Degradation Genes Research Articles

The role of OsBZR4 as a brassinosteroid-signaling component in mediating atrazine and isoproturon degradation in rice

Development of a biotechnological system for rapid degradation of pesticides is important to mitigate the environmental, food security, and health risks that they pose. Degradation of atrazine (ATZ) and isoproturon (IPU) in rice crops promoted by the brassinosteroid (BR) signaling component BRASSINAZOLE RESISTANT4 (OsBZR4) is explored. OsBZR4 is localized in the plasma membrane and nucleus, and is strongly induced by ATZ and IPU exposure. Transgenic rice OsBZR4-overexpression (OE) significantly enhances resistance to ATZ and IPU toxicity, improving growth, and reducing ATZ and IPU accumulation (particularly in grains) in rice crops. Genetic destruction of OsBZR4 (CRISPR/Cas9) increases rice sensitivity and leads to increased accumulation of ATZ and IPU. OE plants promote phase I, II, and III metabolic reactions, and expression of corresponding pesticide degradation genes under ATZ and IPU stress. UPLC-Q-TOF-MS/MS analysis reveals increased relative contents of ATZ and IPU metabolites and conjugates in OE plants, suggesting an increased OsBZR4 expression and consequent detoxification of ATZ and IPU in rice and the environment. The role of OsBZR4 in pesticide degradation is revealed, and its potential application in enhancing plant resistance to pesticides, and facilitating the breakdown of pesticides in rice and the environment, is discussed.

Insights into the distribution characteristic of microbiota in alkaline–sandy soil with inorganic and organic fertiliser treatments: contrasting abundance, structure and functionality

ABSTRACT Fertiliser amendment is the most direct method for improving soil properties of ecologically vulnerable areas (e.g. desertification soil area), and then, understanding the response of microbial community activities and growth to different fertilisation treatments is of great significance in sandy soil restoration. Here, a field experiment with different fertiliser treatments in typical alkaline–sandy soil was conducted. In this study, the difference of physicochemical property, microbial communities and functions in different treatments of no fertiliser (CK), (ii) fly ash chemical fertilisers (CF), (iii) humic straw organic fertiliser (OF), (iv) functional microbial fertiliser (FMF), (v) sulphate-reducing bacterial (SRB) fertiliser (MF) and (vi) humic straw organic fertiliser + functional microbial fertiliser + SRB fertiliser (CMF) were evaluated. The result showed that the contents of soil total organic carbon, NO3-N, P and K in the FMF were highest. The abundance of keystone taxa (Gemmatimonadetes and Thaumarchaeota) increased significantly in the treatments of microbial fertiliser. Microbial fertiliser boosted genes for aerobic nitrite oxidation, nitrogen fixation, ammonia oxidation and aromatic compound degradation. The number of methylotrophy and dark sulphur oxidation genes was reduced. The bbove results indicated that the treatments with the inoculation of functional microbes are better than the others for the restoration of alkaline–sandy soil.

African swine fever virus MGF505-6R attenuates type I interferon production by targeting STING for degradation.

African swine fever (ASF) is an acute hemorrhagic and devastating infectious disease affecting domestic pigs and wild boars. It is caused by the African swine fever virus (ASFV), which is characterized by genetic diversity and sophisticated immune evasion strategies. To facilitate infection, ASFV encodes multiple proteins to antagonize host innate immune responses, thereby contributing to viral virulence and pathogenicity. The molecular mechanisms employed by ASFV-encoded proteins to modulate host antiviral responses have not been comprehensively elucidated. In this study, it was observed that the ASFV MGF505-6R protein, a member of the multigene family 505 (MGF505), effectively suppressed the activation of the interferon-beta (IFN-β) promoter, leading to reduced mRNA levels of antiviral genes. Additional evidence has revealed that MGF505-6R antagonizes the cGAS-STING signaling pathway by interacting with the stimulator of interferon genes (STING) for degradation in the autophagy-lysosomal pathway. The domain mapping revealed that the N-terminal region (1-260aa) of MGF505-6R is the primary domain responsible for interacting with STING, while the CTT domain of STING is crucial for its interaction with MGF505-6R. Furthermore, MGF505-6R also inhibits the activation of STING by reducing the K63-linked polyubiquitination of STING, leading to the disruption of STING oligomerization and TANK binding kinase 1 (TBK1) recruitment, thereby impairing the phosphorylation and nuclear translocation of interferon regulatory factor 3 (IRF3). Collectively, our study elucidates a novel strategy developed by ASFV MGF505-6R to counteract host innate immune responses. This discovery may offer valuable insights for further exploration of ASFV immune evasion mechanisms and antiviral strategies.

Crosstalk in proline biosynthesis regulates proline augmentation and resilience to salt stress in Panicum miliaceum L.

The development and productivity of most agricultural plants can be adversely affected by the presence of salts in soil. It is vital in these situations to increase agricultural yield, especially in barren soil, by developing plants that can endure and thrive in salty environment. For reducing the detrimental salt-induced effects, plants must actively control osmotic balance by accumulating suitable solutes like proline, polyols, and glycine betaine and by activating specific stress-responsive genes and enzymes within their cells. Proline is an important osmolyte which build up endogenously in plants in response to stressful situations and its accumulation is dependent on type of species and severity of stress. Although proline biosynthesis genes and enzymes have been extensively studied, but the preferred substrate in this process is yet not clear. In present study, we aimed to elucidate the preferred pathway of proline biosynthesis and the effect on physiological parameters under salt and Se application in proso millet. It was found that salt stress negatively impacted these parameters, while as the addition of Se improved these parameters. In comparison to control 150 mM NaCl treatment led to a reduction of upto 38.6% in FW and 18.91% in DW, whereas 200 mM NaCl led to reduction of upto 52.29% in FW and 18.91% in DW. The osmolytes, total soluble sugars (TSS), glycine betaine (GB) and total proline content (TPC) increased under salt stress by 53.7%, 2.14% and 113.79% at 150 mM NaCl and 54.89%, 0.53% and 87.1% at 200 mM NaCl. But, the application of Se significantly improved the above parameters. It was observed that the low level of Se (1 µM) had a role in enhancing the activity of P5CS, P5CR, and OAT enzymes while decreasing the activity of ProDH and P5CDH enzymes. It was found that genes responsible for proline biosynthesis were expressed efficiently in response to salt stress which further increased with Se application. During salt stress proline biosynthesis (PmP5CS, PmP5CR and PmOAT) genes were up-regulated which improved further with Se treatment. While as, the proline degrading (PmP5CDH and PmProDH) genes were down-regulated at both salt and se treatments. Overall, the Se treatment appeared to be beneficial for modulating the plant responses by providing tolerance.

Genome-wide identification, molecular evolution and gene expression of P450 gene family in Cyrtotrachelus buqueti

BackgroundInsect Cytochrome P450 monooxygenase (CYPs or P450s) plays an important role in detoxifying insecticides, causing insect populations to develop resistance. However, the molecular functions of P450 gene family in Cyrtotrachelus buqueti genome are still lacking.ResultsIn this study, 71 CbuP450 genes have been identified. The amino acids length of CbuP450 proteins was between 183 aa ~ 1041 aa. They are proteins with transmembrane domains. The main component of their secondary structure is α-helix and random coils. Phylogenetic analysis showed that C. buqueti and Rhynchophorus ferrugineus were the most closely related. This gene family has 29 high-frequency codons, which tend to use A/T bases and A/T ending codons. Gene expression analysis showed that CbuP450_23 in the female adult may play an important role on high temperature resistance, and CbuP450_17 in the larval may play an important role on low temperature tolerance. CbuP450_10, CbuP450_17, CbuP450_23, CbuP450_10, CbuP450_16, CbuP450_20, CbuP450_23 and CbuP450_ 29 may be related to the regulation of bamboo fiber degradation genes in C. buqueti. Protein interaction analysis indicates that most CbuP450 proteins are mainly divided into three aspects: encoding the biosynthesis of ecdysteroids, participating in the decomposition of synthetic insecticides, metabolizing insect hormones, and participating in the detoxification of compounds.ConclusionsWe systematically analyzed the gene and protein characteristics, gene expression, and protein interactions of CbuP450 gene family, revealing the key genes involved in the stress response of CbuP450 gene family in the resistance of C. buqueti to high or low temperature stress, and identified the key CbuP450 proteins involved in important life activity metabolism. These results provided a reference for further research on the function of P450 gene family in C. buqueti.

Temperature sensitivity of aerobic and anaerobic organic carbon mineralization varies with climate and soil depth in riparian zones

The temperature sensitivity (Q10) of soil organic carbon (SOC) mineralization plays a vital role in predicting the global carbon cycle under climate change. Q10 has been extensively examined in various terrestrial ecosystems; however, in riparian zones where soil oxygen levels are highly dynamic owing to frequent flooding, Q10 should change with oxygen conditions and show spatial variation, but the mechanisms are still obscure. In this study, we collected topsoil and subsoil samples from riparian zones along a latitudinal gradient and conducted aerobic and anaerobic incubation experiments to determine the latitudinal and vertical patterns of Q10. The results showed that Q10 under anoxic conditions (average of 1.7) significantly exceeded that under oxic conditions (average of 1.4). In general, aerobic SOC mineralization is more sensitive to warming at higher latitudes than at lower latitudes, whereas the pattern is reversed under anoxic conditions. The Q10 in the topsoil was significantly higher than that in the subsoil only under oxic conditions. Metagenomics showed that the abundance of genes involved in the degradation of lignin, carbohydrate esters, and starch in the topsoil increased with latitude, whereas genes for acetate degradation were more abundant in warmer zones, regardless of soil depth. Q10 under oxic conditions was mainly influenced by soil physicochemical properties (e.g., pH and texture), whereas Q10 under anoxic conditions was jointly controlled by climate, soil texture, and acetate degradation genes. Together, anaerobic carbon (C) mineralization in riparian zones is more sensitive to temperature than aerobic metabolism, but the patterns of Q10 under oxic conditions were dependent on both latitude and depth. Our findings highlight that the discrepancies in aerobic and anaerobic C metabolism, and the C cycling process at different soil depths, might play a non-negligible role in affecting the assessment of global C emissions under climate change.

Effect of in ovo feeding of xylobiose and xylotriose on plasma immunoglobulin, cecal metabolites production, microbial ecology, and metabolic pathways in broiler chickens

BackgroundDietary supplementation of xylooligosaccharides (XOS) has been found to influence gut health by manipulating cecal microbiota and producing microbe-origin metabolites. But no study investigated and compared the effect of in ovo feeding of xylobiose (XOS2) and xylotriose (XOS3) in chickens. This study investigated the effect of in ovo feeding of these XOS compounds on post-hatch gut health parameters in chickens. A total of 144 fertilized chicken eggs were divided into three groups: a) non-injected control (CON), b) XOS2, and c) XOS3. On the 17th embryonic day, the eggs of the XOS2 and XOS3 groups were injected with 3 mg of XOS2 and XOS3 diluted in 0.5 mL of 0.85% normal saline through the amniotic sac. After hatching, the chicks were raised for 21 d. Blood was collected on d 14 to measure plasma immunoglobulin. Cecal digesta were collected for measuring short-chain fatty acids (SCFA) on d 14 and 21, and for microbial ecology and microbial metabolic pathway analyses on d 7 and 21.ResultsThe results were considered significantly different at P < 0.05. ELISA quantified plasma IgA and IgG on d 14 chickens, revealing no differences among the treatments. Gas chromatography results showed no significant differences in the concentrations of cecal SCFAs on d 14 but significant differences on d 21. However, the SCFA concentrations were lower in the XOS3 than in the CON group on d 21. The cecal metagenomics data showed that the abundance of the family Clostridiaceae significantly decreased on d 7, and the abundance of the family Oscillospiraceae increased on d 21 in the XOS2 compared to the CON. There was a reduction in the relative abundance of genus Clostridium sensu stricto 1 in the XOS2 compared to the CON on d 7 and the genus Ruminococcus torques in both XOS2 and XOS3 groups compared to the CON on d 21. The XOS2 and XOS3 groups reduced the genes for chondroitin sulfate degradation I and L-histidine degradation I pathways, which contribute to improved gut health, respectively, in the microbiome on d 7. In contrast, on d 21, the XOS2 and XOS3 groups enriched the thiamin salvage II, L-isoleucine biosynthesis IV, and O-antigen building blocks biosynthesis (E. coli) pathways, which are indicative of improved gut health. Unlike the XOS3 and CON, the microbiome enriched the pathways associated with energy enhancement, including flavin biosynthesis I, sucrose degradation III, and Calvin-Benson-Bassham cycle pathways, in the XOS2 group on d 21.ConclusionIn ovo XOS2 and XOS3 feeding promoted beneficial bacterial growth and reduced harmful bacteria at the family and genus levels. The metagenomic-based microbial metabolic pathway profiling predicted a favorable change in the availability of cecal metabolites in the XOS2 and XOS3 groups. The modulation of microbiota and metabolic pathways suggests that in ovo XOS2 and XOS3 feeding improved gut health during the post-hatch period of broilers.

DDX5 inhibits hyaline cartilage fibrosis and degradation in osteoarthritis via alternative splicing and G-quadruplex unwinding

Hyaline cartilage fibrosis is typically considered an end-stage pathology of osteoarthritis (OA), which results in changes to the extracellular matrix. However, the mechanism behind this is largely unclear. Here, we found that the RNA helicase DDX5 was dramatically downregulated during the progression of OA. DDX5 deficiency increased fibrosis phenotype by upregulating COL1 expression and downregulating COL2 expression. In addition, loss of DDX5 aggravated cartilage degradation by inducing the production of cartilage-degrading enzymes. Chondrocyte-specific deletion of Ddx5 led to more severe cartilage lesions in the mouse OA model. Mechanistically, weakened DDX5 resulted in abundance of the Fn1-AS-WT and Plod2-AS-WT transcripts, which promoted expression of fibrosis-related genes (Col1, Acta2) and extracellular matrix degradation genes (Mmp13, Nos2 and so on), respectively. Additionally, loss of DDX5 prevented the unfolding Col2 promoter G-quadruplex, thereby reducing COL2 production. Together, our data suggest that strategies aimed at the upregulation of DDX5 hold significant potential for the treatment of cartilage fibrosis and degradation in OA.

Kupffer cell diversity maintains liver function in alcohol-associated liver disease.

Liver macrophages are heterogeneous and play an important role in alcohol-associated liver disease (ALD) but there is limited understanding of the functions of specific macrophage subsets in the disease. We used a Western diet alcohol (WDA) mouse model of ALD to examine the hepatic myeloid cell compartment by single cell RNAseq and targeted KC ablation to understand the diversity and function of liver macrophages in ALD. In the WDA liver, KCs and infiltrating monocytes/macrophages each represented about 50% of the myeloid pool. Five major KC clusters all expressed genes associated with receptor-mediated endocytosis and lipid metabolism, but most were predicted to be noninflammatory and antifibrotic with 1 minor KC cluster having a proinflammatory and extracellular matrix degradation gene signature. Infiltrating monocyte/macrophage clusters, in contrast, were predicted to be proinflammatory and profibrotic. In vivo, diphtheria toxin-based selective KC ablation during alcohol exposure resulted in a liver failure phenotype with increases in PT/INR and bilirubin, loss of differentiated hepatocyte gene expression, and an increase in expression of hepatocyte progenitor markers such as EpCAM, CK7, and Igf2bp3. Gene set enrichment analysis of whole-liver RNAseq from the KC-ablated WDA mice showed a similar pattern as seen in human alcoholic hepatitis. In this ALD model, KCs are anti-inflammatory and are critical for the maintenance of hepatocyte differentiation. Infiltrating monocytes/macrophages are largely proinflammatory and contribute more to liver fibrosis. Future targeting of specific macrophage subsets may provide new approaches to the treatment of liver failure and fibrosis in ALD.

Comparative metabolomics combined with genome sequencing provides insights into novel wolfberry-specific metabolites and their formation mechanisms.

Wolfberry (Lycium, of the family Solanaceae) has special nutritional benefits due to its valuable metabolites. Here, 16 wolfberry-specific metabolites were identified by comparing the metabolome of wolfberry with those of six species, including maize, rice, wheat, soybean, tomato and grape. The copy numbers of the riboflavin and phenyllactate degradation genes riboflavin kinase (RFK) and phenyllactate UDP-glycosyltransferase (UGT1) were lower in wolfberry than in other species, while the copy number of the phenyllactate synthesis gene hydroxyphenyl-pyruvate reductase (HPPR) was higher in wolfberry, suggesting that the copy number variation of these genes among species may be the main reason for the specific accumulation of riboflavin and phenyllactate in wolfberry. Moreover, the metabolome-based neighbor-joining tree revealed distinct clustering of monocots and dicots, suggesting that metabolites could reflect the evolutionary relationship among those species. Taken together, we identified 16 specific metabolites in wolfberry and provided new insight into the accumulation mechanism of species-specific metabolites at the genomic level.

Study on the estradiol degradation gene expression and resistance mechanism of Rhodococcus R-001 under low-temperature stress

Estradiol (E2), an endocrine disruptor, acts by mimicking or interfering with the normal physiological functions of natural hormones within organisms, leading to issues such as endocrine system disruption. Notably, seasonal fluctuations in environmental temperature may influence the degradation speed of estradiol (E2) in the natural environment, intensifying its potential health and ecological risks. Therefore, this study aims to explore how bacteria can degrade E2 under low-temperature conditions, unveiling their resistance mechanisms, with the goal of developing new strategies to mitigate the threat of E2 to health and ecological safety. In this paper, we found that Rhodococcus equi DSSKP-R-001 (R-001) can efficiently degrade E2 at 30 °C and 10 °C. Six genes in R-001 were shown to be involved in E2 degradation by heterologous expression at 30 °C. Among them, 17β-HSD, KstD2, and KstD3, were also involved in E2 degradation at 10 °C; KstD was not previously known to degrade E2. RNA-seq was used to characterize differentially expressed genes (DEGs) to explore the stress response of R-001 to low-temperature environments to elucidate the strain's adaptation mechanism. At the low temperature, R-001 cells changed from a round spherical shape to a long rod or irregular shape with elevated unsaturated fatty acids and were consistent with the corresponding genetic changes. Many differentially expressed genes linked to the cold stress response were observed. R-001 was found to upregulate genes encoding cold shock proteins, fatty acid metabolism proteins, the ABC transport system, DNA damage repair, energy metabolism and transcriptional regulators. In this study, we demonstrated six E2 degradation genes in R-001 and found for the first time that E2 degradation genes have different expression characteristics at 30 °C and 10 °C. Linking R-001 to cold acclimation provides new insights and a mechanistic basis for the simultaneous degradation of E2 under cold stress in Rhodococcus adaptation.

Metagenomes from microbial populations beneath a chromium waste tip give insight into the mechanism of Cr (VI) reduction

Dumped Chromium Ore Processing Residue (COPR) at legacy sites poses a threat to health through leaching of toxic Cr(VI) into groundwater. Previous work implicates microbial activity in reducing Cr(VI) to less mobile and toxic Cr(III), but the mechanism has not been explored. To address this question a combined metagenomic and geochemical study was undertaken. Soil samples from below the COPR waste were used to establish anaerobic microcosms which were challenged with Cr(VI), with or without acetate as an electron donor, and incubated for 70 days. Cr was rapidly reduced in both systems, which also reduced nitrate, nitrite then sulfate, but this sequence was accelerated in the acetate amended microcosms. 16S rRNA gene sequencing revealed that the original soil sample was diverse but both microcosm systems became less diverse by the end of the experiment. A high proportion of 16S rRNA gene reads and metagenome-assembled genomes (MAGs) with high completeness could not be taxonomically classified, highlighting the distinctiveness of these alkaline Cr impacted systems. Examination of the coding capacity revealed widespread capability for metal tolerance and Fe uptake and storage, and both populations possessed metabolic capability to degrade a wide range of organic molecules. The relative abundance of genes for fatty acid degradation was 4× higher in the unamended compared to the acetate amended system, whereas the capacity for dissimilatory sulfate metabolism was 3× higher in the acetate amended system. We demonstrate that naturally occurring in situ bacterial populations have the metabolic capability to couple acetate oxidation to sequential reduction of electron acceptors which can reduce Cr(VI) to less mobile and toxic Cr(III), and that microbially produced sulfide may be important in reductive precipitation of chromate. This capability could be harnessed to create a Cr(VI) trap-zone beneath COPR tips without the need to disturb the waste.

Surviving the Potato Stems: Differences in Genes Required for Fitness by Dickeya dadantii and Dickeya dianthicola.

Bacteria belonging to the genus Dickeya cause blackleg and soft rot symptoms on many plant hosts, including potato. Although there is considerable knowledge about the genetic determinants that allow Dickeya to colonize host plants, as well as the genes that contribute to virulence, much is still unknown. To identify the genes important for fitness in potato stems, we constructed and evaluated randomly barcoded transposon mutant (RB-TnSeq) libraries of Dickeya dadantii and Dickeya dianthicola. We identified 169 and 157 genes important for growth in D. dadantii and D. dianthicola in stems, respectively. This included genes related to metabolic pathways, chemotaxis and motility, transcriptional regulation, transport across membranes, membrane biogenesis, detoxification mechanisms, and virulence-related genes, including a potential virulence cluster srfABC, c-di-GMP modulating genes, and pectin degradation genes. When we compared the results of the stem assay with other datasets, we identified genes important for growth in stems versus tubers and in vitro conditions. Additionally, our data showed differences in fitness determinants for D. dadantii and D. dianthicola. These data provide important insights into the mechanisms used by Dickeya when interacting with and colonizing plants and thus might provide targets for management.

Transcriptome Sequencing Provides Insights into High-Temperature-Induced Leaf Senescence in Herbaceous Peony

Global warming causes frequent high temperatures in summer; which negatively impacts herbaceous peonies (Paeonia lactiflora Pall.) by accelerating leaf senescence and reducing biomass accumulation, leading to reduced flower quality in the subsequent year. Our findings revealed that as heat stress progressed, the high-temperature-sensitive cultivar ‘Meigui Zi’ (MGZ) exhibited a higher rate of chlorophyll content reduction and more pronounced premature aging symptoms than the high-temperature-tolerant cultivar ‘Chi Fen’ (CF). To investigate gene expression differences between CF and MGZ under high-temperature stress, we combined PacBio Iso-Seq sequencing (Iso-Seq) with next-generation sequencing (RNA-seq). Iso-seq yielded 352,891 full-length transcripts ranging from 61 bp to 49,022 bp in length. RNA-seq generated 257,562 transcripts across all samples. Further analysis revealed that differentially expressed genes (DEGs) between CF and MGZ were primarily enriched in “Photosynthesis”, with most photosynthesis-related DEGs highly expressed in CF. This indicates that CF has higher stability in its photosystem compared with MGZ, which is crucial for mitigating leaf senescence caused by high temperatures. Additionally, the highly expressed chlorophyll degradation genes stay-green (SGR) and stay-green-like (SGRL) in MGZ may be involved in chlorophyll content reduction induced by high temperature. This study preliminarily revealed the molecular mechanism of high-temperature-induced leaf senescence of in herbaceous peony and provided candidate genes for further studies of the regulation mechanism of high -temperature-induced leaf senescence.

UV-aging reduces the effects of biodegradable microplastics on soil sulfamethoxazole degradation and sul genes development

In recent years, the biodegradable plastics has extensively used in industry, agriculture, and daily life. Herein, the effects of two biodegradable microplastics (BMPs), poly(butyleneadipate-co-terephthalate) (PBAT) and polyhydroxyalkanoate (PHA), on soil sulfamethoxazole (SMX) degradation and sul genes development were comparatively studied based on the type, dosage, and state. The addition of virgin BMPs significantly increased soil DOC following a sequential order PBAT > PHA and high dose > low dose. Meanwhile virgin PBAT significantly reduced soil pH. In general, the addition of BMPs not only promoted soil SMX degradation but also increased the abundance of sul genes, with an exception that pH reduction in virgin PBAT inhibited the proliferation of sul genes. The driving effects of BMPs on soil microbial diversity following the same order as that on DOC. Specific bacteria stimulated by BMPs, such as Arthrobacter and two genera affiliated with phylum TM7, accounted for the accelerated degradation of SMX. Intriguingly, UV-aging hindered the release of DOC from BMPs and the reduction in pH, mitigated the stimulation of microbial communities, and ultimately reduced the promotion effect of BMPs on SMX degradation and sul genes proliferation. Our results suggest that more attention should be paid to the proliferation risk of ARGs in the environment affected by BMPs and UV-aging can be employed sometimes to reduce this risk.

MdWRKY71 promotes the susceptibility of apple to Glomerella leaf spot by controlling salicylic acid degradation.

Glomerella leaf spot (GLS), a fungal disease caused by Colletotrichum fructicola, severely affects apple (Malus domestica) quality and yield. In this study, we found that the transcription factor MdWRKY71 was significantly induced by C. fructicola infection in the GLS-susceptible apple cultivar Royal Gala. The overexpression of MdWRKY71 in apple leaves resulted in increased susceptibility to C. fructicola, whereas RNA interference of MdWRKY71 in leaves showed the opposite phenotypes. These findings suggest that MdWRKY71 functions as a susceptibility factor for the apple-C. fructicola interaction. Furthermore, MdWRKY71 directly bound to the promoter of the salicylic acid (SA) degradation gene Downy Mildew Resistant 6 (DMR6)-Like Oxygenase 1 (DLO1) and promoted its expression, resulting in a reduced SA level. The sensitivity of 35S:MdWRKY71 leaves to C. fructicola can be effectively alleviated by knocking down MdDLO1 expression, confirming the critical role of MdWRKY71-mediated SA degradation via regulating MdDLO1 expression in GLS susceptibility. In summary, we identified a GLS susceptibility factor, MdWRKY71, that targets the apple SA degradation pathway to promote fungal infection.

Effects of biochar immobilization of Serratia sp. F4 OR414381 on bioremediation of petroleum contamination and bacterial community composition in loess soil

Petroleum hydrocarbons pose a significant threat to human health and the environment. Biochar has increasingly been utilized for soil remediation. This study investigated the potential of biochar immobilization using Serratia sp. F4 OR414381 for the remediation of petroleum-contaminated soil through a pot experiment conducted over 90 days. The treatments in this study, denoted as IMs (maize straw biochar-immobilized Serratia sp. F4), degraded 82.5% of the total petroleum hydrocarbons (TPH), 59.23% of the aromatic, and 90.1% of the saturated hydrocarbon fractions in the loess soils. During remediation, the soil pH values decreased from 8.76 to 7.33, and the oxidation-reduction potential (ORP) increased from 156 to 229 mV. The treatment-maintained soil nutrients of the IMs were 138.94 mg/kg of NO3- -N and 92.47 mg/kg of available phosphorus (AP), as well as 11.29% of moisture content. The activities of soil dehydrogenase (SDHA) and catalase (CAT) respectively increased by 14% and 15 times compared to the CK treatment. Three key petroleum hydrocarbon degradation genes, including CYP450, AJ025, and xylX were upregulated following IMs treatment. Microbial community analysis revealed that a substantial microbial population of 1.01E+ 09 cells/g soil and oil-degrading bacteria such as Salinimicrobium, Saccharibacteria_genera_incertae_sedis, and Brevundimonas were the dominant genera in IMs treatment. This suggests that the biochar immobilized on Serratia sp. F4 OR414381 improves soil physicochemical properties and enhances interactions among microbial populations, presenting a promising and environmentally friendly approach for the stable and efficient remediation of petroleum-contaminated loess soil.

Urea fertilization increased CO2 and CH4 emissions by enhancing C-cycling genes in semi-arid grasslands

Global climate change is predicted to increase exogenous N input into terrestrial ecosystems, leading to significant changes in soil C-cycling. However, it remains largely unknown how these changes affect soil C-cycling, especially in semi-arid grasslands, which are one of the most vulnerable ecosystems. Here, based on a 3-year field study involving N additions (0, 25, 50, and 100 kg ha−1 yr−1 of urea) in a semi-arid grassland on the Loess Plateau, we investigated the impact of urea fertilization on plant characteristics, soil properties, CO2 and CH4 emissions, and microbial C cycling genes. The compositions of genes involved in C cycling, including C fixation, degradation, methanogenesis, and methane oxidation, were determined using metagenomics analysis. We found that N enrichment increased both above- and belowground biomasses and soil organic C content, but this positive effect was weakened when excessive N was input (N100). N enrichment also altered the C-cycling processes by modifying C-cycle-related genes, specifically stimulating the Calvin cycle C-fixation process, which led to an increase in the relative abundance of cbbS, prkB, and cbbL genes. However, it had no significant effect on the Reductive citrate cycle and 3-hydroxypropionate bi-cycle. N enrichment led to higher soil CO2 and CH4 emissions compared to treatments without added N. This increase showed significant correlations with C degradation genes (bglA, per, and lpo), methanogenesis genes (mch, ftr, and mcr), methane oxidation genes (pmoA, pmoB, and pmoC), and the abundance of microbial taxa harboring these genes. Microbial C-cycling genes were primarily influenced by N-induced changes in soil properties. Specifically, reduced soil pH largely explained the alterations in methane metabolism, while elevated available N levels were mainly responsible for the shift in C fixation and C degradation genes. Our results suggest that soil N enrichment enhances microbial C-cycling processes and soil CO2 and CH4 emissions in semi-arid ecosystems, which contributes to more accurate predictions of ecosystem C-cycling under future climate change.

High starch and hemicellulose labile C degradation functional genes increase soil CO2 emissions follow straw return

Straw return is a key method to regulate soil carbon (C) by microbial utilization accumulating and CO2 releasing, which mainly depends on microbial metabolism processes. The present knowledge of the mode and mechanism of soil CO2 emission under straw return is limited. We established four straw return treatments, including straw shallow return (SS, 0–20 cm), straw subsoil burial (SD, 20–40 cm), straw mulching (SM), and control with no straw (NS). Microbial metabolic limitation and the abundance of C degradation functional genes were quantified using enzyme stoichiometry and high-throughput quantitative PCR-based chip technology, respectively. The results revealed that the addition of straw inputs resulted in an increase in soil nutrient contents and soil CO2 emissions. The cumulative CO2 emissions of SS and SM treatments were 21,013.53 and 20,819.26 kg hm−2, respectively, which significantly increased by 4.70 % and 3.73 % compared with SD treatment. Compared with SM and SD treatments, microbial C and P limitations of SS treatment were significantly enhanced, increasing by 1.15 %–1.20 % and 2.73 %–1.21 %, respectively. Straw return increased the absolute abundance of genes engaged in decomposing diverse C source compounds, although with a reduction in microbial C use efficiency. The absolute abundance of amyA, apu, sga, abfA, xylA, and manB labile C degradation genes was higher in SM than in SD treatment, increasing by 1.11 %–25.88 %. On the contrary, the absolute abundance of glx and lig recalcitrant C degradation genes was lower in SM than in SD treatment, reducing by 2.96 %–3.68 %. Straw return directly impacts soil nutrient contents and indirectly influences microbial biomass carbon (MBC), nutrient limitation, and C degradation genes, as revealed by the partial least squares pathway model, ultimately leading to changes in soil CO2 emissions. This finding should contribute to the enhancement of soil C retention and the selection of appropriate methods for straw incorporation in tillage fields.

SOC bioavailability significantly correlated with the microbial activity mediated by size fractionation and soil morphology in agricultural ecosystems

Despite the fact that physical and chemical processes have been widely proposed to explicate the stabilization mechanisms of soil organic carbon (SOC), thebioavailability of SOC linked to soil physical structure, microbial community structure, and functional genes remains poorly understood. This study aims to investigate the SOC division based on bioavailability differences formed by physical isolation, and to clarify the relationships of SOC bioavailability with soil elements, pore characteristics, and microbial activity. Results revealed that soil element abundances such as SOC, TN, and DOC ranked in the same order as the soil porosity as clay > silt ≥ coarse sand > fine sand in both top and sub soil. In contrast to silt and clay, which had reduced SOC bioavailability, fine sand and coarse sand had dramatically enhanced SOC bioavailability compared to the bulk soil. The bacterial and fungal community structure was significantly influenced by particle size, porosity, and soil elements. Copiotrophic bacteria and functional genes were more prevalent in fine sand than clay, which also contained more oligotrophic bacteria. The SOC bioavailability was positively correlated with abundances of functional genes, C degradation genes, and copiotrophic bacteria, but negatively correlated with abundances of soil elements, porosity, oligotrophic bacteria, and microbial biomass (p < 0.05). This indicated that the soil physical structure divided SOC into pools with varying levels of bioavailability, with sand fractions having more bioavailable organic carbon than finer fractions. Copiotrophic Proteobacteria and oligotrophic Acidobacteria, Firmicutes, and Gemmatimonadetes made up the majority of the bacteria linked to SOC mineralization. Additionally, the fungi Mortierellomycota and Mucoromycota, which are mostly involved in SOC mineralization, may have the potential for oligotrophic metabolism. Our results indicated that particle-size fractionation could influence the SOC bioavailability by restricting SOC accessibility and microbial activity, thus having a significant impact on sustaining soil organic carbon reserves in temperate agricultural ecosystems, and provided a new research direction for organic carbon stability.