PFKFB3-Meditated Glycolysis via the Reactive Oxygen Species-Hypoxic Inducible Factor 1α Axis Contributes to Inflammation and Proliferation of Staphylococcus aureus in Epithelial Cells.

Mastitis caused by antibiotic-resistant strains of Staphylococcus aureus is a significant concern in the livestock industry due to the economic losses it incurs. Regulating immunometabolism has emerged as a promising approach for preventing bacterial inflammation. To investigate the possibility of alleviating inflammation caused by S aureus infection by regulating host glycolysis, we subjected the murine mammary epithelial cell line (EpH4-Ev) to S aureus challenge. Our study revealed that S aureus can colonize EpH4-Ev cells and promote inflammation through hypoxic inducible factor 1α (HIF1α)-driven glycolysis. Notably, the activation of HIF1α was found to be dependent on the production of reactive oxygen species (ROS). By inhibiting PFKFB3, a key regulator in the host glycolytic pathway, we successfully modulated HIF1α-triggered metabolic reprogramming by reducing ROS production in S aureus-induced mastitis. Our findings suggest that there is a high potential for the development of novel anti-inflammatory therapies that safely inhibit the glycolytic rate-limiting enzyme PFKFB3.

Dynamic variation of Paris polyphylla root-associated microbiome assembly with planting years.

MAIN CONCLUSION: P. polyphylla selectively enriches beneficial microorganisms to help their growth. Paris polyphylla (P. polyphylla) is an important perennial plant for Chinese traditional medicine. Uncovering the interaction between P. polyphylla and the related microorganisms would help to utilize and cultivate P. polyphylla. However, studies focusing on P. polyphylla and related microbes are scarce, especially on the assembly mechanisms and dynamics of the P. polyphylla microbiome. High-throughput sequencing of the 16S rRNA genes was implemented to investigate the diversity, community assembly process and molecular ecological network of the bacterial communities in three root compartments (bulk soil, rhizosphere, and root endosphere) across three years. Our results demonstrated that the composition and assembly process of the microbial community in different compartments varied greatly and were strongly affected by planting years. Bacterial diversity was reduced from bulk soils to rhizosphere soils to root endosphere and varied over time. Microorganisms benefit to plants was selectively enriched in P. polyphylla roots as was its core microbiome, including Pseudomonas, Rhizobium, Steroidobacter, Sphingobium and Agrobacterium. The network's complexity and the proportion of stochasticity in the community assembly process increased. Besides, nitrogen metabolism, carbon metabolism, phosphonate and phosphinate metabolism genes in bulk soils increased over time. These findings suggest that P. polyphylla exerts a selective effect to enrich the beneficial microorganisms and proves the sequential increasing selection pressure with P. polyphylla growth. Our work adds to the understanding of the dynamic processes of plant-associated microbial community assembly, guides the selection and application timing of P. polyphylla-associated microbial inoculants and is vital for sustainable agriculture.

The therapeutic potential for targeting CSE/H2S signaling in macrophages against Escherichia coli infection.

Macrophages play a pivotal role in the inflammatory response to the zoonotic pathogen E. coli, responsible for causing enteric infections. While considerable research has been conducted to comprehend the pathogenesis of this disease, scant attention devoted to host-derived H2S. Herein, we reported that E. coli infection enhanced the expression of CSE in macrophages, accompanied by a significantly increased inflammatory response. This process may be mediated by the involvement of excessive autophagy. Inhibition of AMPK or autophagy with pharmacological inhibitors could alleviate the inflammation. Additionally, cell model showed that the mRNA expression of classic inflammatory factors (Il-1ß, Il-6), macrophage polarization markers (iNOS, Arg1) and ROS production was significantly down-regulated after employing CSE specific inhibitor PAG. And PAG is capable of inhibiting excessive autophagy through the LKB1-AMPK-ULK1 axis. Interestingly, exogenous H2S could suppress inflammation response. Our study emphasizes the importance of CSE in regulating the macrophage-mediated response to E. coli. Increased CSE in macrophages leads to excessive inflammation, which should be considered a new target for drug development to treat intestinal infection.

Purification and water resource circulation utilization of Cd-containing wastewater during microbial remediation of Cd-polluted soil.

The purification and water resource circulation utilization of cadmium-containing leachate is a key link in the field application of microbial remediation in Cd-polluted soil. In this study, through a simulation experiment of microbial remediation of Cd-polluted paddy soil, the feasibility of the purification and recycling process of wastewater derived from microbial remediation of Cd-polluted soil was explored. The results of the microbial mobilization and removal experiment showed that the concentrations of Cd, N, P, and K in the leachate were 88.51 µg/L, 38.06, 0.53, and 98.87 mg/L, respectively. The leachate also contained a large number of microbial resources, indicating that it had high recovery values. To recycle this wastewater, activated carbon (C), humic acid (H), and self-assembled monolayers on mesoporous supports (SAMMS; S) were used as adsorbents. The results showed that the co-existing cations in the leachate had a major influence on the adsorption of Cd. In the ternary system of Fe, Al, and Cd, the removal efficiency of Cd increased to 91.2% when the S dosage was increased to 5‰, and the sorption of Cd occurred after Fe and Al. However, C and H exhibited poor adsorption performances. The isotherm models further showed that the maximum adsorption capacities of S, H, and C were 13.96, 6.41 and 2.94 mg/g, respectively. The adsorption kinetics of S showed that adsorption was a rapid process, and the C-H and O-Si-O of S were the key functional groups. The pH of the leachate significantly affected the adsorption efficiency of Cd. Finally, the purified leachate was successfully applied to microbial cultivation and soil remediation. Overall, the reclamation of Cd-containing wastewater can not only dampen the impacts of water shortages, but also achieve the purposes of Cd removal and resource recovery to lower costs by approximately 1166-3499 yuan per mu.

FABP4-mediated lipid droplet formation in Streptococcus uberis-infected macrophages supports host defence.

Foamy macrophages containing prominent cytoplasmic lipid droplets (LDs) are found in a variety of infectious diseases. However, their role in Streptococcus uberis-induced mastitis is unknown. Herein, we report that S. uberis infection enhances the fatty acid synthesis pathway in macrophages, resulting in a sharp increase in LD levels, accompanied by a significantly enhanced inflammatory response. This process is mediated by the involvement of fatty acid binding protein 4 (FABP4), a subtype of the fatty acid-binding protein family that plays critical roles in metabolism and inflammation. In addition, FABP4 siRNA inhibitor cell models showed that the deposition of LDs decreased, and the mRNA expression of Tnf, Il1b and Il6 was significantly downregulated after gene silencing. As a result, the bacterial load in macrophages increased. Taken together, these data demonstrate that macrophage LD formation is a host-driven component of the immune response to S. uberis. FABP4 contributes to promoting inflammation via LDs, which should be considered a new target for drug development to treat infections.

Immune response variations and intestinal flora changes in mastitis induced by three Streptococcus uberis strains.

Streptococcus uberis is a common cause of mastitis. The pathogenicity among different strains of S. uberis and the resultant host immune responses remain to be elucidated. Herein, we document immune responses among three strains of S. uberis, and preliminary explore whether and how intestinal immunity plays a role in host anti-infection processes. Mice have been proved to be effective experimental animals for bovine mastitis, so utilizing a mouse intramammary infection model, we assay immune responses and gut flora changes of three S. uberis strains by histopathologic examination, RT-PCR, Western blot, and 16s ribosomal DNA sequencing. We find that the immune responses among the three sequence-type (ST) S. uberis strains may be linked to the hasA/B and lbp virulence genes, and the beta diversity of the intestine may be independent of the ST of S. uberis. Twenty phyla and 30 genera of intestinal flora were identified, with Verrucomicrobia and Akkermansia being the most prominent phylum and genus, respectively. These bacteria have strong anti-inflammatory and protective effects against S. uberis challenge. These data provide a foundation for further studies to elucidate gut flora function and exploration of therapeutic targets for mastitis.

Ecological responses of bacterial assembly and functions to steep Cd gradient in a typical Cd-contaminated farmland ecosystem.

The response of soil bacterial communities from farmland ecosystems to cadmium (Cd) pollution, in which a steep concentration gradient of more than 100 mg/kg has naturally formed, has not previously been fully reported. In this study, a field investigation was conducted in a typical severe Cd-polluted farmland ecosystem, and the bacterial community response to the steep Cd gradient was analyzed. The results showed that Cd concentration sharply decreased from 159.2 mg/kg to 4.18 mg/kg among four sampling sites alongside an irrigation canal over a distance of 150 m. Bacterial diversity and richness were significantly lower in highly polluted sites, and random forest analysis indicated that Cd gradient played a decisive role in reducing alpha diversity. Redundancy analysis (RDA) and co-occurrence network indicated that the synergistic effects of pH, Cd, and phosphorus were the main drivers shaping community structure. The functional results predicted by BugBase suggested that the bacterial community may adapt to the harsh environment by recruiting Cd-resistant microbes and improving oxidative stress tolerance of the whole community. Cd-resistant microorganisms such as Burkholderia, Bradyrhizobium, and Sulfurifustis, which directly or indirectly participate in diminishing oxidative damage of Cd, may play essential roles in maintaining community stability and might be potential bacterial resources for the bioremediation of Cd pollution.

Reduction mechanism of Cd accumulation in rice grain by Chinese milk vetch residue: Insight into microbial community.

Chinese milk vetch is an efficient approach to reduce Cd accumulation in rice, nevertheless, its reduction mechanism is not well understood. In this study, we investigated the rice grain Cd, soil properties and microbial community in a Cd-polluted paddy field amended with milk vetch residue (MV) or without (CK) during rice growth period. We found that milk vetch residue averagely decreased the Cd content in rice grain by 45%. Decrease of Cd in rice mainly attributed to the inhibition of Cd activation by milk vetch residue at heading stage probably by the formation of HA-Cd (Humic Acid) and CdS. Increased pH and organic matter (OM) promoted the reduction of available Cd. In addition, nonmetric multidimensional scaling (NMDS) analysis revealed that microbial community structure was significantly different between MV and CK treatment (r = 0.187, p = 0.002), and the core functions of differentially abundant genera were mainly associated with N-cycling, organic matter degradation and sulfate-reducing. The application of milk vetch residue increased the abundance of sulfate-reducing bacteria (SRB) by 8-112% during the rice growth period, which may involve in promoting the transformation of Cd to a more stably residual Cd (CdS). Canonical correspondence analysis (CCA) and mantel test analysis indicated that available K (p = 0.004) and available N (p = 0.005) were the key environmental factors of shaping the SRB. Altogether, changes in soil properties affected microbial structure and functional characteristics, especially the response of SRB in MV treatment would provide valuable insights into reducing the bioavailability of Cd in soil.

Spatial distribution and risk assessment of heavy metals in contaminated paddy fields - A case study in Xiangtan City, southern China.

An extensive investigation on spatial distribution and environmental risk assessment based on total content and fractions of heavy metals, as well as the cancer risk of Cd from seven adjacent contaminated paddy fields at Xiangtan City, southern China, was conducted in this study. A total of 63 soil samples were analyzed for soil physical properties and concentrations of eight heavy metals (Cd, Cr, Co, Cu, Mn, Ni, Pb, Zn). The results showed that concentrations of metals except for Cr, Mn and Ni exceeded the background values to varying degrees, and particularly, content of Cd was as 57.4-612 times higher than background values. Principal components analysis and correlation analysis revealed three groups: industry activities for Cd and Zn; natural sources mainly for Cu, Pb, Ni and Cr, with some slight anthropogenic activities for Cu and Pb accumulation; and manganese ore associated with cobalt for Co and Mn. Combined with different indices, Cd and Zn were the major contributors to the ecological risk, and cancer risk of Cd indicated an unacceptable degree in this area. Altogether, results from this study will facilitate a better understanding of metals distribution characteristics and provide a scientific basis for further comprehensive management for these paddy fields. Combination of functional microbial agent and plants promises to be a feasible and effective remediation method for cadmium pollution in the study area.

A critical role for host-derived cystathionine-ß-synthase in Staphylococcus aureus-induced udder infection.

Cystathionine-ß-synthase (CBS) catalyzes the first step of the transsulfuration pathway. The role of host-derived CBS in Staphylococcus aureus (S. aureus)-induced udder infection remains elusive. Herein, we report that S. aureus infection enhances the expression of CBS in mammary epithelial cells in vitro and in vivo. A negative correlation is present between the expression of CBS and inflammation after employing a pharmacological inhibitor/agonist of CBS. In addition, CBS achieves a fine balance between eliciting sufficient protective innate immunity and preventing excessive damage to cells and tissues preserving the integrity of the blood-milk barrier (BMB). CBS/H2S reduces bacterial load by promoting the generation of antibacterial substances (ROS, RNS) and inhibiting apoptosis, as opposed to relying solely on intense inflammatory reactions. Conversely, H2S donor alleviate inflammation via S-sulfhydrating HuR. Finally, CBS/H2S promotes the expression of Abcb1b, which in turn strengthens the integrity of the BMB. The study described herein demonstrates the importance of CBS in regulating the mammary immune response to S. aureus. Increased CBS in udder tissue modulates excessive inflammation, which suggests a novel target for drug development in the battle against S. aureus and other infections.

Application of Chlorogenic acid as a substitute for antibiotics in Multidrug-resistant Escherichia coli-induced mastitis.

Mastitis affects animal welfare and causes economic losses in the dairy industry. It is caused mainly by bacterial pathogens, among which Escherichia coli (E. coli) is one of the prominent causative agents. To treat bovine mastitis, antibiotics were widely used. However, their extensive and uncontrolled use has led to the emergence of multi-antibiotic-resistant strains. Indeed, a superbug of E. coli was successfully isolated from a mastitis-suffering cow and found resistant to at least 10 antibiotics. Therefore, the development of a universal therapeutic agent used as a replacement for the antibiotic is an immediate need in the dairy industry. To do so, we examined whether chlorogenic acid (CGA), a natural and herbal extract, could be a perfect alternative in mastitis treatment. In this study, we observed that the combination of CGA and antibiotic had an additive or synergistic effect; CGA fought against the superbug by directly targeting bacterial cell wall and membrane; CGA can significantly alleviate the mastitis caused by the superbug E. coli via its antimicrobial, antioxidant and anti-inflammatory activities. Collectively, these data indicated that CGA had a true potential to replace antibiotics during mastitis treatment.

Taurine reduction of injury from neutrophil infiltration ameliorates Streptococcus uberis-induced mastitis.

Mastitis is a common disease of dairy cows characterized by infiltration of leukocytes, especially neutrophils, resulting in increased permeability of the blood-milk barrier (BMB). Taurine, a functional nutrient, has been shown to have anti-inflammatory and antioxidant effects. Here, we investigated the regulatory effects and mechanisms of taurine on the complex immune network of the mammary gland in Streptococcus uberis (S. uberis) infection. We found that taurine had no direct effect on CXCL2-mediated neutrophil chemotaxis. However, it inhibited MAPK and NF-κB signalings by modulating the activity of TAK1 downstream of TLR2, thereby reducing CXCL2 expression in macrophages to reduce neutrophil recruitment in S. uberis infection. Further, the AMPK/Nrf2 signaling pathway was activated by taurine to help mitigate oxidative damage, apoptosis and disruption of tight junctions in mammary epithelial cells caused by hypochlorous acid, a strong oxidant produced by neutrophils, thus protecting the integrity of the mammary epithelial barrier. Taurine protects the BMB from damage caused by neutrophils via blocking the macrophage-CXCL2-neutrophil signaling axis and increasing the antioxidant capacity of mammary epithelial cells.

Flavonoid Synthesis by Deinococcus sp. 43 Isolated from the Ginkgo Rhizosphere.

Flavonoids are crucial in physiological and pharmaceutical processes, especially the treatment of cancer and the prevention of cardiovascular and cerebrovascular diseases. Flavonoid-producing plants and fungi have been extensively reported, but bacteria have been much less investigated as a source of flavonoid production. Deinococcus sp. 43, a spherical flavonoid-producing bacteria from the Ginkgo rhizosphere, was reported in this study. First, the whole genome of Deinococcus sp. 43 was sequenced and a series of flavonoid anabolic genes were annotated. Simultaneously, High Performance Liquid Chromatography (HPLC) results showed that Deinococcus sp. 43 was capable of producing flavonoids, with a maximum quercetin output of 2.9 mg/L. Moreover, the relative expression of key genes involved in flavonoid synthesis was determined to test the completeness of the flavonoid anabolic pathway. The results of LC-MS analysis demonstrated that the flavonoids produced by Deinococcus sp. 43 were significantly different between intracellular and extracellular environments. The concentration of multiple glycosylated flavonoids was substantially higher in extracellular than intracellular environments, while the majority of flavonoids obtained in intracellular environments were hydroxylated multiple times. Lastly, the flavonoid biosynthetic pathway of Deinococcus sp. 43 was constructed based on the genomic analysis and the detected flavonoids. In conclusion, this study represents the first comprehensive characterization of the flavonoid-producing pathway of Deinococcus. The findings demonstrate that the strain has excellent potential as a genetically engineered strain for the industrial production of flavonoids.

Flavonoids affect the endophytic bacterial community in Ginkgo biloba leaves with increasing altitude.

Altitude affects plant growth and metabolism, but the effect of altitude on plant endophytic microorganisms is still unclear. In this study, we selected 16 Ginkgo biloba trees to study the response of leaves' endophytes to flavonoids and altitude (from 530 m to 1,310 m). HPLC results showed that flavonoids in Ginkgo biloba leaves increased by more than 150% with attitude rising from 530 m to 1,310 m, which revealed a positive correlation with altitude. Ginkgo biloba might regulate the increased flavonoids in leaves to resist the increasing light intensity. 16S rDNA sequencing results showed that the endophytic bacterial communities of Ginkgo biloba at different altitudes significantly differed. Ginkgo leaf endophytes' alpha diversity decreased with increasing flavonoids content and altitude. The increased flavonoids might increase the environmental pressure on endophytes and affect the endophytic community in Ginkgo biloba leaves. The bacterial network in Ginkgo biloba leaves became more complex with increasing altitude, which might be one of the strategies of leaf endophytes to cope with increasing flavonoids. Metagenomes results predicted with PICRUSt showed that the abundance of flavonoid biosynthesis and photosynthesis genes were significantly decreased with the increase of flavonoid contents. High flavonoid content in leaves appeared to inhibit microbial flavonoid synthesis. Our findings indicate that altitude can modulate microbial community structure through regulating plant metabolites, which is important to uncovering the interaction of microbes, host and the environment.

The novel distribution of intracellular and extracellular flavonoids produced by Aspergillus sp. Gbtc 2, an endophytic fungus from Ginkgo biloba root.

Here, we reported a Ginkgo endophyte, Aspergillus sp. Gbtc 2, isolated from the root tissue. Its flavonoid biosynthesis pathway was reconstructed, the effect of phenylalanine on the production of flavonoids was explored, and the flavonoid metabolites were identified with the high-resolution Liquid chromatography-mass spectrometry (LC-MS). Some essential genes were annotated to form the upstream of the complete biosynthesis pathway, indicating that Aspergillus sp. Gbtc 2 has the ability to synthesize the C6-C3-C6 flavonoid monomers. HPLC results showed that adding an appropriate amount of phenylalanine could promote the production of flavonoids by Aspergillus Gbtc 2. LC-MS results depicted a significant difference in many flavonoids between intracellularly and extracellularly. Most of the flavonoids gathered in the cell contained glycosylation groups, while almost all components with multiple hydroxyls showed much higher concentrations extracellularly than intracellularly; they likely have different biological functions. A variety of these substances can be mapped back to the pathway pattern of flavonoid biosynthesis and prove the ability of flavonoid production once again. This study expanded the information on flavonoid biosynthesis in Aspergillus and provided a solid theoretical basis for developing the fungi into genetically engineered strains undertaking flavonoid industrialized production.

Molecular Epidemiology and Antimicrobial Resistance of Outbreaks of Klebsiella pneumoniae Clinical Mastitis in Chinese Dairy Farms.

Klebsiella pneumoniae is an opportunistic pathogen that causes serious infections in humans and animals. However, the availability of epidemiological information on clinical mastitis due to K. pneumoniae is limited. To acquire new information regarding K. pneumoniae mastitis, data were mined about K. pneumoniae strains on dairy cattle farms (farms A to H) in 7 Chinese provinces in 2021. Hypermucoviscous strains of K. pneumoniae were obtained by the string test. MICs of antimicrobial agents were determined via the broth microdilution method. Ten antimicrobial resistance genes and virulence genes were identified by PCR. The prevalence of K. pneumoniae was 35.91% (65/181), and 100% of the bacteria were sensitive to enrofloxacin. Nine antimicrobial resistance genes and virulence genes were identified and compared among farms. The hypermucoviscous phenotype was present in 94.44% of isolates from farm B, which may be a function of the rmpA virulence gene. Based on these data, the multidrug-resistant strains SD-14 and HB-21 were chosen and sequenced. Genotypes were assayed for K. pneumoniae isolates from different countries and different hosts using multilocus sequence typing (MLST). Ninety-four sequence types (STs) were found, and 6 STs present a risk for spreading in specific regions. Interestingly, ST43 was observed in bovine isolates for the first time. Our study partially reveals the current distribution characteristics of bovine K. pneumoniae in China and may provide a theoretical basis for the prevention and treatment of bovine K. pneumoniae mastitis. IMPORTANCE K. pneumonia is ubiquitous in nature and infects a wide range of hosts, including animals, and humans. It is one of the leading inducements of clinical mastitis (CM) in dairy cows, a prevalent and costly disease that is predominantly associated with bacterial infection. In general, CM caused by Gram-negative bacteria is more difficult to cure than that associated with Gram-positive pathogens, with an average cost per case of 211.03 U.S. dollars (USD) for Gram-negative bacterial infections compared with 133.73 USD for Gram-positive bacterial CM cases. After Escherichia coli, K. pneumoniae is the second most common Gram-negative cause of bovine CM, but it is the most detrimental in terms of decreased milk yield, discarded milk, treatment costs, death, and culling. In view of the economic implications of K. pneumoniae infection in dairy farming, research into population structure and antibiotic resistance is particularly important.

Reduction of ROS-HIF1α-driven glycolysis by taurine alleviates Streptococcus uberis infection.

Antibiotic-resistant strains of Streptococcus uberis (S. uberis) frequently cause clinical mastitis in dairy cows resulting in enormous economic losses. The regulation of immunometabolism is a promising strategy for controlling this bacterial infection. To investigate whether taurine alleviates S. uberis infection by the regulation of host glycolysis via HIF1α, the murine mammary epithelial cell line (EpH4-Ev) and C57BL/6J mice were challenged with S. uberis. Our data indicate that HIF1α-driven glycolysis promotes inflammation and damage in response to the S. uberis challenge. The activation of HIF1α is dependent on mTOR-mediated ROS production. These results were confirmed in vivo. Taurine, an intracellular metabolite present in most animal tissues, has been shown to effectively modulate HIF1α-triggered metabolic reprogramming and contributes to a reduction of inflammation, which reduces mammary tissue damage and prevents mammary gland dysfunction in S. uberis-induced mastitis. These data provide a novel putative prophylactic and therapeutic strategy for amelioration of dairy cow mastitis and bacterial inflammation.

RNA-seq and nuclear proteomics provide insights into the lactation regulation mechanism of goat transfected IGF-I and GH recombinant vectors.

There exists little available information on the mechanisms of lactation regulation until now. In order to explore the underlying mechanism, we injected IGF-I and GH recombinant vectors into the mammary gland, then RNA-seq analysis and nuclear proteomics were used for rapid high-throughput screening of DEGs and DEPs in the two groups linked to lactation regulation. KEGG analysis of 206 DEGs showed that the same 4 of top 10 enrichment pathways (ECM receptor interaction, protein digestion and absorption, focal adhesion and phagosome) involved in 4 co-expressed genes (IDO, BTG1, ITGB6 and keratin 83), the two groups enriched different metabolic pathways yet. Nuclear proteomics analysis showed 75 and 36 DEPs in the IGF-I and GH group respectively; Sixteen common proteins were identified between the IGF-I group and GH group, four of which (ALB, TPT1, CXXC-5 and ACTR2) significantly decreased and three of which (PRP1, PAG-9 and Hsp70) significantly increased. Similarly, DEPs in the two groups were enriched in same one of top 10 enrichment pathways (PI3K-Akt signaling pathway). Protein-protein interaction networks highlighted the contribution of glycosphingolipid biosynthesis, porphyrin and chlorophyll metabolism and the Jak-STAT signaling pathway to lactation regulation of GH and IGFI. GH and IGF-I improve milk yield, which may be linked to important nodal proteins (ALB and ACTB). Our research advances the understanding of the mammary gland transcriptome and nuclear proteomics during GH and IGF-I overexpression. Individual genes, proteins and pathways in this study point towards potential targets for lactation regulation.

Endophytic Bacterial Communities of Ginkgo biloba Leaves During Leaf Developmental Period.

Plant-specialized secondary metabolites have ecological functions in mediating interactions between plants and their entophytes. In this study, high-throughput gene sequencing was used to analyze the composition and abundance of bacteria from Ginkgo leaves at five different sampling times. The results indicated that the bacterial community structure varied during leaf developmental stage. Bacterial diversity was observed to be the highest at T2 stage and the lowest at T1 stage. Proteobacteria, Firmicutes, Actinobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes were found as the dominant phyla. The major genera also showed consistency across sampling times, but there was a significant variation in their abundance, such as Bacillus, Lysinibacillus, and Staphylococcus. Significant correlations were observed between endophytic bacteria and flavonoids. Especially, Staphylococcus showed a significant positive correlation with quercetin, and changes in the abundance of Staphylococcus also showed a strong correlation with flavonoid content. In order to determine the effect of flavonoids on endophytic bacteria of Ginkgo leaves, an extracorporeal culture of related strains (a strain of Staphylococcus and a strain of Deinococcus) was performed, and it was found that the effect of flavonoids on them remained consistent. The predicted result of Tax4Fun2 revealed that flavonoids might lead to a lower abundance of endophytic microorganisms, which further proved the correlation between bacterial communities and flavonoids. This study provided the first insight into the bacterial community composition during the development of Ginkgo leaves and the correlation between the endophytic bacteria and flavonoids.

Evolutionary, genomic, and biogeographic characterization of two novel xenobiotics-degrading strains affiliated with Dechloromonas.

Xenobiotics are generally known as man-made refractory organic pollutants widely distributed in various environments. For exploring the bioremediation possibility of xenobiotics, two novel xenobiotics-degrading strains affiliated with Azonexaceae were isolated. We report here the phylogenetics, genome, and geo-distribution of a novel and ubiquitous Azonexaceae species that primarily joins in the cometabolic process of some xenobiotics in natural communities. Strains s22 and t15 could be proposed as a novel species within Dechloromonas based on genomic and multi-phylogenetic analysis. Pan-genome analysis showed that the 63 core genes in Dechloromonas include genes for dozens of metabolisms such as nitrogen fixation protein (nifU), nitrogen regulatory protein (glnK), dCTP deaminase, C4-dicarboxylate transporter, and fructose-bisphosphate aldolase. Strains s22 and t15 have the ability to metabolize nitrogen, including nitrogen fixation, NirS-dependent denitrification, and dissimilatory nitrate reduction. Moreover, the novel species possesses the EnvZ-OmpR two-component system for controlling osmotic stress and QseC-QseB system for quorum sensing to rapidly sense environmental changes. It is intriguing that this new species has a series of genes for the biodegradation of some xenobiotics such as azathioprine, 6-Mercaptopurine, trinitrotoluene, chloroalkane, and chloroalkene. Specifically, glutathione S-transferase (GST) and 4-oxalocrotonate tautomerase (praC) in this novel species play important roles in the detoxification metabolism of some xenobiotics like dioxin, trichloroethene, chloroacetyl chloride, benzo[a]pyrene, and aflatoxin B1. Using data from GenBank, DDBJ and EMBL databases, we also demonstrated that members of this novel species were found globally in plants (e.g. rice), guts (e.g. insect), pristine and contaminated regions. Given these data, Dechloromonas sp. strains s22 and t15 take part in the biodegradation of some xenobiotics through key enzymes.