Aboveground and Belowground Plant Traits Explain Latitudinal Patterns in Topsoil Fungal Communities From Tropical to Cold Temperate Forests

Soil fungi predominate the forest topsoil microbial biomass and participate in biogeochemical cycling as decomposers, symbionts, and pathogens. They are intimately associated with plants but their interactions with aboveground and belowground plant traits are unclear. Here, we evaluated soil fungal communities and their relationships with leaf and root traits in nine forest ecosystems ranging from tropical to cold temperate along a 3,700-km transect in eastern China. Basidiomycota was the most abundant phylum, followed by Ascomycota, Zygomycota, Glomeromycota, and Chytridiomycota. There was no latitudinal trend in total, saprotrophic, and pathotrophic fungal richness. However, ectomycorrhizal fungal abundance and richness increased with latitude significantly and reached maxima in temperate forests. Saprotrophic and pathotrophic fungi were most abundant in tropical and subtropical forests and their abundance decreased with latitude. Spatial and climatic factors, soil properties, and plant traits collectively explained 45% of the variance in soil fungal richness. Specific root length and root biomass had the greatest direct effects on total fungal richness. Specific root length was the key determinant of saprotrophic and pathotrophic fungal richness while root phosphorus content was the main biotic factor determining ectomycorrhizal fungal richness. In contrast, spatial and climatic features, soil properties, total leaf nitrogen and phosphorus, specific root length, and root biomass collectively explained >60% of the variance in fungal community composition. Soil fungal richness and composition are strongly controlled by both aboveground and belowground plant traits. The findings of this study provide new evidence that plant traits predict soil fungal diversity distribution at the continental scale

Aboveground and Belowground Plant Traits Explain Latitudinal Patterns in Topsoil Fungal Communities From Tropical to Cold Temperate Forests

International audienceSoil fungi predominate the forest topsoil microbial biomass and participate in biogeochemical cycling as decomposers, symbionts, and pathogens. They are intimately associated with plants but their interactions with aboveground and belowground plant traits are unclear. Here, we evaluated soil fungal communities and their relationships with leaf and root traits in nine forest ecosystems ranging from tropical to cold temperate along a 3,700-km transect in eastern China. Basidiomycota was the most abundant phylum, followed by Ascomycota, Zygomycota, Glomeromycota, and Chytridiomycota. There was no latitudinal trend in total, saprotrophic, and pathotrophic fungal richness. However, ectomycorrhizal fungal abundance and richness increased with latitude significantly and reached maxima in temperate forests. Saprotrophic and pathotrophic fungi were most abundant in tropical and subtropical forests and their abundance decreased with latitude. Spatial and climatic factors, soil properties, and plant traits collectively explained 45% of the variance in soil fungal richness. Specific root length and root biomass had the greatest direct effects on total fungal richness. Specific root length was the key determinant of saprotrophic and pathotrophic fungal richness while root phosphorus content was the main biotic factor determining ectomycorrhizal fungal richness. In contrast, spatial and climatic features, soil properties, total leaf nitrogen and phosphorus, specific root length, and root biomass collectively explained >60% of the variance in fungal community composition. Soil fungal richness and composition are strongly controlled by both aboveground and belowground plant traits. The findings of this study provide new evidence that plant traits predict soil fungal diversity distribution at the continental scale

Expanded encyclopaedias of DNA elements in the human and mouse genomes

AbstractThe human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.11Nsciescopu

Perspectives on ENCODE

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.11Nsciescopu