Urbanization-driven forest soil greenhouse gas emissions: Insights from the role of soil bacteria in carbon and nitrogen cycling using a metagenomic approach.

Increasing population densities and urban sprawl have induced greenhouse gas (GHG) emissions from the soil, and the soil microbiota of urban forests play a critical role in the production and consumption of GHGs, supporting green development. However, the function and potential mechanism of soil bacteria in GHG emissions from forests during urbanization processes need to be better understood. Here, we measured the fluxes of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) in Cinnamomum camphora forest soils along an urbanization gradient. 16S amplicon and metagenomic sequencing approaches were employed to examine the structure and potential functions of the soil bacterial community involved in carbon (C) and nitrogen (N) cycling. In this study, the CH4 and CO2 emissions from urban forest soils (sites U and G) were significantly greater than those from suburban soils (sites S and M). The N2O emissions in the urban center (site U) were 24.0 % (G), 13.8 % (S), and 13.5 % (M) greater than those at the other three sites. These results were related to the increasing bacterial alpha diversity, interactions, and C and N cycling gene abundances (especially those involved in denitrification) in urban forest soils. Additionally, the soil pH and metal contents (K, Ca, Mg) affected key bacterial populations (such as Methylomirabilota, Acidobacteriota, and Proteobacteria) and indicators (napA, nosZ, nrfA, nifH) involved in reducing N2O emissions. The soil heavy metal contents (Fe, Cr, Pb) were the main contributors to CH4 emissions, possibly by affecting methanogens (Desulfobacterota) and methanotrophic bacteria (Proteobacteria, Actinobacteriota, and Patescibacteria). Our study provides new insights into the benefits of conservation-minded urban planning and close-to-nature urban forest management and construction, which are conducive to mitigating GHG emissions and supporting urban sustainable development by mediating the core bacterial population.

De novo assembly of Iron-Heart Cunninghamia lanceolata transcriptome and EST-SSR marker development for genetic diversity analysis.

Iron-Heart Cunninghamia lanceolata, a wild relative of Chinese fir with valuable genetic and breeding traits, has been limited in genetic studies due to a lack of genomic resources and markers. In this study, we conducted transcriptome sequencing of Iron-Heart C. lanceolata leaves using Illumina NovaSeq 6000 and performed assembly and analysis. We obtained 45,326,576 clean reads and 115,501 unigenes. Comparative analysis in five functional databases resulted in successful annotation of 26,278 unigenes, with 6,693 unigenes annotated in all databases (5.79% of the total). UniProt and Pfam databases provided annotations for 22,673 and 18,315 unigenes, respectively. Gene Ontology analysis categorized 23,962 unigenes into three categories. KEGG database alignment annotated 10,195 unigenes, classifying them into five categories: metabolism, genetic information, biological systems, cellular processes, and environmental information processing. From the unigenes, we identified 5,645 SSRs, with dinucleotides repeats being the most common (41.47%). We observed variations in repeat numbers and base compositions, with the majority of markers ranging from 12 to 29 bp in length. We randomly selected 200 primer pairs and successfully amplified 15 pairs of polymorphic SSR primers, which effectively distinguished Chinese fir plants of different origins. This study provides insights into the genetic characteristics of Iron-Heart C. lanceolata and offers a foundation for future molecular marker development, breeding programs, genetic diversity analysis, and conservation strategies.

Integrated Transcriptomic and Metabolomic Analysis Reveals the Mechanism of Gibberellic acid Regulates the Growth and Flavonoid Synthesis in Phellodendron chinense Schneid Seedlings.

The phytohormone gibberellic acids (GAs) play a crucial role in the processes of growth, organ development, and secondary metabolism. However, the mechanism of exogenous GA3 regulating the growth and flavonoid synthesis in Phellodendron chinense Schneid (P. chinense Schneid) seedlings remains unclear. In this study, the physicochemical properties, gene expression level, and secondary metabolite of P. chinense Schneid seedlings under GA3 treatment were investigated. The results showed that GA3 significantly improved the plant height, ground diameter, fresh weight, chlorophyll content, soluble substance content, superoxide dismutase, and peroxidase activities. This was accompanied by elevated relative expression levels of Pc(S)-GA2ox, Pc(S)-DELLA, Pc(S)-SAUR50, Pc(S)-PsaD, Pc(S)-Psb 27, Pc(S)-PGK, Pc(S)-CER3, and Pc(S)-FBA unigenes. Conversely, a notable reduction was observed in the carotenoid content, catalase activity and the relative expression abundances of Pc(S)-KAO, Pc(S)-GID1/2, and Pc(S)-GH 3.6 unigenes in leaves of P. chinense Schneid seedlings (p < 0.05). Furthermore, GA3 evidently decreased the contents of pinocembrin, pinobanksin, isosakuranetin, naringin, naringenin, (-)-epicatechin, tricetin, luteolin, and vitexin belonged to flavonoid in stem bark of P. chinense Schneid seedlings (p < 0.05). These results indicated that exogenous GA3 promoted growth through improving chlorophyll content and gene expression in photosynthesis and phytohormone signal pathway and inhibited flavonoid synthesis in P. chinense Schneid seedlings.

Paclobutrazol Promotes Root Development of Difficult-to-Root Plants by Coordinating Auxin and Abscisic Acid Signaling Pathways in Phoebe bournei.

Phoebe bournei is a rare and endangered plant endemic to China with higher-value uses in essential oil and structural wood production. Its seedlings are prone to death because of its undeveloped system. Paclobutrazol (PBZ) can improve root growth and development in certain plants, but its concentration effect and molecular mechanism remain unclear. Here, we studied the physiological and molecular mechanisms by which PBZ regulates root growth under different treatments. We found that, with moderate concentration treatment (MT), PBZ significantly increased the total root length (69.90%), root surface area (56.35%), and lateral root number (47.17%). IAA content was the highest at MT and was 3.83, 1.86, and 2.47 times greater than the control, low, and high-concentration treatments. In comparison, ABA content was the lowest and reduced by 63.89%, 30.84%, and 44.79%, respectively. The number of upregulated differentially expressed genes (DEGs) induced at MT was more than that of down-regulated DEGs, which enriched 8022 DEGs in response to PBZ treatments. WGCNA showed that PBZ-responsive genes were significantly correlated with plant hormone content and involved in plant hormone signal transduction and MAPK signal pathway-plant pathways, which controls root growth. The hub genes are observably associated with auxin, abscisic acid syntheses, and signaling pathways, such as PINs, ABCBs, TARs, ARFs, LBDs, and PYLs. We constructed a model which showed PBZ treatments mediated the antagonism interaction of IAA and ABA to regulate the root growth in P. bournei. Our result provides new insights and molecular strategies for solving rare plants' root growth problems.

The response of nutrient cycle, microbial community abundance and metabolic function to nitrogen fertilizer in rhizosphere soil of Phellodendron chinense Schneid seedlings.

Nitrogen (N) as an essential macronutrient affects the soil nutrient cycle, microbial community abundance, and metabolic function. However, the specific responses of microorganisms and metabolic functions in rhizosphere soil of Phellodendron chinense Schneid seedlings to N addition remain unclear. In this study, four treatments (CK, N5, N10 and N15) were conducted, and the soil physicochemical properties, enzyme activities, microbial community abundances and diversities, metabolism, and gene expressions were investigated in rhizosphere soil of P. chinense Schneid. The results showed that N addition significantly decreased rhizosphere soil pH, among which the effect of N10 treatment was better. N10 treatment significantly increased the contents of available phosphorus (AP), available potassium (AK), ammonium nitrogen (NH4+-N), nitrate nitrogen (NO3--N) and sucrase (SU) activity, as well as fungal diversity and the relative expression abundances of amoA and phoD genes in rhizosphere soil, but observably decreased the total phosphorus (TP) content, urease (UR) activity and bacterial diversity, among which the pH, soil organic matter (SOM), AP, NH4+-N and NO3--N were the main environmental factors for affecting rhizosphere soil microbial community structure based on RDA and correlation analyses. Meanwhile, N10 treatment notably enhanced the absolute abundances of the uracil, guanine, indole, prostaglandin F2α and γ-glutamylalanine, while reduced the contents of D-phenylalanine and phenylacetylglycine in rhizosphere soil of P. chinense Schneid seedlings. Furthermore, the soil available nutrients represented a significant correlation with soil metabolites and dominant microorganisms, suggesting that N10 addition effectively regulated microbial community abundance and metabolic functions by enhancing nutrient cycle in the rhizosphere soil of P. chinense Schneid seedlings.

Forest succession improves the complexity of soil microbial interaction and ecological stochasticity of community assembly: Evidence from Phoebe bournei-dominated forests in subtropical regions.

Forest succession is a central ecological topic, due to the importance of the associated dynamic processes for terrestrial ecosystems. However, very little is currently known about the community assembly and interaction of soil microbial communities along forest successional trajectories, particularly regarding the microbial community dynamics in contrasting seasons. To bridge these knowledge gaps, we studied soil bacterial and fungal community compositions, assemblages, and co-occurrence networks in a well-established successional gradient of Phoebe bournei-dominated forest, spanning about 65 years of forest development in a subtropical region. Illumina MiSeq sequencing of 16S and ITS genes was employed for the assessment of soil bacterial and fungal community composition and diversity, respectively. The relative abundance and α-diversity of soil bacteria and fungi showed a differential trend over forest succession. The dominant fungal phyla (Basidiomycota and Ascomycota) changed more frequently than the dominant bacterial phyla (Proteobacteria, Acidobacteriota, and Actinobacteriota), indicating that soil fungi have a more sensitive relationship with forest succession compared with bacteria. The soil microbial community variation induced by forest succession was significantly affected by soil total phosphorus, dissolved organic carbon content and pH. Compared to deterministic processes, stochastic processes mainly dominated the community assembly of soil microbial communities. Meanwhile, the relative importance of stochasticity in soil fungal communities increased in the later stages. In Particular, dispersal limitation and drift accounted for a large proportion of bacterial and fungal community assembly, respectively. In addition, the co-occurrence networks of soil microbial communities became more complex as succession proceeds. Soil bacteria and fungi exhibited more competition and cooperation along the forest successional gradient. Collectively, our findings suggest that forest succession improves the complexity of soil microbial interactions and the ecological stochasticity of community assembly in Phoebe bournei-dominated forests, providing key insights into the relationship between microbial communities and forest succession.

View from the Top: Insights into the Diversity and Community Assembly of Ectomycorrhizal and Saprotrophic Fungi along an Altitudinal Gradient in Chinese Boreal Larix gmelinii-Dominated Forests.

The altitudinal patterns of soil fungi have attracted considerable attention; however, few studies have investigated the diversity and community assembly of fungal functional guilds along an altitudinal gradient. Here, we explored ectomycorrhizal (EcM) and saprotrophic (SAP) fungal diversity and community assembly along a 470 m vertical gradient (ranging from 830 to 1300 m) on Oakley Mountain, sampling bulk soils in the 0-10 cm and 10-20 cm soil layers of Larix gmelinii-dominated forests. Illumina MiSeq sequencing of the ITS genes was employed to explore the fungal community composition and diversity. The relative abundance of EcM and SAP fungi showed a divergent pattern along an altitudinal gradient, while we observed a consistent altitudinal tendency for EcM and SAP fungal diversity and community assembly. The diversity of both fungal guilds increased with increasing altitude. Altitude and soil moisture were the key factors affecting the community composition of both fungal guilds. In addition, the plant community composition significantly affected the EcM fungal community composition, whereas the dissolved organic nitrogen and ammonium nitrogen contents were the driving factors of SAP fungal community. Despite the effects of vegetation and soil factors, EcM and SAP fungal communities were mainly governed by stochastic processes (especially drift) at different altitudes and soil depths. These results shed new light on the ecology of different fungal functional guilds along an altitudinal gradient, which will provide a deeper understanding of the biogeography of soil fungi.

Transcriptomic analysis reveals the significant effects of fertilization on the biosynthesis of sesquiterpenes in Phoebe bournei.

Phoebe bournei is a potential medicinal plant. Its essential oils (Eos) are mainly composed of sesquiterpenes that has potential activities of anti-bacteria and anti-tumors. In this study, we evaluated the effects of compost and compound fertilizer on the total amount and main components of Eos in P. bournei, we also studied the molecular mechanism undergoing this process by deep sequencing the genes involved in the biosynthesis of sesquiterpenes. Fertilization enhanced the total amount of main components in Eos from both leaves and twigs. Bicyclogermacrene, the primary sesquiterpene in the leaf EO, was significantly increased under compost treatment, while bicyclogermacrene and δ-cadinene (the second most abundant sesquiterpene) were decreased under compound fertilizer treatment. The two fertilizers had no significant effect on the abundance of the primary (+) - δ-cadinene in the twig EO, but had a positive effect on the second most abundant sesquiterpene copaene. Significant differences were observed in the number of differentially expressed genes (DEGs) with the leaves showing greater number of DEGs as compared to the twigs after compost treatment. Terpenoid backbone biosynthesis (TBB) is a key pathway of sesquiterpenes synthesis. The expression of genes regulating several important enzymes in TBB was altered after fertilization. After the compost treatment, the expression of the leaf DXS gene (ACQ66107.1), being closely related to the sesquiterpene biosynthesis in P. bournei leaves, was decreased. Compost and compound fertilizer altered the expression of the two important branch-point enzymes (FPPS and GGPPS) genes (ART33314.1 and ATT59265.1), which contributed to the changes of the total amount and components of P. bournei sesquiterpenes. This study provides a new insight into the future use of P. bournei for Eos.

High-efficient extraction of principal medicinal components from fresh Phellodendron bark (cortex phellodendri).

There are three key medicinal components (phellodendrine, berberine and palmatine) in the extracts of Phellodendron bark, as one of the fundamental herbs of traditional Chinese medicine. Different extraction methods and solvent combinations were investigated to obtain the optimal technologies for high-efficient extraction of these medicinal components. RESULTS: The results showed that combined solvents have higher extracting effect of phellodendrine, berberine and palmatine than single solvent, and the effect of ultrasonic extraction is distinctly better than those of distillation and soxhlet extraction. CONCLUSION: The hydrochloric acid/methanol-ultrasonic extraction has the best effect for three medicinal components of fresh Phellodendron bark, providing an extraction yield of 103.12 mg/g berberine, 24.41 mg/g phellodendrine, 1.25 mg/g palmatine.