Here we propose to expand the search for new lineages of methanotrophs and methanogens by conducting multi-omic (DNA and RNA) sequencing in methane-rich environments enriched in uncultivated microbial “dark matter” (MDM). Specifically, we will focus on: 1) the distribution of methane metabolism in microbial dark matter; 2) capacity for facultative respiration in methanogenic archaea; 3)…
Metatranscriptome Analysis of Pinus Contorta
Woody biomass makes up the major portion of terrestrial carbon, and forest ecosystems contain enormous reservoirs of lignocellulose belowground, in dead trees, and litter. Decomposition of this recalcitrant material and mobilization of nutrients are major components of the carbon cycle and essential for forest health. Whether releasing carbon dioxide (CO2) or transforming humic substances, the…
Developing an Ice Plant Gene Atlas
The goal is to establish the common or crystalline ice plant (Mesembryanthemum crystallinum L.) as a DOE Plant Flagship Genome species. The ice plant was the first reported halophytic, facultative crassulacean acid metabolism (CAM) species, meaning that the plant can be induced to switch from C3 photosynthesis to CAM following water-deficit or salinity stress treatment….
Brachypodium: a Model Grass Genus for Bioenergy
We propose a series of comparative genomic analyses with the broad aim of identifying transcripts and putative regulatory control elements (conserved non-coding sequences; CNS) that are associated with the evolutionary transition between annual and perennial life history strategies. We will accomplish this via de novo sequencing of additional perennial Brachypodium species and a new outgroup…
Stress in Microbial Communities
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…
Exploring Deep Biosphere Microbial Communities
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…
Functional Genomics of Poplar Endophytes
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…
Photosynthetic Diversity of Cryptophyte Algae
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…
Spatiotemporal Characterization of Microbial Communities
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…
1000 Microbial Genomes-Phase 4
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….