Desert Farming Benefits from Microbial Potential in Arid Soils and Promotes Diversity and Plant Health

BACKGROUND: To convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still not known. METHODOLOGY/PRINCIPAL FINDINGS: We studied the impact of long-term agriculture on desert soil in one of the most prominent examples for organic desert farming in Sekem (Egypt). Using a polyphasic methodological approach to analyse microbial communities in soil as well as associated with cultivated plants, drastic effects caused by 30 years of agriculture were detected. Analysing bacterial fingerprints, we found statistically significant differences between agricultural and native desert soil of about 60%. A pyrosequencing-based analysis of the 16S rRNA gene regions showed higher diversity in agricultural than in desert soil (Shannon diversity indices: 11.21/7.90), and displayed structural differences. The proportion of Firmicutes in field soil was significantly higher (37%) than in the desert (11%). Bacillus and Paenibacillus play the key role: they represented 96% of the antagonists towards phytopathogens, and identical 16S rRNA sequences in the amplicon library and for isolates were detected. The proportion of antagonistic strains was doubled in field in comparison to desert soil (21.6%/12.4%); disease-suppressive bacteria were especially enriched in plant roots. On the opposite, several extremophilic bacterial groups, e.g., Acidimicrobium, Rubellimicrobium and Deinococcus-Thermus, disappeared from soil after agricultural use. The N-fixing Herbaspirillum group only occurred in desert soil. Soil bacterial communities were strongly driven by the a-biotic factors water supply and pH. CONCLUSIONS/SIGNIFICANCE: After long-term farming, a drastic shift in the bacterial communities in desert soil was observed. Bacterial communities in agricultural soil showed a higher diversity and a better ecosystem function for plant health but a loss of extremophilic bacteria. Interestingly, we detected that indigenous desert microorganisms promoted plant health in desert agro-ecosystems

Reviewing treatment outcomes of tuberculosis patients at Zagazig Chest Hospital (2008–2012)

Background: Tuberculosis (TB) is one of major critical heath problem worldwide, where drug treatment is fundamental for controlling TB promoting cure of the patient and breaking the chain of transmission when treatment is completely and correctly followed. Aim of the study: Aim of the study is to assess the treatment outcomes of TB patients at Zagazig Chest Hospital and to identify factors associated with poor outcomes in a trial to achieve the national tuberculosis program (NTP) goals. Patients and methods: This is a cohort study that was carried out at Zagazig Chest Hospital which was in part retrospective and prospective in other part. Analysis of data of 290 tuberculous patients was done where 10 cases were excluded. Demographic, socioeconomic data were reported in addition to radiological, bacteriologic histopathological diagnostic data and history of previous treatment of TB and the used anti-tuberculous treatment regimens with application of directly observed therapy short course (DOTS) strategy. Treatment outcomes were assessed for all patients and were classified either as successful or unsuccessful. Results: Successful treatment outcome was reported in 231 (82.5%) TB cases versus 49 (17.5%) cases with unsuccessful treatment. Successful outcome was significantly associated with middle age (16–35 years) (51.5%) (P < .05), well education (78.8%) (P < .001), absence of history of contact with positive TB case (96.1%) (P < .001), mild to moderate advanced X-ray picture (95.5%) (P < .001) and absence of previous history of anti-tuberculous treatment (87.1%) (P < .01). Multivariate logistic regression analysis for risk factors for unsuccessful outcome revealed that illiteracy (P < .001), history of contact to positive TB cases (P < .001) and far advanced chest X-ray of pulmonary TB (P < .001) were considered as significant predictors. Conclusions: A high rate of successful treatment is reported with application of the NTP (2012) guidelines which was associated with middle age of the patients (16–35 years), well education, mild to moderate advanced X-ray picture and absence of either history of contact with positive TB case or previous history of anti-tuberculous treatment(new case). Illiteracy, history of contact to positive TB cases, far advanced chest X-ray of pulmonary TB and previously treated cases on CAT II regimen could be considered as predictors of unsuccessful outcome

Antibacterial, antibiofilm and antitumor activities of grape and mulberry leaves ethanolic extracts towards bacterial clinical strains

The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were measured at concentrations of 0.01–2.56 mg/mL of grape and mulberry leaves ethanolic extracts. The MIC values were ranged from 0.08 to 0.16 mg/mL against Ps. aeruginosa Ps9, and 0.32 mg/mL against each of S. aureus St3, E. coli Ec3, and S. typhi Sa1. Whereas, the MBC values were ranged from 0.32 to 1.28 mg/mL of the tested extracts. The effects of the tested extracts were also studied representing the bactericidal effect of the grape extract with a ratio of 2 against all investigated isolates, except S. typhi Sa1. Whereas, the mulberry extract had a bactericidal effect towards S. aureus St3 and E. coli Ec3 with ratio of 2, and a bacteriostatic effect against Ps. aeruginosa Ps9 and S. typhi Sa1 with a ratio ≥4. The investigated bacteria found to have a strong ability to form biofilms with densities ranged from 0.67 to 0.80. Both tested extracts inhibited these biofilms with percentages ranged from 48 to 66% at sub-inhibitory concentrations (SICs) ranged from 0.04 to 0.16 mg/mL. In addition, the tested extracts have an excellent cytotoxic activity towards colon cancer cell lines (HCT-16). Five phenolic compounds detected in the tested extracts of grape and mulberry using high performance liquid chromatography (HPLC) after 9.53 min of the retention time. The phenolic compounds of both tested extracts were gallic, coumaric, ferulic, chlorogenic and caffeic with concentrations ranged from 1.28 to 6.56 µg/mL

Effects of bacterial inoculants on the indigenous microbiome and secondary metabolites of chamomile plants

Plant-associated bacteria fulfil important functions for plant growth and health of their host. However, our knowledge about the impact of bacterial treatments on the host’s microbiome and physiology is limited. The present study was conducted to assess the impact of bacterial inoculants on the microbiome of chamomile plants Chamomilla recutita (L.) Rauschert grown in a field under organic management in Egypt. Chamomile seedlings were inoculated with three indigenous Gram-positive strains (Streptomyces subrutilus Wbn2-11, Bacillus subtilis Co1-6, Paenibacillus polymyxa Mc5Re-14) from Egypt and three European Gram-negative strains (Pseudomonas fluorescens L13-6-12, Stenotrophomonas rhizophila P69, Serratia plymuthica 3Re4-18) already known for their beneficial plant-microbe interaction. Molecular fingerprints of 16S rRNA gene as well as real-time PCR analyses did not show statistically significant differences for all applied bacterial antagonists compared to the control. In contrast, a pyrosequencing analysis of the 16S rRNA gene libraries revealed significant differences in the community structure of bacteria between the treatments. These differences could be clearly shown by a shift within the community structure and corresponding beta-diversity indices. Moreover, B. subtilis Co1-6 and P. polymyxa Mc5Re-14 showed an enhancement of the bioactive secondary metabolite apigenin-7-O-glucoside. This indicates a possible new function of bacterial inoculants: to interact with the plant microbiome as well as with the plant metabolome