U.S. Department of Energy Office of Science Office of Biological and…

U.S. Department of Energy
Office of Science
Office of Biological and Environmental Research

ACTION: Recommendations for Sequencing Targets in Support of the
Bioenergy Mission of the Office of Biological and Environmental Research (OBER)

SUMMARY: This Notice seeks the input and nominations of interested parties for
candidate microbes, microbial consortia, and 100Mb-or-less-sized organisms for draft
genomic sequencing in support of Office of Biological and Environmental Research
(BER) Bioenergy Program element within its Genomics:GTL Program. Nominated
candidates must be relevant to the BER mission to determine genomic sequences of
microorganisms involved in energy production (particularly conversion of
lignocellulosic material to ethanol, or hydrogen, or other biofuels). Other
Genomics:GTL missions, e.g., environmental processes including waste remediation, and
carbon management either in the oceans or terrestrially will not be considered under this
Notice. Relevance to the Bioenergy mission will be an explicit criterion for review.
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 the prioritized
organisms being determined at a draft level (typically ~8X coverage) at the Production
Genomics Facility (PGF) at the DOE's Joint Genome Institute (DOE-JGI),
(http://www.jgi.doe.gov). It is the intention that most or all of the selected single
organisms will have their genome sequences finished. This announcement is designed to
assist BER in determining and prioritizing a list of microbes, microbial consortia, or
modest-genome sized (not more than 100Mb) organisms (including eukaryotes) that
address the BER mission of identifying and sequencing genomes from bioenergy relevant
microbes. Following merit review, and a determination of satisfactory programmatic
relevance, draft sequencing will be carried out at the PGF. Henceforth, this
announcement will be incorporated within the DOE-JGI's Community Sequencing
Program (http://www.jgi.doe.gov/CSP/), i.e., this announcement will not be repeated
in future years.

DATES: To assure consideration, nominations in response to this notice should be
received by 4:30 p.m. (E.D.T.), August 10, 2006, to be accepted for merit review. It is
anticipated that review will be completed early in the fall of 2006 with draft sequencing
at the DOE-PGF to commence early in 2007, 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-23.1, Office of Science, U.S.
Department of Energy, 1000 Independence Ave., SW, Washington, DC 20585-1290;
email is acceptable and encouraged for submitting nominations using the following
address: bioenergy.microbes@science.doe.gov .
FOR FURTHER INFORMATION CONTACT: Dr. Daniel W. Drell, SC-23.1, 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,
email: daniel.drell@science.doe.gov . The full text of this notice is available via the
Internet using the following Web site address:
http://www.sc.doe.gov/ober/bioenergy_microbes_call.pdf

SUPPLEMENTARY INFORMATION: The DOE Office of Biological and
Environmental Research supports fundamental research for a variety of missions
(http://www.science.doe.gov/ober/ober_top.html) among them the Genomics:GTL
Program, the Climate Change Research Program, the Terrestrial Carbon Processes
Program, the Environmental Remediation Sciences Program (ERSP), and the Program for
Ecosystem Science. An additional program of relevance is the Biofuels element of the
Biomass Program (http://www.eere.energy.gov/RE/bio_fuels.html) of the Office of
Energy Efficiency and Renewable Energy. The purpose of this request for nominations is
to support one key BER mission by generating and providing initial analyses of microbial
DNA sequence information to further the understanding and application of microbiology
relating to energy production, with emphases on biological degradation of biomass (e.g.,
lignocellulose) and resulting generation of ethanol, hydrogen, or other biofuels. Microbial
sequence information may come from individual microbes or microbial communities or
other single-cell organisms with individual genomes not more than 100Mb in size.

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.
(http://www.jgi.doe.gov; http://www.microbialgenome.org;
http://www.genomesonline.org, http://DOEGenomestolife.org) 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 bioenergy generating processes of BER interest.

For this notice, groups of microbes that may comprise consortia or include species
refractory to laboratory culture that play important roles in the generation of energy
compounds (e.g., ethanol, hydrogen or other biofuels) may be proposed. The candidate(s)
being proposed must mediate or catalyze metabolic events that contribute to these
processes.

For this notice, candidate organisms (either individual organisms, consortia of organisms,
or eukaryotes with small genomes) comprised of archaea, bacteria, fungi, algae, protists,
and other eukaryotes with genome sizes not greater than 100 Mbp can be proposed for
draft sequencing. For all candidates proposed for genomic sequencing, the amount of
sequencing and the degree of sequence coverage being requested must be explicitly
stated. For a current list of microbes that have been and are being sequenced by BER,
see http://www.ornl.gov/microbialgenomes/organisms.html and http://genome.jgi-
psf.org/mic_cur1.html. For a more comprehensive list of genomes (including microbes)
being sequenced in the public sector, see http://www.genomesonline.org. Each
nomination should begin with a statement of the case for the relevance of the
nominated organism(s) for bioenergy production. This should encompass the nature
and forms of the energy produced biologically by the organism(s) and how knowledge of
the sequence would enable or accelerate advances in understandings of biological energy
generation. The nomination should then proceed to address the criteria listed below,
either for single organisms or consortia:

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 100Mb. The criteria that will be
used to evaluate proposed candidates for draft sequencing will include:
   (a) The candidate has significant relevance to the BER mission 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 BER 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) 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 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.

With respect to access to sequencing data, the usual and customary practice for the
DOE-JGI is to put all sequencing data up on its web site (http://www.jgi.doe.gov/) at
frequent and periodic intervals with deposition in a publicly available database within a
maximum of one year. However, for the purposes of this notice, BER's policy is that
after no more than 3 months from the completion of a "first assembly" of the sequence
for a single-genome microbial project, the data will be released on the DOE-JGI web site
or to a publicly accessible database with no use restrictions (see
http://www.jgi.doe.gov/sequencing/collaborators/datarelease.html.) For microbial
community projects, the DOE-JGI will conduct normal QA/QC assessments on the
sequence output (at approximately 2 x coverage), then review with the proposer(s) and
with BER staff the amount of requested sequencing 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 stresses its general commitment to the
rapid release, without any use restrictions, of sequence data into publicly accessible
databases.
Upon selection of a nominated microbial sequencing target, BER expects that Principal
Investigators will collaborate with the DOE-JGI by providing high quality, high
molecular weight 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. (See Information for Collaborators,
http://www.jgi.doe.gov/sequencing/collaborators/index.html.) Notification of successful
proposals will take place sometime in October 2006 at which time the successful
proposer is expected to work out a detailed and mutually satisfactory User Agreement
with the DOE-JGI (see: http://www.jgi.doe.gov/sequencing/collaborators/, click on
"sample_agreement.doc"). This User Agreement will specify the expectations of the
proposer and the commitment of DOE-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
DOE-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-
JGI will provide an assembled and computationally annotated draft (roughly 8X; 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
it is the intention of the DOE-JGI to carry each single-genome project through to
completion.

Submission Information: Interested parties should submit a brief white paper to either of
the two categories (single microbes or environmental consortia) described 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 (bioenergy.microbes@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 email. 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. Finally, the proposer
must indicate the biosafety level of the source culture (microbial or environmental) and
whether the source culture has international, federal or state shipping or possession
restrictions regardless of absence of restrictions on the purified nucleic acids.

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:
http://microbialgenome.org/organisms.shtml

DOE-JGI Microbial Web Page-- http://genome.jgi-psf.org/microbial/index.html

GenBank Home Page-- http://www.ncbi.nlm.nih.gov

DOE Genomics:GTL-- http://DOEGenomestolife.org

DOE EERE Biomass Program--Sugar Platform:
http://www1.eere.energy.gov/biomass/sugar_platform.html

DOE EERE Biomass Program: Ethanol --
http://eereweb.ee.doe.gov/biomass/ethanol.html

DOE EERE Biomass Program: Biofuels: http://www.eere.energy.gov/RE/bio_fuels.html

DOE National Renewable Energy Laboratory Biomass Program --
http://www.nrel.gov/biomass/

BER Genomics:GTL Roadmap Appendix A (Energy Security) --
http://doegenomestolife.org/roadmap/pdf/GTL05_05Energy.pdf

Making Bioethanol Cost Competitive Brochure (PDF) --
http://doegenomestolife.org/pubs/Bioethanol10_27_05_8.5.pdf