of untold diversity in marine environments are the primary catalysts
of energy transformation, and are responsible for > 98% of the
carbon and nitrogen cycling . An estimated 3.6 x 10^30
microbial cells with cellular carbon of ~3 x 1017
grams may account for more than 90 percent of the total oceanic biomass
. The number of bacteriophage and viruses may be one hundred-fold
higher. With such enormous populations, the accumulation of mutations
should lead to very high levels of genetic diversity and phenotypic
variation. Yet, traditional microbiological methods have described
only 30,000 protists [3-5] and fewer than 5000 kinds of prokaryotes
we are witness to a revolution in microbiology. Just as the first
microscopes unveiled an unseen microbial world, the use of molecular
techniques to enumerate different kinds and numbers of single-cell
organisms has forever changed perceptions of the natural world. Microbial
diversity is at least 100-1000 times greater than estimates based
upon cultivation-dependent surveys . Comparisons of genome sequences
from cultivated and naturally occurring microbial populations reveal
unanticipated levels of metabolic diversity and suggest new modes
and mechanisms for evolutionary change. Microbes account for the preponderance
of life's genetic and metabolic variation, but our understanding of
microbial diversity and the evolution of its population structures
in the oceans is only fragmentary.
develop a description of biodiversity in the oceans, the Census of
Marine Life (CoML) must look beyond metazoa and plants. It must develop
a strategy to (1) catalogue all known diversity of single-cell organisms
inclusive of the Bacteria, Archaea, Protista and associated viruses,
(2) to explore and discover unknown microbial diversity, and (3) to
place that knowledge into appropriate ecological and evolutionary
contexts. Several existing or proposed CoML field projects including
CeDAMar, ChEss, MAR-ECO, GoMA, NaGISA, CMarZ, Reefs, Arctic,
Antarctic, Sea Mounts etc. either have microbial initiatives or the
potential to develop microbial-based projects. Yet, there is no global
effort to acquire information about diversity and distribution of
microbes and associated viruses from the three domains of life in
the World's oceans. This proposal describes an International
Census of Marine Microbes (ICoMM).
It will advocate for and coordinate investigations of microbial diversity
(Bacterial, Archaeal, Protistan and Viral) and their population structures
in marine environments. ICoMM will have five major activities.
The first is to support scientific working groups. These will focus
on (1) open ocean and coastal systems, (2) benthic systems, and (3)
technology that is specifically required for a microbial census. The
second is to develop the database resource MICROBIS, which
will organize morphological, molecular and contextual information
for marine microbial diversity within a framework that integrates
into OBIS. The third is to provide resources that can facilitate and
coordinate requests for research support from governmental and private
foundations. The fourth is to facilitate education and outreach of
ICoMM to make it visible to the general public and raise awareness
of its goals. Finally, ICoMM will support pilot projects that
have the potential to shape larger-scale research initiatives in marine
be successful, ICoMM must promote international cooperation
and forge linkages with existing and new CoML field projects for collecting
samples, contextual information and new technologies. At the same
time, ICoMM must engage the broader community of microbiologists
with collateral interests in microbial diversity, evolution, biogeography
and their functional roles in marine systems.
Uncharted Diversity of Marine Microbes: The Known, Unknown and
of Bacteria, Archaea, and Protists account for greater than 90 percent
of oceanic biomass and 98 percent of primary production [1, 2]. Stable
isotopes studies reveal that for more than three billion years, these
microscopic factories "initially anaerobic and later aerobic" mediated
biogeochemical processes that shaped planetary habitability . Today
the oceans world-wide are teeming with microscopic and macroscopic
life forms. Rich, chemosynthetic microbial communities thrive at deep-sea
hydrothermal vents . Abundant Archaea populate oceanic midwaters
. Very large populations of picoplankton including diatoms, dinoflagellates,
picoflagellates and cyanobacteria are the primary catalysts in carbon
fixation , orchestrate the cycling of nitrogen  and form the
base of the traditional marine food web. Heterotrophic SAR11 represents
the dominant clade in communities of ocean-surface bacterioplankton
 while nonphotosynthetic protists of unknown diversity control
the size of picoplankton populations and regulate the supply of nutrients
into the ocean's food webs.
advances in microbiology over the past fifty years force us to think
in terms of ever shifting boundaries between what is known, unknown
and unknowable about single-cell organisms. In the late 60's, microbiologists
had lost hope of constructing a robust natural system for microbial
taxa. New molecular techniques developed during the 1970's opened
pathways for establishing microbial phylogenetic relationships that
were unknowable using traditional techniques (comparisons of phenotypic
characters such as morphology, staining properties,
metabolic capabilities, and physiology) . Modern technologies
(molecular techniques, automated fluorescence cell sorting, etc.)
have demonstrated the great abundance and diversity of microbial life
forms in the oceans, and DNA sequencing of environmental genomes (metagenomics)
provides evidence of hitherto unrecognized physiological categories
among the planktonic microbes. With the acceptance of the significance
of microbial food webs in the 1980's [14, 15] and discoveries of microbial
mediated biogeochemical cycles, oceanographers recognized the pivotal
role of microbial communities as catalysts in oceanic processes. Biologists
reached the profound conclusion that the continued survival of all
multi-cellular life is contingent upon complex microbial communities
of under-described and possibly unknowable diversity.
we are to assemble a comprehensive description of marine biodiversity
and the processes that shape habitats for multi-cellular life, we
must determine what kinds of microorganisms occur in benthic and planktonic
open ocean and coastal systems. For the traditional alpha taxonomist,
a "kind" of organism is comparable to the concept of OTUs (Operational
Taxonomic Units) for describing animal and plant species. Based upon
traditional methods, the number of recognized microbial OTUs
is almost trivial when compared to estimates
of 106 to 108 species for marine fauna. T
his modest assessment of microbial diversity is not consistent with
a 3.5 billion-year evolutionary history during which microbes
have developed an enormous metabolic repertoire to cope with Earth's
dynamic environment. In contrast, culture-independent descriptions
for the microbial world, which rely upon comparisons of homologous
genes (phylotypes), reveal a much richer diversity. Sequence
comparisons of polymerase chain reaction products (PCR amplicons) that
target phylogenetically conserved regions of ribosomal RNA (rRNA)
coding regions, demonstrates that microbial
diversity ranges from 105 to greater than 107
kinds of organisms . Traditional microbiology has failed to culture more than
99.9 percent of these newly discovered "phylotypes" from marine environments.
Using this powerful technology, the microbiologist can also make distinctions
between cells with identical morphologies and enumerate differences
in community structure between microbial populations. Despite the
impact of new information provided by the
molecular biology toolbox, traditional techniques must not be abandoned
since it is within this context that our understanding of marine microbial
ecology has developed.
The hallmark of microbial diversity is biochemical innovation
that single-gene studies cannot fully describe. Within the
next few years, molecular biology will allow us to incorporate a definition
for functional capacity or inducible phenotype in descriptors of microbial
diversity [16, 17]. Microbiologists are able to identify the occurrence
of a particular functional or structural gene and exploit it as a
marker of diversity within an isolate or for members of a naturally
occurring microbial population. In a similar manner, post genomic
technology can measure gene expression patterns as a means to differentiate
between "kinds" of microorganisms. As a direct consequence of increased
activity in marine metagenomics, the combination of high-throughput
DNA sequencing, expression profiling and proteomics can describe new
traits, novel functions, and unusual enzymes in microbial populations.
In some cases, entirely new phyla with novel functions are being discovered
. These aid in understanding the evolution of life in this ancestral
habitat and lead to sounder descriptions of new communities and species.
Sequencing data will also be wedded to newly emerging molecular assays
that incorporate automated sampling technologies and which will lead
to finer temporal and spatial resolution of molecular diversity. If
advances in genome technology and bioinformatics continue on the current
trajectory, sequence scans of entire genomes or communities of genomes
 coupled with high-throughput gene expression or proteomic profiles
may become the standard for defining diversity and monitoring distribution
patterns for microbial species.
fully understand microbial marine diversity it is important to integrate
sequence-based studies with phylogenetically-rich information from
isotopic analyses and characterizations of metabolic and biosynthetic
products. For example, isotopic analyses have pinpointed lipids produced
by novel Archaea that oxidize methane anaerobically . Follow-up
investigations at sites rich in these products have revealed abundant
new phylotypes that are related to methanogens . The abundance
of carbon-14 and carbon-13 in lipids produced by planktonic Archaea
 proves that those organisms are assimilating large amounts of
inorganic carbon from the ocean's midwaters and must be growing as
autotrophs. Unprecedented lipid structures have been traced to previously
unknown planctomycetes and the long-sought capability for anaerobic
oxidation of ammonia. These are just a few examples of the novel insights
that can be achieved when molecular and biochemical information are
International Census of Marine Microbes
proposal implements recommendations that are relevant to CoML objectives
as outlined in the document Unveiling the Ocean's hidden majority:
a roadmap. The most general statement of ICoMM's goal is
to develop a highly-resolved biodiversity database for marine microbes
and to understand how these populations evolve and redistribute on
a global scale. Beginning with Haeckel's reports from the Challenger
expedition of over 100 years ago , traditional microbiological
approaches have made important contributions to our knowledge of microbial
eukaryotes too numerous to recount here, but little about Bacteria
or Archaea. Most of what we must learn about microbial diversity in
the oceans will depend upon the application of molecular techniques.
Early molecular studies of marine microbial diversity only considered
the Archaea and the Bacteria [24-27]. Recent molecular-based searches
have already identified novel eukaryotic lineages in the water column
and in warm anoxic sediments [28, 29]. Combined with fluorescence
in situ hybridization technologies (FISH), it is already possible
to associate novel, molecular-based lineages with specific morphologies.
Efforts should be made to bring newly discovered key taxa into culture
for more detailed investigations. One of our challenges is to create
a bridge to expertise of the past.
what "kinds" of organisms exist within a marine microbial population
and how community structure changes in response to environmental shifts
are high priorities for ICoMM. Sampling strategies and the
collection of contextual information will be important elements of
this census. For example, culture-independent surveys reveal unanticipated
numbers of distinct phylotypes in the benthos and plankton of open
ocean and coastal waters. In contrast, deep-sea vents separated by
thousands of miles sometimes display lower levels of diversity 
but often harbor anaerobic thermophiles that have nearly identical
rRNA sequences, even though these organisms have not been detected
in open ocean waters. Mechanisms that might explain this biogeographical
distribution will require studies of chemically-similar vent environments
and strategically located, intermediate stations. The high-throughput
DNA sequencing of environmental shotgun libraries from an oligotrophic,
low diversity environment , provides another lesson about the
importance of sampling strategies. This landmark study shows that
current de-facto standards of a few hundred to a few thousand sequences
for PCR amplicons of conserved genetic elements e.g. rRNA coding regions-
cannot fully describe microbial diversity. A more complete accounting
of diversity will dictate significant increases in data collection.
But this comes at a considerable cost both in terms of reagents and
in analytical efforts. To maximize the science return from such costly,
high-throughput studies, marine microbiologists must identify the
most important questions to be addressed and the best study sites
and strategies for obtaining unambiguous answers.
historical events and underlying mechanisms that led to contemporary
microbial diversity are mostly uncharted (exceptions might include
the marine foraminifera). The goals of ICoMM include cataloguing
and discovery, but must extend to an understanding of the processes
by which marine microbial diversity has been created and is maintained.
Genome-based studies suggest that large-scale genetic exchange corresponding
to tens of thousands of base pairs from unknown genetic sources can
occur over timescales required by microbes to adapt to shifts in environmental
chemistry. Stunningly, we have only scratched the surface of marine
environments but already learned that the correct conceptual framework
for describing the dynamics of metagenome evolution and shifts in
diversity might not yet be known. Some of the fundamental questions
that we must address and molecular approaches make this possible include:
How many kinds of microorganisms exist in marine environments
and what governs the evolution of microbial lineages within complex
Why do complex microbial consortia retain functionally equivalent
but genetically distinct lineages rather than selecting for a single
"winner" with an optimal suite of metabolic activities?
the diversity of a microbial guild relate to the stability of its
there a biogeography for distinct microbial lineages and, if so, what
are the principal drivers or restrictors? What genomic changes, if
any, are associated with relocation of dormant organisms over large
How widespread is horizontal gene transfer and does it completely
obliterate phylogenetic patterns for microbes? Do viruses mediate
chemical environments select for lineages endowed with particular
metabolic capabilities, or does the unit of selection correspond to
individual genes that can transfer particular metabolic functions
accounts for large-scale genetic variation in microbial genomes that
share a very recent common ancestry? Is there a cryptic source of
genetic information that selectively invades microbial genomes, or
are there undocumented mechanisms that can rapidly generate novel
coding capacity within a bacterial chromosome?
How does genotypic diversity shape phenotypic diversity, and
how does this diversity influence the functioning of ecosystems?
with a larger genomic context, the interpretation of data from molecular-based
field studies will challenge even the most advanced genetic algorithms
and evolutionary theory. This enterprise will demand interdisciplinary
efforts to explore the dynamics of microbial population biology, genome
diversity, and the metabolic basis of biogeochemical processes.
CoML initiatives that focus upon geographical locations (e.g. Arctic,
Antarctic, GoMA, MAR-ECO, NaGISA, POST, TOPP etc.), or restricted
environments (e.g. ChEss, Seamounts, CeDAMAR, etc.), ICoMM
will embrace a world-wide strategy to explore the diversity and distribution
patterns of all kinds of single-cell organisms in marine environments.
Understanding the diversity of marine microbes is a mega-science problem
that requires new approaches to mapping diversity, grand strategies,
integration of diverse communities, and enabling studies that will
explore processes "whether ecological or evolutionary." The community
of marine microbiologists that must participate in this enterprise
is diverse but they do not yet form a unified community. A problem
of this magnitude requires careful planning and international cooperation.
Because we know so little about the limits of microbial diversity
or whether biogeographical distribution patterns exist for microorganisms,
major advances will occur by 2010 albeit complete descriptions may
require decades of research.
address the key scientific questions outlined above (3a. Objectives),
ICoMM must seek community consensus about research priorities and
an integrated experimental plan. Unification of this discipline will
require the development of shared, enabling technologies and standardized
measurements in the same way that DNA sequencing and "bar coding"
has provided a common means to index metazoan and plant biodiversity.
Constituents of ICoMM must agree upon sampling regimes and mechanisms
for sharing samples, contextual information and new data with the
scientific community. We must determine how to bring together the
existing molecular data into a single framework/synthesis or establish
coding standards that promote electronic exchange of information including
close ties with OBIS. An important goal will be to make data from
ICoMM readily accessible to process oriented interest in microbial
oceanography. It will be especially important to form alliances with
relevant CoML and other marine microbiology initiatives. For example,
ICoMM's advisory board and working groups include participants from
ChEss, CeDAMar and GoMA. Because of overlapping interests in certain
protist groups, ICoMM has agreed to cooperate with CMarZ in development
of programmatic infrastructure. Preliminary discussions are also underway
to establish a Protistan focus Group at the interface of both programs.
Other collaborative activities will include participation in the European
Union projects BASICS (Bacterial single-cell approaches to the relationship
between diversity and function in the sea coordinated by J. Gasol,
CSIC, Barcelona, Spain), MIRACLE (Microbial Marine Communities Stability:
from Culture to Function, coordinated by Francisco Romero, Inst Biomar,
Spain), PICODIV (Monitoring Biodiversity of Pico-Phytoplankton in
Marine Waters, coordinated by Daniel Vaulot, Brest France), ALIENS
(Algal Introductions to European Shores, coordinated by Jose M. Rico
Ordas, Univ. Oviedo, Spain), MARBEF (Marine Biodiversity and Ecosystem
Functioning, coordinated by Carlo Heip), EurOcean (coordinated by Paul Treguer, IFREMER Brest
and Louis Legendre, Lab Oceanographique Villefranche sur mer, France)
and participation in the several U.S. programs including the NSF Research
Coordination Network "Seamount Biogeosciences Network" submitted by
Scripps Institution of Oceanography, the NIH/NSF funded Center of
Oceans and Human Health at Woods Hole (organized by John Steggeman
at the Woods Hole Oceanographic Institution), the NSF RIDGE 2000 initiative,
and international collaborations i.e. the MBL and the Alfred Wegener
Institute joint effort to develop the WEB resource plankton*net. Finally,
ICoMM must set an agenda to guide the development of funding strategies
and provide support for pilot projects that have the potential to
generate additional support from governmental agencies and private
foundations. Upon receipt of initial funding in the Fall of 2004,
ICoMM's first task will be to formalize collaborative relationships
with ongoing CoML programs, relevant European and US initiatives
including the Sorcer II expedition, and other existing projects that
contribute towards ICoMM's objectives. The scope of ICoMM's activities
by 2010 will be proportional to available resources from foundations
and governmental funding agencies. An attached supplement provides
cost estimates based upon different kinds of measurements applied
to different sampling regimes. The dynamic range of these cost estimates
is admittedly enormous and it is clear that the marine microbiology
community must establish priorities for initial funding. The total
resource requirement ranges from tens of millions of dollars to NASA-size
efforts costing multiple billions of dollars. None of these projections
takes into account efficiencies that we should expect from advances
in technology. It is entirely reasonable to expect that the cost of
molecular analyses will drop by one or two orders of magnitude over
the next decade.
Organization of ICoMM
will be the lead organization and will support a Secretariat, a small
administrative staff, and a computational biology group charged with
development of the ICoMM data base MICROBIS (see below). NIOZ & NIOO-CEME in The Netherlands will fund a European
coordinator and will employ a data base specialist who will integrate
data from our international collaborators into MICROBIS. The
MBL and NIOZ & NIOO-CEME formed
a partnership in the preparation of this proposal. The Secretariat
will coordinate ICoMM activities including setting agendas, developing
a community-driven database, and providing support (financial and
organizational) for meetings of ICoMMâs constituency.
will coordinate scientific activities through a multi-tiered interface
that will engage the general marine microbiology community, ICoMMâs
specialized working groups and its Scientific Advisory Committee (SAC).
Three working groups (Open ocean and coastal systems, Benthic systems,
and Technology) willconsider the science questions posed under 3.1
Objectives as they develop a plan to address the challenges outlined
under 3.2. The working groups for Benthic systems and for the Water
column will consider the current status of the field, the most promising
approaches for exploring marine microbial diversity, sampling requirements
and potential obstacles. The Technology working group will be cross-cutting
and will consider issues that overlap with the other two working groups.
Their primary charge is to determine what kinds of methods and which
targeted genes will be most appropriate for meeting ICoMMâs scientific
objectives. They will also evaluate alternative methods for sample
processing, standards for data collection and data sharing.
the three working groups will propose objectives, agendas and resource
requirements for consideration by the SAC, which will guide and monitor
development of ICoMM activities. These interactions will provide guidance
for a broader community of representative marine microbiologists who
will meet at least annually in order to move ICoMMâs agenda forward.
Members of the ICoMM Secretariat and the SAC will review funding requests
associated with the preparation of research proposals including either
financial support or DNA sequencing support for small-scale pilot
projects. Examples of four such projects are provided in the Appendix.
of labor into the three working groups allows us to be inclusive of
the taxa to be studied and addresses fundamental differences between
the benthos and the water column that will impact experimental design
and processing of data. Separate working groups for the Benthos and
the Water Column face different challenges in surveys of microbial
diversity. The communities of organisms that inhabit these environments
have different compositions and structures. The physical environments
are dissimilar and different nutrient and energy pathways drive each
of these systems. Chemosynthetic energy and heterotrophy dominate
the Benthos, whereas photosynthesis drives Open ocean and coastal
water systems. There are fundamental differences in the physical stability,
scale and patchiness and therefore sampling protocols for the two
types of habitats will be different. Even the extraction of biopolymers
requires alternative technologies for samples collected from the benthos
versus open ocean and coastal waters (water
column samples). In general, we have a clearer understanding of the
microbiology and physical parameters of open ocean and coastal waters,
where the systems complexity is lower and the technology demands are
better developed. The evaluation of benthic diversity poses special
problems associated with differentiating between organisms that are
endemic versus the introduction of cells that normally live closer
to the surface via sedimentary processes.
Membership of Secretariat, SAC and Working Groups.
Advisory Council (SAC)
PI: Mitchell L. Sogin
|| Â Â
John Baross Univ. Wash.
W. de Leeuw NIOZ
Ariel Gallardo Univ. of Conc.
J. Patterson MBL
ocean and coastal systems
will support the development and maintenance of MICROBIS, which is
a distributed knowledge resource that provides systematic and biogeographic
information for marine viruses, archaea, bacteria, photosynthetic
eukaryotes and heterotrophic protists. The design of MICROBIS allows
it to integrate seamlessly with OBIS and it takes advantage of the
MBLâs development effort for construction of the image-rich WEB resource,
micro*scope. Using the MBLâs star*model
for sharing distributed information about microbial diversity between
different WEB portals, micro*scope currently integrates information
from plankton*net, a network of distributed information that includes
collaborators in Japan, Australia,
Germany, France, Norway,
Denmark and the
seeks to develop encyclopedic knowledge resources for marine phytoplankton
Web sites using the star*template derived from micro*scope are assembled
quickly and allow distributed teams to work co-operatively to create
resources of a grand scope and scale.Â The Data Model meets inter-operability
requirements of OBIS and of other major databases (e,g., TreeBase,
GenBank, the Ribosomal Database Project, the European RISSC, MIRACLE
etc.). Records will include
names and latitude and longitude information, will be annotated with
Dublin core, ISO and TDWG-SDD - metadata standards, and incorporate
DiGIR and SOAP-based protocols to promote cross-resource indexing,
search and retrieval.
will employ a Distributed Workgroup Environment to enable a diverse
community of users to manage unprecedented volumes of largely molecular
data; as well as developing scaleable and flexible internet services
that will allow many users to contribute to, access, organize and
package information to suit the needs of a diverse community of users.
Integration relies heavily on the TNS system developed at the MBL/WHOI
library to emulate taxonomy within internet services. TNS exploits
the universal system of metadata â the names and the classification
of organisms â that has been applied to most biological information,
and uses this to organize and index information locally and remotely,
to create taxon-specific links between data sources, to promote inter-operability
by standardizing the names in previously independent databases, or
to provides services that will mark up documents with taxonomic metadata
and catalogue the resources. TNS is developed in close compliance
with the International
Union of Biological Sciences Taxonomic Database Working Group
the international community to contribute descriptive information
into a communal knowledge repository about marine microbes, the repository
will include, the names, synonyms, taxonomic authorities, descriptions,
images, references, web sites, distribution, ecology, dynamic links
on all marine microbes.Â This system will share resources with micro*scope
Education and Outreach
and education components of ICoMM are important. The lack of familiarity
with the diversity and significance of microbial communities demands
that we make a strategic and targeted commitment to education and
outreach. Our proposed Education and Outreach activities include two
objectives: 1) to raise community awareness of ICoMM; 2) to provide
resources that will underpin the education of marine microbiology
in schools and universities. We will work closely with the Office
of Marine Programs at the University of Rhode Island (URI_OMP) and
draw on their experience of existing CoML projects to implement the
ICoMM education and outreach strategy. That strategy will take advantage
of new informatics initiatives. We will use MICROBIS to open up access
to resources across the ICoMM program narrowing the gap between researchers
and consumers of knowledge.Â Working with the MLER (Microbial Life Educational Resources) project that
has been funded through the NSF National Science Digital Library program,
we will generate a library of digital educational resources with models
for how those resources may be embedded in K-12 and undergraduate
educational packages.Â This will be based on the model already developed
for the geosciences (http://serc.carleton.edu/introgeo/index.html).
provide to URI_OMP the necessary imagery, content, text, and out-link
bundles for CoML portal subprojects.Â Our outreach liaison officer
(Linda Amaral-Zettler) will become a member of the CoML Education
and Outreach network and has already developed contacts with Sara
Hickox.Â Our budget will ensure attendance at annual meetings. We
will add customized access to the resources of the micro*scope, plankton*net,
and MLER web-sites to each area of the CoML portal. The web-based
knowledge environments micro*scope and plankton*net are discussed
above while MLER is summarized below. We will add educational resources
and special navigational pathways to MICROBIS to the âPartner Resourcesâ
page.Â Finally we will hold our own facilitation workshops, and/or
link with existing workshops being developed at the MBL in the context
of other programs.
well positioned to do this.Â The team is committed to outreach and
education includes participation in the Microbial Diversity course
at the MBL, teacher education workshops (MBL) and the Astrobiology
Education and Outreach program.Â We have biodiversity informatics
initiatives that will improve access to resources; and we are actively
involved in educational research programs funded by the NSF.
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