**Microbial Genome Sequencing Program**

**FY 2009 Program Announcement**

**Application Deadline: March 2, 2009**

![](media/image1.png) **U.S. Department of Agriculture**

![](media/image2.png){width="0.5104166666666666in" height="0.71875in"}

**Cooperative State Research, Education, and Extension Service**

![](media/image3.wmf){width="0.6145833333333334in"
height="0.6145833333333334in"} **National Science Foundation**

**Microbial Genome Sequencing Program**

**Program Announcement:**

**Funding Opportunity Number:**

**USDA-CSREES-AFRI-001967**

**USDA Cooperative State Research, Education and Extension Service**

**National Science Foundation**

Directorate for Biological Sciences

**Full Proposal Deadline(s)** (due by 5 p.m. Eastern time):

March 2, 2009

**REVISION NOTES**

In furtherance of the President\'s Management Agenda, Grants.gov
provides a single Government-wide portal for finding and applying for
Federal grants online. In response to this program solicitation,
proposers are required to submit full proposals via Grants.gov.

**This is the last year of this interagency activity.**

SUMMARY OF PROGRAM REQUIREMENTS

General Information

**Program Title:**

Microbial Genome Sequencing Program

**Synopsis of Program:**

As a collaborative, interagency effort the Cooperative State Research,
Education, and Extension Service (CSREES) of the U.S. Department of
Agriculture and the National Science Foundation (NSF)will be inviting
research proposals (i) to support high-throughput sequencing of the
genomes of microorganisms (including plasmids, viruses, bacteria,
archaea, fungi, oomycetes, protists, microeukaryotes and agriculturally
important nematodes) and the metagenomes of mixed microbial communities
and (ii) to develop and implement strategies, tools and technologies to
make currently available and novel genome sequences more valuable to the
user community.

The availability of genome sequences provides the foundation for
understanding how microorganisms function and live, and how they
interact with their environments and with other organisms. The sequences
are expected to be available to and used by a community of investigators
to address issues of scientific and societal importance including:

-   Novel aspects of microbial biochemistry, physiology, metabolism,
    development and cellular biology;

-   The diversity and the roles microorganisms play in complex
    ecosystems and in global geochemical cycles;

-   The impact that microorganisms have on the productivity and
    sustainability of agriculture and natural resources (e.g., forestry,
    soil and water), and on the safety and quality of the nation\'s food
    supply; and

-   The organization and evolution of microbial genomes, and the
    mechanisms of transmission, exchange and reshuffling of genetic
    information.

A Microbial Genomics Workshop will be held; all awardees in this
interagency program are expected to attend.

**Cognizant Program Officer(s):**

Ann Lichens-Park, National Program Leader, CSREES, U.S. Department of
Agriculture, telephone: (202) 401-6460, fax: (202) 401-6488, e-mail to:
<apark@csrees.usda.gov>

Daniel Jones, National Program Leader, CSREES, U.S. Department of
Agriculture, telephone: (202) 401-6854, e-mail to:
<djones@csrees.usda.gov>

Lita M. Proctor, Program Director, Division of Biological
Infrastructure, National Science Foundation, telephone: (703) 292-5190,
fax: (703) 292-9063, e-mail to: <lproctor@nsf.gov>

**Applicable Catalog of Federal Domestic Assistance (CFDA) Number(s):**

-   10.310 \-\-- Agriculture and Food Research Initiative

-   47.074 \-\-- Biological Sciences, National Science Foundation

    Award Information

    **Anticipated Type of Award:** Standard Grant

    **Estimated Number of Awards:** 15 to 20

**Anticipated Funding Amount:** Approximately \$10 million is
anticipated (\$5 million of USDA and \$5 million of NSF funds), pending
availability of funds, with awards ranging between \$100,000 to
\$1,200,000 total, for periods of up to three years.

PLEASE NOTE: USDA funding is subject to the availability of
appropriation to carry out the Agriculture and Food Research Initiative
(AFRI) Competitive Grants Program. Cooperative State Research,
Education, and Extension Service (CSREES) reserves the right to amend,
delete, or otherwise alter it's participation in this program. It is
anticipated that the complete Request for Applications, which will
contain the application submission instructions, will be made available
in January 2009 on the CSREES Web site and the Grants.gov Web site.

Eligibility Information

**Organization Limit:**

Proposals may only be submitted by the following:

**CSREES Eligibility Criteria:**

The source of USDA funds to support the fiscal year (FY) 2009 Microbial
Genome Sequencing Program is subject to the availability of
appropriations to carry out the AFRI program, the Secretary may award
grants to State agricultural experiment stations; colleges and
universities; university research foundations; other research
institutions and organizations; Federal agencies; national laboratories;
private organizations or corporations; individuals; or any group
consisting of two or more of the aforementioned entities. Applications
from scientists at non-U.S. organizations will not be accepted. Award
recipients may subcontract to organizations not eligible to apply,
provided such organizations are necessary for the conduct of the
project.

**NSF Eligibility Criteria:**

Proposals are invited from academic institutions accredited and having a
campus located in the U.S., U.S. non-profit research organizations, and
consortia of such organizations with appropriate research and
educational facilities. A proposal from a multi-organizational
consortium must be submitted by the lead organization as a single
proposal. When a consortium of eligible individuals or organizations
submits a proposal, a single principal investigator must be designated
as the project director (PD) and a single organization must accept
overall management responsibility, including the management of
intellectual property, that may result from the proposed research.

Simultaneous submission of proposals to this program and another federal
agency is permissible with prior written approval of the appropriate
program officers at each agency involved. Proposers are encouraged to
establish international collaborations where appropriate. It is
anticipated that foreign agencies will support the offshore activities
of these programs. The NSF component of this program will not make
awards or allow subcontracts to non-U.S. institutions.

**PI Limit:**

None Specified

**Limit on Number of Proposals per Organization:**

None Specified

**Limit on Number of Proposals per PI:**

None Specified

Proposal Preparation and Submission Instructions

**A. Proposal Preparation Instructions**

-   **Letters of Intent**: Not Applicable

-   **Full Proposal Preparation Instructions**: Full proposals must be
    submitted via Grants.gov:

-   Please note: Additional information on how to access/use Grants.gov
    will be provided by CSREES/USDA. It is anticipated that the complete
    Request for Applications, which will contain the application
    submission instructions, will be made available in early 2009 on the
    CSREES Web site and the Grants.gov Web site.

    **B. Budgetary Information**

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-   Cost Sharing Requirements: Cost Sharing is not required by CSREES or
    by NSF in proposals submitted under this Program Solicitation.

-   Indirect Cost (F&A) Limitations:

    -   The applicant should submit a proposal using their
        Federally**-**negotiated indirect cost rate.

        **CSREES Policy**

Section 7132 of the Food, Conservation, and Energy Act of 2008, amended
the National Agriculture Research, Extension, and Teaching Policy Act of
1977 (7 U.S.C. 3310(a)), limiting indirect costs to 22 percent of the
total Federal funds provided under each award. Therefore, when preparing
budgets, applicants should limit their requests for recovery of indirect
costs to the lesser of their institution's official negotiated indirect
cost rate or the equivalent of 22 percent of total Federal funds
awarded.

To accommodate USDA limit on indirect costs, applicants may be required
at the time of award to submit a revised budget. Proposals selected for
funding by USDA will be asked to comply with the USDA 22 percent limit
on indirect cost rates.

Other Budgetary Limitations: Not Applicable

**NSF Policy**

Standard NSF policy regarding indirect cost rates applies to proposals
funded by the NSF.

**C. Due Dates**

Full Proposal Deadline(s) (due by 5 p.m. Eastern time):

March 2, 2009

Proposal Review Information Criteria

**Merit Review Criteria**: CSREES/USDA and NSF will follow the National
Science Board approved criteria. Additional merit review considerations
apply. Please see the full text of this solicitation for further
information.

Award Administration Information

**Award Conditions**: Additional award conditions apply. Please see the
full text of this solicitation for further information.

**Reporting Requirements**: Additional reporting requirements apply.
Please see the full text of this solicitation for further information.

**TABLE OF CONTENTS**

Summary of Program Requirements

I. Introduction

II\. Program Description

III\. Award Information

IV\. Eligibility Information

V. Proposal Preparation and Submission Instructions

A. Proposal Preparation Instructions

B. Budgetary Information

C. Due Dates

D. Grants.gov Requirements

VI\. CSREES/USDA Proposal Processing and Review Procedures

A. Merit Review Criteria

B. Review and Selection Process

VII\. Award Administration Information

A. Notification of the Award

B. Award Conditions

C. Reporting Requirements

VIII\. Agency Contacts

IX\. Other Information

**I. INTRODUCTION**

Microorganisms dominate the planet in terms of diversity and total
biomass. They represent a vast array of species with enormous genetic,
metabolic, structural, physiological and behavioral diversity. Despite
their ubiquity, beyond human pathogens, a few model organisms, and a few
broad surveys, little is known about their fundamental properties, the
range in their diversity, how they interact with each other, with more
complex life forms and with their environment, and the roles they play
in global biogeochemical cycles. Future progress toward filling these
knowledge gaps can be advanced significantly by the availability of
whole genome sequences, by more complete and accurate information about
the contents of sequenced genomes and through the full complement of
genome sequences from microbial communities (i.e. metagenomes).

The Microbial Genome Sequencing Program is a collaborative interagency
activity of the Cooperative State Research, Education, and Extension
Service (CSREES) of the U.S. Department of Agriculture and the National
Science Foundation (NSF). The program supports (i) high-throughput
sequencing of the genomes of a broad range of microorganisms (including
plasmids, viruses, bacteria, archaea, fungi, oomycetes, protists,
microeukaryotes and agriculturally important nematodes) and the
metagenomes of microbial communities and (ii) the development and
implementation of strategies, tools and technologies to make currently
available genome sequences more valuable to the user community. The
newly acquired sequences are expected to be made available and used by a
community of investigators to address issues of scientific and societal
importance including:

-   Novel aspects of microbial biochemistry, physiology, metabolism,
    development and cellular biology;

-   The diversity and the roles microorganisms play in complex
    ecosystems and in global geochemical cycles;

-   The impact that microorganisms have on the productivity and
    sustainability of agriculture and natural resources (e.g., forestry,
    soil and water), and on the safety and quality of the nation\'s food
    supply; and

-   The organization and evolution of microbial genomes, and the
    mechanisms of transmission, exchange and reshuffling of genetic
    information.

The development and implementation of strategies, tools and technologies
are expected to significantly enhance the value of existing and novel
genome sequences.

This program is part of The Microbe Project, a coordinated effort of
multiple federal agencies to promote genome-enabled microbial science.
(See

[http://www.microbeproject.gov](http://www.microbeproject.gov/).)

**II. PROGRAM DESCRIPTION**

This program supports (i) the high-throughput sequencing of the genomes
from a wide range of microorganisms (including plasmids, viruses,
bacteria, archaea, fungi, oomycetes, protists, microeukaryotes and
agriculturally important nematodes) and the metagenomes of mixed
microbial communities that are either of fundamental biological
interest, are important to the productivity and sustainability of
agriculture and forestry, or to the safety and quality of the nation\'s
food supply and (ii) the development and implementation of strategies,
tools and technologies to make currently available genome sequences more
valuable to the user community. The results will be partial or whole
genome sequence data, more extensive and reliable annotation and whole
genome mapping or scaffolding information. Proposers are encouraged to
incorporate teaching, training, or outreach components within the scope
of the project to facilitate the dissemination of knowledge and the
education of students and the public. Taxon-based functional genomics
studies are not within the scope of the Microbial Genome Sequencing
Program unless they involve the development and implementation of
strategies, tools and technologies to make genome sequences more
valuable to user communities. Taxon-based functional genomics studies
are supported by other Programs offered by CSREES and NSF; e.g.,
Microbial Genomics Program, Microbial Biology Program, and the Animal
Health and Well-Being Program
(<http://www.csrees.usda.gov/fo/funding.cfm>) and activities within the
NSF Division of Molecular and Cellular Biosciences
(<http://www.nsf.gov/div/index.jsp?div=MCB>).

All microorganisms, except strict human pathogens that are not related
to food safety, are candidates for genome sequencing under this program.
Proposers should justify organism selection on the basis of biological
interest or agricultural importance, as well as community involvement,
education and training, and societal impact. Factors to consider include
metabolic potential, novel biochemical, structural or developmental
features, phylogenetic affiliation, ecological or evolutionary
significance, economic importance, and relevance to national security.

Proposals to sequence the genomes of agriculturally important nematodes
will be accepted in the competition; such proposals will be eligible for
funding by CSREES but not by NSF.

Projects will also be considered that include, for example, the
sequencing of (i) expressed sequence tag (EST) libraries, (ii) clones
from mixed environmental microbial populations, (iii) homologous genes
(orthologs and paralogs), islands, plasmids or regions from the genomes
of multiple organisms or (iv) metagenomes of microbial communities.

Complete coverage is generally the most desirable end-point for whole
genome sequencing. However, the choice and justification of complete
versus draft coverage is dependent on the nature and scope of the
proposed project. For example, the genomes of some protists and fungi
are relatively large and their sequencing may not easily be completed
under the support of a single grant. Similarly, sequencing of
prokaryotic genomes for comparative purposes or from environmental
samples may not require or generate complete coverage.

The outcome of all draft sequencing projects is expected to include
generation of high quality sequence data, organization of the sequence
reads into contiguous sequences, correlation with physical maps when
appropriate, annotation of open reading frames, and deposition of all
information into a publicly accessible, **preexisting database**.
Investigators who choose to create their own database must ensure
accessibility and **justify why preexisting databases are not
suitable**. Investigators should indicate how accessibility to the
databases will be maintained after the award period.

For large genome projects, investigators are encouraged to seek
partners, either in the form of consortia or support from other sources,
so that the complete sequence, if appropriate, can be obtained in a
reasonable time frame. If parallel support from another agency is under
consideration or being planned, investigators should inform the
cognizant CSREES and NSF program officers in advance and indicate in the
proposal how the CSREES or NSF funded activity will be organized and
coordinated within the larger project.

The limited ability to decipher the information content of sequenced
genomes has seriously hindered the full experimental exploitation of
this valuable resource. The Microbial Genome Sequencing Program
encourages the development and implementation of strategies, tools and
technologies to make currently available genome sequences more valuable
to the user community. Proposals which contain activities directed
toward the rigorous and unambiguous assignment of function to open
reading frames will be considered. Projects to develop comparative
analytical tools, and other tools and technologies for functional
genomic analyses are encouraged. Plans should be described for
dissemination of these tools and technologies to the broader community.

The program will entertain proposals to support finishing (closure) of
draft genomes under limited circumstances. The resources for finishing
and annotation will be directed toward organisms for which there is a
large community of dedicated experimentalists, where the organism is
unique, amenable to biochemical experimentation and genetic manipulation
and provides a valuable new perspective on a biological question or
phenomenon, and where the proposal is cost effective.

An important activity of this interagency program is the annual
Microbial Genomics Workshop. This workshop is intended to highlight the
breadth of the program and to facilitate exchange of scientific and
technical information between awardees and projects. All awardees are
expected to budget for annual attendance of the workshop and to send one
representative to the workshop.

Organism strains that are being targeted in other, already funded,
sequencing projects should be avoided, unless the sequence information
from these other projects is incomplete or will not be in the public
domain. If one strain of a species has been or is being sequenced, the
proposer should provide strong justification as to why the sequencing of
other strains should be undertaken. Examples of compilations of
microbial genome sequencing projects are available at the following
URLs:

[http://www.genomesonline.org](http://www.genomesonline.org/)

<http://cmr.tigr.org/tigr-scripts/CMR/shared/Genomes.cgi>

<http://genome.jgi-psf.org/mic_home.html>

<http://www3.niaid.nih.gov/research/resources/mscs/default.htm>
<http://www.sanger.ac.uk/Projects/>

<http://www.genome.wustl.edu/>

<http://hgsc.bcm.tmc.edu/>

<http://www.broad.mit.edu/annotation/>

CSREES and NSF will determine which agency will support each award.
These decisions will be based on the relevance of the project goals to
the activities of the agency (CSREES, food and agricultural relevance,
NSF, fundamental biological knowledge) and the availability of funds.
Proposers may request funding for up to three years. The requested
duration should be consistent with the goals of the project. Detailed
information on (i) the organisms chosen, (ii) the coordination,
management and organizational plan, (iii) the method of library
preparation and all other pertinent methodological information, and (iv)
the method for disseminating data and interfacing with the broader
scientific community and the public, should be provided.

Rapid, inexpensive high throughput sequencing technology is advancing
rapidly. All sequencing technologies and strategies, particularly ones
that are novel, as well as the mechanisms to assess validity and
accuracy of the data must be described in the proposal. Proposers should
consider how new technologies might be exploited to achieve the aims of
their projects. Sequencing costs may vary depending on the approach
chosen. **An estimate of, and explanation and justification for
sequencing costs must be provided**.

Activities such as manual annotation, and integral education and
outreach are appropriate for inclusion in the project; when included,
full justification and a description of the appropriateness within the
context of the project is required. Factors resulting in additional
costs (e.g., resulting from methodological complexity, education and
outreach, community integration, resource storage and management, etc.)
should be clearly identified and rationalized. In judging the merits of
a proposal, the speed, level of accuracy, and cost effectiveness of the
proposed work and the identification and involvement of an active
community of experimental users will be among the evaluation criteria.

All proposals should have a project management plan, that will include a
timeline and a clear statement of what the project deliverables (or
products) will be at the end of the project period (i.e., a complete and
finished sequence; a repository site for the sequence; tools for
accessing the sequence; completed automated and manual annotation). The
timeline should cover scheduling, resource allocation, milestones,
contingencies and deliverables. There should be clear examples of what
will be accomplished by each person in the proposal.

Awards will be made in the form of grants to be determined at the time
of the award. Each participating agency will obligate funds separately
and any particular award may be funded by one or both of the
participating agencies. The exact amount of an award will depend on the
advice of the reviewers, agency priorities and the availability of
funds. In FY 2008, the award sizes ranged from \$150,000 to \$1,000,000
for up to three years. Further information on awards made in this
program during FY 2008 is available at the following links:

USDA/CSREES Awards
[http://cris.csrees.usda.gov/cgi-bin/starfinder/0?path=nrimglink.txt&id=anon&pass=&search=(CG=\*35600\*;an=0205775)%20not%20(PS=TERM\*;an=(0212793;0212859;0212772;0212863))&format=WEBTITLESG](http://cris.csrees.usda.gov/cgi-bin/starfinder/0?path=nrimglink.txt&id=anon&pass=&search=(CG=*35600*;an=0205775) not (PS=TERM*;an=(0212793;0212859;0212772;0212863))&format=WEBTITLESG)

NSF Awards <http://www.nsf.gov/bio/pubs/awards/microbgen.htm>

**III. AWARD INFORMATION**

Estimated program budget, number of awards and average award
size/duration are subject to the availability of funds. Between 15 and
20 awards are anticipated in this program in FY 2009, and will be made
as standard grants, with most budgets ranging from \$100,000 to
\$1,200,000 for durations up to three years.

**IV. ELIGIBILITY INFORMATION**

Organization Limit:

Proposals may only be submitted by the following:

Organization Limit:

**CSREES Eligibility Criteria:**

The source of USDA funds to support the fiscal year (FY) 2009 Microbial
Genome Sequencing Program is subject to the availability of
appropriations to carry out the AFRI program, the Secretary may award
grants to State agricultural experiment stations; colleges and
universities; university research foundations; other research
institutions and organizations; Federal agencies; national laboratories;
private organizations or corporations; individuals; or any group
consisting of two or more of the aforementioned entities. Applications
from scientists at non-U.S. organizations will not be accepted. Award
recipients may subcontract to organizations not eligible to apply,
provided such organizations are necessary for the conduct of the
project.

**NSF Eligibility Criteria:**

Proposals are invited from academic institutions accredited and having a
campus located in the U.S., U.S. non-profit research organizations, and
consortia of such organizations with appropriate research and
educational facilities. A proposal from a multi-organizational
consortium must be submitted by the lead organization as a single
proposal. When a consortium of eligible individuals or organizations
submits a proposal, a single principal investigator must be designated
as the project director (PD) and a single organization must accept
overall management responsibility, including the management of
intellectual property, that may result from the proposed research.

Simultaneous submission of proposals to this program and another federal
agency is permissible with prior written approval of the appropriate
program officers at each agency involved. Proposers are encouraged to
establish international collaborations where appropriate. It is
anticipated that foreign agencies will support the offshore activities
of these programs. The NSF component of this program will not make
awards or allow subcontracts to non-U.S. institutions.

**PI Limit:**

None Specified

Limit on Number of Proposals per Organization:

None Specified

**Limit on Number of Proposals per PI:**

None Specified

Additional Eligibility Info:

**V. PROPOSAL PREPARATION AND SUBMISSION INSTRUCTIONS**

**A. Proposal Preparation Instructions**

Full Proposal Preparation Instructions: Proposers are required to submit
proposals in response to the full Program Solicitation which will be
posted on Grants.gov in January 2009. Instructions in the form of a
Grants.gov application guide will be included with the solicitation
posted by CSREES/USDA.

Proposers or applicants who have had prior support from the Microbial
Genome Sequencing Program from CSREES/USDA and/or NSF should indicate
the results of that prior support in the Project Description section of
the application.

Applicants selected for funding by either CSREES or NSF will be required
to submit agency-specific forms prior to the awarding of the grant.
Successful applicants will be notified at the time of award to prepare
and submit applicable forms.

**B. Budgetary Information**

Cost Sharing: Cost sharing is not required by CSREES or by NSF in
proposals submitted under this Program Solicitation.

Indirect Cost (F&A) Limitations:

The applicant should submit a proposal using their Federally negotiated
indirect cost rate.

CSREES Policy

Section 7132 of the Food, Conservation, and Energy Act of 2008, amended
the National Agriculture Research, Extension, and Teaching Policy Act of
1977 (7 U.S.C. 3310(a)), limiting indirect costs to 22 percent of the
total Federal funds provided under each award. Therefore, when preparing
budgets, applicants should limit their requests for recovery of indirect
costs to the lesser of their institution's official negotiated indirect
cost rate or the equivalent of 22 percent of total Federal funds
awarded.

To accommodate USDA limit on indirect costs, applicants may be required
at the time of award to submit a revised budget. Proposals selected for
funding by USDA will be asked to comply with the USDA 22 percent limit
on indirect cost rates.

NSF Policy

Standard NSF policy regarding indirect cost rates applies to proposals
funded by the NSF.

Budget Preparation Instructions:

A budget is required for each year of requested support. In addition, a
cumulative budget is required detailing the requested total support for
the overall project period. Funds may be requested under any of the
categories listed on the budget, provided that the item or service for
which support is requested is allowable under the authorizing
legislation, the applicable statutes, regulations, and Federal cost
principles, and these program guidelines, and can be justified as
necessary for the successful conduct of the proposed project. In the
budget justification, all budget categories for which support is
requested, with the exception of Indirect Costs, must be individually
listed (with costs) in the same order as in the budget and justified on
a separate page.

Proposers are reminded to include in the cumulative budget the cost of
the principal investigator or designee to attend the annual Microbial
Genomics Awardee Workshop that is organized by CSREES and NSF. This
meeting is often held as a satellite to a larger national genomics
meeting.

**C. Due Dates**

Full Proposal Deadline(s) (due by 5 p.m. Eastern time):

March 2, 2009

**D. Grants.gov Requirements**

Proposals Submitted Via Grants.gov:

Before using Grants.gov for the first time, each organization must
register to create an institutional profile. Once registered, the
applicant\'s organization can then apply for any federal grant on the
Grants.gov website. The Grants.gov\'s Grant Community User Guide is a
comprehensive reference document that provides technical information
about Grants.gov. Proposers can download the User Guide as a Microsoft
Word document or as a PDF document. The Grants.gov User Guide is
available at:

http://www.grants.gov/CustomerSupport. For Grants.gov user support,
contact the Grants.gov Contact Center at 1-800-518-4726 or by email:
<support@grants.gov>. The Grants.gov Contact Center answers general
technical questions related to the use of Grants.gov. Specific questions
related to this program solicitation should be referred to the CSREES
and NSF program staff contact(s) listed in Section VIII of this
solicitation.

Submitting the Proposal: Required forms will be posted with the full
solicitation in January 2009. Once all documents have been completed,
the Authorized Representative (AR) must submit the application to
Grants.gov and verify the desired funding opportunity and agency to
which the application is submitted. The AR must then sign and submit the
application to Grants.gov.

**VI. CSREES/USDA PROPOSAL PROCESSING AND REVIEW PROCEDURES**

Proposals received by CSREES are assigned to the appropriate CSREES
program and, if they are compliant with the CSREES proposal preparation
requirements, accepted for review. All proposals are carefully reviewed
by a scientist, engineer, or educator serving as a CSREES or NSF Program
Officer, and usually by three to ten other persons outside each agency
who are experts in the particular fields represented by the proposal.
These reviewers are selected by Program Officers charged with the
oversight of the review process. Care is taken to ensure that reviewers
have no conflicts with the proposer.

**A. Merit Review Criteria**

All proposals are evaluated through use of two merit review criteria:
intellectual merit and the broader impacts of the proposed effort. In
this instance, however, CSREES and NSF will employ additional criteria
as required to highlight the specific objectives of the Microbial Genome
Sequencing Program.

The two merit review criteria are listed below. The criteria include
considerations that help define them. These considerations are
suggestions and not all will apply to any given proposal. While
proposers must address both merit review criteria, reviewers will be
asked to address only those considerations that are relevant to the
proposal being considered and for which the reviewer is qualified to
make judgments.

**What is the intellectual merit of the proposed activity?**

How important is the proposed activity to advancing knowledge and
understanding within its own field or across different fields? How well
qualified is the proposer (individual or team) to conduct the project?
(If appropriate, the reviewer will comment on the quality of the prior
work.) To what extent does the proposed activity suggest and explore
creative, original, or potentially transformative concepts? How well
conceived and organized is the proposed activity? Is there sufficient
access to resources?

**What are the broader impacts of the proposed activity?**

How well does the activity advance discovery and understanding while
promoting teaching, training, and learning? How well does the proposed
activity broaden the participation of underrepresented groups (e.g.,
gender, ethnicity, disability, geographic)? To what extent will it
enhance the infrastructure for research and education, such as
facilities, instrumentation, networks, and partnerships? Will the
results be disseminated broadly to enhance scientific and technological
understanding? What may be the benefits of the proposed activity to
society?

**Additional Review Criteria:**

The following additional evaluation factors will be considered in
reviewing all proposals:

1\. Relevance of the microorganism(s) to be sequenced and the scientific
merit of the project. This criterion addresses the scientific and/or
practical importance of the microorganism chosen for sequencing, the
novelty, uniqueness and originality of the proposal, and the conceptual
adequacy of the sequencing approach including suitability of
methodology, clarity and delineation of objectives, and demonstration of
feasibility through preliminary data (e.g., known or estimated genome
size and techniques for isolation of nucleic acid).

2\. The speed, level of accuracy, and cost effectiveness of the proposed
work.

3\. Project management. This criterion addresses the overall quality of
the technical and managerial aspects of the proposal, including
management oversight, long-range planning, release of the data, and
sharing of the information and resources resulting from the project
within the broader scientific community. To this end, applications are
required to have a section on deliverables that would include a time
line and a clear statement of what the project deliverables (or
products) will be at the end of the project period (i.e., a complete and
finished sequence; a repository site for the sequence; tools for
accessing the sequence; completed automated and manual annotation,
etc.). The time line should cover scheduling, resource allocation,
milestones, contingencies and deliverables. There should be clear
examples of what will be accomplished by each person in the proposal.

4\. Scientific collaboration and information sharing and the
identification and involvement of an active community of experimental
users. Sequencing of the genome of an organism is a community activity.
As such, a close collaboration among the scientists and organizations
involved in sequencing activities and effective dissemination to the
potential users of the information are important components of this
criterion. This criterion also includes adequacy of plans for long-term
maintenance of data accessibility and plans for updating data in
response to new information about functional assignments. Thus, key
criteria are compatibility, accessibility, longevity and the size and
enthusiasm of the user community.

5\. Appropriateness of the proposed budget. Budget requests should be
proportional to the size of the genome(s) to be sequenced or the amount
of sequencing to be done. Sequencing costs must be explained and
justified. Additional activities, such as manual annotation, and
integral education and outreach are appropriate for inclusion in the
project; when included, full justification and a description of
appropriateness within the context of the project is required. Factors
resulting in additional costs (e.g., resulting from methodological
complexity, education and outreach, community integration, resource
storage and management) should be clearly identified and rationalized.

6\. For proposals to enhance existing annotation programs and resources,
it is imperative that enhancements be compatible with existing sites
(e.g. websites in examples of compilations above) and that principal
investigators and submitting institutions foster compatibility. Concrete
examples of how the proposed project would improve current resources are
encouraged.

**B. Review and Selection Process**

All proposals are carefully reviewed by at least three other persons who
are experts in the particular field represented by the proposal.
Proposals submitted under this program solicitation will be carefully
reviewed by a combination of at least three ad hoc (mail) or panel
reviewers who have expertise in some aspect of the proposal. Reviewers
are selected by the responsible program officer and are asked to provide
a written critique of the proposal that addresses the two review
criteria and the special program criteria described above. The written
reviews will also include an overall rating of the proposal. An
individual reviewer may not have expertise in all aspects of a complex
proposal and therefore may choose to focus on areas that are closest to
their areas of expertise. In all cases reviews are treated as
confidential documents.

**Ad hoc Review and/or Panel Review:**

Each proposal, along with the associated written reviews, will be
discussed by a review panel. The panel will rate each proposal relative
to all other proposals under consideration. A summary of the panel
deliberations will be written by one of the panelists. The summary will
describe substantive issues raised by the panel that are not covered in
the written reviews, and in addition, will provide a general impression
of the enthusiasm of the panel for the project and their overall panel
rating of the proposal. The panel rating is not intended to be an
average of the ratings of the written reviews.

The Program Directors assigned to manage the review of the proposals
will consider all available information, including the written ad hoc
and panel reviews, the panel discussion and rating, the panel summary
and all other available information and formulate a recommendation to
award or decline the proposal. After programmatic approval has been
obtained, the proposals recommended for funding will be forwarded to
either the CSREES/USDA Office of Extramural Programs (OEP) or the NSF
Division of Grants and Agreements for review of business, financial, and
policy implications and the processing and issuance of a grant or other
agreement. Proposers are cautioned that only an OEP Authorized
Departmental Officer or a NSF Grants and Agreements Officer may make
commitments, obligations, awards or authorize the expenditure of funds
on behalf of either USDA or NSF. No commitment on the part of either
USDA or NSF should be inferred from technical or budgetary discussions
with a USDA or NSF Program Director. A Principal Investigator or
organization that makes financial or personnel commitments in the
absence of a grant or cooperative agreement signed by the CSREES
Authorized Departmental Officer or the NSF Grants and Agreements
Officer, does so at their own risk.

For both awarded and declined proposals, verbatim copies of all written
reviews and the panel summary, excluding the names of the reviewers, are
sent to the Principal Investigator/Project Director by the Program
Director. In addition, the proposer will receive an explanation of the
decision to award or decline funding.

**VII. AWARD ADMINISTRATION INFORMATION**

**A. Notification of the Award**

Notification of CSREES awards is made to the submitting organization by
the Authorized Departmental Officer in the Awards Management Branch.
Notification of an NSF award is made to the submitting organization by a
Grants Officer in the Division of Grants and Agreements. Organizations
whose proposals are declined will be advised as promptly as possible by
the cognizant CSREES or NSF Program Director administering the program.
Verbatim copies of reviews, not including the identity of the reviewer,
will be provided automatically to the Principal Investigator. (See
Section VI.B. for additional information on the review process.)

**B. Award Conditions**

A CSREES award document shall include at a minimum the following:

1\. Legal name and address of performing organization or institution to
whom the CSREES Administrator has awarded a grant under the terms of
this solicitation;

2\. Title of project;

3\. Name(s) and institution(s) of Project Directors chosen to direct and
control approved activities;

4\. Identifying grant number assigned by CSREES;

5\. Project period, specifying the amount of time CSREES intends to
support the project without requiring recompetition for funds;

6\. Total amount of CSREES financial assistance approved by the CSREES
Administrator during the project period;

7\. Legal authority(ies) under which the grant is awarded;

8\. Appropriate Catalog of Federal Domestic Assistance (CFDA) number;

9\. Applicable award terms and conditions (see
http://www.csrees.usda.gov/business/awards/awardterms.html for CSREES
award terms and conditions);

10\. Approved budget plan for categorizing allocable project funds to
accomplish the stated purpose of the grant award; and

11\. Other information or provisions deemed necessary by CSREES to carry
out its respective granting activities or to accomplish the purpose of a
particular grant.

An NSF award consists of: (1) the award letter, which includes any
special provisions applicable to the award and any numbered amendments
thereto; (2) the budget, which indicates the amounts, by categories of
expense, on which NSF has based its support (or otherwise communicates
any specific approvals or disapprovals of proposed expenditures); (3)
the proposal referenced in the award letter; (4) the applicable award
conditions, such as Grant General Conditions (GC-1); \* or Federal
Demonstration Partnership (FDP) Terms and Conditions \* and (5) any
announcement or other NSF issuance that may be incorporated by reference
in the award letter. Cooperative agreements also are administered in
accordance with NSF Cooperative Agreement Financial and Administrative
Terms and Conditions (CA-FATC) and the applicable Programmatic Terms and
Conditions. NSF awards are electronically signed by an NSF Grants and
Agreements Officer and transmitted electronically to the organization
via e-mail.

These documents may be accessed electronically on NSF\'s Website at
<http://www.nsf.gov/awards/managing/general_conditions.jsp?org=NSF>.
Paper copies may be obtained from the NSF Publications Clearinghouse,
telephone (703) 292-7827 or by e-mail from <pubs@nsf.gov>.

More comprehensive information on NSF Award Conditions and other
important information on the administration of NSF awards is contained
in the NSF Award & Administration Guide (AAG) Chapter II, available
electronically on the NSF Website at

<http://www.nsf.gov/publications/pub_summ.jsp?ods_key=aag>.

**Special Award Conditions:**

CSREES Awards

Within the limit of funds available for such purpose, the awarding
CSREES official shall make grants to those responsible, eligible
applicants whose applications are judged most meritorious under the
procedures set forth in this program solicitation. All funds granted by
CSREES under this solicitation shall be expended solely for the purpose
for which the funds are granted in accordance with the approved
application and budget, the regulations, the terms and conditions of the
award, the applicable Federal cost principles, and the assistance
regulations of the USDA (2 CFR 215 and 3430 of 7 CFR).

Specific management information relating to an applicant shall be
submitted on a one-time basis as part of the responsibility
determination prior to the award of a grant identified under this
solicitation, if such information has not been provided previously under
this or another CSREES program. CSREES will provide copies of forms
recommended for use in fulfilling these requirements as part of the
preaward process. Although an applicant may be eligible based on its
status as one of these entities, there are factors which may exclude an
applicant from receiving Federal financial and nonfinancial assistance
and benefits under this program (e.g., debarment or suspension of an
individual involved or a determination that an applicant is not
responsible based on submitted organizational management information).

**C. Reporting Requirements**

**CSREES Awards**

Applicants selected for funding by CSREES will need to submit the
Current Research Information System (CRIS) forms AD-416 and AD-417 for
NEW awards only. These forms must be submitted electronically via the
CRIS Web Forms site at <http://cwf.uvm.edu/cris>. For assistance with
CRIS forms, please contact the CRIS office at 202-690-0009 or
<cdeckers@cris.csrees.usda.gov>.

**NSF Awards**

For all multi-year grants, the Principal Investigator must submit an
annual project report to the cognizant Program Officer at least 90 days
before the end of the current budget period. Within 90 days after
expiration of a grant, the PI also is required to submit a final project
report.

Failure to provide the required annual or final project reports will
delay NSF review and processing of any future funding increments as well
as any pending proposals for that PI. PIs should examine the formats of
the required reports in advance to assure availability of required data.

PIs are required to use NSF\'s electronic project-reporting system,
available through FastLane, for preparation and submission of annual and
final project reports. Such reports provide information on activities
and findings, project participants (individual and organizational)
publications; and, other specific products and contributions. PIs will
not be required to re-enter information previously provided, either with
a proposal or in earlier updates using the electronic system. Submission
of the report via FastLane constitutes certification by the PI that the
contents of the report are accurate and complete.

**VIII. AGENCY CONTACTS**

General inquiries regarding this program should be made to:

Ann Lichens-Park, National Program Leader, CSREES, U.S. Department of
Agriculture, telephone: (202) 401-6460, fax: (202) 401-6488, e-mail to:
<apark@csrees.usda.gov>

Daniel Jones, National Program Leader, CSREES, U.S. Department of
Agriculture, telephone: (202) 401-6854, e-mail to:
<djones@csrees.usda.gov>

Lita M. Proctor, Program Director, Division of Biological
Infrastructure, National Science Foundation, telephone, (703) 292-5190,
fax (703) 292-9063, e-mail to: <lproctor@nsf.gov>

**For questions relating to Grants.gov contact:**

Grants.gov Contact Center: If the Authorized Organizational
Representatives (AOR) has not received a confirmation message from
Grants.gov within 48 hours of submission of application, please contact
via telephone: 1-800-518-4726; mail to: <support@grants.gov>

**IX. OTHER INFORMATION**

CSREES supports a wide variety of agricultural research and educational
programs. Further information concerning funding opportunities may be
obtained on the CSREES web site at
<http://www.csrees.usda.gov/fo/funding.cfm>.

The NSF Website provides the most comprehensive source of information on
NSF Directorates (including contact information), programs and funding
opportunities. Use of this Website by potential proposers is strongly
encouraged. In addition, MyNSF (formerly the Custom News Service) is an
information-delivery system designed to keep potential proposers and
other interested parties apprised of new NSF funding opportunities and
publications, important changes in proposal and award policies and
procedures, and upcoming NSF Regional Grants Conferences. Subscribers
are informed through e-mail or the user\'s Web browser each time new
publications are issued that match their identified interests. MyNSF
also is available on NSF\'s Website at <http://www.nsf.gov/mynsf/>.

Grants.gov provides an additional electronic capability to search for
Federal government-wide grant opportunities. CSREES and NSF funding
opportunities may be accessed via this new mechanism. Further
information on Grants.gov may be obtained at
[http://www.grants.gov](http://www.grants.gov/).

**ABOUT THE U.S. DEPARTMENT OF AGRICULTURE COOPERATIVE STATE, RESEARCH,
EDUCATION AND EXTENSION SERVICE**

The Cooperative State Research, Education, and Extension Service
(CSREES) is an agency within the U.S. Department of Agriculture (USDA).
CSREES is one of four USDA agencies that make up its Research,
Education, and Economics (REE) mission area. The other three agencies
are:

-   [Agricultural Research Service
    (ARS)](http://www.ars.usda.gov/main/main.htm)

-   [Economics Research Service (ERS)](http://ers.usda.gov/)

-   [National Agricultural Statistics Service
    (NASS)](http://www.nass.usda.gov/)

The USDA-REE agencies provide federal leadership in creating and
disseminating knowledge spanning the biological, physical, and social
sciences related to agricultural research, economic analysis,
statistics, extension, and higher education.

CSREES\' unique mission is to advance knowledge for agriculture, the
environment, human health and well-being, and communities by supporting
[research](http://www.csrees.usda.gov/qlinks/research.html),
[education](http://www.csrees.usda.gov/nea/education/education.html),
and [extension](http://www.csrees.usda.gov/qlinks/extension.html)
programs in the Land-Grant University System and other partner
organizations.

CSREES\' targeted areas of interest---its 60 identified programs---are
grouped in the following [National Emphasis
Areas](http://www.csrees.usda.gov/nea/emphasis_area.html):

-   [Agricultural & Food
    Biosecurity](http://www.csrees.usda.gov/nea/ag_biosecurity/ag_biosecurity.cfm)

-   [Agricultural
    Systems](http://www.csrees.usda.gov/nea/ag_systems/ag_systems.cfm)

-   [Animals & Animal
    Products](http://www.csrees.usda.gov/nea/animals/animals.cfm)

-   [Biotechnology &
    Genomics](http://www.csrees.usda.gov/nea/biotech/biotech.cfm)

-   [Economics &
    Commerce](http://www.csrees.usda.gov/nea/economics/economics.cfm)

-   [Education](http://www.csrees.usda.gov/nea/education/education.html)

-   [Families, Youth &
    Communities](http://www.csrees.usda.gov/nea/family/family.cfm)

-   [Food, Nutrition &
    Health](http://www.csrees.usda.gov/nea/food/food.cfm)

-   [International](http://www.csrees.usda.gov/nea/international/international.cfm)

-   [Natural Resources &
    Environment](http://www.csrees.usda.gov/nea/nre/nre.cfm)

-   [Pest Management](http://www.csrees.usda.gov/nea/pest/pest.cfm)

-   [Plants & Plant
    Products](http://www.csrees.usda.gov/nea/plants/plants.cfm)

-   [Technology &
    Engineering](http://www.csrees.usda.gov/nea/technology/technology.cfm)

CSREES\' two key mechanisms for accomplishing its mission of \"advancing
knowledge\" are:

-   [**National program
    leadership**](http://www.csrees.usda.gov/about/leadership.html). We
    help states identify and meet research, extension, and education
    priorities in areas of public concern that affect agricultural
    producers, small business owners, youth and families, and others.

-   [**Federal
    assistance**](http://www.csrees.usda.gov/about/fed_asst.html). We
    provide annual formula grants to land-grant universities and
    competitively granted funds to researchers in land-grant and other
    universities.

CSREES and its partners focus on critical issues affecting people\'s
daily lives and the nation\'s future. The advanced research and
educational technologies we support empower people and communities to
solve problems and improve their lives on the local level.

We respond to quality-of-life problems such as:

-   Improving agricultural productivity

-   Creating new products

-   Protecting animal and plant health

-   Promoting sound human nutrition and health

-   Strengthening children, youth, and families

-   Revitalizing rural American communities

Through all of these activities, CSREES
[impacts](http://www.csrees.usda.gov/about/prog_impacts.html) the lives
of millions of Americans each day.

**ABOUT THE NATIONAL SCIENCE FOUNDATION**

The National Science Foundation (NSF) is an independent Federal agency
created by the National Science Foundation Act of 1950, as amended (42
USC 1861-75). The Act states the purpose of the NSF is \"to promote the
progress of science; \[and\] to advance the national health, prosperity,
and welfare by supporting research and education in all fields of
science and engineering.\"

NSF funds research and education in most fields of science and
engineering. It does this through grants and cooperative agreements to
more than 2,000 colleges, universities, K-12 school systems, businesses,
informal science organizations and other research organizations
throughout the US. The Foundation accounts for about one-fourth of
Federal support to academic institutions for basic research.

NSF receives approximately 40,000 proposals each year for research,
education and training projects, of which approximately 11,000 are
funded. In addition, the Foundation receives several thousand
applications for graduate and postdoctoral fellowships. The agency
operates no laboratories itself but does support National Research
Centers, user facilities, certain oceanographic vessels and Antarctic
research stations. The Foundation also supports cooperative research
between universities and industry, US participation in international
scientific and engineering efforts, and educational activities at every
academic level.

Facilitation Awards for Scientists and Engineers with Disabilities
provide funding for special assistance or equipment to enable persons
with disabilities to work on NSF-supported projects. See Grant Proposal
Guide Chapter II, Section D.2 for instructions regarding preparation of
these types of proposals.

The National Science Foundation has Telephonic Device for the Deaf (TDD)
and Federal Information Relay Service (FIRS) capabilities that enable
individuals with hearing impairments to communicate with the Foundation
about NSF programs, employment or general information. TDD may be
accessed at (703) 292-5090 and (800) 281-8749, FIRS at (800) 877-8339.

The National Science Foundation Information Center may be reached at
(703) 292-5111.

The National Science Foundation promotes and advances scientific
progress in the United States by competitively awarding grants and
cooperative agreements for research and education in the sciences,
mathematics, and engineering.

To get the latest information about program deadlines, to download
copies of NSF publications, and to access abstracts of awards, visit the
NSF Website at [http://www.nsf.gov](http://www.nsf.gov/).

Location:

4201 Wilson Blvd. Arlington, VA 22230

For General Information (703) 292-5111

(NSF Information Center):

-   TDD (for the hearing-impaired): (703) 292-5090

-   To Order Publications or Forms:

    -   Send mail to: <pubs@nsf.gov> or telephone: (703) 292-7827

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-   To Locate NSF Employees: (703) 292-5111