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A Novel Technique for Studying Nitrifiers

Ammonia-oxidizing bacteria and nitrite-oxidizing bacteria (AOB and NOB) catalyze nitrification and are key drivers of the nitrogen cycle. As nitrification is an important step of nitrogen removal from sewage, AOB and NOB are essential bacteria in most wastewater treatment plants. However, both groups are understudied as most nitrifiers are uncultured and the few cultured strains… [Read More]

Microbial and Viral Responses to Low Oxygen Zones

Oxygen minimum zones (OMZs) occur throughout the world’s oceans but vary substantially in biological, chemical, and physical properties, notably the levels of primary production and oxygen availability. These areas are expanding due to climate warming and human modification of coastal zones. Complex microbial communities dominate OMZs and OMZ expansion is predicted to affect microbial biogeochemical… [Read More]

Microbial Dark Matter, Phase II

Though more than 5,000 bacterial and archaeal genomes have been sequenced worldwide, the great majority are of rather limited phylogenetic diversity. Through the Microbial Dark Matter Project targeted 200 representatives of candidate phyla belonging to 29 major uncharted branches of the tree. The findings provided a first glimpse into the coding potential and the phylogeny… [Read More]

Peat Moss as a Comparative Genomics Resource

Spikemoss (Physcomitrella patens) is one DOE JGI’s Plant Flagship Genomes. However, researchers note that despite its many advantages as a model Flagship organism, the moss is exceedingly rare in nature, is poorly characterized ecologically, and forms miniscule quantities of biomass worldwide. In contrast, peat mosses have tremendous impacts on global carbon budgets and climate.Both arctic… [Read More]

Poplar and Epigenomic Reprogramming

The ability to engineer genomes or selectively breed for traits desirable for bioenergy crops is a costly and time-intensive process. Innovative methods that enable rapid reprogramming of stable gene expression patterns is desired. To this end, for this project, researchers plan to combine common practices for Populus plant regeneration from tissue culture or stem cuttings… [Read More]

Unraveling the Rhizosphere Carbon Cycle

Two-thirds of the carbon in the terrestrial biosphere is stored as soil organic matter, and plant roots are the primary source of this stabilized soil organic carbon. While the soil surrounding roots accounts for only 1-2% of the total soil volume, the rhizosphere can provide 30-40% of the total soil organic carbon input. The microbes… [Read More]

Functional Diversity of the Populus Root Microbiome

Complex microbial communities provide benefits to host plants such as ability to grow on marginal lands, pathogen resistance, abiotic stress tolerance, and increase in biomass productivity. Populus has received attention in bioenergy research as a source of cellulose-derived biofuels and as a model tree species. Populus trees are host to a diverse microbial community that… [Read More]

Sorghum GENCODE Project

The overall goal of the Sorghum GENCODE project is to obtain in-depth knowledge of key gene regulatory networks that will enable the design of high yielding feedstocks of the DOE JGI Flagship Plant sorghum and other C4 grasses that can be sustainably produced and efficiently converted by the U.S. biofuels industry. As part of this… [Read More]

Characterizing BDLs in MycoCosm’s fungal genomes

Benzenediol lactones or BDLs are a subclass of polyketides whose known representatives show widely varied biological activities, including stress tolerance and other roles related to plant health and productivity. Through a novel technique dubbed “comparative metaparvomics,” this project uses genome sequence information from the fungal genomes in the DOE JGI portal MycoCosm and interpreted by… [Read More]

A Brachypodium ENCODE-like project

The Brachypodium reference genome was sequenced, assembled and annotated by the DOE JGI. This project builds upon the reference genome by generating gene regulatory networks in Brachypodium in order to identify genes capable of conferring enhanced traits in bioenergy crop plants. In particular, the project will focus on generating fundamental systems-level information on drought tolerance and water… [Read More]