Phylogeny and genetic diversity of native rhizobia nodulating common bean (Phaseolus vulgaris L.) in Ethiopia

The diversity and phylogeny of 32 rhizobial strains isolated from nodules of common bean plants grown on 30 sites in Ethiopia were examined using AFLP fingerprinting and MLSA. Based on cluster analysis of AFLP fingerprints, test strains were grouped into six genomic clusters and six single positions. In a tree built from concatenated sequences of recA, glnII, rpoB and partial 16S rRNA genes, the strains were distributed into seven monophyletic groups. The strains in the groups B, D, E, G1 and G2 could be classified as Rhizobium phaseoli, R. etli, R. giardinii, Agrobacterium tumefaciens complex and A. radiobacter, respectively, whereas the strains in group C appeared to represent a novel species. R. phaseoli, R. etli, and the novel group were the major bean nodulating rhizobia in Ethiopia. The strains in group A were linked to R. leguminosarum species lineages but not resolved. Based on recA, rpoB and 16S rRNA genes sequences analysis, a single test strain was assigned as R. leucaenae. In the nodC tree the strains belonging to the major nodulating groups were clustered into two closely linked clades. They also had almost identical nifH gene sequences. The phylogenies of nodC and nifH genes of the strains belonging to R. leguminosarum, R. phaseoli, R. etli and the putative new species (collectively called R. leguminosarum species complex) were not consistent with the housekeeping genes, suggesting symbiotic genes have a common origin which is different from the core genome of the species and indicative of horizontal gene transfer among these rhizobia.     

Efficacy of two artemisinin combination therapies for uncomplicated falciparum malaria in children under 5 years, Malakal, Upper Nile, Sudan

Background

The treatment for Plasmodium falciparum malaria in Sudan has been in process of change since 2003. Preceding the change, this study aimed to determine which artemisinin-based combination therapies is more effective to treat uncomplicated malaria in Malakal, Upper Nile, Sudan.

Methods

Clinical trial to assess the efficacy of 2 antimalarial therapies to treat P. falciparum infections in children aged 6–59 months, in a period of 42 days after treatment.

Results

A total of 269 children were followed up to 42 days. Artesunate plus Sulfadoxine/Pyrimethamine (AS+SP) and Artesunate plus Amodiaquine (AS+AQ) were both found to be efficacious in curing malaria infections by rapid elimination of parasites and clearance of fever, in preventing recrudescence and suppressing gametocytaemia. The combination of AS+SP appeared slightly more efficacious than AS+AQ, with 4.4% (4/116) versus 15% (17/113) of patients returning with malaria during the 6-week period after treatment (RR = 0.9, 95% CI 0.81–0.96). PCR analysis identified only one recrudescence which, together with one other early treatment failure, gave efficacy rates of 99.0% for AS+AQ (96/97) and 99.1% for AS+SP (112/113). However, PCR results were incomplete and assuming part of the indeterminate samples were recrudescent infections leads to an estimated efficacy ranging 97–98% for AS+SP and 88–95% for AS+AQ.

Conclusion

These results lead to the recommendation of ACT, and specifically AS+SP, for the treatment of uncomplicated falciparum malaria in this area of Sudan. When implemented, ACT efficacy should be monitored in sentinel sites representing different areas of the country.     

Impact of HIV Status on Treatment Outcome of Tuberculosis Patients Registered at Arsi Negele Health Center,Southern Ethiopia: A Six Year Retrospective Study

BackgroundDespite implementation of different strategies, the burden and mortality of human immunodeficiency virus (HIV)-associated tuberculosis (TB) remains a challenge in Ethiopia. The aim of this study was to assess the impact of HIV status on treatment outcome of tuberculosis patients registered at Arsi Negele Health Center, Southern Ethiopia.MethodsA six-year retrospective data (from September 2008 to August 2014) of tuberculosis patients (n = 1649) registered at the directly observed therapy short-course (DOTS) clinic of Arsi Negele Health Center was reviewed. Treatment outcome and tuberculosis type were categorized according to the national tuberculosis control program guideline. Data were entered and analyzed using SPSS version 20. Multinomial logistic regression analysis was used to examine the effect of HIV status separately on default/failure and death in relation to those who were successfully treated. Odds ratios with 95% confidence intervals were used to check the presence and strength of association between TB treatment outcome and HIV status and other independent variables.ResultsOut of the 1649 TB patients, 94.7% (1562) have been tested for HIV of whom 156(10%) were HIV co-infected. The mean (standard deviation) age of the patients was 28.5(15.5) years. The majority were new TB cases (96.7%), male (53.7%), urban (54.7%), and had smear negative pulmonary TB (44.1%). Overall, the treatment success rate of TB patients with or without HIV was 87.3%. Using cure/completion as reference, patients without known HIV status had significantly higher odds of default /failure [aOR, 4.26; 95%CI, 1.684–10.775] and transfer-out [aOR, 2.92; 95%CI, 1.545–5.521] whereas those who tested positive for HIV had a significantly higher odds of death [aOR, 6.72; 95%CI, 3.704–12.202] and transfer-out [aOR, 2.02; 95%CI, 1.111–3.680].ConclusionOverall, treatment outcome and HIV testing coverage for TB patients is promising to reach the WHO target in the study area. However, default/failure among patients without known HIV status, and higher rate of mortality among HIV positive TB patients and transfer-out cases deserves concern. Therefore further prospective studies on quality of services, socioeconomics and psychology of this group should be conducted.     

Diversity of sporadic symbionts and nonsymbiotic endophytic bacteria isolated from nodules of woody, shrub, and food legumes in Ethiopia

Fifty-five bacterial isolates were obtained from surface-sterilized nodules of woody and shrub legumes growing in Ethiopia: Crotalaria spp., Indigofera spp., and Erythrina brucei, and the food legumes soybean and common bean. Based on partial 16S rRNA gene sequence analysis, the majority of the isolates were identified as Gram-negative bacteria belonging to the genera Achromobacter, Agrobacterium, Burkholderia, Cronobacter, Enterobacter, Mesorhizobium, Novosphingobium, Pantoea, Pseudomonas, Rahnella, Rhizobium, Serratia, and Variovorax. Seven isolates were Gram-positive bacteria belonging to the genera Bacillus, Paenibacillus, Planomicrobium, and Rhodococcus. Amplified fragment length polymorphism (AFLP) fingerprinting showed that each strain was genetically distinct. According to phylogenetic analysis of recA, glnII, rpoB, and 16S rRNA gene sequences, Rhizobium, Mesorhizobium, and Agrobacterium were further classified into six different genospecies: Agrobacterium spp., Agrobacterium radiobacter, Rhizobium sp., Rhizobium phaseoli, Mesorhizobium sp., and putative new Rhizobium species. The strains from R. phaseoli, Rhizobium sp. IAR30, and Mesorhizobium sp. ERR6 induced nodules on their host plants. The other strains did not form nodules on their original host. Nine endophytic bacterial strains representing seven genera, Agrobacterium, Burkholderia, Paenibacillus, Pantoea, Pseudomonas, Rhizobium, and Serratia, were found to colonize nodules of Crotalaria incana and common bean on co-inoculation with symbiotic rhizobia. Four endophytic Rhizobium and two Agrobacterium strains had identical nifH gene sequences with symbiotic Rhizobium strains, suggesting horizontal gene transfer. Most symbiotic and nonsymbiotic endophytic bacteria showed plant growth-promoting properties in vitro, which indicate their potential role in the promotion of plant growth when colonizing plant roots and the rhizosphere.     

Phylogenetically diverse groups of Bradyrhizobium isolated from nodules of Crotalaria spp., Indigofera spp., Erythrina brucei and Glycine max growing in Ethiopia

Ethiopian Bradyrhizobium strains isolated from root nodules of Crotalaria spp., Indigofera spp., Erythina brucei and soybean (Glycine max) represented genetically diverse phylogenetic groups of the genus Bradyrhizobium. Strains were characterized using the amplified fragment length polymorphism fingerprinting technique (AFLP) and multilocus sequence analysis (MLSA) of core and symbiotic genes. Based on phylogenetic analyses of concatenated recA-glnII-rpoB-16S rRNA genes sequences, Bradyrhizobium strains were distributed into fifteen phylogenetic groups under B. japonicum and B. elkanii super clades. Some of the isolates belonged to the species B. yuanmingense, B. elkanii and B. japonicum type I. However, the majority of the isolates represented unnamed Bradyrhizobium genospecies and of these, two unique lineages that most likely represent novel Bradyrhizobium species were identified among Ethiopian strains. The nodulation nodA gene sequence analysis revealed that all Ethiopian Bradyrhizobium isolates belonged to nodA sub-clade III.3. Strains were further classified into 14 groups together with strains from Africa, as well as some originating from the other tropical and subtropics regions. Strains were also clustered into 14 groups in nodY/K phylogeny similarly to the nodA tree. The nifH phylogenies of the Ethiopian Bradyrhizobium were generally also congruent with the nodA gene phylogeny, supporting the monophyletic origin of the symbiotic genes in Bradyrhizobium. The phylogenies of nodA and nifH genes were also partially congruent with that inferred from the concatenated core genes sequences, reflecting that the strains obtained their symbiotic genes vertically from their ancestor as well as horizontally from more distantly related Bradyrhizobium species.     

UV-B-induced Inhibition of Stem Elongation and Leaf Expansion in Pea Depends on Modulation of Gibberellin Metabolism and Intact Gibberellin Signalling

Information on the involvement of elongation-controlling hormones, particularly gibberellin (GA), in UV-B modulation of stem elongation and leaf growth, is limited. We aimed to study the effect of UV-B on levels of GA and indole-3-acetic acid (IAA) as well as involvement of GA in UV-B inhibition of stem elongation and leaf expansion in pea. Reduced shoot elongation (13%) and leaf area (37%) in pea in response to a 6-h daily UV-B (0.45 W m^?2) exposure in the middle of the light period for 10 days were associated with decreased levels of the bioactive GA₁ in apical stem tissue (59%) and young leaves (69%). UV-B also reduced the content of IAA in young leaves (35%). The importance of modulation of GA metabolism for inhibition of stem elongation in pea by UV-B was confirmed by the lack of effect of UV-B in the le GA biosynthesis mutant. No UV-B effect on stem elongation in the la cry-s (della) pea mutant demonstrates that intact GA signalling is required. In conclusion, UV-B inhibition of shoot elongation and leaf expansion in pea depends on UV-B modulation of GA metabolism in shoot apices and young leaves and GA signalling through DELLA proteins. UV-B also affects the IAA content in pea leaves.     

Search for nodulation-related CLE genes in the genome of Glycine max

CLE peptides are potentially involved in nodule organ development and in the autoregulation of nodulation (AON), a systemic process that restricts nodule number. A genome-wide survey of CLE peptide genes in the soybean glycine max genome resulted in the identification of 39 GmCLE genes, the majority of which have not yet been annotated. qRT-PCR analysis indicated two different nodulation-related CLE expression patterns, one linked with nodule primordium development and a new one linked with nodule maturation. Moreover, two GmCLE gene pairs, encoding group-III CLE peptides that were previously shown to be involved in AON, had a transient expression pattern during nodule development, were induced by the essential nodulation hormone cytokinin, and one pair was also slightly induced by the addition of nitrate. Hence, our data support the hypothesis that group-III CLE peptides produced in the nodules are involved in primordium homeostasis and intertwined in activating AON, but not in sustaining it.     

Prevalence of contagious caprine pleuropneumonia in the Borana pastoral areas of Ethiopia

The study was conducted in selected districts of Borana pastoral areas of Ethiopia, namely Yabello, Dire, Moyale and Liban, during June–September 2004 to determine the status of contagious caprine pleuropneumonia (CCPP). The study includes a retrospective study, fieldwork, serology, an abattoir investigation and isolation of the causative Mycoplasma. Outbreaks of CCPP were reported from almost all regions of the country, especially from lowland areas, which are known goat-rearing regions, with the highest in 2002. The predominant clinical findings observed in affected flocks were coughing, nasal discharge, weakness, reluctance to move, abduction of elbow and laboured breathing. A total of 35 sheep and goats, of 183 examined, were sero-positive for MCCP F₃₈ antibodies using CFT. From the total of 217 goats examined in the abattoir for the presence of CCPP lesions, 21 (9.7%) showed pathological lesions, inflamed lungs with marbled appearance, fibrous pleuropneumonia, yellowish-coloured pleural fluid and swollen bronchial and mediastinal lymph nodes. The causative agent (Mycoplasma capricolum sp. capripneumoniae) was isolated and identified from tissue samples and thoracic fluid treated bacteriologically. In conclusion, the study indicates that CCPP is becoming a very important goat disease in Borana pastoral areas.     

Awash National Park,Ethiopia: use policy,ethnic conflict and sustainable resources conservation in the context of decentralization

In response to recent decentralization in Ethiopia, we investigated pressure exerted on Awash National Park (ANP), vis‐a‐vis park resources; causes of park‐related conflicts and the impact of policy on sustainable resources conservation before decentralization (pre‐1995) and after decentralization (post‐1995). The study's aim was to assess the implementation of sustainable resources conservation in terms of use policy and conflicts in protected areas. We sampled a total of 210 respondents by stratified random sampling and group discussion participants and key informants using purposive sampling technique. Our results show that while policy problems were perceived to be the main threats to the park pre‐1995, demand for pasture land and water, resource‐caused conflicts, expansion of private and state farms were identified as main threats to the park post‐1995. Before decentralization (pre‐1995), inequitable resource sharing and poor organizational structures were the main causes of ethnic conflicts, whereas after decentralization, increasing demand for various resources were the main causes of conflict. We recommend experiences from the Simen National Park be tested to the benefit of improving the state of ANP.