Soil microbes are of great significance to driving the biogeochemical cycles and are affected by multiple factors, including urbanization. However, the response of soil microbes to urbanization remains unclear. Therefore, we designed an urban-to-rural gradient experiment to investigate the response of soil microbial composition and diversity to urbanization. Here, we used a high-throughput sequencing method to analyze the biotic and abiotic effects on soil microbial composition and diversity along the urban-to-rural gradient. Our results showed that soil bacterial diversity was the highest in urban areas, followed by suburban areas, and was the lowest in exurbs; however, fungal diversity did not vary significantly among the three areas. Plant traits, i.e., tree richness, shrub richness, the number of tree stems, diameter at breast height of trees, and soil properties, i.e., pH, soil organic carbon, soil exchangeable calcium and magnesium, and soil water content, were only significantly influenced bacterial diversity, but not fungal diversity. The effect of trees and shrubs was higher than that of herbs on microbial composition. Soil organic carbon, pH, soil available nitrogen, soil exchangeable calcium, and magnesium were the major soil factors influencing the soil bacterial and fungal composition. Soil properties had a greater influence on bacterial than on fungal composition at genus level, while plant traits contributed more to fungal than to bacterial composition at genus level. Our study suggests that the urban-to-rural gradient affect the composition and diversity of bacterial community as well as the fungal composition, but not the fungal diversity.

The wild population of Madhuca pasquieri (Dubard) H. J. Lam is currently dwindling; its understory seedlings are rare, and there is a lack of molecular studies, which impedes the conservation of this species. This study exploited second-generation sequencing and widely targeted metabolomics analysis to uncover the dynamic changes in differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) in five post-germination stages of M. pasquieri whole organism. Notably, the weighted gene co-expression network analysis (WGCNA), transcriptome, and metabolome association analyses all indicated significant enrichment of the flavonoid biosynthesis pathway in stage 4 (two-leaf), and an upregulation of the genes encoding flavonol biosynthesis in this stage. In stage 5 (nine-leaf), the flavonols were significantly accumulated, indicating that the changes in metabolites were driven at the transcript level. According to the significant changes in gene expression encoding auxin transport carriers and their correlation with flavonols during stage 5, the flavonols were speculated to have a direct inhibitory effect on the expression of PIN4 encoding gene, which may inhibit the process of polar auxin transport. The results provided important insights into the molecular network relationships between the transcription and metabolism of this rare and endangered species during the post-germination stages and explained the reasons for the slow growth of its seedlings at the molecular level.

Madhuca pasquieri (Dubard) Lam. is a tree on the International Union for Conservation of Nature Red List and a national key protected wild plant (II) of China, known for its seed oil and timber. However, lacking of genomic and transcriptome data for this species hampers study of its reproduction, utilization, and conservation. Here, single-molecule long-read sequencing (PacBio) and next-generation sequencing (Illumina) were combined to obtain the transcriptome from five developmental stages of M. pasquieri. Overall, 25,339 transcript isoforms were detected by PacBio, including 24,492 coding sequences (CDSs), 9440 simple sequence repeats (SSRs), 149 long non-coding RNAs (lncRNAs), and 182 alternative splicing (AS) events, a majority was retained intron (RI). A further 1058 transcripts were identified as transcriptional factors (TFs) from 51 TF families. PacBio recovered more full-length transcript isoforms with a longer length, and a higher expression level, whereas larger number of transcripts (124,405) was captured in de novo from Illumina. Using Nr, Swissprot, KOG, and KEGG databases, 24,405 transcripts (96.31%) were annotated by PacBio. Functional annotation revealed a role for the auxin, abscisic acid, gibberellin, and cytokinine metabolic pathways in seed germination and post-germination. These findings support further studies on seed germination mechanism and genome of M. pasquieri, and better protection of this endangered species.

Madhuca longifolia (M. longifolia), a tropical tree valued for its medicinal, nutritional, and industrial applications, exhibits severe sensitivity to low-temperature stress in subtropical regions, particularly during seedling establishment. To address this challenge, this study systematically identified 109 NAC genes in M. longifolia and characterized their functional roles in cold adaptation via multi-omics analyses. All NAC proteins were hydrophilic. Key members (e.g., MlNAC026, MlNAC077, MlNAC076) were localized in the nucleus. Phylogenetic analysis grouped them with ANAC072 (RD26), a homolog involved in leaf senescence and ABA-regulated cold stress responses. The NAC family expanded primarily through segmental duplication. And low Ka/Ks ratios (<1) indicated purifying selection. Promoter analysis highlighted the prevalence of dehydration-responsive DRE and LTR cis-acting elements. Transcriptomic profiling under cold stress identified five continuous differentially expressed genes (MlNAC026, MlNAC040, MlNAC059, MlNAC077, and MlNAC078) linked to regulatory functions. Homology modeling predicted 3D structures of cold-responsive NAC proteins, and STRING network analysis indicated independent regulatory mechanisms due to the absence of prominent interaction nodes. These findings advance our understanding of NAC-mediated cold tolerance and offer genetic targets to enhance M. longifolia resilience in subtropical climates.

Background.: Ovary culture is a useful technique used to generate double haploid (DH) cucumber (Cucumis sativusL.) plants. However, cucumber ovary culture have a low rate of embryo induction and plant regeneration. Moreover, the cucumber embryogenesis mechanism remains unclear. In this study, we explored the molecular basis of cucumber embryogenesis in order to establish a foundation for a more efficient ovary culture method. Using transcriptome sequencing, we also investigated the differential expression of genes during the embryogenesis process.Methods.: Cytological and morphological observations have divided cucumber ovary culture into three stages: early embryo development (T0), embryo morphogenesis (T1, T2, T3 and T4), and shoot formation (T5). We selected six key time points for transcriptome sequencing and analysis: T0 (the ovules were cultured for 0 d), T1 (the ovules were cultured for 2 d), T2 (the embryos were cultured for 10 d), T3 (the embryos were cultured for 20 d), T4 (the embryos were cultured for 30 d), and T5 (the shoots after 60 d culture).Results.: We used cytology and morphology to observe the characteristics of the cucumber’s developmental transformation during embryogenesis and plant regeneration. The differentially expressed genes(DEGs) at developmental transition points were analyzed using transcriptome sequencing. In the early embryogenesis stage, the cells expanded, which was the signal for gametophytes to switch to the sporophyte development pathway. RNA-seq revealed that when compared to the fresh unpollinated ovaries, there were 3,468 up-regulated genes in the embryos, including hormone signal transduction genes, hormone response genes, and stress-induced genes. The reported embryogenesis-related genesBBM, HSP90andAGLwere also actively expressed during this stage. In the embryo morphogenesis stage (from cell division to cotyledon-embryo formation), 480 genes that functioned in protein complex binding, microtubule binding, tetrapyrrole binding, tubulin binding and other microtubule activities were continuously up-regulated during the T1, T2, T3 and T4 time points. This indicated that the cytoskeleton structure was continuously being built and maintained by the action of microtubule-binding proteins and enzyme modification. In the shoot formation stage, 1,383 genes were up-regulated that were mainly enriched in phenylpropanoid biosynthesis, plant hormone signal transduction, phenylalanine metabolism, and starch and sucrose metabolism. These up-regualted genes included six transcription factors that contained a B3 domain, nine genes in the AP2/ERF family, and two genes encodingWUShomologous domain proteins.Conclusions.: Evaluation of molecular gynogenesis events may contribute to a better understanding of the molecular mechanism of cucumber ovarian culture.

Warming effects on agricultural and forest ecosystems have been well documented at broad spatiotemporal scales but less so at stand and landscape scales. To detect the changes in soil organic carbon (SOC) and carbon:nitogen:phosphorus (C:N:P) stoichiometry in response to a short-range warming gradient, we defined an inverse elevation-dependent warming gradient and developed a novel index of warming based on a common environmental lapse rate. We associated the warming gradient and warming index with the changes in SOC and C:N:P stoichiometry and tested the independence of warming effects using partial correlation analysis. SOC content and C:N:P stoichiometric ratios significantly decreased with warming, and the effect of warming on C:N:P stoichiometric ratios were stronger than on SOC content. The relationships of SOC content and C:N:P stoichiometric ratios with warming did not change after controlling for two other energy-related variables, i.e., transmitted total radiation and potential direct incident radiation. However, the strength in the relationships of C:N:P stoichiometric ratios with vegetation-related variables significantly decreased after the warming index was controlled for. As indicated by the random forest regression model, the warming index was the most important variable for predicting SOC variability and the second most important for predicting total N variability, while vegetation-related variables were the most important for predicting C:N:P stoichiometric ratios. Our results showed that warming was responsible for the decrease in SOC content and C:N:P stoichiometric ratios and the warming index was the most important variable for predicting SOC variability. Although the most important variables for C:N:P stoichiometric ratios were related to vegetation, the relationships between C:N:P stoichiometric ratios and vegetation-related variables were significantly affected by warming. These findings demonstrate that warming is the major driver of SOC variability and the decrease in SOC content, as well as of C:N:P stoichiometry, even along a short-range warming gradient.