabilizing the N-cycling microbial community. Straw and manure are widely applied to agricultural systems, and greatly shape soil N-cycling microflora. However, we still lack a comprehensive understanding of how these organic materials structure soil N-cycling microbial communities. In this study, metagenomic analysis was performed to investigate the compositional variation in N-cycling microbial communities in a 30-year long-term experiment under five fertilization regimes: no fertilization (Control), chemical fertilization only (NPK), and NPK with wheat straw (NPK + HS), pig manure (NPK + PM), and cow manure (NPK + CM). Long-term NPK application differentially changed N-cycling gene abundance and greatly altered N-cycling microbial community structure. NPK + HS resulted in a similar pattern to NPK in terms of gene abundance and community structure. However, NPK + PM and NPK + CM significantly increased most genes and resulted in a community similar to that of the Control. Further analysis revealed that serious soil acidification caused by long-term NPK fertilization was a major factor for the variation in N-cycling microbial communities. The addition of alkaline manure, rather than wheat straw, stabilized the N-cycling microbial community structure presumably by alleviating soil acidification. These results revealed the strong impact of soil acidification on microbial N-cycling communities and illustrated the possibility of resolving nitrogen-related environmental problems by manipulating pH in acidified agricultural soils.

For achieving long-term sustainability of intensive agricultural practices, it is pivotal to understand belowground functional stability as belowground organisms play essential roles in soil biogeochemical cycling. It is commonly believed that resource availability is critical for controlling the soil biodiversity and belowground organism interactions that ultimately lead to the stabilization or collapse of terrestrial ecosystem functions, but evidence to support this belief is still limited. Here, we leveraged field experiments from the Chinese National Ecosystem Research Network (CERN) and two microcosm experiments mimicking high and low resource conditions to explore how resource availability mediates soil biodiversity and potential multi-trophic interactions to control functional trait stability. We found that agricultural practice-induced higher resource availability increased potential cross-trophic interactions over 316

Managing above-ground plant carbon inputs can pave the way toward carbon neutrality and mitigating climate change. Chemical complexity of plant residues largely controls carbon sequestration. There exist conflicting opinions on whether residue chemistry diverges or converges after long-term decomposition. Moreover, whether and how microbial communities regulate residue chemistry remains unclear. This study investigated the decomposition processes and residue composition dynamics of maize straw and wheat straw and related microbiomes over a period of 9 years in three climate zones. Residue chemistry exhibited a divergent-convergent trajectory during decomposition, that is, the residue composition diverged during the 0.5–3 year period under the combined effect of straw type and climate and then converged to an array of common compounds during the 3–9 year period. Chemical divergence during the first 2–3 years was primarily driven by the changes in extracellular enzyme activity influenced by keystone taxa-guided bacterial networks, and the keystone taxa belonged to Alphaproteobacteria, particularly Rhizobiales. After 9 years, microbial assimilation became dominant, leading to chemical convergence, and fungi, particularly Chaetomium, were the main contributors to microbial assimilation. Overall, this study demonstrated that keystone taxa regulate the divergent-convergent trajectory in residue chemistry.

Traditional intercropping of tall and short crops often maintain productivity at the expense of the fitness of the short crop due to planting orientation. There is a need to understand how light interception as influenced by row orientation, affects the vertical allocation of photosynthesized carbon, and how this impacts the rhizosphere microbiota of short crops. This understanding would allow for the optimization of aboveground design to utilize the belowground microbiota for plant and soil health in diversified cropping systems. We manipulated the row orientation (east-west vs. north-south) of peanut and maize in a field and conducted simulated pot experiment where peanut plants were shaded. By using 13C tracer approach and DNA stable isotope probing (DNA-SIP) method, we quantified C allocation by peanuts in its rhizosphere including the rhizosphere microorganisms. Moreover, by combining high-throughput sequencing and bacterial cultivation, we evaluated photosynthesized carbon driven the change of rhizosphere microbial composition and its interaction for fungal pathogen resistance. Field intercropping in the north-south orientation increased peanut photosynthetically active radiation to over two times compared to the east-west orientation. The higher light interception increased the relative abundance of photosynthesized carbon which selectively enriched the rhizosphere biomarker Burkholderia to effectively suppressed the pathogenic fungus Alternaria alstroemeriae. North-south row orientation of peanut and maize intercropping can enhance the allocation of photosynthesized carbon in peanut rhizosphere by changing the light interception. The more photosynthesized carbon triggers the reshape of rhizosphere microbiota and induce beneficial Burkholderia to antagonize peanut pathogen to optimize peanut health.

SPX genes play important roles in the coordinated utilization of nitrogen (N) and phosphorus (P) in plants. However, a genome-wide analysis of the SPX family is still lacking. In this study, the gene structure and phylogenetic relationship of 160 SPX genes were systematically analyzed at the genome-wide level. Results revealed that SPX genes were highly conserved in plants. All SPX genes contained the conserved SPX domain containing motifs 2, 3, 4, and 8. The 160 SPX genes were divided into five clades and the SPX genes within the same clade shared a similar motif composition. P1BS cis–elements showed a high frequency in the promoter region of SPXs, indicating that SPX genes could interact with the P signal center regulatory gene Phosphate Starvation Response1 (PHR1) in response to low P stress. Other cis–elements were also involved in plant development and biotic/abiotic stress, suggesting the functional diversity of SPXs. Further studies were conducted on the interaction network of three SpSPXs, revealing that these genes could interact with important components of the P signaling network. The expression profiles showed that SpSPXs responded sensitively to N and P deficiency stresses, thus playing a key regulatory function in P and N metabolism. Furthermore, the expression of SpSPXs under P and N deficiency stresses could be affected by environmental factors such as ABA treatment, osmotic, and LT stresses. Our study suggested that SpSPXs could be good candidates for enhancing the uptake ability of Spirodela polyrhiza for P nutrients in wastewater. These findings could broaden the understanding of the evolution and biological function of the SPX family and offer a foundation to further investigate this family in plants.