Arbuscular mycorrhizal fungal community structures differ between co-occurring tree species of dry Afromontane tropical forest, and their seedlings exhibit potential to trap isolates suited for reforestation

The diversity of arbuscular mycorrhizal (AM) fungi and their broad or narrow association with distinct plant species in natural environments are crucial information in the understanding of the ecological role of AM fungi on plant co-existence. This knowledge is also needed for appropriate mycorrhization of nursery-grown seedlings for forestation efforts. Here, we report results from comparative studies on three co-occurring indigenous tree species of the dry Afromontane forests of Ethiopia and their seedlings grown under controlled conditions in soil collected from the sites. AM fungal SSU rDNA fragment was amplified and sequenced from mycorrhizas of adult plants and seedlings of Olea europaea subsp. cuspidata and Prunus africana, and from Podocarpus falcatus seedlings. AM fungal identity, diversity and community structure were analyzed based on sequence types defined by the NS31-AM1 SSU rDNA fragment similarity in order to compare with data from other habitats. A total of 409 sequences, grouped in 32 sequence types, belonging to Glomeraceae, Diversisporaceae and Gigasporaceae were found. Some sequence types are close to the widespread Glomus intraradices, G. hoi, G. etunicatum, G. cf. etunicatum and Gigaspora margarita. However, the majority (59%) of sequence types are so far specific for the sites including 11 new types when compared with previous data from the same area. The AM fungal community associated with adult plants, including data previously obtained from adult Podocarpus falcatus seedlings, and seedlings of a host species differed significantly, where seedlings trapping a surprising large number of native fungi. AM fungal community structure also differed significantly between host species and sites, respectively. The results confirm previous results from the same area indicating distinct fungal communities associated with the diverse tree species and suggests the potential of these indigenous tree seedlings to trap a wide range of AM fungi appropriate for successful afforestation.     

3'-Fluoro-3'-deoxy-5'-noraristeromycin derivatives: synthesis and antiviral analysis

The promising antiviral properties of 3'-fluoro-3'-deoxyadenosine and 4',4'-difluoro-4'-deoxy-5'-noraristeromycin prompted the synthesis of the corresponding 3'-fluoro derivatives of 5'-noraristeromycin. These target compounds, which were prepared from the same readily accessible cyclopentenol, were found to be inactive when subjected to 31 viral assays. The results have some implications on the mechanism of antiviral action of 5'-noraristeromycin and provide guidance for future geminal-difluoro analog design.     

Horizon-Specific Bacterial Community Composition of German Grassland Soils,as Revealed by Pyrosequencing-Based Analysis of 16S rRNA Genes

The diversity of bacteria in soil is enormous, and soil bacterial communities can vary greatly in structure. Here, we employed a pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to characterize the overall and horizon-specific (A and B horizons) bacterial community compositions in nine grassland soils, which covered three different land use types. The entire data set comprised 752,838 sequences, 600,544 of which could be classified below the domain level. The average number of sequences per horizon was 41,824. The dominant taxonomic groups present in all samples and horizons were the Acidobacteria, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, Firmicutes, and Bacteroidetes. Despite these overarching dominant taxa, the abundance, diversity, and composition of bacterial communities were horizon specific. In almost all cases, the estimated bacterial diversity (H′) was higher in the A horizons than in the corresponding B horizons. In addition, the H′ was positively correlated with the organic carbon content, the total nitrogen content, and the C-to-N ratio, which decreased with soil depth. It appeared that lower land use intensity results in higher bacterial diversity. The majority of sequences affiliated with the Actinobacteria, Bacteroidetes, Cyanobacteria, Fibrobacteres, Firmicutes, Spirochaetes, Verrucomicrobia, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria were derived from A horizons, whereas the majority of the sequences related to Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospira, TM7, and WS3 originated from B horizons. The distribution of some bacterial phylogenetic groups and subgroups in the different horizons correlated with soil properties such as organic carbon content, total nitrogen content, or microbial biomass.Soil is probably the most complex microbial environment on Earth with respect to species richness and community size. The microbial richness in soils exceeds that of other environments (44) and is higher by orders of magnitude than the biodiversity of plants and animals. Cultivated soil or grassland soil contains an estimated 2 × 10⁹ prokaryotic cells per gram (12). Soil microbial communities are an important factor of agriculturally managed systems, as they are responsible for most nutrient transformations in soil and influence the above-ground plant diversity and productivity (53).To analyze the bacterial community in soils, most approaches target the 16S rRNA gene by PCR amplification and subsequent analysis employing sequencing of clone libraries (10, 24), denaturing gradient gel electrophoresis (DGGE) (38), or terminal restriction fragment length polymorphism (T-RFLP) (17, 52). Most of these approaches provided limited insights into the structure of soil bacterial communities, as the survey sizes and the number of compared sampling sites were small with respect to the enormous bacterial diversity present in different soil samples. For example, the reported clone libraries vary considerably in size, but small sample sizes (500 or fewer 16S rRNA gene sequences) are usually analyzed and employed for the theoretical estimation of species richness (39). This provides snapshots of the predominant bacterial community members, but phylogenetic groups that are present in a low abundance and which may possess important ecosystem functions are not assessed (47). In addition, it has been shown that rich sampling (several thousands of clones) of complex bacterial communities is required to perform robust measurements and estimations of community diversity parameters (37). Thus, the detection bias accompanying analyses of small sample sizes can lead to invalidated assumptions. Genetic profiling techniques such as DGGE and T-RFLP have high-throughput capability. These approaches allow researchers to unravel differences in community structure but are limited for assessing diversity (23, 40). To deeply survey the diversity and the composition of the bacterial communities within different soil samples, large-scale pyrosequencing of partial 16S rRNA genes has been employed recently. Previous pyrosequencing-based studies of soil (1, 30, 34, 43) have generated large data sets, which comprised 39,707 (30) to 152,359 (34) 16S rRNA partial gene sequences. Those studies provided comprehensive insights into the biogeography of bacterial soil communities and taxa that were present in a low abundance. However, all those studies focused on the analysis of microbial communities present in topsoil. The subsoil is also known to harbor an important part of the soil microbial biomass (18). It has been shown that the microbial population in the shallow subsurface is impacted by agricultural production to a similar extent as that in topsoil (5).In this study, we performed large-scale pyrosequencing-based analyses of 16S rRNA genes to assess the bacterial community composition in topsoil and the corresponding subsoil of nine different grassland sites in the Hainich region (Thuringia, Germany). To provide a high level of coverage at the species level (97% genetic distance) and minimize detection bias, we exceeded the above-described numbers of analyzed 16S rRNA gene sequences (752,838 in this study). To examine the impact of land use on bacterial diversity and community composition, the selected grassland sites covered a range of three different land use types, including samples from unfertilized pastures grazed by cattle, fertilized mown pastures grazed by cattle, and fertilized meadows. In many recent studies, surveys were focused on comprehensive analyses of a single soil or a few soil samples (1, 14, 37, 43). This allowed the determination of overall bacterial species richness and community composition, but the assessment of spatial patterns and environmental factors that drive these patterns is hampered by the limited number of examined soils. To assess spatial distribution and the impact of soil edaphic factors and land use on community structure, we used triplicate samples of each land use type from different locations. In addition, composite samples derived from five soil cores after the separation of soil horizons were employed.     

Glomus africanum and G. iranicum, two new species of arbuscular mycorrhizal fungi (Glomeromycota)

Two new arbuscular mycorrhizal fungal species (Glomeromycota) of genus Glomus, G. africanum and G. iranicum, are described and illustrated. Both species formed spores in loose clusters and singly in soil and G. iranicum sometimes inside roots. G. africanum spores are pale yellow to brownish yellow, globose to subglobose, (60-)87(-125) μm diam, sometimes ovoid to irregular, 80-110 x 90-140 μm. The spore wall consists of a semipermanent, hyaline, outer layer and a laminate, smooth, pale yellow to brownish yellow, inner layer, which always is markedly thinner than the outer layer. G. iranicum spores are hyaline to pastel yellow, globose to subglobose, (13-)40(-56) μm diam, rarely egg-shaped, prolate to irregular, 39-54 x 48-65 μm. The spore wall consists of three smooth layers: one mucilaginous, short-lived, hyaline, outermost; one permanent, semirigid, hyaline, middle; and one laminate, hyaline to pastel yellow, innermost. Only the outermost spore wall layer of G. iranicum stains red in Melzer's reagent. In the field G. africanum was associated with roots of five plant species and an unrecognized shrub colonizing maritime sand dunes of two countries in Europe and two in Africa, and G. iranicum was associated with Triticum aestivum cultivated in southwestern Iran. In one-species cultures with Plantago lanceolata as the host plant G. africanum and G. iranicum formed arbuscular mycorrhizae. Phylogenetic analyses of partial SSU sequences of nrDNA placed the two new species in Glomus group A. Both species were distinctly separated from sequences of described Glomus species.     

Geographical variation in the response of visceral leishmaniasis to paromomycin in East Africa: a multicentre, open-label, randomized trial

Background

Visceral leishmaniasis (VL) is a major health problem in developing countries. The untreated disease is fatal, available treatment is expensive and often toxic, and drug resistance is increasing. Improved treatment options are needed. Paromomycin was shown to be an efficacious first-line treatment with low toxicity in India.

Methods

This was a 3-arm multicentre, open-label, randomized, controlled clinical trial to compare three treatment regimens for VL in East Africa: paromomycin sulphate (PM) at 15 mg/kg/day for 21 days versus sodium stibogluconate (SSG) at 20 mg/kg/day for 30 days; and the combination of both dose regimens for 17 days. The primary efficacy endpoint was cure based on parasite-free tissue aspirates taken 6 months after treatment.

Findings

Overall, 135 patients per arm were enrolled at five centres in Sudan (2 sites), Kenya (1) and Ethiopia (2), when the PM arm had to be discontinued due to poor efficacy. The trial has continued with the higher dose of PM as well as the combination of PM and SSG arms. These results will be reported later. Baseline patient characteristics were similar among treatment arms. The overall cure with PM was significantly inferior to that with SSG (63.8% versus 92.2%; difference 28.5%, 95%CI 18.8% to 38.8%, p<0.001). The efficacy of PM varied among centres and was significantly lower in Sudan (14.3% and 46.7%) than in Kenya (80.0%) and Ethiopia (75.0% and 96.6%). No major safety issues with PM were identified.

Conclusion

The efficacy of PM at 15 mg/kg/day for 21 days was inadequate, particularly in Sudan. The efficacy of higher doses and the combination treatment warrant further studies.     

The BOS loci of Arabidopsis are required for resistance to Botrytis cinerea infection

Three Botrytis-susceptible mutants bos2, bos3, and bos4 which define independent and novel genetic loci required for Arabidopsis resistance to Botrytis cinerea were isolated. The bos2 mutant is susceptible to B. cinerea but retains wild-type levels of resistance to other pathogens tested, indicative of a defect in a response pathway more specific to B. cinerea. The bos3 and bos4 mutants also show increased susceptibility to Alternaria brassicicola, another necrotrophic pathogen, suggesting a broader role for these loci in resistance. bos4 shows the broadest range of effects on resistance, being more susceptible to avirulent strain of Pseudomonas syringae pv. tomato. Interestingly, bos3 is more resistant than wild-type plants to virulent strains of the biotrophic pathogen Peronospora parasitica and the bacterial pathogen P. syringae pv. tomato. The Pathogenesis Related gene 1 (PR-1), a molecular marker of the salicylic acid (SA)-dependent resistance pathway, shows a wild-type pattern of expression in bos2, while in bos3 this gene was expressed at elevated levels, both constitutively and in response to pathogen challenge. In bos4 plants, PR-1 expression was reduced compared with wild type in response to B. cinerea and SA. In bos3, the mutant most susceptible to B. cinerea and with the highest expression of PR-1, removal of SA resulted in reduced PR-1 expression but no change to the B. cinerea response. Expression of the plant defensin gene PDF1-2 was generally lower in bos mutants compared with wild-type plants, with a particularly strong reduction in bos3. Production of the phytoalexin camalexin is another well-characterized plant defense response. The bos2 and bos4 mutants accumulate reduced levels of camalexin whereas bos3 accumulates significantly higher levels of camalexin than wild-type plants in response to B. cinerea. The BOS2, BOS3, and BOS4 loci may affect camalexin levels and responsiveness to ethylene and jasmonate. The three new mutants appear to mediate disease responses through mechanisms independent of the previously described BOS1 gene. Based on the differences in the phenotypes of the bos mutants, it appears that they affect different points in defense response pathways.     

Hydroxylated N-alkyl-4-piperidinyl-2,3-diarylpyrrole derivatives as potent broad-spectrum anticoccidial agents

Diaryl-(4-piperidinyl)-pyrrole derivatives bearing hydroxylated N-alkyl substituents have been synthesized and evaluated as anticoccidial agents. High potency in Et-PKG inhibition and broad-spectrum anticoccidial activities have been observed on compounds, such as 4b and 5h, which are fully efficacious in vivo at 50 ppm in feed.     

Diet overlap of non‐native common carp and native Nile tilapia: A potential cause for population reduction of Nile tilapia stock in Lake Ziway,Ethiopia

Lake Ziway harbours indigenous and exotic fish species including Nile tilapia (Oreochromis niloticus) and common carp (Cyprinus carpio). Nile tilapia was the dominant and preferred fish. However, its contribution to total catch has dramatically declined from 89.3% in 1994 to 27% in 2014 while the introduced common carp has increased from 0% before 2012 to 25% in 2014. Common carp potentially compete with Nile tilapia for available resources and could be a cause for the decline. Thus, the study explored the dietary overlap of the two species from April to August 2017. Schoener's overlap index (α) revealed significant dietary overlap between the two species (α = 0.84, between juveniles and α = 0.63, between adults). Juveniles fed mainly on animal origin (zooplankton and insects), while adult Nile tilapia have consumed plant origin (macrophyte and phytoplankton), and adult common carp fed on macrophytes and detritus. The presence of significant dietary overlap between the two species, particularly due to intense competition among juveniles, might cause the reduction of Nile tilapia stock because the native species has shown a competitive disadvantage for food in the presence of common carp. This study provides baseline information to researchers and decision makers working towards the sustainable resource utilisation of the system.