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« เมื่อ: สิงหาคม 03, 2007, 03:33:03 PM »
Recommendations for Future Research
● The continued development of environmental
genomics with particular attention
to capturing ecological heterogeneity;
● The continued development of environmental
microarray technology with particular
emphasis on understanding sensitivity
and complexity;
● The development of environmental
proteomics;
● The expansion of molecular environmental
methods to include eukaryotic organisms;
● The encouragement of bioinformatics and
modeling as research tools for solving
critical problems (e.g., reconstructing
genomic information from mixed samples,
understanding the ecological significance
of genomic complexity and evolution); and
● The development of cost-effective mechanisms
for environmental sample and
culture collection archiving and for dissemination
to microbial-life researchers.
Novel Approaches for Isolating and
Culturing Microorganisms
Interestingly, the recent emphasis on
molecular characterization of microbial
communities is leading to a renewed interest
in cultivating representatives of microbes
known only through nucleic acid-based
studies. It is generally argued that less than
one percent of all microorganisms is known
and culturable. But are any microorganisms
truly “unculturable,” or have our attempts
simply failed to provide the environmental
conditions essential for growth? The challenges
now lie in overcoming the limitations
of traditional culturing techniques—those of
selectivity—and improving culturing techniques
to isolate novel organisms known
only from 16S rRNA sequences.
Recommendations for Future Research
● The continued development of culturebased
technologies that take advantage
of recent advances in materials,
microfluidics, and other micro- and
nanotechnologies;
● Development of improved microsensor
techniques to identify and quantitate
important organic and inorganic metabolites
in situ, as well as to follow reactant
sources and products in real time; and
● Building of new data schema for rapidly
identifying novel microbes that can be
coupled with advances in molecular
genotyping and phenotyping methods.
Environmental Sequence
Databases
Existing public sequence databases
are insufficient for ecological purposes. The
development of sequence databases with
an environmental slant will build knowledge
of where, when, and under what conditions
microbial sequences were retrieved. Such
databases can provide mechanisms for data
exchange within the research community,
enhance the value of sequences obtained in
single laboratories, and provide a data
catalog that can be mined at different times
and with different questions by microbial
diversity and microbial biogeography researchers.
Recommendations for Future Research
● Determination of the feasibility and desirability
of building a centralized, ecological
sequence database that will serve as a
community-wide resource; and
● Consideration of the relationship of an
environmental database to existing gene
archives, including the Ribosomal Database
Project (RDP; rdp.cme.msu.edu/
html) and NCBI/GenBank
(www.ncbi.nlm.nih.gov).
Recommendations for Microbial
Life Research Funding at NSF
Workshop participants judged the MO
program to be overwhelmingly successful in
addressing a critical research need in sitebased
microbial discovery and activity. Yet,
despite the success of this and other NSF
environmental microbiology funding opportunities,
significant funding gaps were identified.
Critical areas that currently fall outside
existing programs and special competitions
include:
● Microbial discovery that is not site-based;
● Microbe-microbe interactions;
● Microbial community interactions (physiological,
biochemical, genetic);
● Natural patterns of microbial distribution;
● Environmental proteomics and functional
genomics;
● Exploring extreme environments for biochemical
and phylogenetic diversity;
● Specific programs to support eukaryotic
microbial studies and soil microbial studies
at a high level;
● Bioremediation; and
● Discovering natural products from microorganisms.
Final Recommendations
1. The MO Program has played a major role
in advancing research on microbial life and
should be continued in its current form,
perhaps broadening its scope to include
extreme environments and cover habitat
types, rather than single sites.
2. Nonetheless, significant and critical gaps
exist in funding research on microbial life
that can only be filled with an increased
investment by NSF.
3. Consideration should be given to establishing
long-term, renewable MO projects,
perhaps analogous to the Long-Term Ecological
Research (LTER) projects that focus
on diversity and function, and are not necessarily
restricted to a single locale.
4. Consideration should be given to establishing
a core funding program for ecological
microbiology.
5. Special short-term programs are a particularly
valuable approach for funding
research on microbial life, since they allow
flexibility in responding to a rapidly changing
field.
6. Continued support of multidisciplinary
research that welcomes collaborations
between microbiologists, geochemists, and
molecular biologists should be encouraged.
7. New mechanisms for funding needs
unique to research on microbial life should
be considered. These needs include: maintenance
of culture collections, sample
archiving, establishment of environmental
sequence databases, updating instrumentation,
and increasing accessibility of molecular
and in situ technologies to environmental
microbiologists.
5
Conclusion
Despite the great successes of the
LExEn and MO programs, there still is a
need for expanded funding for research on
microbial life: from identifying organisms in
all environments (soil, ocean, air, and extreme
environments), to determining the role
of the organisms in the ecosystem, to sequencing
the organisms’ genetic material for
phylogenetic and evolutionary studies.
The meeting of LExEn and MO grantees
lauded the programs’ successes, but
also pointed out some areas that remain
unfunded and others that require additional
funding. The grantees listed areas of critical
concern, and requested that programs
developed to address them be continued
and expanded. NSF is one of the few
sources of research funds for microbial
biology. For such research to continue and
expand, additional NSF programs remain
essential.
6
Introduction
The National Science Foundation
(NSF) Microbial Observatory (MO) and Life
in Extreme Environments (LExEn) programs
have fostered significant advances in microbial
ecosystems research in a wide variety
of natural environments. The investigators
funded by these programs have extended
the frontiers of microbial diversity and microbial
biogeochemistry research, discovering
novel microbial lineages, describing the
complexity of natural microbial communities,
and linking microbial taxa to critical ecosystem
functions. This workshop, the first of its
kind, provided a platform for MO and LExEn
researchers to discuss recent accomplishments
and future directions in microbial
ecosystem research. Principal investigators
included molecular and ecological microbiologists,
geomicrobiologists and geochemists,
biochemists, chemical engineers, and
computer modelers. This report highlights a
number of insightful contributions generated
by MO and LExEn projects, and underscores
areas for which future funding is
needed and can have a significant impact.
An important theme for the MO program—
one that emerged from the LExEn
program—is the need for comprehensive
multidisciplinary characterization of microbial
systems. The LExEn program, funded
for five years (1996-2001), focused on
microorganisms in extreme environments.
Since many of these ecosystems were only
recently discovered, comprehensive characterization
of the microbiology, geochemistry,
and physical constraints of these ecosystems
were research priorities. This work
provides an environmental context for advanced
studies of these systems, such as
those of the ongoing MO program that focus
on the discovery and characterization of
undescribed microorganisms.
Development of new technologies
and instruments for studying microbial
ecosystems—another theme initiated
through the LExEN program—represents a
timely and significant aspect of future microbial
research. A combination of technological
advances applied to ecosystem characterization
studies promises to accelerate our
understanding of the interactions between
organisms and the physical and chemical
constraints of their environment.
The inherent cross-disciplinary nature
of MO and LExEn projects produced a new
generation of cross-disciplinary scientists,
an added value of microbial ecosystem
studies fostered by investigators from a wide
range of disciplines. Many of these scientists,
including postdoctoral associates and
students of the principal investigators, along
with postdoctoral
associates funded
through the NSF
Microbial Biology
Postdoctoral program,
participated
in the workshop.
NSF Microbial Observatory/Life in Extreme Environments
Principal Investigators’ Workshop
Sept. 22-24, 2002, Arlington, VA
Mary Ann Moran and Sherry L. Cady, editors
MICROBIAL RESEARCH: PROGRESS AND
POTENTIAL
7
“The investigators funded by these
programs have extended the
frontiers of microbial diversity and
microbial biogeochemistry research”.
Developing Molecular
Technologies
LExEn and MO projects have greatly
benefited from the use of new molecular
technologies to identify organisms and their
activities in natural environments. Molecular
methods have provided microbial ecologists
with invaluable information on the enormous
reservoir of microbes that have not been
cultured; 16S rRNA work alone has identified
the presence of more than 13,000 new
prokaryotes. These technologies have also
allowed access to functional genes, providing
a mechanism to assess both capability
for and expression of ecologically important
microbial processes in natural environments.
However, these successes have only
scratched the surface of the diversity and
activity of the microbial world. Now the
challenges are to: 1) move beyond the
limitations of 16S rRNA-based approaches
to link members of microbial communities
with function and 2) move beyond the limitations
of characterized functions into unknown
and unexpected microbial activities.
These approaches can provide insights into
known microbial processes, glimpses of
unsuspected microbial processes, and
access to novel microbial products, such as
naturally produced antibiotics, immunosuppressants,
antitumor agents, and other
potential pharmaceuticals
manufactured
within microbes.
Metagenomics
Genomic analysis, now used primarily
to observe the structures of genomes of
individual organisms, can also be used to
study the genetic reservoir of entire communities,
i.e., the metagenome (Vergin et al.,
1998; Rondon et al., 2000; Béjà et al.,
2000b). Several metagenomics studies have
recovered large fragments of DNA from an
environment, cloned them into vectors, and
sequenced them to produce either endsequence
fragments or completely sequenced
regions (Béjà et al., 2000a;
Gillespie et al., 2002; Brady, Chao, and
Clardy, 2002). Thus, genetic material from a
natural community can be analyzed without
first culturing the organisms. Although technical
challenges and funding limitations are
important concerns, environmental
metagenomics has the potential to provide
new biological insights, recover and detect
novel functional genes in the environment,
and determine physiological diversity of
environmental samples. This methodology is
currently being pioneered in several MO
projects, and has enormous potential for
future microbial life research in all types of
environments.
“16S rRNA work alone has identified
the presence of more than 13,000
new prokaryotes.”
Before metagenomics can take a
leading position in microbial-life research,
there are many challenges that must be
met. For example, access to microorganisms
in extreme or inaccessible environments
can be difficult, and obtaining sufficient
DNA to build genomic libraries (e.g.,
from insect guts or the human mouth) will be
a true challenge. One multicellular organism
can be host to untold numbers of microbes,
but can we build metagenomic libraries from
a single host?
8
Understanding the heterogeneity in
microbial communities over time and space,
the hallmark of most natural environments,
must also be captured in future
metagenomic approaches. For example, in
the marine environment, changes in microbial
community structure, functional gene
reservoirs, and activities can be extremely
rapid, sometimes occurring over the course
of minutes rather than days, months, or
years. Developing high-throughput
metagenomic analysis that can adequately
represent the dynamics of natural microbial
communities is a significant challenge.
The difficulty of obtaining high-quality DNA
from certain microbes or microbial habitats
is another potential hurdle. Some
metagenomics studies require large (ideally,
~100 kb) fragments for library construction;
yet Bacteria and Archaea with hard-to-break
cell walls necessitate extraction procedures
that yield fragmented DNA. Many environments,
particularly soils and sediments,
have contaminants that are co-extracted
with DNA and, thus, limit its quality and
susceptibility to cloning.
Once isolated, how will the DNA be
cloned and maintained for metagenomic
analysis? Present methods use E. coli as
the primary vector for cloned environmental
DNA; but there is concern that sequences
harboring genes that produce proteins toxic
to E. coli will never be retrieved (Béjà et al.,
2000b). Alternate vectors, new extraction
methods, and smaller sample requirements
will all be important technical challenges as
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