Recommendations for Sequencing Targets in Support of the Science Missions of the Office of Biological and Environmental Research (BER), 13489-13492 [05-5492]

Agencies

• DEPARTMENT OF ENERGY

[Federal Register Volume 70, Number 53 (Monday, March 21, 2005)]
[Notices]
[Pages 13489-13492]
From the Federal Register Online via the Government Printing Office [www.gpo.gov]
[FR Doc No: 05-5492]


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DEPARTMENT OF ENERGY


Recommendations for Sequencing Targets in Support of the Science 
Missions of the Office of Biological and Environmental Research (BER)

AGENCY: Office of Science; Office of Biological and Environmental 
Research; U.S. Department of Energy (DOE).

ACTION: Notice of recommendations for sequencing targets.

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SUMMARY: This Federal Register Notice seeks the input and nominations 
of interested parties for candidate microbes, microbial consortia, and 
250Mb-or-less-sized organisms for draft genomic sequencing in support 
of Office of Biological and Environmental Research (BER) programs, 
among them, the Genomics: GTL Program, the Climate Change Research 
Program, the Terrestrial Carbon Processes Program, the Natural and 
Accelerated Bioremediation Research (NABIR) Program, the Environmental 
Management Science Program (EMSP), the Ocean Science Program, and the 
Program for Ecosystem Research. Additional programs of relevance 
include the Energy Biosciences, and Nanoscale Science, Engineering and 
Technology Programs in the Office of Basic Energy Sciences. Nominated 
candidates should be relevant to DOE mission needs, e.g., organisms 
involved in environmental processes, including waste remediation, 
carbon management, and energy production. This announcement is not an 
offer of direct financial support for research on these organisms. 
Those nominations selected will result in the DNA sequence of selected 
organisms being determined at a draft level (6-8 X coverage) at the DOE 
Production Genomics Facility (PGF) at the Joint Genome Institute (JGI), 
(https://www.jgi.doe.gov). A subset of the selected organisms may be 
identified for sequence finishing. This announcement is designed to 
assist DOE in determining and prioritizing a list of microbes, 
microbial consortia, or modest-genome sized (not more than 250Mb) 
organisms (including eukaryotes) that address DOE mission needs. 
Following merit review, and a determination of satisfactory 
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. (e.d.t.), July 14, 2005, to be accepted 
for merit review. It is anticipated that review will be completed early 
in the fall of 2005 with draft sequencing at the DOE PGF to commence 
early in 2006, conditional upon the provision of high quality DNA.

ADDRESSES: 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, 1000 Independence 
Ave., SW., Washington, DC 20585-1290; e-mail is acceptable and 
encouraged for submitting nominations using the following addresses: 
kim.laing@science.doe.gov and daniel.drell@science.doe.gov.

FOR FURTHER INFORMATION CONTACT: Dr. Daniel W. Drell, SC-72, Office of 
Biological and Environmental Research, Office of Science, U.S. 
Department of Energy, 1000 Independence Ave. SW., Washington, DC 20585-
1290, phone: (301) 903-4742, e-mail: daniel.drell@science.doe.gov. The 
full text of this notice is available via the Internet using the 
following Web site address: https://microbialgenome.org/.

SUPPLEMENTARY INFORMATION: The DOE Office of Biological and 
Environmental Research supports fundamental research for a variety of 
missions (https://www.science.doe.gov/ober/ober_top.html). Relevant BER 
programs may include the the Genomics: GTL Program, the Climate Change 
Research Program, the Terrestrial Carbon Processes Program, the Natural 
and Accelerated Bioremediation Research (NABIR) Program, the 
Environmental Management Science Program (EMSP), the Ocean Science 
Program, and the Program for Ecosystem Science. Additional programs of 
relevance include the Energy Biosciences, and Nanoscale Science, 
Engineering and Technology Programs in the Office of Basic Energy 
Sciences. The Genomics:GTL Program, a partnership with the DOE Office 
of Advanced Scientific Computing Research, supports research into 
systems microbiology towards the comprehensive understanding of 
proteins and protein machines, gene regulatory networks, and microbial 
communities, and the development of computing and information 
infrastructure to enable a predictive understanding of biological 
systems. The Climate Change Research Program supports investigations of 
microbially-mediated fixation of atmospheric CO2. The NABIR 
program supports research on microbial biotransformations and/or 
immobilization of metal and radionuclide wastes. The EMSP supports 
research into microbially-mediated biotransformations of DOE-relevant 
organic wastes such as chlorinated solvents. The Ocean

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Sciences Program supports research to understand the ocean carbon 
cycle. The Program for Ecosystem Science supports research to 
understand and predict effects of environmental changes associated with 
energy production on the structure and functioning of important 
terrestrial ecosystems. In the Office of Basic Energy Sciences, the 
Energy Biosciences Program supports fundamental research in molecular-
level studies on solar energy capture through natural photosynthesis; 
the mechanisms and regulation of carbon fixation and carbon energy 
storage; the synthesis, degradation, and molecular interconversions of 
complex hydrocarbons and carbohydrates. Aligned with this, the 
Nanoscale Science, Engineering and Technology Program supports studies 
of novel biosystems and their potential for materials synthesis, 
chemical catalysis, and materials synthesized at the nanoscale needed 
to develop future biotechnologies related to energy.
    The purpose of this solicitation is to support these key DOE 
missions by generating and providing initial analyses of microbial DNA 
sequence information to further the understanding and application of 
microbiology relating to energy production, biochemical and 
biomaterials production, environmental carbon management, and 
environmental cleanup. Both terrestrial and ocean environments in which 
microbial flora contribute to the sequestration of carbon, particularly 
carbon dioxide, are of interest. Within the ocean environment, 
microbial flora that sequester or process carbon dioxide in both the 
eutrophic and ``twilight'' zones are of interest.
    For more than ten years, sequencing of a variety of microorganisms 
that live in diverse environments has provided a considerable 
information base for scientific research related not only to DOE 
missions, but also to other federal agency missions and U.S. industry. 
(https://www.tigr.org/tdb/mdb/mdbcomplete.html https://
microbialgenome.org/organisms.shtml and https://genome.jgi-psf.org/ microbial/). Nonetheless, most of our current knowledge of microbiology 
still is derived from individual species that either cause disease 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. Many are thought to grow as part of 
interdependent consortia in which one species supplies a nutrient 
necessary for the growth of another. Little is known of the 
organization, membership, or functioning of these consortia, especially 
those involved in environmental processes of DOE interest.
    Genomic analyses of sequenced microbes have suggested that 
processes such as lateral gene transfers at various times in the 
evolutionary history of some microbial lineages may have blurred the 
understanding of their phylogenetic relationships. For this notice, 
groups of microbes that may have exchanged (or may be exchanging) 
genetic information via lateral gene exchange or plasmid mediated 
exchanges can be proposed if the processes of genetic exchange result 
in functions relevant to the DOE missions noted above.
    Genomic analyses are badly needed of microbial consortia and 
species refractory to laboratory culture that play important roles in 
environments challenged with metals, radionuclides, or chlorinated 
solvents; can potentially generate energy compounds (e.g., hydrogen or 
methane); or are involved in carbon sequestration. The candidate(s) 
being proposed must mediate or catalyze metabolic events that 
contribute to these processes. Priority will be given to studies on 
those microbes or microbial consortia that can bioremediate metals and 
radionuclides, degrade biomass and significant biopolymers such as 
celluloses and lignins, produce potentially useful energy-related 
materials (H2, CH4, ethanol, etc.), or fix or 
sequester CO2.
    For this notice, candidate organisms (either individual organisms, 
consortia of organisms, or eukaryotes with small genomes) comprised of 
archaea, bacteria, fungi, algae, protests, and other eukaryotes with 
genome sizes not greater than 250 Mbp can be proposed for draft 
sequencing. For a current list of microbes that have been and are being 
sequenced by the DOE see https://microbialgenome.org/organisms.shtml. 
For a more comprehensive list of genomes (including microbes) being 
sequenced in the public sector, see https://www.genomesonline.org.
    Aims: This request for nominations of candidate sequencing targets 
has two broad foci:
    (1) Single organisms. These may be bacteria, archaea, fungi, 
microalgae or multicellular organisms with genomes not larger than 
250Mb. The criteria that will be used to evaluate proposed candidates 
for draft sequencing will include:
    (a) The candidate has significant relevance to the DOE missions 
noted above;
    (b) To assess suitability for whole genome shotgun sequencing, 
preliminary data on genome size, repeat content, genome structure, GC 
content, polymorphism, and other characteristics are provided, 
especially for larger genomes;
    (c) The source of genomic DNA (i.e., strain or isolate, and 
researcher) is identified, and a clonal sample (or samples with low and 
characterized polymorphism) is available;
    (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, although funding will not be provided for these 
activities;
    (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 scientific user community for the 
sequence information, and for the organism in general, is given;
    (i) The potential impact on science is large;
    (j) Explicit commitment to a data-release schedule, consistent with 
the guidelines given below is provided.
    (k) Explicit commitment to the deposition of a culture of the 
proposed microbe to a publicly accessible repository is made.
    (2) Currently unculturable or hard-to-culture organisms 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 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 consortium 
being proposed, e.g., approximate number of species, size(s) of 
genomes, and proportions of different members (it is understood that in 
most cases, only estimates of these parameters may be available) is 
discussed. When the environmental consortia are complex, approaches 
should be described to normalize the DNA libraries in order to reduce 
the

[[Page 13491]]

amount of sequencing required and assure adequate sampling of the 
complexity of the consortia. Additionally, the proposer(s) should be 
prepared to work together with JGI scientists to optimize the yield 
from the sequencing effort required;
    (b) Past attempts to cultivate consortium members are described, 
e.g., have any members of this consortium been successfully cultured;
    (c) Some spatial/temporal/hydrochemical/geochemical or other 
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 consortium are 
described;
    (e) Some indication of the biological function of the 
relationships, within consortium members where available, along with a 
discussion of the scientific and programmatic importance of 
understanding these relationships is given;
    (f) Information where available is given about the phylogenetic 
position(s) of the members of the consortium and what is known about 
closely related organisms.
    (g) Available informatics tools and annotation plan (e.g., for 
annotating genes from a consortium analysis or grouping identified 
genes into a putative ``consortium phenotype'' within the chosen 
environment) are described;
    (h) Explicit commitment to a data-release schedule, consistent with 
the guidelines given below is provided.
    Scientific community standards regarding access to sequencing data 
are evolving. BER conforms to the general guidance contained within the 
Draft Rapid Data Release Policy https://www.genome.gov/
page.cfm?pageID=10506537) for ``community resource projects.'' The 
usual and customary practice for the JGI is to put all sequencing data 
up on its Web site (https://www.jgi.doe.gov) at frequent and periodic 
intervals. However, for the purposes of this notice, BER does not 
regard individual genome sequencing efforts involving less than 250Mb, 
or microbial community sequencing efforts, as requested herein, as 
``community resource projects'' within the definition of the Draft 
Rapid Data Release policy. BER's position, which is provisional and 
subject to evolution, is that no more than 3 months from the completion 
of a ``first assembly'' of the sequence for a single-genome project, 
the data will be released on the JGI web site or to a publicly 
accessible database with no use restrictions. For microbial community 
projects, the JGI will conduct normal QA/QC assessments on the sequence 
output (at approximately 2 X coverage), then discuss with the 
proposer(s) and with BER staff the extent to which sequencing will be 
continued to achieve a satisfactory genomic ``view'' of the selected 
microbial community. From the time of initiation of this discussion, 
not more than 3 months will be permitted to elapse before unconditional 
release of these data. Proposers should clearly understand that the 
priority in the sequencing queue that a selected project is given may 
be linked to the willingness of the proposer(s) to shorten this 
``embargo'' period. BER is fully aware that some ambiguity remains in 
the precise initiation of this embargo period but stresses its 
intention and commitment to the rapid release, without any use 
restrictions, of this data into publicly accessible databases.
    Upon selection of a nominated microbial sequencing target, BER 
expects that Principal Investigators will collaborate with the JGI by 
providing high quality, high MW genomic DNA for library construction as 
well as assisting in annotating the draft sequence data until a 
sufficiently complete annotation is achieved, understanding that this 
will be sensitive to hypothetical gene predictions and the usual 
uncertainties of annotation. Notification of successful proposals will 
take place sometime in November 2005 at which time the successful 
proposer is expected to work out a detailed and mutually satisfactory 
User Agreement with the JGI. This User Agreement will specify the 
expectations of the proposer and the commitment of JGI resources to the 
project, including the amount of sequencing capacity or megabases to be 
sequenced. Sequencing will NOT begin prior to the finalization of this 
User Agreement. Thus proposers are strongly encouraged to begin 
preparation of DNA BEFORE notification of successful proposals because 
from the date of the conclusion of the User Agreement, the proposer is 
expected to furnish the JGI with usable, high quality DNA within 6 
months or risk losing her/his place in the sequencing. A separate 
communication with the detailed requirements for DNA will be sent to 
proposers whose nominations are accepted for sequencing. Following data 
acquisition and annotation, DOE expects that Principal Investigators 
whose nominations have been sequenced will make good faith efforts to 
publish the results of their subsequent work in the open scientific 
literature, including both the genome sequences of the organisms 
sequenced under this notice as well as the annotation. BER also expects 
the Principal Investigator of a selected effort to either deposit a 
culture of the microbe or consortium into a publicly accessible 
collection or repository, or make it available directly so others can 
have access. 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 6 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. Finally, there is no commitment 
to finish a given drafted sequence, although this option may be 
considered at a later time for a selected subset of proposed 
candidates.
    Submission Information: Interested parties should submit a brief 
white paper to either of the foci given above, consisting of not more 
than 5 pages of narrative exclusive of attachments (which should be 
kept to a minimum) responding to each of the specific criteria set 
forth. Electronic submission to (kim.laing@science.doe.gov and 
daniel.drell@science.doe.gov) is strongly encouraged. It is expected 
that the Principal Investigator 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 (or e-mails) 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 programs cited above. A brief response to each 
nomination will be provided electronically following merit and 
programmatic reviews.
    Other useful Web sites include:
    DOE JGI Microbial Sequencing Priorities for FY2005: https://
microbialgenome.org/.
    DOE Joint Genome Institute Microbial Web Page--https://genome.jgi-
psf.org/microbial/.

[[Page 13492]]

    GenBank Home Page--https://www.ncbi.nlm.nih.gov.
    DOE Genomics: GTL--https://DOEGenomestolife.org.
    DOE Natural and Accelerated Bioremediation Research (NABIR) 
Program--https://www.lbl.gov/nabir.
    Climate Change Research Program: https://www.science.doe.gov/ober/
CCRD_top.html.
    Terrestrial Carbon Processes Program: https://www.science.doe.gov/
ober/CCRD/tcp.html.
    Environmental Management Science Program (EMSP): https://
www.science.doe.gov/ober/ERSD/ersd_emsp.html.
    Ocean Science Program: https://www.science.doe.gov/ober/CCRD/
oceans.html.
    Program for Ecosystem Research: https://www.science.doe.gov/ober/
CCRD/per.html.

Ari Patrinos,
Associate Director of Science for Biological and Environmental 
Research.
[FR Doc. 05-5492 Filed 3-18-05; 8:45 am]
BILLING CODE 6450-01-P