Substitution of manure for chemical fertilizer affects soil microbial community diversity, structure and function in greenhouse vegetable production systems

Soil microbial communities and enzyme activities together affect various ecosystem functions of soils. Fertilization, an important agricultural management practice, is known to modify soil microbial characteristics; however, inconsistent results have been reported. The aim of this research was to make a comparative study of the effects of different nitrogen (N) fertilizer rates and types (organic and inorganic) on soil physicochemical properties, enzyme activities and microbial attributes in a greenhouse vegetable production (GVP) system of Tianjin, China. Results showed that manure substitution of chemical fertilizer, especially at a higher substitution rate, improved soil physicochemical properties (higher soil organic C (SOC) and nutrient (available N and P) contents; lower bulk densities), promoted microbial growth (higher total phospholipid fatty acids and microbial biomass C contents) and activity (higher soil hydrolase activities). Manure application induced a higher fungi/bacteria ratio due to a lower response in bacterial than fungal growth. Also, manure application greatly increased bacterial stress indices, as well as microbial communities and functional diversity. The principal component analysis showed that the impact of manure on microbial communities and enzyme activities were more significant than those of chemical fertilizer. Furthermore, redundancy analysis indicated that SOC and total N strongly influenced the microbial composition, while SOC and ammonium-N strongly influenced the microbial activity. In conclusion, manure substitution of inorganic fertilizer, especially at a higher substitution rate, was more efficient for improving soil quality and biological functions.</p

Physiological and transcriptomic analysis reveal the crucial factors in heat stress response of red raspberry ‘Polka’ seedlings

With global climate warming, recurring extreme heat and high temperatures irreversibly damage plants. Raspberries, known for their nutritional and medicinal value, are in high demand worldwide. Thus, it is important to study how high-temperature stress (HTS) affects raspberries. The physiological and biochemical responses and molecular genetic mechanisms of raspberry leaves to different HTS treatments were investigated: mild high temperature at 35°C (HT35), severe high temperature at 40°C (HT40), and the control at room temperature of 25°C (CK). The physiological results suggested that leaves in both the 35°C and 40°C treatments showed maximum relative conductivity at 4 d of stress, increasing by 28.54% and 43.36%, respectively, compared to CK. Throughout the stress period (0–4 d), malondialdehyde (MDA) and soluble protein contents of raspberry leaves increased under HT35 and HT40 treatments, while soluble sugar content first decreased and then increased. Catalase (CAT) activity increased, superoxide dismutase (SOD) activity first increased and then decreased, and peroxidase (POD) activity gradually decreased. Photosynthetic and fluorescence responses of raspberry leaves showed the most severe impairment after 4 d of stress. Transcriptomics results revealed significant alterations in 42 HSP family genes, two SOD-related differentially expressed genes (DEGs), 25 POD-related DEGs, three CAT-related DEGs, and 38 photosynthesis-related DEGs under HTS. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that these DEGs were mainly enriched in photosynthesis-antenna proteins, pentose and glucuronide interconversion, phenylpropane biosynthesis, and indole alkaloid biosynthesis. HTS induced excessive ROS accumulation in raspberry leaves, causing oxidative damage in plant cells and subsequently reducing photosynthesis in raspberry leaves. This reduction in photosynthesis, in turn, affects photosynthetic carbon fixation and starch and sucrose metabolism, which, combined with phenol propane biosynthesis, mitigates the HTS-induced damage

Combined Fertilization Could Increase Crop Productivity and Reduce Greenhouse Gas Intensity through Carbon Sequestration under Rice-Wheat Rotation

Quantifying greenhouse gas intensity (GHGI) and soil carbon sequestration is a method to assess the mitigation potential of agricultural activities. However, the effects of different fertilizer amendments on soil carbon sequestration and net GHGI in a rice-wheat cropping system are poorly understood. Here, fertilizer treatments including PK (P and K fertilizers); NPK (N, P and K fertilizers), NPK + OM (NPK plus manure), NPK + SR (NPK plus straw returning), and NPK + CR (NPK plus controlled-release fertilizer) with equal N input were conducted to gain insight into the change of soil organic carbon (SOC) derived from the net ecosystem carbon budget (NECB), net global warming potential (GWP), and GHGI under rice-wheat rotation. Results showed that compared with NPK treatment, NPK + OM significantly increased wheat yield and NPK + SR caused significant increase in rice yield. Meanwhile, NPK + SR and NPK + CR treatments reduced net GWP by 30.80% and 21.83%, GHGI by 36.84% and 28.07%, respectively, which suggested that improved grain production could be achieved without sacrificing the environment. With the greatest C sequestration, lowest GHGI, the NPK plus straw returning practices (NPK + SR) might be the best strategy to mitigate net GWP and improve grain yield and NUE in the current rice-wheat rotation system

Temperature Matters More than Fertilization for Straw Decomposition in the Soil of Greenhouse Vegetable Field

As the largest organic carbon input to agroecosystems, crop straw can solve the problem of soil quality degradation in greenhouse vegetable fields, harmonize the balance between soil nutrients and energy, and improve soil quality to maintain the sustainable production of greenhouse vegetables. However, the microbial mechanism of the straw decomposition process under different temperatures and fertilization treatments in greenhouse vegetable soils has not been clarified. Soil samples were used to investigate the biology of straw decomposition in the soil at three incubation temperatures (15, 25, and 35 °C) through a soil incubation experiment (60 d) under different fertilization treatments. Fertilization treatments for this long-term field experiment included chemical fertilizer (CF), substitution of half of the chemical N fertilizer with manure (CM), straw (CS), or combined manure and straw (CMS). The results showed that soil hydrolase activities tended to decrease with increasing temperature during straw decomposition. Compared with the CF, organic substitutions (CM, CMS, and CS) increased soil β-glucosidase, β-cellobiosidase, N-acetyl-glucosaminidase, and β-xylosidase activities during straw decomposition. Soil CO2 emission rates were the highest at each incubation temperature on the first day, rapidly declining at 25 °C and 35 °C and slowly declining at 15 °C. The soil CO2 cumulative emissions tended to increase with increasing temperature under different fertilization treatments. PCA showed that the responses of soil enzyme activities to temperature at 7, 15, and 30 d of straw decomposition were stronger than those of fertilization. In summary, both fertilization treatment and incubation temperature could influence soil CO2 emissions by affecting soil physicochemical properties and enzyme activities during straw decomposition, whereas incubation temperature had a stronger effect on straw decomposition than fertilization, as indicated by PLS-PM and three-way ANOVA. Considering the influence for fertilization on the straw decomposition process at different incubation temperatures, the straw applications (CMS and CS) were more suitable to temperature changes

Transcriptomics and metabolomics provide insight into the anti-browning mechanism of selenium in freshly cut apples

Enzymatic browning has a considerable negative impact on the acceptability and marketability of freshly cut apples. However, the molecular mechanism by which selenium (Se) positively affects freshly cut apples in this regard is not yet clear. In this study, 0.75 kg/plant of Se-enriched organic fertilizer was applied to “Fuji” apple trees during the young fruit stage (M5, May 25), the early fruit enlargement stage (M6, June 25), and the fruit enlargement stage (M7, July 25), respectively. The same amount of Se-free organic fertilizer was applied as a control. Herein, the regulatory mechanism by which exogenous Se exerts its anti-browning effect in freshly cut apples was investigated. The results showed that the M7 treatment applied in Se-reinforced apples could remarkably inhibit their browning at 1 h after being freshly cut. Additionally, the expression of polyphenol oxidase (PPO) and peroxidase (POD) genes treated with exogenous Se was significantly reduced compared to controls. Moreover, the lipoxygenase (LOX) and phospholipase D (PLD) genes, which are involved in membrane lipid oxidation, were expressed at higher levels in the control. The gene expression levels of the antioxidant enzymes catalase (CAT), superoxide dismutase (SOD), glutathione S-transferase (GST), and ascorbate peroxidase (APX) were upregulated in the different exogenous Se treatment groups. Similarly, the main metabolites measured during the browning process were phenols and lipids; thus, it could be speculated that the mechanism by which exogenous Se produces its anti-browning effect may be by reducing phenolase activity, improving the antioxidant capacity of the fruits, and alleviating membrane lipid peroxidation. In summary, this study provides evidence regarding and insight into the response mechanism employed by exogenous Se to inhibit browning in freshly cut apples

Organic amendment increases soil respiration in a greenhouse vegetable production system through decreasing soil organic carbon recalcitrance and increasing carbon-degrading microbial activity

Purpose: Recent works have shown that fertilization has an important influence on soil respiration (Rs); however, the underlying mechanisms involved in regulating Rs in greenhouse vegetable production (GVP) systems remain unclear.Materials and methods: Samples from six kinds of soils that were amended with different fertilization patterns (8 years) were incubated for 36 days to determine soil microbial community (PLFA), enzyme activities, soil organic C (SOC) quality (13C NMR), and Rs in a GVP system in Tianjin, China. Treatments included 100% chemical N (CN) and different substitution rates of CN with manure-N and/or straw-N.Results and discussion: Compared with 100%CN treatment, organic amendment strongly promoted microbial (e.g., fungi, bacteria, and actinomycetes) growth, enhanced the majority of C-degrading enzyme activities, affected SOC chemical composition with increasing O-alkyl (labile) C and reducing aromatic (stable) C, decreased SOC recalcitrance, and enhanced Rs. Redundancy analysis indicated that variations in microbial community and SOC chemical composition were closely linked to light fraction organic C (LFC) and readily oxidizable C (ROC), respectively. Further, structural equation modeling and linear regression analysis revealed that SOC recalcitrance (negative effects) and C-degrading enzyme activities (positive effects) together mediate Rs rates; meanwhile, microbial community can indirect affect Rs rates through altering C-degrading enzyme activities. Conclusions: Agricultural soil abiotic properties (mainly labile C fractions, i.e., LFC and ROC) are altered by adding organic resources (i.e., manure and straw), the changes of which can promote soil microbial growth, enhance C-degrading microbial activity, and reduce SOC recalcitrance, and in turn accelerate Rs in GVP systems

Metabolomics and Transcriptomics Provide Insights into Lipid Biosynthesis in the Embryos of Walnut (Juglans regia L.)

Walnut (Juglans regia L.) is an important woody oilseed tree species due to its commercial value. However, the regulation mechanism of walnut oil accumulation is still poorly understood, which restricted the breeding and genetic improvement of high-quality oil-bearing walnuts. In order to explore the metabolic mechanism that regulates the synthesis of walnut oil, we used transcriptome sequencing technology and metabolome technology to comprehensively analyze the key genes and metabolites involved in oil synthesis of the walnut embryo at 60, 90, and 120 days after pollination (DAP). The results showed that the oil and protein contents increased gradually during fruit development, comprising 69.61% and 18.32% of the fruit, respectively, during ripening. Conversely, the contents of soluble sugar and starch decreased gradually during fruit development, comprising 2.14% and 0.84%, respectively, during ripening. Transcriptome sequencing generated 40,631 unigenes across 9 cDNA libraries. We identified 51 and 25 candidate unigenes related to the biosynthesis of fatty acid and the biosynthesis of triacylglycerol (TAG), respectively. The expression levels of the genes encoding Acetyl-CoA carboxylase (ACCase), long-chain acyl-CoA synthetases (LACS), 3-oxoacyl-ACP synthase II (KASII), and glycerol-3-phosphate acyl transfer (GPAT) were upregulated at 60 DAP relative to the levels at 90 and 120 DAP, while the stearoyl-ACP-desaturase (SAD) and fatty acid desaturase 2 (FAD2) genes were highly abundantly expressed during all walnut developmental periods. We found that ABSCISIC ACID INSENSEITIVE3 (ABI3), WRINKLEDl (WRI1), LEAFY COTYLEDON1 (LEC1), and FUSCA3 (FUS3) may be key transcription factors involved in lipid synthesis. Additionally, the metabolomics analysis detected 706 metabolites derived from 18 samples, among which, 4 are implicated in the TAG synthesis, 2 in the glycolysis pathway, and 5 in the tricarboxylic acid cycle (TCA cycle) pathway. The combined analysis of the related genes and metabolites in TAG synthesis showed that phospholipid:diacylglycerol acyltransferase (PDAT) genes were highly abundantly expressed across walnut fruit developmental periods, and their downstream metabolite TAG gradually accumulated with the progression of fruit development. The FAD2 gene showed consistently higher expression during fruit development, and its downstream metabolites 18:2-PC and 18:3-PC gradually accumulated. The ACCase, LACS, SAD, FAD2, and PDAT genes may be crucial genes required for walnut oil synthesis. Our data will enrich public databases and provide new insights into functional genes related to lipid metabolism in walnut

Systematical Characterization of the <i>AT-Hook</i> Gene Family in <i>Juglans regia</i> L. and the Functional Analysis of the <i>JrAHL2</i> in Flower Induction and Hypocotyl Elongation

AT-hook motif nuclear localization (AHL) proteins play essential roles in various plant biological processes. Yet, a comprehensive understanding of AHL transcription factors in walnut (Juglans regia L.) is missing. In this study, 37 AHL gene family members were first identified in the walnut genome. Based on the evolutionary analysis, JrAHL genes were grouped into two clades, and their expansion may occur due to segmental duplication. The stress-responsive nature and driving of developmental activities of JrAHL genes were revealed by cis-acting elements and transcriptomic data, respectively. Tissue-specific expression analysis showed that JrAHLs had a profound transcription in flower and shoot tip, JrAHL2 in particular. Subcellular localization showed that JrAHL2 is anchored to the nucleus. Overexpression of JrAHL2 in Arabidopsis adversely affected hypocotyl elongation and delayed flowering. Our study, for the first time, presented a detailed analysis of JrAHL genes in walnut and provided theoretical knowledge for future genetic breeding programs

Genome-Wide Characterization of the Mitogen-Activated Protein Kinase Gene Family and Their Expression Patterns in Response to Drought and Colletotrichum Gloeosporioides in Walnut (Juglans regia)

Mitogen-activated protein kinases (MAPKs) are a family of Ser/Thr (serine/threonine) protein kinases that play very important roles in plant responses to biotic and abiotic stressors. However, the MAPK gene family in the important crop walnut (Juglans regia L.) has been less well studied compared with other species. We discovered 25 JrMAPK members in the Juglans genome in this study. The JrMAPK gene family was separated into four subfamilies based on phylogenetic analysis, and members of the same subgroup had similar motifs and exons/introns. A variety of cis-acting elements, mainly related to the light response, growth and development, stress response, and hormone responses, were detected in the JrMAPK gene promoters. Collinearity analysis showed that purification selection was the main driving force in JrMAPK gene evolution, and segmental and tandem duplications played key roles in the expansion of the JrMAPK gene family. The RNA-Seq (RNA Sequencing) results indicated that many of the JrMAPK genes were expressed in response to different levels of Colletotrichum gloeosporioides infection. JrMAPK1, JrMAPK3, JrMAPK4, JrMAPK5, JrMAPK6, JrMAPK7, JrMAPK9, JrMAPK11, JrMAPK12, JrMAPK13, JrMAPK17, JrMAPK19, JrMAPK20, and JrMAPK21 were upregulated at the transcriptional level in response to the drought stress treatment. The results of this study will help in further investigations of the evolutionary history and biological functions of the MAPK gene family in walnut

Heat map of the association between major soil bacterial taxa and soil chemical properties at the genus level.

* indicates significant correlation P<0.05; ** indicates highly significant correlation P<0.01.</p