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The makeup of soil microbial communities may serve as a crucial predictor of the alpine grassland ecosystem. Climate change and human disturbance have resulted in intensified ecosystem degradation, such as grassland rocky desertification, which may modify the structures and composition of the microorganisms. However, little is known about the effects of rocky desertification on soil microbial communities of soil. Here, we investigated five different layers of rocky desertification grassland in the Qinghai-Tibet Plateau, including nil rock desertification (NRD); potential rocky desertification (PRD); light rocky desertification (LRD); moderate rocky desertification (MRD); and severe rocky desertification (SRD), we compared soil bacterial community with soil physiochemical properties in different rocky desertification conditions. The result showed that rocky desertification significantly altered the physiochemical properties of the soil but did not significantly affect the bacterial community microbial abundance and diversity. At the same time as rocky desertification increased, soil organic carbon (SOC), total nitrogen (TN), alkali hydrolyzable nitrogen (AN), available phosphorus (AP), and available potassium (AK) decreased significantly, while soil pH, total phosphorus (TP); and total potassium (TK) increased. Redundancy analysis revealed that pH, AK, TP, and SOC are key factors influencing soil bacterial communities. Our finding provides basic information and scientific reference for the restoration of the rocky desertification of alpine grasslands. [ABSTRACT FROM AUTHOR]

Rhombic-spot disease, caused mainly by Neostagonosporella sichuanensis , significantly impacts the yield and quality of fishscale bamboo (Phyllostachys heteroclada). Xylanases are essential for pathogenic fungi infection, yet their specific functions in the physiology and pathogenicity of N. sichuanensis remain unclear. Here, we characterized three xylanase proteins with glycosyl hydrolase 11 domains from the N. sichuanensis SICAUCC 16–0001 genome and examined the function of Nsxyn1 and Nsxyn2. Purified Nsxyn1 and Nsxyn2 proteins displayed specific xylanase activity in vitro and induced cell death in Nicotiana benthamiana , independent of their enzymatic function. Both proteins possessed signal peptides and were confirmed as secreted proteins using a yeast secretion system. Subcellular localization revealed that Nsxyn1 and Nsxyn2 localized in both the cytoplasm and nucleus and can trigger cell death in N. benthamiana through Agrobacterium tumefaciens -mediated transient transformation. qRT-PCR results showed notable upregulation of Nsxyn1 and Nsxyn2 during infection, with Nsxyn1 exhibiting an 80-fold increase at 15 days post-inoculation. Deletion of Nsxyn1 and Nsxyn2 in N. sichuanensis impaired xylan degradation, adaptation to osmotic and oxidative stress, and pathogenic full virulence. Deletion of Nsxyn1 notably slowed fungal growth and reduced spore production, whereas only a reduction in microconidial production was observed in Nsxyn2 mutants. Complementation of Nsxyn1 and Nsxyn2 only partially restored these phenotypic defects in the ∆ Nsxyn1 and ∆ Nsxyn2 mutants. These findings suggest that Nsxyn1 and Nsxyn2 contribute to N. sichuanensis virulence and induced plant defense responses, providing new insights into the function of xylanases in the interaction between fishscale bamboo and N. sichuanensis. [ABSTRACT FROM AUTHOR]

Bamboo resources have garnered significant global attention due to their excellent capacity for regeneration and high yield. Rhombic-spot disease, a substantial threat to fishscale bamboo (Phyllostachys heteroclada), is primarily caused by Neostagonosporella sichuanensis. This study first reported the genome assemblies and characteristics of two N. sichuanensis isolates using PacBio and Illumina sequencing platforms. The genomes of N. sichuanensis strain SICAUCC 16–0001 and strain SICAUCC 23–0140, with sizes of 48.0 Mb and 48.4 Mb, respectively, revealed 10,289 and 10,313 protein-coding genes. Additionally, they contained 34.99 and 34.46% repetitive sequences within AT-rich regions, with notable repeat-induced point mutation activity. Comparative genome analysis identified 1,049 contracted and 45 expanded gene families in the genome of N. sichuanensis , including several related to pathogenicity. Several gene families involved in mycotoxin metabolism, secondary metabolism, sterol biosynthesis and transport, and cell wall degradation were contracted. Compared to most analyzed necrotrophic, hemibiotrophic, and phaeosphaeriacous pathogens, the genomes of two N. sichuanensis isolates exhibited fewer secondary metabolite enzymes, carbohydrate-active enzymes, plant cell wall degrading enzymes, secreted proteins, and effectors. Comparative genomics analysis suggested that N. sichuanensis shares more similar characteristics with hemibiotrophic pathogens. Based on single carbon source tests, N. sichuanensis strains demonstrated a higher potential for xylan decomposition than pectin and cellulose. The proportion of cell wall-degrading enzyme effectors occupied a high proportion of the total effectors of the N. sichuanensis genomes. These findings provide valuable insights into uncovering the pathogenesis of N. sichuanensis toward the efficient management of rhombic-spot disease of fishscale bamboo. [ABSTRACT FROM AUTHOR]

Walnut (Juglans regia L.) is a widely grown nut plant worldwide, including in Guizhou Province, located in southwest China. The high quality and special taste make Guizhou walnuts, particularly those produced in Hezhang County, a "Chinese National Geographical Indication Product" that substantially contributes to the local economy and grower's income. In July 2022, a serious occurrence of leaf spot disease was observed in a walnut plantation area, Shuitang Town, Hezhang County, Guizhou Province, China (27°07'67"N, 104°64'61"E). The causal agent was identified as Didymella segeticola through morphological characterization and amplification and sequencing of the internal transcribed spacer (ITS) region, beta-tubulin (TUB) gene, and glyceraldehyde-3-phosphate dehydrogenase (G3PD) gene. Koch's postulates, including re-isolation and identification, were performed to confirm its pathogenicity on healthy leaves. To our knowledge, this is the first report of D. segeticola causing leaf spot on walnuts worldwide. Further, to determine its biological characteristics, which could be utilized for future disease management, the effects of temperature, light, and carbon and nitrogen resources on mycelial growth, conidia production, and conidia germination and the effects of humidity on conidia germination were studied. The optimum temperature for mycelial growth of representative strain D. segeticola C27 was 20°C. Increasing the light period significantly decreased conidia production and conidia germination. Maltose and beef extract were the best carbon and nitrogen sources, respectively, for the pathogen. Conidia germination was enhanced at 90% humidity. In vitro screening of effective fungicides was conducted. Among the 20 screened fungicides, difenoconazole showed the best inhibition rate, with an EC50 (concentration for 50% of the maximal effect) of 0.0007 µg/mL. Tetramycin also showed sufficient inhibitory effects against D. segeticola, with an EC50 value of 0.0009 µg/mL. Our study provides new insights into the causal agent of walnut leaf spot in Guizhou, China, as well as the first pathogen characteristics and promising candidate fungicides for its management. [ABSTRACT FROM AUTHOR]

Bacterial infections pose a significant clinical burden on global health. The growing incidence of drug-resistant pathogens highlights the critical necessity to identify and isolate bioactive compounds from marine resources. Marinederived fungi could provide novel lead compounds against pathogenic bacteria. Due to the particularity of the marine environment, Aspergillus species derived from marine sources have proven to be potent producers of bioactive secondary metabolites and have played a considerable role in advancing drug development. This study reviews the structural diversity and activities against pathogenic bacteria of secondary metabolites isolated from marine-derived Aspergillus species over the past 14 years (January 2010-June 2024), and 337 natural products (including 145 new compounds) were described. The structures were divided into five major categories--terpenoids, nitrogen-containing compounds, polyketides, steroids, and other classes. These antimicrobial metabolites will offer lead compounds to the development and innovation of antimicrobial agents. [ABSTRACT FROM AUTHOR]

Bamboo resources have garnered significant global attention due to their excellent capacity for regeneration and high yield. Rhombic-spot disease, a substantial threat to fishscale bamboo (Phyllostachys heteroclada), is primarily caused by Neostagonosporella sichuanensis. This study first reported the genome assemblies and characteristics of two N. sichuanensis isolates using PacBio and Illumina sequencing platforms. The genomes of N. sichuanensis strain SICAUCC 16-0001 and strain SICAUCC 23-0140, with sizes of 48.0 Mb and 48.4 Mb, respectively, revealed 10,289 and 10,313 protein-coding genes. Additionally, they contained 34.99 and 34.46% repetitive sequences within ATrich regions, with notable repeat-induced point mutation activity. Comparative genome analysis identified 1,049 contracted and 45 expanded gene families in the genome of N. sichuanensis, including several related to pathogenicity. Several gene families involved in mycotoxin metabolism, secondary metabolism, sterol biosynthesis and transport, and cell wall degradation were contracted. Compared to most analyzed necrotrophic, hemibiotrophic, and phaeosphaeriacous pathogens, the genomes of two N. sichuanensis isolates exhibited fewer secondary metabolite enzymes, carbohydrate-active enzymes, plant cell wall degrading enzymes, secreted proteins, and effectors. Comparative genomics analysis suggested that N. sichuanensis shares more similar characteristics with hemibiotrophic pathogens. Based on single carbon source tests, N. sichuanensis strains demonstrated a higher potential for xylan decomposition than pectin and cellulose. The proportion of cell wall-degrading enzyme effectors occupied a high proportion of the total effectors of the N. sichuanensis genomes. These findings provide valuable insights into uncovering the pathogenesis of N. sichuanensis toward the efficient management of rhombic-spot disease of fishscale bamboo. [ABSTRACT FROM AUTHOR]

Introduction: Grazer exclosure is widely regarded as an effective measure for restoring degraded grasslands, having positive effects on soil microbial diversity. The Intergovernmental Panel on Climate Change (IPCC) predicts that global surface temperatures will increase by 1.5-4.5°C by the end of the 21st century, which may affect restoration practices for degraded grasslands. This inevitability highlights the urgent need to study the effect of temperature on grassland soil microbial communities, given their critical ecological functions. Methods: Here, we assessed the effects of heavy grazing (control), grazer exclosure, and grazer exclosure plus warming by 1.5°C on soil microbial community diversity and network properties as well as their relationships to soil physicochemical properties. Results and discussion: Our results showed that grazer closure increased soil microbial richness relative to heavy grazing controls. Specifically, bacterial richness increased by 7.9%, fungal richness increased by 20.2%, and the number of fungal network nodes and edges increased without altering network complexity and stability. By contrast, grazer exclosure plus warming decreased bacterial richness by 9.2% and network complexity by 12.4% compared to heavy grazing controls, while increasing fungal network complexity by 25.8%. Grazer exclosure without warming increased soil ammonium nitrogen content, while warming increased soil nitrate nitrogen content. Soil pH and organic carbon were not affected by either exclosure strategy, but nitrate nitrogen was the dominant soil factor explaining changes in bacterial communities. Conclusion: Our findings show that grazer exclosure increases soil microbial diversity which are effective soil restoration measures for degraded desert steppe, but this effect is weakened under warming conditions. Thus, global climate change should be considered when formulating restoration measures for degraded grasslands. [ABSTRACT FROM AUTHOR]

Bletilla striata is an endangered traditional medicinal herb in China. In May 2020, the emergence of white root rot severely impacted the quality and yield of B. striata, affecting about 5% of the plants at plant nurseries of the Chengdu Academy of Agricultural and Forestry Sciences. Through a series of experiments and evaluations, the pathogen was identified as Fusarium solani. This is the first report of B. striata white root rot caused by F. solani in Sichuan, China. To better understand this disease and provide data support for its control, a combination of morphological, molecular characterisation and pathogenicity determination was used in this study for assessment. Meanwhile, the effects of different carbon and nitrogen sources, culture medium, temperature, photoperiod and pH on mycelial growth and spore production of F. solani were investigated. In addition, effective fungicides were screened and the concentration ratios of fungicides were optimized using response surface methodology (RSM). The experimental results showed that sucrose was the optimum carbon source for the pathogen, and the optimum temperature and pH were 25°C and pH 7, respectively, while light did no significant effect. Effective fungicides were screened, among which difenoconazole showed the strongest inhibition with EC50 of 142.773 µg/mL. The optimum fungicide concentration scheme (difenoconazole, pyraclostrobin, and thiophanatemethyl at 395.42, 781.03, and 561.11 µg/mL, respectively) was obtained using response surface methodology (RSM) to improve the inhibition rate of 92.24 ± 0.34%. This study provides basic data for the pathogen characterization of B. striata white root rot and its potential fungicides in Sichuan, China. In addition, the optimal fungicide concentration ratios were obtained through response surface methodology (RSM) optimization, which significantly enhanced the fungicidal effect and provided a scientific basis for the future control of B. striata white root rot. [ABSTRACT FROM AUTHOR]

Influenza A virus (IAV) is a highly contagious pathogen causing dreadful losses to humans and animals around the globe. As is known, immune escape is a strategy that benefits the proliferation of IAVs by antagonizing, blocking, and suppressing immune surveillance. The HA protein binds to the sialic acid (SA) receptor to enter the cytoplasm and initiate viral infection. The conserved components of the viral genome produced during replication, known as the pathogen-associated molecular patterns (PAMPs), are thought to be critical factors for the activation of effective innate immunity by triggering dependent signaling pathways after recognition by pattern recognition receptors (PRRs), followed by a cascade of adaptive immunity. Viral infectioninduced immune responses establish an antiviral state in the host to effectively inhibit virus replication and enhance viral clearance. However, IAV has evolved multiple mechanisms that allow it to synthesize and transport viral components by "playing games" with the host. At its heart, this review will describe how host and viral factors interact to facilitate the viral evasion of host immune responses. [ABSTRACT FROM AUTHOR]

Ammonia oxidation is the rate-limiting step in nitrification and the key step in the nitrogen (N) cycle. Most soil nutrients and biological indicators are extremely sensitive to irrigation systems, from the perspective of improving soil fertility and soil ecological environment, the evaluation of different irrigation systems and suitability of selection, promote crop production and soil quality, study the influence of the soil microenvironment contribute to accurate evaluation of irrigation farmland soil health. Based on the amoA gene, the abundance and community diversity of ammonia-oxidizing archaea (AOA) and ammonia- oxidizing bacteria (AOB) and their responses to soil physicochemical factors and enzyme activities were studied in semi-arid areas of Northeast China. The study consisted of three irrigation systems: flood irrigation (FP), shallow buried drip irrigation (DI), and mulched drip irrigation (MF). The results showed that DI and MF significantly increased the contents of alkaline hydrolyzed nitrogen (AN), nitrate nitrogen (NO3--N), soil moisture, and the activities of ammonia monooxygenase (AMO) and hydroxylamine oxidase (HAO). Compared with FP, DI significantly increased the abundance of soil AOA and AOB, while MF significantly increased the abundance of soil AOB. Irrigation systems significantly affected the community composition of ammonia-oxidizing microorganisms (AOM). Also, AN and soil moisture had the greatest influence on the community composition of AOA and AOB, respectively. The AOB community had better stability and stress resistance. Moreover, the symbiotic network of AOB in the three irrigation systems was more complex than that of AOA. Compared with FP, the AOA community under treatment DI had higher complexity and stability, maintaining the versatility and sustainability of the ecosystem, while the AOB community under treatment MF had higher transfer efficiency in terms of matter and energy. In conclusion, DI and MF were more conducive to the propagation of soil AOM in the semi-arid area of Northeast China, which can provide a scientific basis for rational irrigation and N regulation from the perspective of microbiology. [ABSTRACT FROM AUTHOR]

Despite extensive research on the impact of warming and nitrogen deposition on soil organic carbon components, the response mechanisms of microbial community composition and enzyme activity to soil organic carbon remain poorly understood. This study investigated the effects of warming and nitrogen deposition on soil organic carbon components in the Tibetan Plateau alpine meadow and elucidated the regulatory mechanisms of microbial characteristics, including soil microbial community, enzyme activity, and stoichiometry, on organic carbon components. Results indicated that both warming and nitrogen deposition significantly increased soil organic carbon, readily oxidizable carbon, dissolved organic carbon, and microbial biomass carbon. The interaction between warming and nitrogen deposition influenced soil carbon components, with soil organic carbon, readily oxidizable carbon, and dissolved organic carbon reaching maximum values in the W0N32 treatment, while microbial biomass carbon peaked in the W3N32 treatment. Warming and nitrogen deposition also significantly increased soil Cellobiohydrolase, β-1,4-N-acetylglucosaminidase, leucine aminopeptidase, and alkaline phosphatase. Warming decreased the soil enzyme C: N ratio and C:P ratio but increased the soil enzyme N:P ratio, while nitrogen deposition had the opposite effect. The bacterial Chao1 index and Shannon index increased significantly under warming conditions, particularly in the N32 treatment, whereas there were no significant changes in the fungal Chao1 index and Shannon index with warming and nitrogen addition. Structural equation modeling revealed that soil organic carbon components were directly influenced by the negative impact of warming and the positive impact of nitrogen deposition. Furthermore, warming and nitrogen deposition altered soil bacterial community composition, specifically Gemmatimonadota and Nitrospirota, resulting in a positive impact on soil enzyme activity, particularly soil alkaline phosphatase and β-xylosidase, and enzyme stoichiometry, including N:P and C:P ratios. In summary, changes in soil organic carbon components under warming and nitrogen deposition in the alpine meadows of the Tibetan Plateau primarily depend on the composition of soil bacterial communities, soil enzyme activity, and stoichiometric characteristics. [ABSTRACT FROM AUTHOR]

Six new polyketides, which includes three new lactones (talarotones A-C) (1-3), one new polyketide (talarotide A) (4), two new polyenes (talaroyenes A, B) (5, 6), together with one new meroterpenoid (talaropenoid A) (7) and 13 known compounds (8-20) were isolated from the mangrove-derived fungus Talaromyces flavus TGGP35. The structure and configuration of the compounds 1-7 were elucidated from the data obtained from HR-ESI-MS, IR, 1D/2D NMR spectroscopy, Mo2 (OAc)4-induced electronic circular dichroism (ECD), CD spectroscopy, and modified Mosher's method. Compounds 5 and 20 displayed antioxidant activity with IC50 values of 0.40 and 1.36mM, respectively. Compounds 3, 6, 11, 16, and 17 displayed cytotoxic activity against human cancer cells Hela, A549, and had IC50 values ranging from 28.89 to 62.23 µM. Compounds 7, 10-12, and 14-18 exhibited moderate or potent anti-insect activity against newly hatched larvae of Helicoverpa armigera Hubner, with IC50 values in the range 50-200µg/mL. Compound 18 showed antibacterial activity against Ralstonia solanacearum with the MIC value of 50 µg/mL.. [ABSTRACT FROM AUTHOR]

Powdered infant formula (PIF) is prone to Cronobacter sakazakii (C. sakazakii) contamination, which can result in infections that endanger the lives of newborns and infants. Slightly acidic electrolytic water (SAEW) has shown antibacterial effects on a variety of foodborne pathogens and has a wide applicability in the food industry. Here, the antibacterial activity of SAEW against C. sakazakii and its use as a disinfectant on contact surfaces with high infection transmission risk were investigated. The inactivation of SAEW on C. sakazakii was positively correlated to the SAEW concentration and treatment time. The antibacterial effect of SAEW was achieved by decreasing the intracellular adenosine triphosphate (ATP), K+, protein, and DNA contents of C. sakazakii, reducing the intracellular pH (pHin) and destroying the cell morphology, which led to inactivation of C. sakazakii ultimately. To test the applicability of this study, the results showed that approximately 10³ CFU/cm² of C. sakazakii were successfully inactivated on stainless steel and rubber surfaces after a 30 mg/L SAEW treatment for 20 s. These results indicate the antibacterial mechanism and potential application of SAEW against C. sakazakii, as well as a new strategy for the prevention and control of C. sakazakii on stainless steel and rubber surfaces. [ABSTRACT FROM AUTHOR]

Through whole-genome re-sequencing of 18 Hymenopellis radicata germplasm resources collected from diverse regions in China, we identified significant variations in the form of Single Nucleotide Polymorphisms (SNPs) and Insertions and Deletions (InDels). These variations were comprehensively annotated, shedding light on the mutation types present in the entire genome of the H. radicata germplasm. This analysis revealed the number and position information of each mutation and provided insights into the overall genomic landscape of H. radicata germplasm. Utilizing SNP data, we delved into the population structure of the 18 H. radicata germplasm resources. The results indicated the presence of 2,335,179 Indel sites and 12,050,448 SNP sites. The population structure analysis unveiled two distinct subgroups among the H. radicata germplasm resources. Phenotypic statistics, principal component analysis, and phylogenetic tree results echoed the findings of the population structure analysis. Different strains of H. radicata from various regions in China exhibited notable differences in genetic diversity, mycelial growth rate, yield, and fruiting body characteristics. Significant disparities were observed between the two subgroups, while strains within each subgroup shared common characteristics. This research establishes a solid foundation for integrating H. radicata into diverse breeding programs. The data underscore the potential of H. radicata for genetic improvement and exploitation in breeding initiatives, paving the way for future advancements in this field. [ABSTRACT FROM AUTHOR]

As the environmental nuclear radiation pollution caused by nuclear-contaminated water discharge and other factors intensifies, more plant-microorganism-soil systems will be under long-term low-dose ionizing radiation (LLR). However, the regulatory mechanisms of the plant-microorganism-soil system under LLR are still unclear. In this study, we study a system that has been stably exposed to low-dose ionizing radiation for 10 years and investigate the response of the plant-microorganism-soil system to LLR based on the decay of the absorbed dose rate with distance. The results show that LLR affects the carbon and nitrogen migration process between plant-microorganism-soil through the "symbiotic microbial effect." The increase in the intensity of ionizing radiation led to a significant increase in the relative abundance of symbiotic fungi, such as Ectomycorrhizal fungi and Rhizobiales, which is accompanied by a significant increase in soil lignin peroxidase (LiP) activity, the C/N ratio, and C%. Meanwhile, enhanced radiation intensity causes adaptive changes in the plant functional traits. This study demonstrates that the "symbiotic microbial effect" of plant-microorganism-soil systems is an important process in terrestrial ecosystems in response to LLR. [ABSTRACT FROM AUTHOR]

Salmonella enterica serovar Typhimurium (S. Typhimurium) is a common foodborne pathogen which is frequently used as the reference strain for Salmonella. Investigating the sigma factor network and protomers is crucial to understand the genomic and transcriptomic properties of the bacterium. Its promoters were identified using various methods such as dRNA-seq, ChIP-chip, or ChIP-Seq. However, validation using ChIP-exo, which exhibits higher-resolution performance compared to conventional ChIP, has not been conducted to date. In this study, using the representative strain S. Typhimurium LT2 (LT2), the ChIP-exo experiment was conducted to accurately determine the binding sites of catalytic RNA polymerase subunit RpoB and major sigma factors (RpoD, RpoN, RpoS, and RpoE) during exponential phase. Integrated with the results of RNA-Seq, promoters and sigmulons for the sigma factors and their association with RpoB have been discovered. Notably, the overlapping regions among binding sites of each alternative sigma factor were found. Furthermore, comparative analysis with Escherichia coli str. K-12 substr. MG1655 (MG1655) revealed conserved binding sites of RpoD and RpoN across different species. In the case of small RNAs (sRNAs), 50 sRNAs observed their expression during the exponential growth of LT2. Collectively, the integration of ChIP-exo and RNA-Seq enables genome-scale promoter mapping with high resolution and facilitates the characterization of binding events of alternative sigma factors, enabling a comprehensive understanding of the bacterial sigma factor network and condition-specific active promoters. [ABSTRACT FROM AUTHOR]

The current study aims to evaluate and characterize the probiotic andantidiabetic properties of lactic acid bacteria (LAB) obtained from milk and other dairy-based products. The strains were tested physiologically, biochemically, and molecularly. Based on biochemical tests and 16S rRNA gene amplification and sequencing, all three isolates RAMULAB18, RAMULAB19, and RAMULAB53 were identified as Lacticaseibacillus paracasei with homology similarity of more than 98%. The inhibitory potential of each isolate against carbohydrate hydrolysis enzymes (a-amylase and a-glucosidase) was assessed using three different preparations of RAMULAB (RL) isolates: the supernatant (RL-CS), intact cells (RL-IC), and cellfree extraction (RL-CE). Additionally, the isolate was evaluated for its antioxidant activity against free radicals (DPPH and ABTS). The strain's RL-CS, RL-CE, and RL-IC inhibited a-amylase (17.25 to 55.42%), a-glucosidase (15.08-59.55%), DPPH (56.42-87.45%), and ABTS (46.35-78.45%) enzymes differently. With the highest survival rate (>98%) toward tolerance to gastrointestinal conditions, hydrophobicity (>42.18%), aggregation (>74.21%), as well as attachment to an individual's colorectal cancer cell line (HT-29) (>64.98%), human buccal and chicken crop epithelial cells, all three isolates exhibited extensive results. All three isolates exhibited high resistance toward antibiotics (methicillin, kanamycin, cefixime, and vancomycin), and other assays such as antibacterial, DNase, hemolytic, and gelatinase were performed for safety assessment. Results suggest that the LAB described are valuable candidates for their significant health benefits and that they can also be utilized as a beginning or bio-preservative tradition in the food, agriculture, and pharmaceutical sectors. The LAB isolates are excellent in vitro probiotic applicants and yet additional in vivo testing is required. [ABSTRACT FROM AUTHOR]

This study was conducted to compare the effects of rumen-protected (RP-Leu) and unprotected L-leucine (RU-Leu) on the fermentation parameters, bacterial composition, and amino acid metabolism in vitro rumen batch incubation. The 5.00  g RP-Leu or RU-Leu products were incubated in situ in the rumen of four beef cattle (Bos taurus) and removed after 0, 2, 4, 6, 12, 16, and 24  h to determine the rumen protection rate. In in vitro incubation, both RP-Leu and RU-Leu were supplemented 1.5  mmol/bottle (L-leucine HCl), and incubated after 0, 2, 4, 6, 8, 12, and 16  h to measure gas production (GP), nutrient degradability, fermentation parameters, bacterial composition, and amino acids metabolism. Results from both in vitro and in situ experiments confirmed that the rumen protection rate was greater (p  <  0.01) in RP-Leu than in RU-Leu, whereas the latter was slow (p  <  0.05) degraded within incubation 8  h. Free leucine from RP-Leu and RU-Leu reached a peak at incubation 6  h (p  <  0.01). RU-Leu supplementation increased (p  <  0.05) gas production, microbial crude protein, branched-chain AAs, propionate and branched-chain VFAs concentrations, and Shannon and Sobs index in comparison to the control and RP-Leu supplementation. RU-Leu and RP-Leu supplementation decreased (p  <  0.05) the relative abundance of Bacteroidota, which Firmicutes increased (p  <  0.05). Correlation analysis indicated that there are 5 bacteria at the genus level that may be positively correlated with MCP and propionate (p  <  0.05). Based on the result, we found that RP-Leu was more stable than RU-Leu in rumen fluid, but RU-Leu also does not exhibit rapid degradation by ruminal microbes for a short time. The RU-Leu was more beneficial in terms of regulating rumen fermentation pattern, microbial crude protein synthesis, and branched-chain VFAs production than RP-Leu in vitro rumen conditions. [ABSTRACT FROM AUTHOR]

The flavor of cigar tobacco leaf determines the quality of finished cigar tobacco, and the enhancement of flavor generally relies on microbial fermentation. In this paper, the correlation between the dominant microorganisms and the main flavor substances of cigar tobacco leaves during fermentation and the correlation between the two were investigated to reveal the correlation between microorganisms and flavor and the metabolic pathways of microorganisms affecting the flavor substances. During the fermentation process, the main flavors of cigar tobacco leaves were sweet, light and grassy, with hexanal, 2,6-dimethylpyridine, nonanal, phenylacetaldehyde, naphthalene, and methyl benzoate as the main constituents, and the key microorganisms Haloferax mediterranei, Haloterrigena limicola, Candidatus Thorarchaeota archaeon SMTZ-45, the genera Methyloversatilis, Sphingomonas, Thauera, Pseudomonas, Penicillium, and Aspergillus. Correlation analysis revealed that fungi were negatively correlated with the main aroma and inhibited the main flavor substances, while bacteria were positively correlated with Benzoic acid, methyl ester in the main flavor substances, which was conducive to the accumulation of green aroma. Functional analysis revealed that the dominant bacterial population was producing aroma by metabolizing glycoside hydrolases and glycosyltransferases, performing amino acid metabolism, carbohydrate metabolism and film transport metabolism. The present study showed that the bacterial and fungal dominant microorganisms during the fermentation of cigar tobacco were influencing the production and degradation of the main flavor substances through the enzyme metabolism by the occurrence of the Merad reaction. [ABSTRACT FROM AUTHOR]

Rapid growth in the mining industry has brought about a large formation of tailings, which result in serious destruction of the ecological environment and severe soil pollution problems. This study assesses soil nutrients, soil bacterial community and soil microbes' metabolic function in heavily polluted areas (W1), moderately polluted areas (W2), lightly polluted areas (W3) and clean areas (CK) using 16S Illumina sequencing. The results of this study showed that compared with CK, a severe loss of soil nutrients and richness of OTUs (Chao1 and ACE indices) were observed with the aggravated pollution of tailings. The Chao1 and ACE indices in the W1 group decreased significantly by 15.53 and 16.03%, respectively, (p < 0.01). Besides, the relative abundance of Actinobacteria and Proteobacteria was high whereas and relative abundance of Chloroflexi in the polluted areas. Among them, W1 groups increased significantly the relative abundance of Actinobacteria and decreased significantly the relative abundance of Chloroflexi, these can be used as indicator phyla for changes in soil community structures under polluted stress. Tax4 Fun analysis showed that W1 groups affected the soil bacterial community and altered the primary types of biological metabolism in polluted areas. Tailings have adverse impacts on soil bacterial community and metabolic functions, and the deterioration in soil quality is dependent on the levels of tailings pollution. Cumulatively, this study provides valuable information on the bacterial community structure and metabolic functions in the tailing polluted soil. [ABSTRACT FROM AUTHOR]

The interaction between poisonous weeds and neighboring plants is complex. Poisonous weeds frequently have a competitive advantage in the interaction between poisonous weeds and neighboring plants. Arbuscular mycorrhizal fungi (AMF) and plant pathogenic fungi (PPF) are closely related to the interspecific relationships of plants. However, the role of AMF and PPF between poisonous weeds and neighboring grasses remains unclear. Here, we designed a pot experiment to determine the interspecific relationship between Leymus chinensis and Stellera chamaejasme and the regulation of AMF and PPF. The results showed that interactive effects between L. chinensis and S. chamaejasme significantly inhibited the aboveground growth of both but promoted the underground growth of L. chinensis. As the proportions of S. chamaejasme increased, the total nitrogen content and pH in the rhizosphere soil of L. chinensis were reduced, the soil pH of S. chamaejasme was reduced, and the relative abundance of AMF in the rhizosphere soil of L. chinensis significantly increased and that of S. chamaejasme decreased considerably. The relative abundances of PPF in the rhizosphere soil of both in the mono-cultures were significantly higher than those in the mixed cultures. Structural equation modeling indicated that soil abiotic (pH and N availability) and biotic (AMF and PPF) factors are major drivers explaining the interactive effects between L. chinensis and S. chamaejasme. We provided new evidence for the interspecific interactions between poisonous weeds and neighboring grasses and revealed the regulatory role of AMF and PPF in the interactive effects of both plants. This study will provide a scientific basis for the prevention and control of poisonous weeds and the vegetation restoration of degraded grasslands in the future. [ABSTRACT FROM AUTHOR]

Legume crops in rice cultivation are typically rotated and incorporated into the soil as green manure to improve soil fertility. Biochar has recently been co-incorporated with green manure to simultaneously stimulate soil organic carbon (SOC) mineralization and increase carbon (C) sequestration. However, few studies examine the effects of the co-incorporation of biochar and green manure on C cycling and the underlying microbial mechanisms in paddy fields. In this study, the effects of the co-incorporation of green manure and biochar on C mineralization, dissolved organic carbon (DOC) characteristics, and microbial community structures were investigated. A pot study was conducted with three treatments: inorganic NPK (NPK), inorganic NPK + green manure (GM), and inorganic NPK+green manure + biochar (GMC). Organic amendments significantly increased cumulative C mineralization, with amounts in the order GMC (3,434 mg⋅kg-1)> GM (2,934 mg⋅kg-1) > NPK (2,592 mg⋅kg-1). Fertilizer treatments had similar effects on DOC concentrations, with amounts in the order GMC (279 mg⋅kg-1) > GM (255 mg⋅kg-1) > NPK (193 mg⋅kg-1). According to fluorescence spectra, the highest microbial humic acid-like fraction and biological index were also in GMC. Co-incorporation of green manure and biochar shifted the composition of bacterial and fungal communities but more importantly, increased fungal network complexity and decreased bacterial network complexity. The increase in fungal network complexity with the increase in DOC concentrations and microbially derived components was the dominant factor in promoting C mineralization. Overall, this study reveals the underlying biochemical mechanism, the interaction between DOC and fungal network of C cycling in paddy soil under the co-incorporation of green manure and biochar management, and provides fundamental knowledge for exploring effective approaches to improve soil fertility and health in the future. [ABSTRACT FROM AUTHOR]

Satellite RNAs (satRNAs) are molecular parasites that depend on their nonhomologous helper viruses (HVs) for essential biological functions. While there are multiple molecular and phylogenetic studies on satRNAs, there is no experimental evolution study on how satRNAs may evolve in common infection conditions. In this study, we serially passaged the Bamboo mosaic virus (BaMV) associated-satRNA (satBaMV) under conditions in which satBaMV either coinfects an uninfected host plant, Nicotiana benthamiana, with BaMV or superinfects a transgenic N. benthamiana expressing the full-length BaMV genome. Singlenucleotide polymorphisms (SNPs) of satBaMV populations were analyzed by deep sequencing. Forty-eight SNPs were identified across four different experimental treatments. Most SNPs are treatment-specific, and some are also ephemeral. However, mutations at positions 30, 34, 63, and 82, all located at the 5′ untranslated region (UTR), are universal in all treatments. These universal SNPs are configured into several haplotypes and follow different population dynamics. We constructed isogenic satBaMV strains only differing at positions 30 and 82 and conducted competition experiments in protoplasts and host plants. We found that the haplotype that reached high frequency in protoplasts and inoculation leaves also exhibited poor dissemination to systemic leaves and vice versa, thus suggesting an apparent trade-off between local replication and longdistance dissemination. We posit that the trade-off is likely caused by antagonistic pleiotropy at the 5′ UTR. Our findings revealed a hitherto under-explored connection between satRNA genome replication and movement within a host plant. The significance of such a connection during satRNA evolution warrants a more thorough investigation. [ABSTRACT FROM AUTHOR]

Introduction: This study aimed to investigate the genetic factors promoting widespread Q6 dissemination of tet(X4) between Escherichia coli and to characterize the genetic contexts of tet(X4). Methods: We isolated E. coli from feces, water, soil and flies collected across a largescale chicken farm in China in 2020. Antimicrobial susceptibility testing and PFGE typing were used to identify tigecycline resistance and assess clonal relationships among isolates. Plasmids present and genome sequences were analyzed by conjugation, S1 pulsed-field gel electrophoresis (PFGE), plasmid stability testing and whole-genome sequencing. Results: A total of 204 tigecycline-resistant E. coli were isolated from 662 samples. Of these, we identified 165 tet(X4)-carrying E. coli and these strains exhibited a high degree of multidrug resistance. Based on the geographical location distribution of the sampled areas, number of samples in each area and isolation rate of tigecyclineresistant strains and tet(X4)-carrying isolates, 72 tet(X4)-positive isolates were selected for further investigation. Tigecycline resistance was shown to be mobile in 72 isolates and three types of tet(X4)-carrying plasmids were identified, they were IncHI1 (n= 67), IncX1 (n= 3) and pO111-like/IncFIA(HI1) (n= 2). The pO111-like/IncFIA(HI1) is a novel plasmid capable of transferring tet(X4). The transfer efficiency of IncHI1 plasmids was extremely high in most cases and IncHI1 plasmids were stable when transferred into common recipient strains. The genetic structures flanked by IS1, IS26 and ISCR2 containing tet(X4) were complex and varied in different plasmids. Discussion: The widespread dissemination of tigecycline-resistant E. coli is a major threat to public health. This data suggests careful use of tetracycline on farms is important to limit spread of resistance to tigecycline. Multiple mobile elements carrying tet(X4) are in circulation with IncHI1 plasmids the dominant vector in this setting. [ABSTRACT FROM AUTHOR]

Introduction: The Three-River Source Nature Reserve is located in the core area of the Qinghai-Tibetan Plateau, with the alpine swamp, meadow and steppe as the main ecosystem types. However, the microbial communities in these alpine ecosystems, and their carbon and nitrogen degrading metabolic networks and limiting factors remain unclear. Methods: We sequenced the diversity of bacteria and fungi in alpine swamps, meadows, steppes, and their degraded and artificially restored ecosystems and analyzed soil environmental conditions Results: The results indicated that moisture content had a greater influence on soil microbial community structure compared to degradation and restoration. Proteobacteria dominated in high moisture alpine swamps and alpine meadows, while Actinobacteria dominated in low moisture alpine steppes and artificial grasslands. A metabolic network analysis of carbon and nitrogen degradation and transformation using metagenomic sequencing revealed that plateau microorganisms lacked comprehensive and efficient enzyme systems to degrade organic carbon, nitrogen, and other biological macromolecules, so that the shortterm degradation of alpine vegetation had no effect on the basic composition of soil microbial community. Correlation analysis found that nitrogen fixation was strong in meadows with high moisture content, and their key nitrogen-fixing enzymes were significantly related to Sphingomonas. Denitrification metabolism was enhanced in water-deficient habitats, and the key enzyme, nitrous oxide reductase, was significantly related to Phycicoccus and accelerated the loss of nitrogen. Furthermore, Bacillus contained a large number of amylases (GH13 and GH15) and proteases (S8, S11, S26, and M24) which may promote the efficient degradation of organic carbon and nitrogen in artificially restored grasslands. Discussion: This study illustrated the irrecoverability of meadow degradation and offered fundamental information for altering microbial communities to restore alpine ecosystems. [ABSTRACT FROM AUTHOR]

Wetlands are an important source of atmospheric methane (CH4) and are sensitive to global climate change. Alpine swamp meadows, accounting for ~50% of the natural wetlands on the Qinghai-Tibet Plateau, were considered one of the most important ecosystems. Methanogens are important functional microbes that perform the methane producing process. However, the response of methanogenic community and the main pathways of CH4 production to temperature rise remains unknown in alpine swamp meadow at different water level in permafrost wetlands. In this study, we investigated the response of soil CH4 production and the shift of methanogenic community to temperature rise in the alpine swamp meadow soil samples with different water levels collected from the Qinghai-Tibet Plateau through anaerobic incubation at 5°C, 15°C and 25°C. The results showed that the CH4 contents increased with increasing incubation temperature, and were 5-10 times higher at the high water level sites (GHM1 and GHM2) than that at the low water level site (GHM3). For the high water level sites (GHM1 and GHM2), the change of incubation temperatures had little effect on the methanogenic community structure. Methanotrichaceae (32.44-65.46%), Methanobacteriaceae (19.30-58.86%) and Methanosarcinaceae (3.22-21.24%) were the dominant methanogen groups, with the abundance of Methanotrichaceae and Methanosarcinaceae having a significant positive correlation with CH4 production (p < 0.01). For the low water level site (GHM3), the methanogenic community structure changed greatly at 25°C. The Methanobacteriaceae (59.65-77.33%) was the dominant methanogen group at 5°C and 15°C; In contrast, the Methanosarcinaceae (69.29%) dominated at 25°C, and its abundance showed a significant positive correlation with CH4 production (p < 0.05). Collectively, these findings enhance the understanding of methanogenic community structures and CH4 production in permafrost wetlands with different water levels during the warming process. [ABSTRACT FROM AUTHOR]

Under climate warming conditions, storage and conversion of soil inorganic carbon (SIC) play an important role in regulating soil carbon (C) dynamics and atmospheric CO2 content in arid and semi-arid areas. Carbonate formation in alkaline soil can fix a large amount of C in the form of inorganic C, resulting in soil C sink and potentially slowing global warming trends. Therefore, understanding the driving factors affecting carbonate mineral formation can help better predict future climate change. Till date, most studies have focused on abiotic drivers (climate and soil), whereas a few examined the effects of biotic drivers on carbonate formation and SIC stock. In this study, SIC, calcite content, and soil microbial communities were analyzed in three soil layers (0-5 cm, 20-30 cm, and 50-60 cm) on the Beiluhe Basin of Tibetan Plateau. Results revealed that in arid and semi-arid areas, SIC and soil calcite content did not exhibit significant differences among the three soil layers; however, the main factors affecting the calcite content in different soil layers are different. In the topsoil (0-5 cm), the most important predictor of calcite content was soil water content. In the subsoil layers 20-30 cm and 50-60 cm, the ratio of bacterial biomass to fungal biomass (B/F) and soil silt content, respectively, had larger contributions to the variation of calcite content than the other factors. Plagioclase provided a site for microbial colonization, whereas Ca2+ contributed in bacteria-mediated calcite formation. This study aims to highlight the importance of soil microorganisms in managing soil calcite content and reveals preliminary results on bacteriamediated conversion of organic to inorganic C. [ABSTRACT FROM AUTHOR]

Adenylate cyclase (AC) regulates growth, reproduction, and pathogenicity in many fungi by synthesizing cyclic adenosine monophosphate (cAMP) and activating downstream protein kinase A (PKA). Botrytis cinerea is a typical necrotrophic plant-pathogenic fungus. It shows a typical photomorphogenic phenotype of conidiation under light and sclerotia formation under dark; both are important reproduction structures for the dispersal and stress resistance of the fungus. The report of B. cinerea adenylate cyclase (BAC) mutation showed it affects the production of conidia and sclerotia. However, the regulatory mechanisms of the cAMP signaling pathways in photomorphogenesis have not been clarified. In this study, the S1407 site was proven to be an important conserved residue in the PP2C domain which poses a remarkable impact on the phosphorylation levels and enzyme activity of the BAC and the overall phosphorylation status of total proteins. The point mutation bacS1407P, complementation bacP1407S, phosphomimetic mutation bacS1407D, and phosphodeficient mutation bacS1407A strains were used for comparison with the light receptor white-collar mutant Δbcwcl1 to elucidate the relationship between the cAMP signaling pathway and the light response. The comparison of photomorphogenesis and pathogenicity phenotype, evaluation of circadian clock components, and expression analysis of light response transcription factor genes Bcltf1, Bcltf2, and Bcltf3 showed that the cAMP signaling pathway could stabilize the circadian rhythm that is associated with pathogenicity, conidiation, and sclerotium production. Collectively, this reveals that the conserved S1407 residue of BAC is a vital phosphorylation site to regulate the cAMP signaling pathway and affects the photomorphogenesis, circadian rhythm, and pathogenicity of B. cinerea. [ABSTRACT FROM AUTHOR]

Introduction: Toll-like receptor 4 (TLR4) identifies Gram-negative bacteria or their products and plays a crucial role in host defense against invading pathogens. In the intestine, TLR4 recognizes bacterial ligands and interacts with the immune system. Although TLR4 signaling is a vital component of the innate immune system, the influence of TLR4 overexpression on innate immune response and its impact on the composition of the intestinal microbiota is unknown. Methods: Here, we obtained macrophages from sheep peripheral blood to examine phagocytosis and clearance of Salmonella Typhimurium (S. Typhimurium) in macrophages. Meanwhile, we characterized the complex microbiota inhabiting the stools of TLR4 transgenic (TG) sheep and wild-type (WT) sheep using 16S ribosomal RNA (rRNA) deep sequencing. Results: The results showed that TLR4 overexpression promoted the secretion of more early cytokines by activating downstream signaling pathways after stimulation by S. Typhimurium. Furthermore, diversity analysis demonstrated TLR4 overexpression increased microbial community diversity and regulated the composition of intestinal microbiota. More importantly, TLR4 overexpression adjusted the gut microbiota composition and maintained intestinal health by reducing the ratio of Firmicutes/Bacteroidetes and inflammation and oxidative stress-producing bacteria (Ruminococcaceae, Christensenellaceae) and upregulating the abundance of Bacteroidetes population and short-chain fatty acid (SCFA)-producing bacteria, including Prevotellaceae. These dominant bacterial genera changed by TLR4 overexpression revealed a close correlation with the metabolic pathways of TG sheep. Discussion: Taken together, our findings suggested that TLR4 overexpression can counteract S. Typhimurium invasion as well as resist intestinal inflammation in sheep by regulating intestinal microbiota composition and enhancing anti-inflammatory metabolites. [ABSTRACT FROM AUTHOR]

In this study, the effects of the immobilized bacterial mixture (IM-FN) of Arthrobacter sp. NJ-1 and Klebsiella variicola strain FH-1 using sodium alginate-CaCl2 on the degradation of atrazine were investigated. The results showed that the optimal ratio of three types of carrier materials (i.e., rice straw powder, rice husk, and wheat bran) was 1:1:1 with the highest adsorption capacity for atrazine (i.e., 3774.47 mg/kg) obtained at 30°C. On day 9, the degradation efficiency of atrazine (50 mg/L) reached 98.23% with cell concentration of 1.6 × 108 cfu/ml at pH 9 and 30°C. The Box-Behnken method was used to further optimize the culture conditions for the degradation of atrazine by the immobilized bacterial mixture. The IM-FN could be reused for 2-3 times with the degradation efficiency of atrazine maintained at 73.0% after being stored for 80 days at 25°C. The population dynamics of IM-FN was explored with the total soil DNA samples specifically analyzed by real-time PCR. In 7 days, the copy numbers of both PydC and estD genes in the IM-FN were significantly higher than those of bacterial suspensions in the soil. Compared with bacterial suspensions, the IM-FN significantly accelerated the degradation of atrazine (20 mg/kg) in soil with the halflife shortened from 19.80 to 7.96 days. The plant heights of two atrazine-sensitive crops (wheat and soybean) were increased by 14.99 and 64.74%, respectively, in the soil restored by immobilized bacterial mixture, indicating that the IM-FN significantly reduced the phytotoxicity of atrazine on the plants. Our study evidently demonstrated that the IM-FN could significantly increase the degradation of atrazine, providing a potentially effective bioremediation technique for the treatment of atrazine-polluted soil environment and providing experimental support for the wide application of immobilized microorganism technology in agriculture. [ABSTRACT FROM AUTHOR]

Methyl-branched aldehydes, especially 3-methylbutanal, have been reported to be perceived either as a malty or as a nutty/chocolate-like aroma and were considered an important flavor contributor in fermented meat products. Decomposition of leucine (Leu) by branched-chain amino acid transaminase (BACT) is a crucial step in the metabolism of Leu to 3-methylbutanal. This study was conducted to explore the effects of mixed-starter culture (Lactobacillus fermentum YZU-06 and Staphylococcus saprophyticus CGMCC 3475) and addition of Leu (0, 1, and 3 mM) on the flavor and quality of fermented sausages. The pH, water activity, texture profile analysis, color, counts of lactic acid bacteria (LAB) and staphylococci, peptide, and flavor compounds were detected during fermentation. The results showed that the starter culture group increased hardness, elasticity, the counts of LAB and staphylococci, peptide content, volatile flavor compounds, as well as the sensorial scores of sausage, while decreasing pH, aw, and L* and b* values compared with the non-inoculation group. The mixed starter of adding with 3 mM Leu enhanced the content of 3-methylbutanal and overall flavor of fermented sausages. It is applicable to directionally produce methyl-branched aldehydes and improve the overall quality of fermented sausage by the addition of Leu and using starter of L. fermentum YZU-06 and S. saprophyticus CGMCC 3475. [ABSTRACT FROM AUTHOR]

The physicochemical property, volatile flavor compounds, and microbial community structure of Jinhua fatty ham (FH) and lean ham (LH) were investigated and compared by high-throughput sequencing and HS-GC-IMS. Results showed that FH had higher pH and slightly lighter and yellower color than LH. Meanwhile, 33 volatile flavor compounds were identified from FH and LH, among which LH showed higher abundance of total alcohols and acids, but FH had generally richer aldehydes, ketones, esters, heterocyclic, and sulfur-containing compounds. Moreover, FH and LH did not have significant difference in α-diversity of bacterial community, but LH presented a much lower α-diversity of fungal community than FH. Besides, the dominant microorganisms (relative abundance >2%) in FH were Ruminococcaceae UCG-005, Staphylococcus, Ruminococcaceae UCG-014, Meyerozyma, and Aspergillus at the genus level, while in LH were Staphylococcus, Psychrobacter, Halomonas, Propionicicella, Ruminococcaceae UCG-005, Meyerozyma, Yamadazyma, and Aspergillus. Furthermore, the analysis of Pearson’s correlation and metabolic network confirmed that the discriminative flavor compounds of FH were mainly β-oxidation and degradation products of fatty acids, while those of LH were mostly derived from the Strecker reaction or microbial metabolism of amino acids. The present study could help understand the potential pathway of characteristic microorganisms affecting flavor formation of fat-deficient dry-cured hams and provide theoretical supports for developing healthier fermented meat products. [ABSTRACT FROM AUTHOR]

Ganoderma lucidum is a traditional Chinese medicine and its major active ingredients are ganoderma triterpenoids (GTs). To screen for transcription factors (TFs) that involved in the biosynthetic pathway of GTs in G. lucidum, the chemical composition in mycelia, primordium and fruiting body were analyzed, and the transcriptomes of mycelia induced by methyl jasmonate (MeJA) were analyzed. In addition, the expression level data of MeJAresponsive TFs in mycelia, primordia and fruiting body were downloaded from the database, and the correlation analysis was carried out between their expression profiles and the content of total triterpenoids. The results showed that a total of 89 components were identified, and the content of total triterpenoids was the highest in primordium, followed by fruiting body and mycelia. There were 103 differentially expressed TFs that response to MeJA-induction including 95 upregulated and 8 downregulated genes. These TFs were classified into 22 families including C2H2 (15), TFII-related (12), HTH (9), fungal (8), bZIP (6), HMG (5), DADS (2), etc. Correlation analysis showed that the expression level of GL23559 (MADS), GL26472 (HTH), and GL31187 (HMG) showed a positive correlation with the GTs content, respectively. While the expression level of GL25628 (fungal) and GL26980 (PHD) showed a negative correlation with the GTs content, respectively. Furthermore, the over expression of the Glmhr1 gene (GL25628) in Pichia pastoris GS115 indicated that it might be a negative regulator of GT biosynthesis through decreasing the production of lanosterol. This study provided useful information for a better understanding of the regulation of TFs involved in GT biosynthesis and fungal growth in G. lucidum. [ABSTRACT FROM AUTHOR]

Soil microorganisms play an irreplaceable role in agricultural production, however, an understanding of response of soil microorganisms to slow-release and common fertilizer applications is limited. In this study, different amounts of slow-release fertilizer were used to overwintering Chinese chives growing area in a plastic greenhouse to investigate the effects of on rhizosphere soil physicochemical properties and soil microbial communities (bacteria and fungi) of Chinese chives. The result displayed that application of slowrelease fertilizer significantly improved soil nutrients, soil enzyme activity, and soil microbial community structure and diversity compared to conventional fertilizer application. Compared with T1 treatment, the content of total nitrogen (TN) and available phosphorus (AP), and the SU-E activity in the soil of T2 (NPK: 62.8 kg · 667 m-2) increased by 42.58%, 16.67%, and 9.70%, respectively, showing the best effects. In addition, soil bacterial diversity index and soil microbial community structure were improved as indicated by increased relative abundance of each species, such as Byssovorax, Sandaracinus, and Cellvibrio. Oppositely, the both soil fungal diversity and the number of species decreased after fertilizationthe relative abundance of Ascomycota increased in each fertilization treatment detected by ITS sequencing. Further, the relative abundance of pathogenic fungi such as Pezizomycetes, Cantharellales, and Pleosporales decreased in the T2 treatment. Principal Coordinates Analysis (PCoA) showed that both the amount of fertilizer applied and the type of fertilizer applied affected the soil microbial community structure. RDA evidenced that soil bacteria, Proteobacteria and Gemmatimonadetes, were closely correlated with soil AN, SOM, and AK. Acidobacteria were closely correlated with soil pH, TN, and AP. Ascomycota was closely correlated with soil pH and TN. In conclusion, the application of slow-release fertilizers and reduced fertilizer applicationcould improve soil physical and chemical properties as well as soil microbial community structure and diversity, contributing to sustainable soil development. The recommended fertilization rate for overwintering Chinese chives is NPK: 62.8 kg · 667 m-2. [ABSTRACT FROM AUTHOR]

Land-use conversion affects the composition and assembly of plant-associated microbiomes, which in turn affects plant growth, development, and ecosystem functioning. However, agroforestry systems, as sustainable land types, have received little attention regarding the dynamics of different plant-associated microbes. In this study, we used high-throughput sequencing technology to analyze the assembly mechanisms and the driving factors of pine-and Panax notoginseng (P.n.)-associated microbiomes during the conversion of different pine forests (Pinus kesiya var. langbianensis and Pinus armandii) into P.n.-pine agroforestry systems. The results showed that the conversion of pure pine forest into P.n.-pine agroforestry systems significantly altered the diversity of pine-associated fungi rather than the community structure, and the community structure of P.n.-associated fungi rather than the diversity. Additionally, plant-associated fungi were more responsive to land-use change than bacteria. Main effect analysis revealed that compartment rather than genotype was the driving factor of pine- and P.n.-associated microbiomes, but P.n. cultivation also significantly affected the assembly of pine-associated microbiomes. In addition, there was a transfer of P.n. endophytes to pine trees in agroforestry systems and the beneficial microbiomes (Massilia, Marmoricola, Herbaspirillum, etc.) were enlarged in pine roots. Therefore, the diversity of the assembly mechanisms of P.n.- and pine-associated microbiomes played an important role in the P.n.--pine agroforestry systems and were the basis for the sustainable development of the P.n.--pine agroforestry systems. [ABSTRACT FROM AUTHOR]

Candida albicans is a symbiotic fungus that commonly colonizes on oral mucosal surfaces and mainly affects immuno-compromised individuals. Polymicrobial interactions between C. albicans and oral microbes influence the cellular and biochemical composition of the biofilm, contributing to change clinically relevant outcomes of biofilm-related oral diseases, such as pathogenesis, virulence, and drug-resistance. Notably, the symbiotic relationships between C. albicans and oral bacteria have been welldocumented in dental caries, oral mucositis, endodontic and periodontal diseases, implant-related infections, and oral cancer. C. albicans interacts with co-existing oral bacteria through physical attachment, extracellular signals, and metabolic cross-feeding. This review discusses the bacterial–fungal interactions between C. albicans and different oral bacteria, with a particular focus on the underlying mechanism and its relevance to the development and clinical management of oral diseases. [ABSTRACT FROM AUTHOR]

In Sichuan province, walnuts, consisting of Juglans regia, Juglans sigillata, and the hybrid J. regia × J. sigillata, are commercially important edible nuts, and J. regia is the most widespread plant. To date, the diversity and distribution of fungi inhabiting on Juglans have not received enough attention, although there have been studies focusing on pathogens from fruit and stem. In order to update the checklist of fungi associated with Sichuan walnuts, a survey on fungi associated with the three Juglans species from 15 representative regions in Sichuan was conducted. In this article, ten fungi distributed in two classes of Ascomycota (Dothideomycetes and Sordariomycetes) were described based on morpho-molecular analyses, and two novel species, Neofusicoccum sichuanense and Sphaerulina juglandina, a known species of Ophiognomonia leptostyla, and seven new hosts or geographical records of Cladosporium tenuissimum, Diatrypella vulgaris, Helminthosporium juglandinum, Helminthosporium velutinum, Loculosulcatispora hongheensis, Periconia byssoides, and Rhytidhysteron subrufulum were included. Morphological descriptions and illustrations of these fungi are provided. [ABSTRACT FROM AUTHOR]

Microbial decomposition plays a crucial role in the incorporation of straw and straw biochar (SSB) into soil. Lime concretion black soil (LCBS) is a typical low-medium crop yield soil, and it is also one of the main soil types for grain production in China. However, the link between SSB additions and soil bacterial communities in LCBS remains unclear. This study explored the effects of SSB incorporation on bacterial community composition, structure and co-occurrence network patterns at different soil depths and maize growth stages. The results showed that soil PH, soil organic matter and total nitrogen significantly affected the seasonality and stratification of the soil bacterial community. The composition and diversity of bacterial communities were significantly affected by growth period and treatment rather than soil depth. Specifically, the bacterial community diversity increased significantly with crop growth at 0–20 cm, decreased the relative abundance of Actinobacteria, and increased the relative abundance of Proteobacteria and Acidobacteria. SF (straw with fertilizer) and BF (straw biochar with fertilizer) treatments decreased bacterial community diversity. Co-occurrence networks are more complex in BF, S (straw), and SF treatments, and the number of edge network patterns is increased by 92.5, 40, and 60% at the maturity stage compared with F (fertilizer) treatment, respectively. Moreover, the positive effect of straw biochar on the bacterial network pattern increased with time, while the effect of straw weakened. Notably, we found that rare species inside keystone taxa (Gemmatimonadetes and Nitrospirae) play an indispensable role in maintaining bacterial network construction in LCBS. This study offers a comprehensive understanding of the response of soil bacterial communities to SSB addition in LCBS areas, and provides a reference for further improvement of LCBS productivity. [ABSTRACT FROM AUTHOR]

Giant pandas have developed a series of foraging strategies to adapt to their special bamboo diets. Although bamboo is an important food resource for giant pandas in Liziping National Nature Reserve (Liziping NR), China, there are relatively few studies on their phyllosphere fungal community and its influencing factors. Herein, we used ITS1 amplification and metagenomic sequencing to analyze the phyllosphere fungi diversity and functions (KEGG, CAZyme, and antibiotic resistance gene) and explore the influencing factors for the three giant pandas foraging bamboo species (Arundinaria spanostachya, AS; Yushania lineolate, YL; and Fargesia ferax, FF) over different seasons (spring vs. autumn) in Liziping NR, China. We found that Ascomycota and Basidiomycota were the most dominant phyla in the bamboo phyllosphere. The alpha diversity (e.g., the Sobs index and Shannon index) was relatively higher in autumn samples than in spring samples, and the community structure differed significantly between the three bamboo species in spring and autumn. Some biotic and abiotic variables (e.g., the elevation and mean base diameter of bamboo) significantly influenced the abundance, diversity, and community structure of the bamboo phyllosphere fungal community. Moreover, the functional analysis showed the differences in the glycoside hydrolase community and antibiotic resistance gene (ARG) profile between spring and autumn samples. Co--occurrence network modeling suggested that AS phyllosphere fungal communities in autumn employed a much more complex network than that in spring, and the abundance of multidrug, tetracycline, and glycopeptide resistance genes was high and closely correlated with other ARGs. These results indicate that fungal community's abundance, diversity, and community structure are mainly affected by the season, host species, and elevation. The season and host species are major factors affecting the biological functions (KEGG and CAZyme), ARGs, and interactions between sympatric bacterial and fungal communities in bamboo phyllosphere. This integrated study can provide a reference basis for the seasonal management of bamboo resources foraged by wild giant pandas, and predict the risk of antibiotic resistance in bamboo phyllosphere fungal flora in Liziping NR (Xiaoxiangling mountains), China. [ABSTRACT FROM AUTHOR]

Candida albicans is a prevalent, opportunistic human fungal pathogen. It usually dwells in the human body as a commensal, however, once in its pathogenic state, it causes diseases ranging from debilitating superficial to life-threatening systemic infections. The switch from harmless colonizer to virulent pathogen is, in most cases, due to perturbation of the fungushost-microbiota interplay. In this review, we focused on the interactions between C. albicans and the host microbiota in the mouth, gut, blood, and vagina. We also highlighted important future research directions. We expect that the evaluation of these interplays will help better our understanding of the etiology of fungal infections and shed new light on the therapeutic approaches. [ABSTRACT FROM AUTHOR]

Cypermethrin is an important synthetic pyrethroid pesticide that widely used to control pests in agriculture. However, extensive use has caused its residue and the metabolite 3-phenoxybenzoic acid (3-PBA) to seriously pollute the environments and agricultural products. In this study, a highly efficient cypermethrin-degrading bacterial consortium was acclimated from long-term pyrethroid-contaminated soil. Two strains, designated JQ-L and A-3, were screened from the consortium, and identified as Rhodococcus sp. and Comamonas sp., respectively. Strain JQ-L transformed 100 mg/L of cypermethrin to 3-PBA within 60 h of incubation; however, 3-PBA could not be further degraded by the strain. Strain A-3 utilized 3-PBA as sole carbon for growth, and completely degraded 100 mg/L of 3-PBA within 15 h of incubation. Co-culture of JQ-L and A-3 completely degraded 100 mg/L of cypermethrin within 24 h of incubation. Furthermore, a complete catabolic pathway of cypermethrin and the metabolite 3-PBA by the co-culture was proposed. This study provided a promising strategy for efficient elimination of cypermethrin residue-contaminated environments and agricultural products. [ABSTRACT FROM AUTHOR]

In this study, silage Pennisetum sinese Roxb-based diet was replaced with fermented pineapple residue (FPR) at the replacement ratio of 0% (CON), 25% (T25), and 50% (T50) in fattening Simmental bulls for 30 days to evaluate the effects of FPR on growth performance, serum indexes, and ruminal characteristics. A total of 30 Simmental bulls (546 ± 44 kg initial BW) were allocated to three groups according to a completely randomized design. On day 30, the slaughter performance and meat quality were determined. Rumen fluids were collected for analyzing the rumen fermentation parameters and microbiota composition on day 30. The results showed that the average daily weight gain increased (P < 0.05) as the proportion of FPR rose. Within treatments, the T25 group reached more profit (5.34 RMB per day per bull) than CON while T50 was 3.69. The content of crude fat, cysteine, and proline in the muscle of T50 increased significantly (P < 0.05). The amounts of tyrosine, proline, and phenylalanine were significantly increased in the T25 (P < 0.05). The beta diversity analysis showed significant differences among the rumen bacterial flora of each group (P < 0.05). In the T25 group, the relative abundance of Spirochaetes decreased significantly (P < 0.05). The relative abundance of Lachnospiraceae_bacterium_RM44 was significantly lower (P < 0.05). Thus, FPR could improve the growth performance, economic benefits, and meat quality without adverse effects on ruminal characteristics. [ABSTRACT FROM AUTHOR]

Dendrobium nobile, an epiphytic plant, is a traditional medicinal herb with abundant endophytes. It is unclear whether the variation in the diversity and abundance of endophytes could stimulate the biosynthesis of medicinal compounds in the plant. In this study, we collected fresh stems of D. nobile from four habitats for investigating the fungal community structure, dendrobine content, and environment factors and their correlations. The results indicated no significant difference in endophytic fungal diversity among the habitats; however, different dominant or special endophytic genera were observed in the hosts from different habitats. The altitude was observed to be positively related to the dendrobine content, as the stems collected from the altitude of 692 m exhibited the highest level of dendrobine. Furthermore, the relative abundance of Toxicocladosporium was found to be positively correlated with the altitude and dendrobine content. The epiphytic matrix exhibited a significant negative correlation with the relative abundance of the endophytic fungus Gibberella but did not exhibit any significant correlation with the dendrobine content. The results indicated that the abundance of endophytes in D. nobile was affected by the altitude and epiphytic matrix and that high Toxicocladosporium abundance and high altitude were conducive to dendrobine production. [ABSTRACT FROM AUTHOR]

Aim: The aroma-producing strain of Geotrichum candidum GDMCC60675 was taken as the research object, the composition of aroma-producing substances of G. candidum was studied, and the target strains of G. candidum suitable for food additives were screened out by mutagenesis. Methods: Mutants were obtained by space breeding. The colony morphology and cell morphology of the mutant strain were identified, the phylogenetic tree of the two strains was constructed, and the whole-genome sequences of the wild strain and the mutant strain were compared. The aroma components and key odor compounds of the two strains were analyzed and compared by HS-SPME-GC-MS and E-nose detection, and the data were processed by using the relative odor activity value (ROAV) analysis method. Results: A mutant strain of G. candidum was found with different characteristics of aroma production compared with wild-type G. candidum. It was found that its colony morphology and cell morphology were similar. However, it was found that the aroma-producing substances produced by the two strains were different, and the key difference compound was phenyl ethyl alcohol, which also proved that the two strains were different, and the main aroma note was different. [ABSTRACT FROM AUTHOR]

Currently, how rice roots interact with straw return in structuring rhizosphere communities and nitrogen (N) cycling functions is relatively unexplored. In this study, paddy soil was amended with wheat straw at 1 and 2% w/w and used for rice growth. The effects of the rhizosphere, straw, and their interaction on soil bacterial community composition and N-cycling gene abundances were assessed at the rice maturity stage. For the soil without straw addition, rice growth, i.e., the rhizosphere effect, significantly altered the bacterial community composition and abundances of N-cycling genes, such as archaeal and bacterial amoA (AOA and AOB), nirK, and nosZ. The comparison of bulk soils between control and straw treatments showed a shift in bacterial community composition and decreased abundance of AOA, AOB, nirS, and nosZ, which were attributed to sole straw effects. The comparison of rhizosphere soils between control and straw treatments showed an increase in the nifH gene and a decrease in the nirK gene, which were attributed to the interaction of straw and the rhizosphere. The number of differentially abundant genera in bulk soils between control and straw treatments was 13–23, similar to the number of 16–22 genera in rhizosphere soil between control and straw treatment. However, the number of genera affected by the rhizosphere effect was much lower in soil amended with straw (3–4) than in soil without straw addition (9). Results suggest possibly more pronounced impacts of straw amendments in shaping soil bacterial community composition. [ABSTRACT FROM AUTHOR]

Plateau pikas (Ochotona curzoniae) are high-altitude model animals and famous "ecosystem engineers" on the Qinghai-Tibet Plateau. Pika activities may accelerate the degradation of alpine meadows. Nevertheless, little is known about the responses of bacterial, fungal, and archaeal communities, and ecosystem multifunctionality to pika perturbations. To address this question, we studied the impacts of only pika disturbance and combined disturbance (pika disturbance and grazing) on ecological networks of soil microbial communities and ecosystem multifunctionality. Our results demonstrated that Proteobacteria, Ascomycota, and Crenarchaeota were dominant in bacteria, fungi, and archaea, respectively. Bacteria, fungi, and archaea were all influenced by the combined disturbance of grazing and pika. Most fungal communities became convergent, while bacterial and archaeal communities became differentiated during the succession of surface types. In particular, the bacterial and fungal networks were less stable than archaeal networks. In response to the interference, cross-domain cooperation between bacterial and fungal communities increased, while competitive interactions between bacterial and archaeal communities increased. Pika disturbance at high intensity significantly reduced the ecosystem multifunctionality. However, the mixed effects of grazing and pika weakened such influences. This study revealed how pika activities affected microbial networks and ecosystem multifunctionality. These results provide insights to designing reasonable ecological management strategies for alpine grassland ecosystems. [ABSTRACT FROM AUTHOR]

Soil microbes play a crucial role in a forest ecosystem. However, whether the distribution of bacteria and fungi in different forest succession stages is random or following ecological specialization remains to be further studied. In the present study, we characterized soil bacterial and fungal communities to determine their distribution preference, with different succession communities in a temperate mountain forest. The Kruskal–Wallis method was used to analyze structural differences between bacterial and fungal communities in different succession processes. The specificity of soil microbial distribution in a secondary forest was studied by network analysis. The torus-translation test was used to analyze the species distribution preference of soil microbes in different succession stages. Results showed that the species composition of soil bacteria and fungi differed significantly in different succession processes. The modularity index of fungi (0.227) was higher than that of bacteria (0.080). Fungi (54.47%) had specific preferences than bacteria (49.95%) with regard to forests in different succession stages. Our work suggests that the distribution pattern of most soil microbes in a temperate mountain forest was not random but specialized in temperate mountain forests. Different microbes showed different distribution preferences. Fungi were more sensitive than bacteria during secondary succession in a temperate mountain forest. In addition, microbe–environment relations varied during secondary succession. Our results provided new insight into the mechanism through which complex soil microbial communities responded to changes in forest community succession. [ABSTRACT FROM AUTHOR]

Interactions of Shiga toxin–producing E. coli (STEC; O103:H2) with lactic acid bacteria (LAB) or spoilage bacteria (SP) multispecies biofilms on polyurethane (TPU) and stainless-steel (SS) were assessed at 10 and 25°C under wet and dry conditions after 6, 30, and 60 days of storage. One LAB T1: Carnobacterium piscicola + Lactobacillus bulgaricus , and two SP T2: Comamonas koreensis + Raoultella terrigena; T3: Pseudomonas aeruginosa + C. koreensis were assessed for their ability to form multispecies biofilms with O103:H2. O103:H2 single-species biofilms served as a control positive (T4). Coupons were stored dry (20–50% relative humidity; RH) or moist (60–90% RH) for up to 60 days, at which point O103:H2 transfer to beef and survival was evaluated. At 25°C, T3 decreased beef contamination with O103:H2 by 2.54 log10 CFU/g (P < 0.001). Overall, at 25°C contamination of beef with O103:H2 decreased (P < 0.001) from 3.17 log10 CFU/g on Day 6 to 0.62 log10 CFU/g on Day 60. With 60 days dry biofilms on TPU, an antagonistic interaction was observed among O103:H2 and multispecies biofilm T1 and T3. E. coli O103:H2 was not recovered from T1 and T3 after 60 days but it was recovered (33%) from T2 and T4 dry biofilms. At 10°C, contamination of beef with O103:H2 decreased (P < 0.001) from 1.38 log10 CFU/g after 6 days to 0.47 log10 CFU/g after 60 days. At 10°C, recovery of O103:H2 from 60 days dry biofilms could only be detected after enrichment and was always higher for T2 than T4 biofilms. Regardless of temperature, the transfer of O103:H2 to beef from the biofilm on TPU was greater (P < 0.001) than SS. Moist biofilms also resulted in greater (P < 0.001) cell transfer to beef than dry biofilms at 10 and 25°C. Development of SP or LAB multispecies biofilms with O103:H2 can either increase or diminish the likelihood of beef contamination. Environmental conditions such as humidity, contact surface type, as well as biofilm aging all can influence the risk of beef being contaminated by STEC within multi-species biofilms attached to food contact surfaces. [ABSTRACT FROM AUTHOR]

Bursaphelenchus xylophilus , a plant parasitic nematode, is the causal agent of pine wilt, a devastating forest tree disease. Essentially, no efficient methods for controlling B. xylophilus and pine wilt disease have yet been developed. Enterobacter ludwigii AA4, isolated from the root of maize, has powerful nematocidal activity against B. xylophilus in a new in vitro dye exclusion test. The corrected mortality of the B. xylophilus treated by E. ludwigii AA4 or its cell extract reached 98.3 and 98.6%, respectively. Morphological changes in B. xylophilus treated with a cell extract from strain AA4 suggested that the death of B. xylophilus might be caused by an increased number of vacuoles in non-apoptotic cell death and the damage to tissues of the nematodes. In a greenhouse test, the disease index of the seedlings of Scots pine (Pinus sylvestris) treated with the cells of strain AA4 plus B. xylophilus or those treated by AA4 cell extract plus B. xylophilus was 38.2 and 30.3, respectively, was significantly lower than 92.5 in the control plants treated with distilled water and B. xylophilus. We created a sdaB gene knockout in strain AA4 by deleting the gene that was putatively encoding the beta-subunit of L-serine dehydratase through Red homologous recombination. The nematocidal and disease-suppressing activities of the knockout strain were remarkably impaired. Finally, we revealed a robust colonization of P. sylvestris seedling needles by E. ludwigii AA4, which is supposed to contribute to the disease-controlling efficacy of strain AA4. Therefore, E. ludwigii AA4 has significant potential to serve as an agent for the biological control of pine wilt disease caused by B. xylophilus. [ABSTRACT FROM AUTHOR]

Candida glabrata is a common cause of Candida infections. In our present study, we investigated the antifungal susceptibility and molecular epidemiology of vaginal and non-vaginal C. glabrata isolates. Seventy-six vaginal C. glabrata strains isolated from patients with vulvovaginal candidiasis and 57 non-vaginal C. glabrata isolates were collected at two hospitals in Shanghai, China. Antifungal susceptibility was examined using a broth microdilution method. Multilocus sequence typing was used for genotyping. Overall, 28 (21.1%), 28 (21.1%), and 29 (21.8%) C. glabrata isolates were resistant to fluconazole, itraconazole, and voriconazole, respectively. Briefly, 18 (23.7%), 18 (23.7%), and 19 (25%) vaginal strains were resistant to fluconazole, itraconazole, and voriconazole. While the resistance to these antifungals were all 17.5% (10/57) in non-vaginal strains. All isolates retained susceptibility to amphotericin B, and only four non-vaginal isolates were caspofungin resistant. Genotyping identified 17 ST patterns. In non-vaginal samples, the same genotypes appear as in the vaginal samples, except for one genotype (ST-182), while in the vaginal samples more genotypes appear (ST8, ST19, ST45, ST55, ST66, ST80, ST138, and ST17). The most common genotype was ST7 (81 strains), followed by ST10 (14 strains) and ST15 (11 strains). The majority of resistant phenotype strains (25/30, 83.3%) correlated to the predominant genotype (ST7), and the rest belonged to ST3 (2/30, 6.7%), ST10 (1/30, 3.3%), ST19 (1/30, 3.3%), and ST45 (1/30, 3.3%). Our survey revealed cross-resistance in vaginal and non-vaginal C. glabrata isolates. Moreover, there is no genotype associated with the resistance phenotype. [ABSTRACT FROM AUTHOR]