The study of transcription regulatory networks in bacterial communities will greatly benefit our mechanistic understanding of C and N cycling in soil ecosystems and reveal how individual bacterial taxa integrate into whole community responses. Moreover, the study will generate essential information on life-history traits and ecological strategies for hundreds of bacterial taxa, many of which… [Read More]

The proposed study will answer fundamental questions regarding microbial diversity, metabolism, and growth in one in one of the least understood habitats on Earth. The data will have implications for our understanding of global energy and nutrient cycles, the potential for deep terrestrial disposal of nuclear waste and geo-engineering for CO2 storage, while also providing… [Read More]

The basic molecular mechanisms by which bacterial endophytes improve plant growth and health and reduce phytotoxic responses and promote remediation are not well understood. To learn more, one approach is to use the RB-TnSeq approach to elucidate which genes are required for N2-fixation by a diazotrophic endophyte of poplar. Using the same approach, researchers then plan… [Read More]

The researchers aim to understand the genetic diversity of cryptophyte photosynthesis in the context of their ability to capture a broad spectrum of available light. These genomes will provide a valuable resource to researchers studying cryptophytes, microalgal photosynthesis and systematics, and marine metagenomics by providing a better catalog of the diversity within this clade of… [Read More]

Nitrogen (N) availability is an important factor controlling productivity in estuaries. Relatively little is known about how the abundance, diversity, and distribution of estuarine N-cycling microbes are affected by environmental change. The researchers will investigate the structure and function of microbial communities, particularly those related to N and carbon (C) cycling, in the San Francisco… [Read More]

The Genomic Encyclopedia of Bacteria and Archaea pilot and the Kilo Microbial Genomes project demonstrated that strain selection to maximize sequence coverage of phylogenetic space is of tremendous help in discovering new protein families, facilitating metagenome interpretation and identifying numerous biosynthetic clusters. It also reinforced the notion that isolate sequence space is far from saturated…. [Read More]

The aim is to sequence the genomes of a closely related pair of C3 and Crassulacean acid metabolism (CAM) species of Yucca (Asparagaceae). While CAM has been studied for over four decades, little is known about the genetic molecular mechanisms regulating this adaptive photosynthetic pathway. Whereas over 35 independent transitions from C3 to CAM have been… [Read More]

Bloom-forming marine phytoplankton are major contributors to primary production and key regulators of local biogeochemistry.  Here, the team proposes a genome sequencing and assembly project that will facilitate (1) phylogenomic comparisons of photo- and heterotrophic Mesodinium species, (2) accurate attribution of metabolic pathways to host versus prey, and (3) identification of horizontal gene exchange. Proposer: Matthew… [Read More]

This proposal seeks support to generate a platinum grade genome sequence for Andropogon gerardii subsp. gerardii (big bluestem). This genome will be valuable for disparate communities of researchers, including many working on projects closely connected to the DOE mission. A. gerardii is the dominant plant of the tallgrass prairie and is the species most often… [Read More]

Populus is one of DOE’s “flagship” plant species that is of special interest as a biofuel feedstock. Sphaerulina musiva, the cause of Septoria stem canker and leaf-spot disease, is one of the most economically important pathogens and a major limiting factor in the use of Populus as a biofuel feedstock in North America. We propose… [Read More]