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]

The team is investigating desiccation tolerance in a very phylogenetically broad group of green microalgae isolated from microbiotic crusts of the desert southwestern United States. These algae fall in multiple, evolutionarily independent lineages (in at least 7 algal classes) that made the leap from aquatic to desert habitats. They exhibit clearly stronger desiccation tolerance than… [Read More]

Recent findings of genomic complexity in the form of mobile elements and evidence for extensive horizontal gene transfer, as well as community complexity in the form of trophic associations with other bacteria, drives the team to gain a better understanding of these communities and their molecular underpinnings. The team plans to generate “single-cell” (meta-)genomes of… [Read More]

The goal of this CSP is deep-sequencing of highly diverse sorghum lines to assemble and analyze the pan-genome of this important bioenergy crop. Sorghum is a promising lignocellulosic and saccharine bioenergy crop, one of the DOE-JGI’s flagship species, and an important food and feed crop. In order to accelerate breeding and development of elite sorghum… [Read More]

The team aims to study organic sulfur biogeochemistry in a coastal ocean ecosystem. In fall 2014, the Monterey Bay Aquarium Research Institute (MBARI) Environmental Sample Processor (ESP) was deployed in Monterey Bay, CA to collect a high-resolution microbial community time-series for analysis of bacterially-mediated organic sulfur transformations. Concurrent data on chlorophyll concentrations, bacterial and phytoplankton cell… [Read More]