scholarly journals Microbiome Community Structure and Functional Gene Partitioning in Different Micro-Niches Within a Sporocarp-Forming Fungus

2021 ◽  
Vol 12 ◽  
Author(s):  
Dong Liu ◽  
Xinhua He ◽  
Caspar C. C. Chater ◽  
Jesús Perez-Moreno ◽  
Fuqiang Yu
Keyword(s):  
Sulfur Oxidation ◽  
Edible Mushroom ◽  
Amplicon Sequencing ◽  
Functional Gene ◽  
Functional Genes ◽  
Functional Roles ◽  
Genomic Complexity ◽  
Polyphosphate Degradation ◽  
Wild Edible Mushroom ◽  
Shed Light

Thelephora ganbajun is a wild edible mushroom highly appreciated throughout China. The microbiomes of some fungal sporocarps have been studied, however, their potential functional roles currently remain uncharacterized. Here, functional gene microarrays (GeoChip 5.0) and amplicon sequencing were employed to define the taxonomic and functional attributes within three micro-niches of T. ganbajun. The diversity and composition of bacterial taxa and their functional genes differed significantly (p < 0.01) among the compartments. Among 31,117 functional genes detected, some were exclusively recorded in one sporocarp compartment: 1,334 genes involved in carbon (mdh) and nitrogen fixation (nifH) in the context; 524 genes influencing carbon (apu) and sulfite reduction (dsrB, dsra) in the hymenophore; and 255 genes involved in sulfur oxidation (soxB and soxC) and polyphosphate degradation (ppx) in the pileipellis. These results shed light on a previously unknown microbiome and functional gene partitioning in sporome compartments of Basidiomycota. This also has great implications for their potential ecological and biogeochemical functions, demonstrating a higher genomic complexity than previously thought.

A Gravity Model to Explain Flows of Wild Edible Mushroom Picking. A Panel Data Analysis

2019 ◽  
Vol 156 ◽  
pp. 164-173 ◽  
Author(s):  
Pablo de Frutos ◽  
Beatriz Rodriguez-Prado ◽  
Joaquín Latorre ◽  
Fernando Martinez-Peña
Keyword(s):  
Data Analysis ◽  
Panel Data ◽  
Gravity Model ◽  
Panel Data Analysis ◽  
Edible Mushroom ◽  
Wild Edible Mushroom

scholarly journals Microbial Functional Gene Diversity with a Shift of Subsurface Redox Conditions duringIn SituUranium Reduction

2012 ◽  
Vol 78 (8) ◽  
pp. 2966-2972 ◽  
Author(s):  
Yuting Liang ◽  
Joy D. Van Nostrand ◽  
Lucie A. N′Guessan ◽  
Aaron D. Peacock ◽  
Ye Deng ◽  
...  
Keyword(s):  
Functional Diversity ◽  
Field Experiments ◽  
Gene Diversity ◽  
Functional Gene ◽  
Redox Conditions ◽  
Functional Genes ◽  
Microbial Functional Diversity ◽  
Content Type ◽  
Microbial Functional Gene

ABSTRACTTo better understand the microbial functional diversity changes with subsurface redox conditions duringin situuranium bioremediation, key functional genes were studied with GeoChip, a comprehensive functional gene microarray, in field experiments at a uranium mill tailings remedial action (UMTRA) site (Rifle, CO). The results indicated that functional microbial communities altered with a shift in the dominant metabolic process, as documented by hierarchical cluster and ordination analyses of all detected functional genes. The abundance ofdsrABgenes (dissimilatory sulfite reductase genes) and methane generation-relatedmcrgenes (methyl coenzyme M reductase coding genes) increased when redox conditions shifted from Fe-reducing to sulfate-reducing conditions. The cytochrome genes detected were primarily fromGeobactersp. and decreased with lower subsurface redox conditions. Statistical analysis of environmental parameters and functional genes indicated that acetate, U(VI), and redox potential (Eh) were the most significant geochemical variables linked to microbial functional gene structures, and changes in microbial functional diversity were strongly related to the dominant terminal electron-accepting process following acetate addition. The study indicates that the microbial functional genes clearly reflect thein situredox conditions and the dominant microbial processes, which in turn influence uranium bioreduction. Microbial functional genes thus could be very useful for tracking microbial community structure and dynamics during bioremediation.

A Comparison Analysis for Protein-Protein Interaction Network-Based Methods in Prioritizing Arabidopsis Functional Genes

2021 ◽  
Vol 16 ◽  
Author(s):  
Chun-Jing Si ◽  
Si-Min Deng ◽  
Yuan Quan ◽  
Hong-Yu Zhang
Keyword(s):  
Hybrid Model ◽  
Protein Interaction ◽  
High Throughput Sequencing ◽  
Functional Gene ◽  
Functional Genes ◽  
Systems Genetics ◽  
Ppi Network ◽  
Protein Protein Interaction ◽  
Gene Enrichment ◽  
Comprehensive Score

Background: Connecting genes to phenotypes is still a great challenge in genetics. Research related to gene-phenotype associations has made remarkable progress recently due to high-throughput sequencing technology and genome-wide association study (GWAS). However, these genes, which are considered to be significantly associated with a target phenotype according to traditional GWAS, are less precise or subject to greater confounding. Objective: The present study is an attempt to prioritize functional genes for complex phenotypes employing protein-protein interaction (PPI) network-based systems genetics methods on available GWAS results. Method: In this paper, we calculated the functional gene enrichment ratios of the trait ontology of A. thaliana for three common systems genetics methods (i.e. GeneRank, K-shell and HotNet2). Then, comparison of gene enrichment ratios obtained by PPI network-based methods was performed. Finally, a hybrid model was proposed, integrating GeneRank, comprehensive score algorithm and HotNet diffusion-oriented subnetworks (HotNet2) to prioritize functional genes. Results: These PPI network-based systems genetics methods were indeed useful for prioritizing phenotype-associated genes. And functional gene enrichment ratios calculated from the top 20% of GeneRank-identified genes were higher than these ratios of K-shell and these ratios of HotNet2 for most phenotypes. However, the hybrid model can improve the efficiency of functional gene enrichment for A. thaliana (up to 40%). Conclusion: The present study provides a hybrid method integrating GeneRank, comprehensive score algorithm and HotNet2 to prioritize functional genes. The method will contribute to functional genomics in plants. The source data and codes are freely available at http://47.242.161.60/Plant/.

Fatty Acid Compositions of Five Wild Edible Mushroom Species Collected from Turkey

2012 ◽  
Vol 8 (5) ◽  
pp. 463-466 ◽  
Author(s):  
Pelin Gunc Ergon ◽  
Bulent Ergonul ◽  
Fatih Kalyoncu ◽  
Ilgaz Akata
Keyword(s):  
Fatty Acid ◽  
Edible Mushroom ◽  
Mushroom Species ◽  
Wild Edible Mushroom ◽  
Fatty Acid Compositions
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