About This Program
The Small-scale Microbial/Metagenome program seeks to target specific project types listed in the call, with an emphasis on providing pilot data to enable future large-scale proposal submission. Projects from first-time JGI investigators are strongly encouraged. Proposals may include up samples from up to three project types. The number of samples proposed must adhere to call guidelines for the proposal to be considered for scientific review.
Proposals for this call may be submitted at any time as brief white papers and will be reviewed every six months. Applicants may submit up to two proposals per cycle (but may be listed as co-PI on an unlimited number of proposals).
All proposals will undergo an internal pre-review to ensure technical feasibility and alignment with JGI and DOE missions. Screened proposals will then be reviewed for scientific merit, DOE relevance, proposed data usage by the applicant/community, and track record of the applicant. After proposal approval, and at an established time (roughly two months after approval), the proposer will be asked to provide DNA/RNA meeting JGI’s sample requirements. Samples that are not available at that time, or are of insufficient quality or quantity, will delay or potentially defer approval for sequencing.
For questions about the appropriateness of projects, program specifics or application process, please contact us.
Current Call (Proposals due February 24, 2017)
Bacterial and archaeal isolates and single cells
Proposed organisms should broaden phylogenetic representation among sequenced representatives or participate in processes directly relevant to DOE missions. Type strains, including proposed strains prior to publication, are highly encouraged. For single-cell sequencing projects, MDA products of single amplified genomes should either be in hand at the time of proposal submission or samples can be sent directly to JGI for single-cell sorting and amplification. Single cells from candidate phyla are encouraged. Between 48 and 92 isolates or single-cell genomes may be proposed. For projects with >92 genomes, please refer to the CSP Annual Call.
Bacterial and archaeal resequencing
The JGI seeks proposals centered on resequencing of bacterial and archaeal isolates for which a reference genome exists. Projects may focus on bacterial community structure, understanding gene function in bacteria under selective pressure or in mutagenized strains. We will also consider collections of highly related strains from nature that display differences in phenotypes related to DOE missions, e.g. lignocellulose decomposition, fermentation of sugar substrates or degradation of environmental toxins. Between 36 and 72 samples may be proposed. For projects with >72 samples, please refer to the CSP Annual Call.
Bacterial and archaeal RNA sequencing
The JGI solicits smaller scale RNA sequencing projects for bacterial and archaeal isolates, for which a reference genome is available. RNA-seq data may be used for improvement of genome annotation or for transcript counting applications (e.g. gene expression profiling during growth on an array of cellulosic substrates to decipher degradation pathways). Projects should be directly relevant to DOE missions. Between 36 and 54 samples (including replicates) may be proposed. For projects with >54 samples, please refer to the CSP Annual Call.
Bacterial and archaeal epigenomes
DNA base modifications (6mA, 5mC, 4mC and others) are known to be important in host defense (as part of restriction systems), but may have additional functional roles that have previously been difficult to detect. New technologies now allow direct sequencing of DNA base modifications, providing a first opportunity for genome-wide exploration of bacterial epigenomes. JGI is seeking proposals to examine the possible regulatory roles of DNA base modification in Bacteria and Archaea. Up to 12 samples may be proposed. For projects with >12 samples, please refer to the CSP Annual Call.
Metagenomes and metatranscriptomes
Most microbes live in complex communities in oftentimes dynamic environments where the impact of changing environmental parameters on community structure and function are largely unknown. JGI is accepting proposals that include up to 24 metagenomes or metatranscriptomes (in any combination). Up to 184 samples may also be proposed for 16S, 18S or ITS2 tag sequencing on the Illumina MiSeq (itags), although itag-only proposals will not be considered. Each proposal will have a sequencing allocation of up to 360 Gb. Proposals must show clear DOE mission relevance in areas such as bioenergy-related plant-microbe interactions, carbon/nitrogen cycling and/or carbon sequestration processes in soils and sediments, and biogeochemical processes contributing to contaminant biotransformation and/or immobilization. For projects that fall outside these criteria, please refer to the CSP Annual Call.
Proposals are accepted on a continuous basis and will be reviewed twice a year. Letters of intent are not required. Deadline for submission is 60 days prior to the review date.
Submission deadlines (review dates in parentheses):
- February 24, 2017 (April 2017)
- September 4, 2017 (October 2017)
- March 1, 2018 (April 2018)