Showing papers by "Mohammad Bahram published in 2017"

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients

Abstract: Parkinson’s disease (PD) presently is conceptualized as a protein aggregation disease in which pathology involves both the enteric and the central nervous system, possibly spreading from one to another via the vagus nerves. As gastrointestinal dysfunction often precedes or parallels motor symptoms, the enteric system with its vast diversity of microorganisms may be involved in PD pathogenesis. Alterations in the enteric microbial taxonomic level of L-DOPA-naive PD patients might also serve as a biomarker. We performed metagenomic shotgun analyses and compared the fecal microbiomes of 31 early stage, L-DOPA-naive PD patients to 28 age-matched controls. We found increased Verrucomicrobiaceae (Akkermansia muciniphila) and unclassified Firmicutes, whereas Prevotellaceae (Prevotella copri) and Erysipelotrichaceae (Eubacterium biforme) were markedly lowered in PD samples. The observed differences could reliably separate PD from control with a ROC-AUC of 0.84. Functional analyses of the metagenomes revealed differences in microbiota metabolism in PD involving the ẞ-glucuronate and tryptophan metabolism. While the abundances of prophages and plasmids did not differ between PD and controls, total virus abundance was decreased in PD participants. Based on our analyses, the intake of either a MAO inhibitor, amantadine, or a dopamine agonist (which in summary relates to 90% of PD patients) had no overall influence on taxa abundance or microbial functions. Our data revealed differences of colonic microbiota and of microbiota metabolism between PD patients and controls at an unprecedented detail not achievable through 16S sequencing. The findings point to a yet unappreciated aspect of PD, possibly involving the intestinal barrier function and immune function in PD patients. The influence of the parkinsonian medication should be further investigated in the future in larger cohorts.

Novel soil-inhabiting clades fill gaps in the fungal tree of life

Abstract: Fungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water. We provide rough phylogenetic placement and principal niche analysis for >40 previously unrecognized fungal groups at the order and class level from global soil samples based on combined 18S (nSSU) and 28S (nLSU) rRNA gene sequences. Especially, Rozellomycota (Cryptomycota), Zygomycota s.lat, Ascomycota, and Basidiomycota are rich in novel fungal lineages, most of which exhibit distinct preferences for climate and soil pH. This study uncovers the great phylogenetic richness of previously unrecognized order- to phylum-level fungal lineages. Most of these rare groups are distributed in different ecosystems of the world but exhibit distinct ecological preferences for climate or soil pH. Across the fungal kingdom, tropical and non-tropical habitats are equally likely to harbor novel groups. We advocate that a combination of traditional and high-throughput sequencing methods enable efficient recovery and phylogenetic placement of such unknown taxonomic groups.

PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data.

Abstract: High-throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be ...

Plant species richness and productivity determine the diversity of soil fungal guilds in temperate coniferous forest and bog habitats.

Abstract: Fungi have important roles as decomposers, mycorrhizal root symbionts and pathogens in forest ecosystems, but there is limited information about their diversity and composition at the landscape scale. This work aimed to disentangle the factors underlying fungal richness and composition along the landscape-scale moisture, organic matter and productivity gradients. Using high-throughput sequencing, we identified soil fungi from 54 low-productivity Pinus sylvestris-dominated plots across three study areas in Estonia and determined the main predictors of fungal richness based on edaphic, floristic and spatial variables. Fungal richness displayed unimodal relationship with organic matter and deduced soil moisture. Plant richness and productivity constituted the key predictors for taxonomic richness of functional guilds. Composition of fungi and the main ectomycorrhizal fungal lineages and hyphal exploration types was segregated by moisture availability and soil nitrogen. We conclude that plant productivity and diversity determine the richness and proportion of most functional groups of soil fungi in low-productive pine forests on a landscape scale. Adjacent stands of pine forest may differ greatly in the dominance of functional guilds that have marked effects on soil carbon and nitrogen cycling in these forest ecosystems.

Bacterial Communities in Boreal Forest Mushrooms Are Shaped Both by Soil Parameters and Host Identity.

Abstract: Despite recent advances in understanding the microbiome of eukaryotes, little is known about microbial communities in fungi. Here we investigate the structure of bacterial communities in mushrooms, including common edible ones, with respect to biotic and abiotic factors in the boreal forest. Using a combination of culture-based and Illumina high-throughput sequencing, we characterized the bacterial communities in fruitbodies of fungi from eight genera spanning four orders of the class Agaricomycetes (Basidiomycota). Our results revealed that soil pH followed by fungal identity are the main determinants of the structure of bacterial communities in mushrooms. While almost half of fruitbody bacteria were also detected from soil, the abundance of several bacterial taxa differed considerably between the two environments. The effect of host identity was significant at the fungal genus and order level and could to considerable extent be ascribed to the distinct bacterial community of the chanterelle, representing Cantharellales – the earliest diverged group of mushroom-forming basidiomycetes. These data suggest that besides the substantial contribution of soil as a major taxa source and environmental determinant of bacterial communities in mushrooms, the structure of these communities is to a great degree affected by the identity of the host. Thus, bacteria inhabiting fungal fruitbodies may be non-randomly selected from environment based on their symbiotic functions and/or habitat requirements.

Pole-to-Pole Connections : Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change

Abstract: The global biogeography of microorganisms remains poorly resolved, which limits the current understanding of microbial resilience toward environmental changes. Using high-throughput 16S rRNA gene amplicon sequencing, we characterized the microbial diversity of terrestrial and lacustrine biofilms from the Arctic, Antarctic and temperate regions. Our analyses suggest that bacterial community compositions at the poles are more similar to each other than they are to geographically closer temperate habitats, with 32% of all operational taxonomic units (OTUs) co-occurring in both polar regions. While specific microbial taxa were confined to distinct regions, representing potentially endemic populations, the percentage of cosmopolitan taxa was higher in Arctic (43%) than in Antarctic samples (36%). The overlap in polar microbial OTUs may be explained by natural or anthropogenically-mediated dispersal in combination with environmental filtering. Current and future changing environmental conditions may enhance microbial invasion, establishment of cosmopolitan genotypes and loss of endemic taxa.

Local-scale spatial structure and community composition of orchid mycorrhizal fungi in semi-natural grasslands.

Abstract: Orchid mycorrhizal (OrM) fungi play a crucial role in the ontogeny of orchids, yet little is known about how the structure of OrM fungal communities varies with space and environmental factors. Previous studies suggest that within orchid patches, the distance to adult orchids may affect the abundance of OrM fungi. Many orchid species grow in species-rich temperate semi-natural grasslands, the persistence of which depends on moderate physical disturbances, such as grazing and mowing. The aim of this study was to test whether the diversity, structure and composition of OrM fungal community are influenced by the orchid patches and management intensity in semi-natural grasslands. We detected putative OrM fungi from 0 to 32 m away from the patches of host orchid species (Orchis militaris and Platanthera chlorantha) in 21 semi-natural calcareous grasslands using pyrosequencing. In addition, we assessed different ecological conditions in semi-natural grasslands but primarily focused on the effect of grazing intensity on OrM fungal communities in soil. We found that investigated orchid species were mostly associated with Ceratobasidiaceae and Tulasnellaceae and, to a lesser extent, with Sebacinales. Of all the examined factors, the intensity of grazing explained the largest proportion of variation in OrM fungal as well as total fungal community composition in soil. Spatial analyses showed limited evidence for spatial clustering of OrM fungi and their dependence on host orchids. Our results indicate that habitat management can shape OrM fungal communities, and the spatial distribution of these fungi appears to be weakly structured outside the orchid patches.

Specificity of fungal associations of Pyroleae and Monotropa hypopitys during germination and seedling development.

Abstract: Mycoheterotrophic plants obtain organic carbon from associated mycorrhizal fungi, fully or partially. Angiosperms with this form of nutrition possess exceptionally small 'dust seeds' which after ge ...

Biogeography and Specificity of Ectomycorrhizal Fungi of Coccoloba uvifera

Abstract: Ectomycorrhizal fungal assemblages in tropical regions have remained relatively understudied compared to temperate ecosystems. Sea grape (Coccoloba uvifera) from the Polygonaceae family is a common ectomycorrhizal tree species inhabiting coastal habitats in neotropical forests. We sampled roots of C. uvifera in six locations around the Caribbean basin to characterize the associated ectomycorrhizal fungal assemblages at the regional scale. In accordance with earlier reports, sea grape ectomycorrhizal fungal communities were species-poor, implying ecological host specificity. Species of the /tomentella-thelephora lineage were the most species-rich group inhabiting roots of C. uvifera. Inclusive phylogenetic analyses of Thelephoraceae from Northeast, Central and South America indicated that the mycobionts of C. uvifera tend to cluster with taxa associated with North and Central American Pinus and Fagaceae rather than with South American taxa. This suggests that C. uvifera may have received multiple EcM symbionts from host switching events due to a common habitat in maritime sand dunes or more widely shared historical habitat in North America and the Caribbean Islands. Considering the absence of shared fungal taxa with other Coccoloba species from inland rain forest habitats, we hypothesize that distinct ectomycorrhizal associations of sea grape are primarily driven by stressful environmental conditions in maritime sand dunes.

Physiological and molecular responses of resistant and susceptible wheat cultivars to Fusarium graminearum mycotoxin extract

Abstract: Fusarium graminearum, causing Fusarium head blight (FHB), is one of the most important diseases on cereals worldwide leading to a reduction in both grain yield and quality. Currently, there is limited knowledge about the physiological and molecular mechanisms involved in wheat resistance against F. graminearum mycotoxins. Crude culture extract of F. graminearum was used to determine the physiological and molecular responses of wheat cultivars ‘Falat’ and ‘Sumai3‘, susceptible and resistant to FHB, respectively. Point inoculation of crude extract in the wheat spikelets resulted in significant increases in hydrogen peroxide (H2O2) and malondialdehyde (MDA) content in both cultivars, most likely due to oxidative stress. A greater induction level and activity of H2O2, MDA, peroxidase (POX), phenylalanine ammonia lyase (PAL) and polyphenol oxidase (PPO) was observed in the resistant versus the susceptible cultivar. In addition, quantitative real-time PCR indicated earlier and greater induction of PAL, ...