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Deep Sequencing of Dikarya

Fungi perform essential ecological functions, both beneficial and harmful. The ecology of most of the 1.5- 6 million fungal species is unknown. The current 1000 Fungal Genomes (1KFG) and associated CSPs (e.g., Mycorrhizal Genomics Initiative, Saprotrophic Basidiomycetes) have been mostly successful in sampling genomes of members of the Dikarya. The results have included an increased… [Read More]

Shale Gas Extraction Impact on Microbes

Due to the high cost of drilling and maintaining sample integrity, there has been very little research on microbial life in pristine hydrocarbon-bearing shale ecosystems. This project provides necessary information needed to plan for future energy and resource needs. Advances in high throughput genomics afford the first opportunity to deeply characterize microbial phylogenetic diversity and… [Read More]

Understanding Sugar Accumulation in Sorghum

The goal of the project is to identify and characterize the biological pathways and their regulators that enable sucrose accumulation in sweet sorghum, whose genome was sequenced by the DOE JGI. Understanding the genetic mechanisms underlying sugar production and storage in sorghum is of great interest to both biologists and breeders, and the genes in… [Read More]

Genomic Survey of Lentinula genus

Lentinula is a group of white-rot, wood-decaying fungi that is famous as the genus of shiitake mushrooms, Lentinula edodes. Today, shiitake is cultivated worldwide, and it is second only to the button mushroom, Agaricus bisporus, a previous DOE JGI project, in terms of production volume. However, the diversity within cultivars is dwarfed by the genetic… [Read More]

Microbial Controls on Carbon Cycling in Freshwater Lakes

The role of lakes in the global carbon budget has previously been underestimated. The total amount of organic matter stored in the sediments of lakes and reservoirs is estimated to exceed that stored in the sediments of the world’s oceans. Freshwater lakes can act as net sources or sinks of atmospheric carbon, and microbes mediate… [Read More]

ASR Pathogen Reference Genome

Phakopsora pachyrhizi is responsible for Asian Soybean Rust (ASR) and is the major pathogen of soybean, causing severe losses in almost all soybean-growing areas. Nearly 300 billion tons of the legume are produced annually, and used primarily as feedstock and for bioenergy production. Yield damage caused by ASR can be dramatic (reported cases from 60… [Read More]

Global Diversification of Pisolithus

The mutualistic ectomycorrhizal (ECM) fungal genus Pisolithus colonizes the roots of trees in forests around the world and are inoculated on bioenergy crops such as Eucalyptus sp. and Pinus sp. due to their role in promoting plant health and productivity under different environmental constraints. The mutualistic relationship between tree roots and ECM fungi, and the… [Read More]

Methane cycling in arid and semi-arid ecosystems

Roughly one-third of the world’s land surface is characterized by severe water deficiency, and these semi-arid and desert areas around the world are currently expanding, impacting local and global climate. Very little is known about the microbial communities inhabiting the natural dry ecosystems, but environmental genetic studies showed that diverse and active bacteria inhabit arid soils,… [Read More]

Better Microbial Genome Binning with MetaBAT

DOE JGI researchers develop an automated software tool that can scale to handle complex metagenome datasets. The Science: DOE JGI researchers have developed an automated tool called MetaBAT that automatically groups large genomic fragments assembled from metagenome sequences to reconstruct single microbial genomes. The Impact: The ability to accurately and efficiently reconstruct individual microbial genomes… [Read More]

Tanja Woyke: 2015 Women @ Berkeley Lab Honoree

Tanja Woyke, head of our Microbial Program, was one of the honorees at Berkeley Lab’s 2015 Women @ The Lab, held November 18, 2015. She was among 14 women selected from labwide nominations in the following categories: Postdoctoral Fellow Early/Mid-Career Scientist or Engineer Senior Scientists or Engineer Operations Professional Administrative Professional Technician Click here to read about Dr. Woyke… [Read More]