Secondary Structure and Molecular Evolution of the Mitochondrial Small Subunit Ribosomal RNA in Agaricales (Euagarics clade,Homobasidiomycota)

The complete sequences and secondary structures of the mitochondrial small subunit (SSU) ribosomal RNAs of both mostly cultivated mushrooms Agaricus bisporus (1930 nt) and Lentinula edodes (2164 nt) were achieved. These secondary structures and that of Schizophyllum commune (1872 nt) were compared to that previously established for Agrocybe aegerita. The four structures are near the model established for Archae, Bacteria, plastids, and mitochondria; particularly the helices 23 and 37, described as specific to bacteria, are present. Within the four Agaricales (Homobasidiomycota), the SSU-rRNA core is conserved in size (966 to 1009 nt) with the exception of an unusual extension of 40 nt in the H17 helix of S. commune. The four core sequences possess 76% of conserved positions and a cluster of C in their 3 end, which could constitute a signal involved in the RNA maturation process. Among the nine putative variable domains, three (V3, V5, V7) do not show significant length variations and possess similar percentages of conserved positions (69%) than the core. The other six variable domains show important length variations, due to independent large size inserted/deleted sequences, and higher rates of nucleotide substitutions than the core (only 31% of conserved positions between the four species). Interestingly, the inserted/deleted sequences are located in few preferential sites (hot spots for insertion/deletion) where they seem to arise or disappear haphazardly during evolution. These sites are located on the surface of the tertiary structure of the 30S ribosomal subunit, at the beginning of hairpin loops; the insertions lead to a lengthening of existing hairpins or to branching loops bearing up to five additional helices.     

High Prevalence of Severe Food Insecurity and Malnutrition among HIV-Infected Adults in Senegal,West Africa

Background

Malnutrition and food insecurity are associated with increased mortality and poor clinical outcomes among people living with HIV/AIDS; however, the prevalence of malnutrition and food insecurity among people living with HIV/AIDS in Senegal, West Africa is unknown. The objective of this study was to determine the prevalence and severity of food insecurity and malnutrition among HIV-infected adults in Senegal, and to identify associations between food insecurity, malnutrition, and HIV outcomes.

Methods

We conducted a cross-sectional study at outpatient clinics in Dakar and Ziguinchor, Senegal. Data were collected using participant interviews, anthropometry, the Household Food Insecurity Access Scale, the Individual Dietary Diversity Scale, and chart review.

Results

One hundred and nine HIV-1 and/or HIV-2 participants were enrolled. The prevalence of food insecurity was 84.6% in Dakar and 89.5% in Ziguinchor. The prevalence of severe food insecurity was 59.6% in Dakar and 75.4% in Ziguinchor. The prevalence of malnutrition (BMI <18.5) was 19.2% in Dakar and 26.3% in Ziguinchor. Severe food insecurity was associated with missing clinic appointments (p = 0.01) and not taking antiretroviral therapy due to hunger (p = 0.02). Malnutrition was associated with lower CD4 cell counts (p = 0.01).

Conclusions

Severe food insecurity and malnutrition are highly prevalent among HIV-infected adults in both Dakar and Ziguinchor, and are associated with poor HIV outcomes. Our findings warrant further studies to determine the root causes of malnutrition and food insecurity in Senegal, and the short- and long-term impacts of malnutrition and food insecurity on HIV care. Urgent interventions are needed to address the unacceptably high rates of malnutrition and food insecurity in this population.     

Application of the white rot fungus <Emphasis Type="Italic">Phanerochaete chrysosporium</Emphasis> in biotreatment of bagasse effluent

Biotreatment of bagasse effluent using Phanerochaete chrysosporium (white rot fungus) is investigated. This study confirmed that lignin is the major pollutant component in this effluent followed by different carbohydrates. The treatment conditions must be very proper, especially in terms of biomass culture to achieve a successful treatment. The best conditions of temperature, biomass concentration, pH and duration for biotreatment of this effluent were 35°C, 552 mg l⁻¹, 6 and 5 to 9 days, respectively. Under these conditions, a 9 days long treatment reduced by 98.7% the original biochemical oxygen demand (of 2,780 mg l⁻¹) and by 98.5% the dissolved chemical oxygen demand (initial 4,200 mg l⁻¹). Moreover, fungal treatment reduced total dissolved solids from 3,950 to 575 mg l⁻¹ and color from 560 mg l⁻¹ PtCo to 111 mg l⁻¹ PtCo.     

Changes in ant communities along an age gradient of cocoa cultivation in the Oumé region,central Côte d'Ivoire

We identified the extent to which ant diversity occurs despite conversion of forests into cocoa plantations by examining the communities across four age classes of plantations (classes I–IV with increasing age from 0–5 to 21–40 years) and in their original forests. An extensive sampling protocol consisting of pitfall trapping, leaf litter sampling, soil sampling and hand sampling was used to characterize ant species richness and composition in three replicates of each age class and in the remaining forest patches. A total of one hundred ant species was found in all habitats combined. While the forest was the richest habitat (73 species), species richness in the different plantation age classes varied as follows (sorted in descending order): class IV (69 species) > class III (57 species) > class I (52 species) > class II (43 species). Age gradient was thus significantly positively correlated with mean species richness and with the relative abundance of some subfamilies. The species composition differed greatly between some plantation age classes and the forest. The two youngest cocoa age classes (I and II) were most dissimilar to the forest. In contrast, forest ants were well represented in the old cocoa age classes (III and IV). Three functional guilds (generalist predators, specialist predators and territorially dominant arboreal species) were in their relative abundance significantly correlated to the age gradient. Overall, cocoa cultivations retaining a floristically diverse and structurally complex forest structure are a suitable management system for the conservation of ant species of the formerly forested habitats.     

Potentiality of the cox1 gene in the taxonomic resolution of soil fungi

We explored the potential of the cox1 gene in the species resolution of soil fungi and compared it with the nuclear internal transcribed spacer (ITS) and small subunit (SSU)-rDNA. Conserved primers allowing the amplification of the fungal cox1 gene were designed, and a total of 47 isolates of Zygomycota and Ascomycota were investigated. The analysis revealed a lack of introns in >90% of the isolates. Comparison of the species of each of the six studied genera showed high interspecific sequence polymorphisms. Indeed, the average of nucleotide variations (4.2–11%) according to the genus, due mainly to the nucleotide substitutions, led to the taxonomic resolution of all the species studied regarding both ITS and SSU-rDNA, in which <88% were discriminated. The phylogenetic analysis performed after alignment of the cox1 gene across distant fungal species was in accordance with the well-known taxonomic position of the species studied and no overlap was observed between intra- and interspecific variations. These results clearly demonstrated that the cox1 sequences could provide good molecular markers for the determination of the species composition of environmental samples and constitute an important advance to study soil fungal biodiversity.     

Population structuring of the tsetse Glossina tachinoides resulting from landscape fragmentation in the Mouhoun River basin,Burkina Faso

The impact of landscape fragmentation resulting from human‐ and climate‐mediated factors on the structure of a population of Glossina tachinoides Westwood (Diptera: Glossinidae) in the Mouhoun River basin, Burkina Faso, was investigated. Allele frequencies at five microsatellite loci were compared in four populations. The average distance between samples was 72 km. The sampling points traversed an ecological cline in terms of rainfall and riverine forest ecotype, along a river loop that enlarged from upstream to downstream. Microsatellite DNA demonstrated no structuring among the groups studied (F_ST = 0.015, P = 0.07), which is contrary to findings pertaining to Glossina palpalis gambiensis Vanderplank in the same geographical area. The populations of G. tachinoides showed complete panmixia (F_IS = 0, P = 0.5 for the whole sample) and no genetic differentiation among populations or global positioning system trap locations. This is in line with the results of dispersal studies which indicated higher diffusion coefficients for G. tachinoides than for G. p. gambiensis. The impact of these findings is discussed within the framework of control campaigns currently promoted by the Pan African Tsetse and Trypanosomosis Eradication Campaign.     

Effects of mowing on fungal endophytes and arbuscular mycorrhizal fungi in subalpine grasslands

In French subalpine grasslands, cessation of mowing promotes dominance of Festuca paniculata, which alters plant diversity and ecosystem functioning. One of the mechanisms underpinning such effects may be linked to simultaneous changes in the abundance of fungal symbionts such as endophytes and arbuscular mycorrhizal fungi. In field conditions, mowing reduced the abundance of the endophyte Neotyphodium sp. in leaves of F. paniculata by a factor of 6, and increased mycorrhizal densities by a factor of 15 in the soil. In greenhouse experiments, the mycorrhizal colonization of Trifolium pratense and Allium porrum increased 3- fold and 3.8- fold respectively in mown vs unmown grassland soil. Significantly reduced growth of the two host plants was also observed on soil from the unmown grassland. Such opposite effects of mowing on the two functional groups of fungal symbionts could suggest interactions between these two groups, which in turn could contribute to structuring plant communities in subalpine grasslands.     

Potential of autochthonous fungal strains isolated from contaminated soils for degradation of polychlorinated biphenyls

Up to now, most studies on polychlorinated biphenyl (PCB) bioremediation have examined the ability of model fungal strains to biodegrade PCBs. Yet, there is limited information concerning the potential of autochthonous filamentous fungal strains in the biodegradation of PCBs and their possible use in the environmental technologies. In this study, we investigated the capacity of autochthonous fungal strains in the biodegradation of PCBs by isolating 24 taxa from former industrial sites highly contaminated by PCBs. Microscopic and molecular analyses using the internal transcribed spacer (ITS) region revealed that the fungal strains belonged to the phyla Ascomycota (19 strains) and Zygomycota (five strains). The chromatography gas analysis revealed evidence of degradation of seven PCB congeners. With the exception of Circinella muscae which presented no degradation potential, the other fungal strains exhibited a rate of biodegradation ranging from 29 to 85 % after 7 d of incubation in liquid medium. Among these strains, Doratomyces nanus, Doratomyces purpureofuscus, Doratomyces verrucisporus, Myceliophthora thermophila, Phoma eupyrena, and Thermoascus crustaceus showed remarkable degradation ability (>70 %) regardless of the number of chlorine substituents on the biphenyl nucleus and a high tolerance towards PCBs. To our knowledge, this is the first study that demonstrates the ability of PCB degradation by these species and indicates the potential effectiveness of some autochthonous fungal strains in bioremediation systems.     

High sexual reproduction and limited contemporary dispersal in the ectomycorrhizal fungus Tricholoma scalpturatum: new insights from population genetics and spatial autocorrelation analysis

Dispersal and establishment are fundamental processes influencing the response of species to environmental changes, and the long-term persistence of populations. A previous study on the symbiotic ectomycorrhizal fungus Tricholoma scalpturatum revealed strong genetic differentiations between populations in Western Europe, suggesting restricted dispersal for this wind-dispersed cosmopolitan fungus. Two distinct genetic groups (genetic groups 1 and 2), co-occurring in some locations, were also identified and could correspond to cryptic species. In the present work, we examine the reproductive strategy and dispersal biology of the two T. scalpturatum's genetic groups. Variable molecular markers (intersimple sequence repeats and intergenic spacer 2-restriction fragment length polymorphisms) and spatial autocorrelation analyses were used to examine fine-scale patterns (< 140 m) of genetic structure, in an effort to determine the physical scale at which genetic structure exists. A total of 473 fruit bodies were mapped and collected over 3 years from two plots located in the south of France, including 219 and 254 samples from group 1 and group 2, respectively. High genetic diversity and the presence of numerous small genets were observed in both groups. Autocorrelation analyses revealed significant positive spatial genetic structures of genets at close distances (up to few metres for both groups). Mantel tests confirmed this isolation-by-distance pattern. These results clearly demonstrate high sexual reproduction and spatial structuring of genets at very small geographical scales in this wind-dispersed ectomycorrhizal fungal species, a pattern consistent with restricted contemporary dispersal of spores.     

Population Evidence of Cryptic Species and Geographical Structure in the Cosmopolitan Ectomycorrhizal Fungus, Tricholoma scalpturatum

Tricholoma scalpturatum is an ectomycorrhizal fungus that forms symbioses with roots of diverse trees and shrubs. It is commonly encountered in a wide range of habitats, across temperate ecosystems. A previous study has revealed a high genetic diversity at a local scale, and ruderal abilities. To examine genetic structure at a large geographical scale, a total of 164 basidiocarps were collected from 30 populations located in Western Europe, from Spain to Scandinavia. These samples were analyzed by three molecular methods with different levels of resolution: inter-simple sequence repeats (ISSRs), restriction fragment length polymorphisms (RFLPs) in the rDNA internal transcribed spacer (ITS), and ITS sequence analysis. Considerable genetic variation was found, and the morphospecies was separated into two genetic groups that were distinct from each other. The ISSR data and the relatively low percentage value (96%) of shared sequence polymorphisms in the ITS between isolates from the two groups, strongly suggest cryptic species and long-lasting separation. No geographical exclusion was detected for these two widely distributed taxa. However, high estimates of population differentiation were observed in each group, including between populations less than a few kilometers apart. This result provides evidence for limited gene flow and/or founding effects. It also indicates that T. scalpturatum does not constitute a random mating population, and the hypothesis of endemism cannot be excluded for this cosmopolitan wind-dispersed fungus.