Taxonomic and functional assembly cues enrich the endophytic tobacco microbiota across epiphytic compartments.

The plant microbiome plays a critical role in plant growth, development, and health, with endophytes being recognized as essential members due to their close interactions with host plants. However, knowledge gaps remain in understanding the mechanisms driving the colonization and establishment of endophytic communities. To address this issue, we investigated the microbiota of tobacco roots and leaves, including both epiphytic and endophytic microorganisms. We found that Actinobacteria and Alphaproteobacteria were significantly enriched in the root endosphere. Additionally, we identified higher abundances of functional traits involved in antibiotic synthesis, plant cell wall degradation, iron metabolism, secretion systems, and nicotine degradation enzymes in the endosphere. We further studied metagenome-assembled genomes from the rhizosphere and root endosphere, revealing a greater diversity of secondary metabolites in bacteria within the root endosphere. Together, this study provides insights into the taxonomic and functional assembly cues that may contribute to shaping the endophytic plant microbiota.IMPORTANCEThe presence of diverse microorganisms within plant tissues under natural conditions is a well-established fact. However, due to the plant immune system's barrier and the unique microhabitat of the plant interior, it remains unclear what specific characteristics bacteria require to successfully colonize and thrive in the plant endosphere. Recognizing the significance of unraveling these functional features, our study focused on investigating the enriched traits in the endophytic microbiota compared to the epiphytes. Through our research, we have successfully identified the taxonomic and functional assembly cues that drive the enrichment of the endophytic microbiota across the epiphytic compartments. These findings shed new light on the intricate mechanisms of endophyte colonization, thereby deepening our understanding of plant-microbe interactions and paving the way for further advancements in microbiome manipulation.

Distinct microbiota assembly and functional patterns in disease-resistant and susceptible varieties of tobacco.

The plant microbiota is believed to be an accessory genome that extends plant functions, forming holobionts together with the host plant. Plant disease resistance, therefore, is inextricably linked with plant microbiota, which play important roles in plant growth and health. To explore the relationship between plant microbiota and disease resistance, we investigated the tobacco microbiome of two varieties with contrasting disease-resistance levels to bacterial wilt and black shank diseases. Comparative microbiome analysis indicated that the resistant variety assembled a distinct microbiota with higher network complexity and diversity. While Pseudomonas and Ensifer, which contain biocontrol and beneficial members, were enriched in the rhizosphere of the resistant variety, Ralstonia, a genus including the known causative pathogen, was enriched in the susceptible variety. Metagenome sequencing revealed that biocontrol functions, such as hydrogen cyanide synthase, pyochelin biosynthesis, and arthrofactin-type cyclic lipopeptide synthetase, were more abundant in the resistant variety. Further analysis indicated that contigs encoding the corresponding genes were mostly assigned to Pseudomonas. Among all the metagenome-assembled genomes, positive selection was suggested in the genome assigned to Pseudomonas only in the rhizosphere of the resistant variety. The search of biosynthetic gene clusters in the Pseudomonas genome revealed a non-ribosomal peptide synthetase, the compound of which was brabantamide A, with known antimicrobial activity. Collectively, our study suggests that the plant microbiota might be involved in microbe-mediated disease resistance. Particularly, our results highlight Pseudomonas in the rhizosphere of the disease-resistant variety as a promising biocontrol candidate. Our study may facilitate further screening of bacterial isolates and the targeted design of microbial communities.

Denitrification performance and microbial diversity in a packed-bed bioreactor using PCL as carbon source and biofilm carrier.

Polycaprolactone (PCL) was used as both carbon source and biofilm support for denitrifying bacteria in a packed-bed bioreactor. The denitrification performance and microbial diversity were investigated. The microbial community of biofilm developed on the surface of PCL in the reactor was analyzed by pyrosequencing method. The experimental results showed the average nitrate removal efficiency reached 93 % at stable operation. ESEM observation and FTIR analysis were conducted to characterize the PCL structure before and after microbial utilization. For the microbial community, Betaproteobacteria predominated, and most of the PCL-degrading denitrifying bacteria assigned to the family of Comamonadacea. Denitrifying bacteria accounted for more than 20 % in the total population, indicating that PCL is a good carrier and carbon source for biological denitrification.

Urbanization Reduces Phyllosphere Microbial Network Complexity and Species Richness of Camphor Trees.

Studies on microbial communities associated with foliage in natural ecosystems have grown in number in recent years yet have rarely focused on urban ecosystems. With urbanization, phyllosphere microorganisms in the urban environment have come under pressures from increasing human activities. To explore the effects of urbanization on the phyllosphere microbial communities of urban ecosystems, we investigated the phyllosphere microbial structure and the diversity of camphor trees in eight parks along a suburban-to-urban gradient. The results showed that the number of ASVs (amplicon sequence variants), unique on the phyllosphere microbial communities of three different urbanization gradients, was 4.54 to 17.99 times higher than that of the shared ASVs. Specific microbial biomarkers were also found for leaf samples from each urbanization gradient. Moreover, significant differences (R2 = 0.133, p = 0.005) were observed in the phyllosphere microbial structure among the three urbanization gradients. Alpha diversity and co-occurrence patterns of bacterial communities showed that urbanization can strongly reduce the complexity and species richness of the phyllosphere microbial network of camphor trees. Correlation analysis with environmental factors showed that leaf total carbon (C), nitrogen (N), and sulfur (S), as well as leaf C/N, soil pH, and artificial light intensity at night (ALIAN) were the important drivers in determining the divergence of phyllosphere microbial communities across the urbanization gradient. Together, we found that urbanization can affect the composition of the phyllosphere bacterial community of camphor trees, and that the interplay between human activities and plant microbial communities may contribute to shaping the urban microbiome.

Response of Barley Plants to Drought Might Be Associated with the Recruiting of Soil-Borne Endophytes.

Mechanisms used by plants to respond to water limitation have been extensively studied. However, even though the inoculation of beneficial microbes has been shown to improve plant performance under drought stress, the inherent role of soil microbes on plant response has been less considered. In the present work, we assessed the importance of the soil microbiome for the growth of barley plants under drought stress. Plant growth was not significantly affected by the disturbance of the soil microbiome under regular watering. However, after drought stress, we observed a significant reduction in plant biomass, particularly of the root system. Plants grown in the soil with disturbed microbiome were significantly more affected by drought and did not recover two weeks after re-watering. These effects were accompanied by changes in the composition of endophytic fungal and bacterial communities. Under natural conditions, soil-derived plant endophytes were major colonizers of plant roots, such as Glycomyces and Fusarium, whereas, for plants grown in the soil with disturbed microbiome seed-born bacterial endophytes, e.g., Pantoea, Erwinia, and unclassified Pseudomonaceae and fungal genera normally associated with pathogenesis, such as Gibberella and Gaeumannomyces were observed. Therefore, the role of the composition of the indigenous soil microbiota should be considered in future approaches to develop management strategies to make plants more resistant towards abiotic stress, such as drought.

Enrichment of endophytic Actinobacteria in roots and rhizomes of Miscanthus × giganteus plants exposed to diclofenac and sulfamethoxazole.

This study investigates how wastewater containing 2 mg l-1 of sulfamethoxazole (SMX) and 2 mg l-1 of diclofenac (DCF) affects the composition of bacterial communities present in the roots and rhizomes of Miscanthus × giganteus plants grown in laboratory-scale constructed wetlands. Bacterial communities in plant roots and rhizomes were identified in treated and control samples by 16S rRNA amplicon sequencing. Moreover, bacterial endophytes were isolated in R2A and 1/10 869 media and screened for their ability to metabolize SMX and DCF in liquid medium by HPLC. Our results show significant changes in the abundance of main genera, namely Sphingobium and Streptomyces between control and treated plants. Around 70% of the strains isolated from exposed plants belonged to the phylum Actinobacteria and were classified as Streptomyces, Microbacterium, and Glycomyces. In non-exposed plants, Proteobacteria represented 43.5% to 63.6% of the total. We identified 17 strains able to remove SMX and DCF in vitro. From those, 76% were isolated from exposed plants. Classified mainly as Streptomyces, they showed the highest SMX (33%) and DCF (41%) removal efficiency. These isolates, alone or in combination, might be used as bio-inoculants in constructed wetlands to enhance the phytoremediation of SMX and DCF during wastewater treatment.

Reduced microbial potential for the degradation of phenolic compounds in the rhizosphere of apple plantlets grown in soils affected by replant disease.

BACKGROUND: Apple replant disease (ARD) is a syndrome that occurs in areas where apple plants or closely related species have been previously cultivated. Even though ARD is a well-known phenomenon, which has been observed in different regions worldwide and occurs independent of the soil type, its causes still remain unclear. RESULTS: As expected, the biomass of plants grown in replant soil was significantly lower compared to those grown in control (virgin) soil. A shotgun metagenome analysis showed a clear differentiation between the rhizosphere and bulk soil compartments independent from the soil used. However, significant differences associated with apple replant disease were only observed in the rhizosphere compartment, for which we detected changes in the abundance of major bacterial genera. Interestingly, reads assigned to Actinobacteria were significantly reduced in relative abundance in rhizosphere samples of the soil affected by replant disease. Even though reads assigned to pathogenic fungi were detected, their relative abundance was low and did not differ significantly between the two different soils. Differences in microbiome structure also resulted in shifts in functional pattern. We observed an increase in genes related to stress sensing in the rhizosphere of soils affected by replant disease, whereas genes linked to nutrient sensing and uptake dominated in control soils. Moreover, we observed a lower abundance of genes coding for enzymes which trigger the degradation of aromatic compounds in rhizosphere of soils affected by replant disease, which is probably connected with higher concentration of phenolic compounds, generally associated with disease progression. CONCLUSIONS: Our study shows, for the first time, how apple replanting affects soil functioning by altering the soil microbiome. Particularly, the decrease in the abundance of genes which code for enzymes catalyzing the degradation of aromatic compounds, observed in the rhizosphere of plants grown in soil affected by apple replant disease, is of interest. Apple rootstocks are known to synthetize many phenolic compounds, including defense related phytoalexins, which have been considered for long to be connected with the emergence of replant disease. The knowledge gained in this study might help to develop targeted strategies to overcome or at least reduce the effects of ARD symptoms.

Population prevalence of myopia, glasses wear and free glasses acceptance among minority versus Han schoolchildren in China.

AIM: To measure myopia, glasses wear and free glasses acceptance among minority and Han children in China. METHODS: Visual acuity testing and questionnaires assessing ethnicity, study time, and parental and teacher factors were administered to a population-based sample of 9-12 year old minority and Han children in Yunnan and Guangdong, and their teachers and parents. Refraction was performed on children with uncorrected visual acuity (VA) < = 6/12 in either eye, and acceptance of free glasses assessed. MAIN OUTCOME MEASURES: Baseline myopia (uncorrected visual acuity < = 6/12 in > = 1 eye and spherical equivalent refractive power < = -0.5D in both eyes); baseline glasses wear; free glasses acceptance. RESULTS: Among 10,037 children (mean age 10.6 years, 52.3% boys), 800 (8.0%) were myopic, 4.04% among Yunnan Minority children (OR 0.47, 95%CI 0.33, 0.67, P<0.001), 6.48% in Yunnan Han (OR 0.65, 95%CI 0.45, 0.93, P = 0.019), 9.87% in Guangdong Han (Reference). Differences remained significant after adjusting for study time and parental glasses wear. Difference in baseline glasses ownership (Yunnan Minority 4.95%, Yunnan Han 6.15%, Guangdong Han 15.3%) was not significant after adjustment for VA. Yunnan minority children (71.0%) were more likely than Yunnan Han (59.6%) or Guangdong Han (36.8%) to accept free glasses. The difference was significant after adjustment only compared to Guangdong Han (OR 3.34, 95% CI 1.62, 6.90, P = 0.001). CONCLUSION: Myopia is more common among Han children and in wealthier Guangdong. Baseline differences in glasses wear could be explained by student, teacher and parental factors. Yunnan Minority children were more likely to accept free glasses.

Enhanced nitrogen removal using solid carbon source in constructed wetland with limited aeration.

In this study, the performances of nitrogen removal in constructed wetlands using solid carbon source with limited aeration were investigated. The blends of poly-3-hydroxybutyrate-co-3-hydroxyvalerate (PHBV) and polyacetic acid (PLA) were used as the carbon source and biofilm support. The performances of nitrogen removal, microbial abundance and microbial community structure in the biofilm attached on PHBV/PLA were investigated. Higher ammonia removal efficiency (91.00%) and total nitrogen removal efficiency (97.03%) than non-aerated constructed wetland (System NA) were achieved in constructed wetland with limited aeration (System A). The limited aeration decreased the average concentrations of COD in effluent. And, System A had higher microbial abundance than System NA. Pyrosequencing analysis showed that denitrifying bacteria Brevinema (41.85%) and Thiothrix (12.33%) were the predominant genus in the biofilm attached on the carbon source in System NA and System A, respectively.

Dominant Groups of Potentially Active Bacteria Shared by Barley Seeds become Less Abundant in Root Associated Microbiome.

Endophytes are microorganisms colonizing plant internal tissues. They are ubiquitously associated with plants and play an important role in plant growth and health. In this work, we grew five modern cultivars of barley in axenic systems using sterile sand mixture as well as in greenhouse with natural soil. We characterized the potentially active microbial communities associated with seeds and roots using rRNA based amplicon sequencing. The seeds of the different cultivars share a great part of their microbiome, as we observed a predominance of a few bacterial OTUs assigned to Phyllobacterium, Paenibacillus, and Trabusiella. Seed endophytes, particularly members of the Enterobacteriacea and Paenibacillaceae, were important members of root endophytes in axenic systems, where there were no external microbes. However, when plants were grown in soil, seed endophytes became less abundant in root associated microbiome. We observed a clear enrichment of Actinobacteriacea and Rhizobiaceae, indicating a strong influence of the soil bacterial communities on the composition of the root microbiome. Two OTUs assigned to Phyllobacteriaceae were found in all seeds and root samples growing in soil, indicating a relationship between seed-borne and root associated microbiome in barley. Even though the role of endophytic bacteria remains to be clarified, it is known that many members of the genera detected in our study produce phytohormones, shape seedling exudate profile and may play an important role in germination and establishment of the seedlings.

Cluster-randomized controlled trial of the effects of free glasses on purchase of children's glasses in China: The PRICE (Potentiating Rural Investment in Children's Eyecare) study.

BACKGROUND: Offering free glasses can be important to increase children's wear. We sought to assess whether "Upgrade glasses" could avoid reduced glasses sales when offering free glasses to children in China. METHODS: In this cluster-randomized, controlled trial, children with uncorrected visual acuity (VA)< = 6/12 in either eye correctable to >6/12 in both eyes at 138 randomly-selected primary schools in 9 counties in Guangdong and Yunnan provinces, China, were randomized by school to one of four groups: glasses prescription only (Control); Free Glasses; Free Glasses + offer of $15 Upgrade Glasses; Free Glasses + offer of $30 Upgrade Glasses. Spectacle purchase (main outcome) was assessed 6 months after randomization. RESULTS: Among 10,234 children screened, 882 (8.62%, mean age 10.6 years, 45.5% boys) were eligible and randomized: 257 (29.1%) at 37 schools to Control; 253 (28.7%) at 32 schools to Free Glasses; 187 (21.2%) at 31 schools to Free Glasses + $15 Upgrade; and 185 (21.0%) at 27 schools to Free Glasses +$30 Upgrade. Baseline ownership among these children needing glasses was 11.8% (104/882), and 867 (98.3%) children completed follow-up. Glasses purchase was significantly less likely when free glasses were given: Control: 59/250 = 23.6%; Free glasses: 32/252 = 12.7%, P = 0.010. Offering Upgrade Glasses eliminated this difference: Free + $15 Upgrade: 39/183 = 21.3%, multiple regression relative risk (RR) 0.90 (0.56-1.43), P = 0.65; Free + $30 Upgrade: 38/182 = 20.9%, RR 0.91 (0.59, 1.42), P = 0.69. CONCLUSIONS: Upgrade glasses can prevent reductions in glasses purchase when free spectacles are provided, providing important program income. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT02231606. Registered on 31 August 2014.

Correlation of interferon-lambda 4 ss469415590 with the hepatitis C virus treatment response and its comparison with interleukin 28b polymorphisms in predicting a sustained virological response: a meta-analysis.

BACKGROUND: Interferon-lambda 4 (IFNL4) ss469415590 is a newly discovered polymorphism that could predict the treatment response in hepatitis C virus (HCV)-infected patients. This meta-analysis was performed in order to clarify its specific effect on the treatment response and to compare it with interleukin 28b (IL28B). METHOD: The commonly used literature databases were searched. Meta-analyses were performed with fixed/random-effects models using Stata 12.0. The sustained virological response (SVR) rate was summarized using R software. Publication bias was examined through Egger's test. RESULTS: A total of seven studies were finally included in this meta-analysis. IFNL4 ss469415590 was demonstrated to be associated with SVR (odds ratio (OR) 3.83, 95% confidence interval (CI) 3.22-4.56, p<0.001). Asians had a higher likelihood of achieving SVR than Caucasians (OR=7.36 vs. 3.54). When stratifying all the patients according to HCV genotype, a significant association was observed in HCV genotype 1 patients (OR 4.5, 95% CI 2.91-6.95, p<0.001). In HCV genotype 2/3 patients, the favorable TT/TT genotype patients tended to have a statistically higher SVR rate than the non-TT/TT genotype patients (84.4% vs. 78.3%, p=0.058). Compared with IL28B rs12979860 (OR 3.45) and rs8099917 (OR 3.50), ss469415590 TT/TT genotype patients showed a slightly higher probability of achieving a SVR (OR 3.61 calculated from studies investigating both IFNL4 and rs12979860; OR 4.86 for studies investigating both IFNL4 and rs8099917). Furthermore, ss469415590 showed a slightly higher predictive value than rs12979860 using the diagnostic test tool (area under the curve=0.71 vs. 0.70). IFNL4 was also correlated with rapid virological response (RVR) (OR 4.35, 95% CI 1.43-13.20, p=0.01), viral clearance (OR 0.31, 95% CI 0.24-0.39, p<0.001), and HCV susceptibility (OR 0.76, 95% CI 0.65-0.89, p=0.001). CONCLUSIONS: IFNL4 ss469415590 is significantly associated with SVR in HCV genotype 1 patients, irrespective of race; there is a tendency towards an association in HCV genotype 2/3 patients. Comparable to IL28B, IFNL4 is correlated with natural viral clearance and HCV susceptibility, additionally IFNL4 ss469415590 has a slightly higher predictive performance over IL28B polymorphisms in regard to SVR.

Efficacy of poly-unsaturated fatty acid therapy on patients with nonalcoholic steatohepatitis.

AIM: To examine whether poly-unsaturated fatty acid (PUFA) therapy is beneficial for improving nonalcoholic steatohepatitis (NASH). METHODS: In total, 78 patients pathologically diagnosed with NASH were enrolled and were randomly assigned into the control group and the PUFA therapy group (added 50 mL PUFA with 1:1 ratio of EHA and DHA into daily diet). At the initial analysis and after 6 mo of PUFA therapy, parameters of interest including liver enzymes, lipid profiles, markers of inflammation and oxidation, and histological changes were evaluated and compared between these two groups. RESULTS: At the initial analysis, in patients with NASH, serum levels of alanine aminotransferase (ALT) and aspartase aminotransferase (AST) were slightly elevated. Triglyceride (TG), total cholesterol (TC) and low-density lipoprotein cholesterol levels, markers of systemic inflammation [C-reactive protein (CRP)] and oxidation [malondialdehyde (MDA)], as well as fibrosis parameters of type IV collagen and pro-collagen type III pro-peptide were also increased beyond the normal range. Six months later, ALT and AST levels were significantly reduced in the PUFA group compared with the control group. In addition, serum levels of TG and TC, CRP and MDA, and type IV collagen and pro-collagen type III pro-peptide were also simultaneously and significantly reduced. Of note, histological evaluation showed that steatosis grade, necro-inflammatory grade, fibrosis stage, and ballooning score were all profoundly improved in comparison to the control group, strongly suggesting that increased PUFA consumption was a potential way to offset NASH progression. CONCLUSION: Increased PUFA consumption is a potential promising approach for NASH prevention and reversal.

IL-28B polymorphisms correlated with treatment response in HCV-4 mono-infected patients: a meta-analysis.

BACKGROUND: The role of interleukin 28B (IL-28B) polymorphisms played in hepatitis C virus (HCV) infection has been gradually explicit, especially in HCV genotype 1, 2 and 3. However, no confirmative conclusion was acquired in genotype 4 HCV patients. Thus we conducted this meta-analysis. METHODS: We searched the commonly used databases both in English and Chinese. Meta-analysis was performed in fixed/random effects models using STATA 12.0 or R software. Publication bias was examined through Egger's test and Begg's funnel plot. RESULTS: In total, 11 studies were included in this meta-analysis, encompassing 1284 patients who were mono-infected with HCV-4 and received Peg-interferon (Peg-IFN) plus Ribavirin (Rbv). Around 53.0% patients would achieve sustained virologic response (SVR), 36.6% achieve rapid virologic response (RVR) and 62.4% achieve end of treatment response (ETR). Egyptian patients had a higher rate achieving SVR than non-Egyptian patients (56.3% vs. 47.8%). IL-28B rs12979860 CC genotype not only favored SVR (OR = 3.95, 95%CI = 3.03-5.16), regardless of citizenship, but also favored RVR (OR = 3.82, 95%CI = 2.46-5.95) and ETR (OR = 4.22, 95%CI = 2.81-6.34). IL-28B rs8099917 genotype TT also correlated with SVR (OR = 3.41, 95%CI = 1.92-6.07), but might not with RVR. IL-28B rs12980275 might still correlate with SVR, but warrant more studies to validate. CONCLUSIONS: The favorable IL-28B rs12979860 genotype is a statistically significant predictor of SVR, RVR and ETR in HCV-4 monoinfected patients treated with Peg-IFN plus Rbv. Rs8099917 might predict SVR but not RVR. Egyptian HCV-4 patients would achieve better outcomes than non-Egyptian patients when treated with standard care.

Denitrification using PBS as carbon source and biofilm support in a packed-bed bioreactor.

Biodegradable polymer was used as carbon source and biofilm support for nitrate removal from aqueous solution as an attractive alternative for biological denitrification. The objective of this paper was to investigate the denitrification performance and microbial community of a packed-bed bioreactor using poly (butanediol succinate) (PBS), a biodegradable polymer, as carbon source and biofilm support. NO(3)-N concentration was determined by UV spectrophotometer. NO(2)-N concentration was assayed by hydrochloric acid naphthyl ethylenediamine spectrophotometry method. Total organic carbon (TOC) was measured using a TOC analyzer. The morphology of the samples was observed using an environmental scanning electron microscope (ESEM). The microbial community was analyzed by pyrosequencing method. The experimental results showed that an average removal efficiency of nitrate was 95 %. ESEM observation and FTIR analysis indicated the changes of PBS granules before and after microbial utilization. Pyrosequencing results showed that Betaproteobacteria predominated, and most of PBS-degrading denitrifying bacteria were assigned to the family Comamonadaceae. Denitrifying bacteria accounted for 13.02 % in total population. The PBS granules were suitable support and carbon source for denitrifying bacteria.

Biological denitrification with a novel biodegradable polymer as carbon source and biofilm carrier.

A novel biodegradable polymer composed of PHBV and PLA was prepared for advanced wastewater treatment. It could serve as both biofilm carrier and carbon source for denitrification. Results of batch test showed the average denitrification rate was 0.07 mg NO(3)-N/(gh). The kinetic study demonstrated that when nitrate concentration was above 10.00 mg/L, DOC could not be detected in the effluent. In continuous packed-bed reactor, the average nitrogen removal efficiency was 94.11%. Nitrite concentration throughout the experiment was below 0.15 mg/L. The formation of NH(4)-N was observed, though small. DOC released in the effluent did not exceed 16.00 mg/L in the whole process, and it finally dropped below 1.20 mg/L.