[Federal Register Volume 66, Number 248 (Thursday, December 27, 2001)]
[Notices]
[Pages 66891-66893]
From the Federal Register Online via the Government Publishing Office [www.gpo.gov]
[FR Doc No: 01-31717]



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DEPARTMENT OF ENERGY


Office of Science; Office of Biological and Environmental 
Research; Recommendations for Sequencing Targets in Support of the 
Microbial Genome Program and the Genomes to Life Program

AGENCY: U.S. Department of Energy (DOE).

ACTION: Recommendations for sequencing targets.

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SUMMARY: This Federal Register Notice seeks the input and nominations 
of interested parties for candidate microbes and candidate microbial 
communities, for draft genomic sequencing in support of the Microbial 
Genome Program (MGP) and the Genomes to Life (GTL) Program. Candidate 
microbes and microbial communities should be relevant to DOE mission 
needs, e.g., microbes involved in environmental processes, including 
waste remediation, carbon management, energy production, and 
biodefense. This announcement is not an offer of direct financial 
support for research on these microbes. Those nominations selected will 
result in the DNA sequence of selected microbes being determined at a 
draft level (6-8 X coverage) at the DOE Production Genomics Facility 
(PGF) at the Joint Genome Institute (JGI), 
(http://www.jgi.doe.gov). This announcement is designed to assist DOE 
in determining and prioritizing a list of microbes, or microbial 
consortia that address DOE mission needs. Following merit review, and 
subject to the availability of funding and programmatic relevance, 
draft sequencing will be carried out at the PGF.

DATES: To assure consideration, nominations in response to this notice 
should be received by 4:30 p.m. (EST), March 28, 2002, to be accepted 
for merit review. It is anticipated that review will be completed early 
in the summer of 2002 with draft sequencing at the DOE PGF to commence 
later in 2002, but not before high quality DNA has been provided.

ADDRESSES: Written nominations responding to this notice should be sent 
to Dr. Daniel W. Drell, Office of Biological and Environmental 
Research, SC-72, Office of Science, U.S. Department of Energy, 19901 
Germantown Road, Germantown, MD 20874-1290; e-mail is acceptable for 
submitting nominations using the following addresses: 
[email protected] and [email protected].

FOR FURTHER INFORMATION CONTACT: Dr. Daniel W. Drell, SC-72, Office of 
Biological and Environmental Research, Office of Science, U.S. 
Department of Energy, 19901 Germantown Road, Germantown, MD 20874-1290, 
phone: (301) 903-4742, e-mail: [email protected]. The full 
text of this notice is available via the Internet using the following 
Web site addresses: http://doegenomestolife.org and http://www.sc.doe.gov/ober/microbial.html.

SUPPLEMENTARY INFORMATION: The MGP supports key DOE business areas by 
providing and analyzing microbial DNA sequence information to further 
the understanding and application of microbiology relating to energy 
production, chemical and materials production, environmental carbon 
management, environmental cleanup, and biodefense. The GTL Program 
builds on the successes of the DOE Human Genome Program (HGP) by 
seeking to understand biological functioning with emphases on 
identifying the multi-component protein complexes in cells, 
characterizing gene regulatory networks, probing the functional 
capabilities of the environmental microbial repertoire of genes, and 
beginning to model these processes computationally. A major goal is to 
support research on microbes that address DOE Office of Biological and 
Environmental Research (BER) missions and programs. Relevant BER 
programs may include Terrestrial and Ocean Carbon Sequestration, the 
Natural and Accelerated Bioremediation Research (NABIR) Program, the 
Biotechnological Investigation of Ocean Margins Program (BI-OMP), the 
Microbial Genome Program (MGP), the Genomes to Life (GTL) program, and 
the National Nuclear Security Administration's Chemical and Biological 
National Security Program.
    These programs are natural outgrowths of past and current BER 
Programs, including DNA sequencing from the HGP, structural biology 
studies utilizing BER-supported facilities at synchrotron and neutron 
sources located at DOE laboratories, and molecular microbiological 
research supported by BER environmental programs. These programs 
benefit from, and provide new scientific challenges to, the DOE 
national laboratories, the DOE and National Institutes of Health (NIH) 
Human Genome Centers, the U. S. Department of Agriculture (USDA), the 
National Science Foundation (NSF), the National Center for 
Biotechnology Information (NCBI) at the NIH, and the capabilities of 
universities and non-profit organizations.
    Over the last 5 years, sequencing of a range of microorganisms that 
live in a wide diversity of environments has provided considerable 
information base for scientific research related not only to DOE 
missions, but also to other federal agency missions and U.S. industry. 
(http://www.tigr.org/tdb/mdb/mdbcomplete.html http://www.ornl.gov/microbialgenomes/organisms.html and http://www.jgi.doe.gov/JGI_microbial/html/). Nonetheless, most of our current knowledge of 
microbiology still is derived from individual species that either cause 
diseases or grow easily and readily as monocultures under laboratory 
conditions and are thus easy to study. The preponderance of species in 
the environment remains largely unknown to science. Most are thought to 
grow as part of interdependent consortia in which one species supplies 
a nutrient necessary for the growth of another. Virtually nothing is 
known of the organization, membership, or functioning of these 
consortia, especially those involved in environmental processes in 
which DOE is interested.
    A related issue emerging from genome sequence analyses is the need 
to develop a better understanding of relatedness or phylogeny using 
genomics as a tool. Genomic analyses of sequenced microbes have 
suggested that processes such as lateral gene transfers early in the 
evolutionary history of some microbial ``species'' have blurred this 
understanding, and therefore the phylogeny, among microorganisms that 
had been thought to have known relationships. For this notice, groups 
of microbes that are thought to have a species relationship can be 
proposed to explore what the concept of a microbial species entails and 
how much sequence divergence defines different species.
    Genomic analyses of microbial consortia, and of those species that 
have proven refractory to laboratory culture, but are either plentiful 
in environments challenged with chemical contamination, metals, and/or 
radionuclide wastes, or involved in carbon sequestration are badly 
needed. These are expected to be the most challenging studies. The 
candidate(s) must mediate or catalyze metabolic events of energy or 
environmental importance. Priority will be given to studies on those 
microbes or microbial consortia that can bioremediate metals and 
radionuclides, that can degrade significant biopolymers such as 
celluloses and lignins, or that produce potentially useful energy-
related materials (H2, CH4,, ethanol, etc.), or 
that

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are involved in environmental carbon management, e.g., fix or sequester 
CO2,.
    An additional interest of this notice is microbes that are 
phylogenetically related to potential biowarfare (BW) threat agents. 
The Centers for Disease Control and Prevention defines three categories 
of BW threats (see at http://www.bt.cdc.gov/Agent/Agentlist.asp). DOE 
encourages nominations to sequence microbes or groups of microbes 
related to the category A and B agents.
    For this notice, candidate microorganisms, either individual 
microbes, groups of microbes, or a consortia of microbes, for draft 
sequencing can comprise archaea, bacteria, fungi or eukaryotic microbes 
with genome sizes 60 Mbp, or communities made up of these same types of 
microbes. For a current list of microbes that have been and are being 
sequenced see http://www.ornl.gov/microbial genomes/organisms.html.
    Aims: This request for nominations of candidate microbial 
sequencing targets has two broad foci:
    (1) Single culturable organisms. The criteria that will be used to 
evaluate proposed candidates for draft sequencing will include:
    (a) The candidate is likely to have significant relevance to the 
DOE missions noted above;
    (b) The genome size and structure are known;
    (c) The source of genomic DNA (i.e., strain or isolate, and 
researcher) is identified;
    (d) A brief description of post sequencing follow-up work (e.g., a 
data use plan and how will data be annotated to enable rapid and open 
use) is included;
    (e) The availability of a DNA/gene transfer system supporting 
genetic analyses is known;
    (f) Biological novelty or uniqueness (i.e., unusual genetically 
determined characteristics pertinent to DOE missions) is described;
    (g) Place in the currently understood, 16s RNA based, ``Tree of 
Life'' is identified, e.g., is the proposed candidate in a sparsely 
populated or more heavily populated section of the tree?
    (h) A brief description of the user community is given;
    (i) The potential impact on the scientific community is large;
    (j) Explicit commitment to data-release policy given below is 
provided.
    (2) Currently unculturable or hard-to-culture microbes and 
environmental consortia. The review criteria that will be used to 
evaluate proposed candidates for draft sequencing will include most of 
the criteria listed above for single culturable organisms (with less 
emphasis on genome size/structure, presence/absence of a genetic 
system, or position in the ``Tree of Life'' since it is recognized that 
few data on these attributes will be available), but in addition, the 
following considerations will be included:
    (a) Some measure of the ``complexity'' of the target community is 
proposed, e.g., approximate number of species, size(s) of genomes, and 
proportions of different community members (it is understood that in 
most cases, only estimates of these parameters may be available);
    (b) Past attempts to cultivate community members are described, 
e.g., have any members of this community been successfully cultured;
    (c) Some spatial/temporal/geochemical characterization of the 
environment is given, e.g., the physicochemical parameters of the site 
from which the selected community is derived; a description of the site 
contaminants; the accessibility of the site for future sampling; the 
adequacy of site documentation;
    (d) If proposed, technical approaches and technology development 
specific for defining and isolating members of a given community are 
described;
    (e) Some indication of the biological function of the consortial 
relationships where available along with a discussion of the scientific 
and programmatic importance of understanding these relationships;
    (f) Information where available about the phylogenetic affinities 
of the members of the consortia and what is known about the closely 
related organisms.
    (g) Available informatics tools and annotation plan (e.g. for 
annotating genes from a community analysis or grouping identified genes 
into a putative ``community phenotype'' within the chosen environment).
    Usual and customary practice is for the JGI to put all sequencing 
data up on its web site (http://www.jgi.doe.gov/) at frequent and 
periodic intervals. DOE expects that the Principal Investigators (PI) 
will collaborate with the JGI and assist in annotating the draft 
sequence data. Following data acquisition and annotation, DOE expects 
that those whose nominations have been sequenced will make good faith 
efforts to publish in the open scientific literature the results of 
their subsequent work, including both the genome sequences of microbes 
sequenced under this notice as well as the annotation. These parties 
are encouraged to create process- and cost-effective partnerships that 
will maximize data production and analysis, data dissemination, and 
progress towards understanding basic biological mechanisms that can 
further the aims of this effort. Additionally, it must be explicitly 
understood that DOE will provide an assembled and computationally 
annotated ``draft'' (roughly 8 x; carried out in a paired-end 
sequencing approach) sequence of the microbe(s) selected, but that 
research using that sequence data should be funded from separate 
sources and/or separate solicitations. This draft sequence is provided, 
without use restrictions, to the scientific community at large for any 
and all subsequent research purposes. (DOE data release requirements, a 
condition of any award, are available at: http://www.sc.doe.gov/ober/EPR/data.html)
    Submission Information: Interested parties should submit a brief 
white paper, consisting of not more than 5 pages of narrative exclusive 
of attachments (which are discouraged) responding to the criteria set 
forth above. It is expected that the PI will serve as the main point of 
contact for additional information on the nominated microbe. 
Nominations must contain a very short abstract or project summary and a 
cover page with the name of the applicant, mailing address, phone, fax, 
and e-mail. The nomination should include 2-page curriculum vitae of 
the key investigators; letters of intent from collaborators (suggesting 
the size of the interested community) are permitted.
    Nominations will be reviewed relative to the scope and research 
needs of the BER Microbial Genome and Genomes to Life Programs. A brief 
response to each nomination will be provided following merit and 
programmatic reviews.
    Other useful web sites include:
    Microbial Genome Program Home Page--http://www.sc.doe.gov/ober/microbial.html
    DOE Joint Genome Institute Microbial Web Page--http://www.jgi.doe.gov/JGI_microbial/html/
    GenBank Home Page--http://www.ncbi.nlm.nih.gov/
    Human Genome Home Page--http://www.ornl.gov/hgmis
    DOE Genomes to Life--http://DOEGenomestoLife.org
    DOE Natural and Accelerated Bioremediation Research (NABIR) 
Program--http://www.lbl.gov/nabir
    Biotechnology Investigations--Ocean Margins Program--http://www.sc.doe.gov/ober/GC/omp.html
    Chemical and Biological National Security Program-- http://www.nn.doe.gov/cbnp/


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    Issued in Washington, DC.
John Rodney Clark,
Associate Director of Science for Resource Management.
[FR Doc. 01-31717 Filed 12-26-01; 8:45 am]
BILLING CODE 6450-01-P