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Understanding patterns of use and scientific opportunities in the emerging global microbial commons

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Abstract

Rapidly growing global networking has induced and supported an increased interest in the life sciences in such general issues as health, climate change, food security and biodiversity. Therefore, the need to address and share research data and materials in a systematic way emerged almost simultaneously. This movement has been described as the so-called global research commons. Also in microbiology, where the sharing of microbiological materials is a key issue, microbial commons is attracting attention. Microbiology is currently facing great challenges with the advances of high throughput screening and next-generation whole genome sequencing. Furthermore, the exploration and use of microorganisms in agriculture and food production are increasing so as to safeguard global food and feed production. Further to several meetings on the subject, a special issue of Research in Microbiology is dedicated to Microbial Research Commons with a series of reviews elaborating its major pay-offs and needs in basic and applied microbiology. This paper gives an introduction to these articles covering a range of topics. These include the role of public culture collections and biological resource centers and legal aspects in the exchange of materials, microbial classification, an internet-based platform for data-sharing, applications in agriculture and food production, and challenges in metagenomics and extremophile research.
Understanding patterns of use and scientific opportunities
in the emerging global microbial commons
Tom Dedeurwaerdere (FRS-FNRS/UCL)
Bibliographical reference
Dijkshoorn, L., De Vos, P., and Dedeurwaerdere, T., 2010, "Understanding patterns of use and
scientific opportunities in the emerging global microbial commons", Research in Microbiology 161(6):
407-413.
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Copyright © 2015 Elsevier Masson SAS. All rights reserved
Understanding patterns of use and scientific opportunities in the emerging
global microbial commons
Lenie Dijkshoorn
a,
*, Paul De Vos
b
, Tom Dedeurwaerdere
c
a
Department of Infectious Diseases C5-P, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300 RC Leiden, The Netherlands
b
Department of Biochemistry and Microbiology (WE 10), University of Gent, Laboratory for Microbiology, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
c
Universite
´catholique de Louvain (UCLouvain), Centre de Philosophie du Droit, Colle
`
ge Thomas More, Place Montesquieu 2, box15, B-1348, Belgium
Received 6 June 2010; accepted 8 June 2010
Available online 19 June 2010
Abstract
Rapidly growing global networking has induced and supported an increased interest in the life sciences in such general issues as health,
climate change, food security and biodiversity. Therefore, the need to address and share research data and materials in a systematic way emerged
almost simultaneously. This movement has been described as the so-called global research commons. Also in microbiology, where the sharing of
microbiological materials is a key issue, microbial commons is attracting attention. Microbiology is currently facing great challenges with the
advances of high throughput screening and next-generation whole genome sequencing. Furthermore, the exploration and use of microorganisms
in agriculture and food production are increasing so as to safeguard global food and feed production. Further to several meetings on the subject,
a special issue of Research in Microbiology is dedicated to Microbial Research Commons with a series of reviews elaborating its major pay-offs
and needs in basic and applied microbiology. This paper gives an introduction to these articles covering a range of topics. These include the role
of public culture collections and biological resource centers and legal aspects in the exchange of materials, microbial classification, an internet-
based platform for data-sharing, applications in agriculture and food production, and challenges in metagenomics and extremophile research.
Ó2010 Elsevier Masson SAS. All rights reserved.
Keywords: Microbial commons; Public culture collections; Agriculture; Food production
1. Introduction
As scientists and user groups become better connected with
each other, particularly through the internet, and as research
focuses on issues of global importance, such as human health,
climate change, food security and biodiversity, there is
a growing need to systematically address sharing of and access
to research data and materials beyond national jurisdictions,
and thereby create greater value from international coopera-
tion. This movement has been described in the literature as the
emergence of so-called global commons, which have been
defined as resources that are shared by groups of people
participating in decisions about how those resources should be
managed and used (Hess and Ostrom, 2006). This also applies
to research in microbiology, where the need to access refer-
ence materials for identification purposes, the specialization
amongst collections of microbial materials, and collaborative
efforts for increasing our understanding of the biodiversity of
microorganisms result in interdependency amongst research
communities on the global scale.
Despite considerable interest in specific areas regarding
microorganisms and the existence of substantial and diverse
public culture collections and research collections, the breadth
of the subject has meant that the sector has so far received
little systematic attention. Moreover, at present, this situation
of exchange of biological materials within a global commons,
is facing a set of important challenges, mainly related to the
high cost of appropriate quality management (OECD, 2001)
and the change in the international legal environment, which
* Corresponding author.
E-mail addresses: l.dijkshoorn@lumc.nl (L. Dijkshoorn), paul.devos@
Ugent.be (P. De Vos), tom.dedeurwaerdere@uclouvain.be (T. Dedeurwaerdere).
0923-2508/$ - see front matter Ó2010 Elsevier Masson SAS. All rights reserved.
doi:10.1016/j.resmic.2010.06.001
Research in Microbiology 161 (2010) 407e413
www.elsevier.com/locate/resmic
may hamper some of the most promising new scientific
opportunities made possible by current advances in high
throughput screening and increasing availability of full
genome sequencing of entire microorganisms (Reichman, J.
H., Dedeurwaerdere, T., and Uhlir, P.F., unpublished data). For
all these reasons, microbial genetic resources deserve to be
analyzed in a systematic way, focusing on global trends in
gene flow and uses and their possible benefits to life science
research.
The first international meeting of the microbial commons
initiative was held on the 7th and 8th of July 2005 in Brussels,
Belgium (Dawyndt et al., 2006). This initiative was followed
by two other international meetings into the questions of the
legal, institutional and technical design of the microbial
commons, one in Ghent on the 12th and 13th of June 2008,
and a second in Washington DC on the 8th and 9th of October
2009 at the US National Academies. A major monograph on
the legal, institutional and organizational design of the
microbial commons is also in preparation, early versions of
which have been presented and discussed at both the Ghent
and Washington meetings (Reichman, J.H., Dedeurwaerdere,
T., and Uhlir, P.F., unpublished data). In the context of this
work on the emerging microbial commons, however, a more
systematic analysis of the existing patterns of exchange and
the scientific pay-offs that can be expected from a more fully
organized microbial commons is needed. In 2009, two inter-
national workshops on “Analyzing Patterns of Exchange and
Use in the Global Microbial Commons” with microbial
scientists and culture collection managers were organized to
address these issues (18th and 19th of February and 25th and
26th of March, Brussels 2009). At the outcome of the work-
shops, a set of papers were commissioned which provide
a systematic overview of the incipient global microbial
research commons and present some in-depth case studies
illustrating the socio-economic benefits of use and exchange of
microorganisms, both regionally and internationally. The
papers presented in the special issue on “Microbial Research
Commons” in Research in Microbiology are the result of that
effort.
2. Public collections of microorganisms, spiders in the
web
Many microbiologists will occasionally need particular
strains as taxonomic reference, but also as test material, and
they order these from a public microbiological culture
collection. These culture collections (biological resource
centers, or BRCs) serve an essential infrastructure function by
making available biological materials and information of
guaranteed identity and quality, for scientific investigation and
development in an international context. As described by
Janssens et al. (2010), the global distribution and exchange of
microorganisms is organized on a formal basis by the network
of over 500 public culture collections which are members of
the World Federation of Culture Collections (WFCC). It is
their historical mission to organize the collection, authenti-
cation, maintenance and distribution of cultures of
microorganisms and cultured cells. Through the culture
collection network, cultures are distributed and made available
for research and development with marginal distribution costs,
often with the possibility of further distributing the cultures to
qualified third parties and with major benefits for the devel-
opment of downstream applications.
The situation of the public culture collections is charac-
terized by a high level of interdependency (Dedeurwaerdere
et al., 2009). The largest public culture collection, with
approximately 25,000 strains, holds less than 2% of the total
strain holdings of the WFCC members and only a minor
fraction of currently known microbial biodiversity. Intense
collaboration and exchange amongst culture collections is
a necessary consequence of this situation. Furthermore,
scientists may also exchange strains in an informal way
between their in-house research collections where the bulk of
microbial research is done. These research collections play an
important role in the overall research cycle, because this is
where the first selection and screening of reference materials is
undertaken. On average, deposits from these research collec-
tions represent 30% of the yearly accession of new holdings in
the public culture collections, while both academia (58%) and
the private sector (23%) are important recipients from cultures
of the public culture collections (Dedeurwaerdere, 2010a).
Many of the services provided by BRCs and knowledge
accumulated in these institutions are relatively unknown to the
applied microbiologist or scientist. Yet these centers are
essential infrastructures for life sciences and biotechnology.
Therefore, researchers should be encouraged to deposit
important microorganisms with these collections. Editorial
boards of scientific journals along with funding bodies should
support this by demanding these deposits as part of their
review process and research output.
3. Standardized electronic information exchange, the
StrainInfo initiative
Many BRCs have built up their collections over decades.
Due to exchange policies, BRCs have in their holdings
subcultures of so-called original strains. Only during the past
decade have digital databases with information on the holdings
of the individual BRCs become available. Many of these
include, apart from cataloguing of their biological material,
additional strain information (meta-information) that is in
most cases not overlapping and also provided under different
formats between the BRCs for mutual subcultures. Various
attempts have been made to standardize the information in
such databases to allow easy linking (e.g. Stalpers et al.,
1990). A recent platform, StrainInfo (http://www.straininfo.
net)(Dawyndt et al., 2005) is becoming the reference for
information and meta-information on microorganisms at the
strain level. It integrates the information from various BRCs as
well as related information retrieved from other databases and
makes it available in a common electronic format. To realize
this, a microbial common language (MCL) for the exchange of
microbial information has been developed (Verslyppe et al.,
2010). As a result, strain designations, historic information
408 L. Dijkshoorn et al. / Research in Microbiology 161 (2010) 407e413
on their deposit in BRCs, growth characteristics, genomics and
other data, and relevant publications are shown to the user in
an integrated way. This system has the potential to evolve, to
some extent comparable to the Wikipedia-information
network, into a global microbiological data-network of which
the data can be directly used in scientific research, for example
in combination with genomics for comparative studies.
4. Taxonomy and its implications in microbial commons
In clinical or environmental microbiology, it is a frequent
task to determine the species to which an isolate recovered
from a sample belongs. This process of identification has
practical implications since, by inductive generalization, it is
assumed that the isolated organism has the same features as
other members of this species. Consequently, identification of
a bacterium from a patient’s sputum as Mycobacterium
tuberculosis or from a general infection as methicillin-resistant
Staphylococcus aureus (the so-called MRSA) has severe
implications in the sense of treatment and/or infection control.
Thus, the determination of the name of the species to which an
isolate belongs is an important act in applied microbiology.
It happens that an isolate cannot be assigned to an already
known species and that it is hence a representative of a newly
discovered species. Description of new species and nomen-
clatural changes are part of the specialized field regarded as
microbial taxonomy, and which encompasses three successive
elements, characterization, classification and nomenclature.
Recent reviews on bacterial taxonomy have been given by
Tindall et al. (2010) and by Moore et al. (2010). Reviews on
virological taxonomy have been given by Fauquet et al. (2005)
(see also http://www.ictvdb.org/), on the taxonomy of fungi by
Hibbett et al. (2007) and Lutzoni et al. (2004) (see also http://
www.indexfungorum.org/), and of yeasts by Kurtzman et al.
(in press). Here we will focus on some aspects of bacterial
taxonomy.
Although the bacterial species concept is man-made and
subjective, microbiologists nowadays generally accept
a phylogenetic species concept (Stackebrandt et al., 2002;
Wayne et al., 1987) in which overall DNA relatedness
(measured by DNA:DNA hybridization) is crucial for species
delineation that must be supported by phenotypic differences
measured e.g. by a polyphasic study (Vandamme et al., 1996).
Although alternatives for this concept have been proposed (e.
g. by Staley, 2006), overall genome sequencing followed by
comparative analysis taking into account the common genome
content seems to support the bacterial species concept (Goris
et al., 2007; Konstantinidis and Tiedje, 2005).
An overview of all currently described bacterial species can
be found on the Internet (Euzeby: http://www.bacterio.cict.fr/).
New species names must be published in the International
Journal of Systematic and Evolutionary Microbiology (IJSEM)
before being valid. Over the past years, the number of described
species has increased enormously (Moore et al., 2010), mainly
due to the description of species encompassing one strain only.
This development is a matter of debate since the diversity of
those species is unknown, which makes it difficult to identify
isolates among them (Christensen et al., 2001).
5. Exchange of microbial materials among scientists
Outside BRCs, much greater numbers of strains are kept in
non-public collections, including those at universities and
other research institutes, companies and reference centers like
public health institutes. These collections have been set up for
special purposes and their existence depends on local policies
and considerations of the institutions that keep them,
including research targets of the institutions, resources and
facilities, or employment of scientists with particular interest
in certain microorganisms. Since these policies and consid-
erations may change over time, the long-term maintenance of
these collections is uncertain. The non-public collections are
usually part of a particular project or purpose, as can be the
case for reference institutes. Database management, storage
conditions and quality control measures of these collections
can differ considerably from those of BRCs. Awareness of the
existence of such collections follows from publications,
conferences, personal contacts, etc. Materials from these
collections can be requested by scientists wishing to verify
published results of these organisms or to perform other
research on these organisms. As discussed by Staley et al.
(2010), free exchange of materials by scientists has long
been practiced and is important both from a scientific and
ethical point of view. However, free exchange may not always
happen. For example, requests can be ignored or the corre-
sponding author replies that he/she no longer has direct access
to the material. Furthermore, the logistics and required
administration can make it difficult or impossible to comply
with requests for exchange. Apart from this, certain organisms
with important value for future publications or known or
likely commercial value (Reichman, J.H., Dedeurwaerdere, T.,
and Uhlir, P.F., unpublished data) will not always be
exchanged freely due to institutional policies or demands from
contributing scientists and/or collections who expect to have
a fair share of the benefits of commercial uses in recognition
of their contribution to the research on the organisms. Their
disposal will require formal material transfer agreements
(MTAs) (Staley et al., 2010).
To improve the accessibility of these special culture
collections and protect them against loss, several measures
could be taken:
- Holders (curators) of these collections should be stimu-
lated to report the existence of the collections at a given
(internet-based) platform, for example, set up with support
from national or international scientific societies.
- Holders (curators) of the collections (for example, the
scientists who brought the material together) should be
trained to comply as much as possible with those of formal
public culture collections. Initiatives like those supported
by the FP7 EU program (e.g. the EMbaRC eEuropean
Consortium of Microbial Resource Centers ehttp://www.
embarc.eu/) should be strengthened and national public
409L. Dijkshoorn et al. / Research in Microbiology 161 (2010) 407e413
culture collections might play a role in giving advice and
training.
- Governments, institutions and funding agencies should be
convinced of the importance of particular special purpose
collections and provide finances and conditions to main-
tain them.
- Standard MTAs should be designed by scientific agencies
and policymakers in order to decrease the administrative
costs for the scientists and culture collection managers in
dealing with case by case MTAs, and to provide sufficient
legal guarantees for maximum availability of the organ-
isms for further downstream research use (Reichman, J.H.,
Dedeurwaerdere, T., and Uhlir, P.F., unpublished data).
Altogether, a great effort needs to be made in the safe-
guarding of research or other special purpose collections
which are not formal BRCs.
6. A global microbial commons in practice
In the preceding paragraphs, we have discussed the
concept of a microbial commons and the required infra-
structure in terms of BRCs and ‘private’ culture collections,
an internet-based platform for exchange of data (Straininfo)
and well-defined taxonomies of the organisms involved to
realize its aims. In this section, we will discuss a number of
examples in agriculture and food microbiology in which
a microbial commons can play or is already playing an
important role.
6.1. Rhizobial symbiotic nitrogen fixation
Symbiotic nitrogen fixation is the main route for sustain-
able input of nitrogen into agro-ecosystems. In agriculture,
inoculation of legume crops soil with suitable rhizobia can
improve nitrogen fixation. Soybeans and forage legumes are
important nitrogen-fixing crops. Knowledge of the biodiversity
at large and of local populations of rhizobia is important for
the development of successful inoculation strategies. In
a review, Lindstro
¨m et al. (2010) discuss inoculation practices,
the biodiversity and classification of rhizobia and recent
insights gained from genome analysis of these organisms.
Taxonomically important strains (i.e. type strains and other
taxonomically relevant strains) are deposited in BRCs and can
be easily obtained. However, inoculant strains for agriculture
are not regularly deposited in culture collections, but are
maintained by companies or research institutes and not listed
in public databases which make them less accessible for
exchange. Furthermore, strains studied by taxonomists,
molecular biologists and those used for inoculation may differ
because of different importance for the users. A combined
effort to combine knowledge on biological nitrogen fixation
(BNF), taxonomy, population biology and genomics of
rhizobia might contribute to further development of the
rhizobial commons (Lindstro
¨m et al., 2010).
6.2. Biological control in agriculture
Artificial introduction of living microorganisms into the
environment to control a pathogen is another application of
microorganisms in sustainable agricultural systems. Species
belonging to different bacterial genera i.e. Bacillus,Pseudo-
monas,Agrobacterium and Streptomyces, have been registered
in the United States as biocontrol agents (Fravel, 2005).
A review of the role of fluorescent pseudomonads in biocon-
trol is given by Ho
¨fte and Altier (2010). These organisms can
increase plant growth and improve plant health, and occur in
soil and plant hosts worldwide. The genus Pseudomonas is
very diverse, with 128 species including the fluorescent
pseudomonads. There is no general congruence between
biocontrol mechanisms and phylogeny of strains. Screening of
isolates for biocontrol activity is usually done by testing large
sets of strains effective on local crops under local environ-
mental conditions. Reference strains from BRCs are required
as control strains to assess the taxonomic and phylogenetic
position of new field isolates and to test the specificity of
detection of pathogenic and beneficial pseudomonads.
Although there are dedicated BRCs mainly dealing with
plant pathogenic microorganisms and nitrogen-fixing organ-
isms, there are no culture collections exclusively specialized in
bacterial biocontrol agents. Altogether, both public and private
collections are important in the application and basic studies
of biocontrol agents.
6.3. Networks for the diagnosis of plant pathogens
Plant diseases are caused by a variety of microorganisms
including, amongst others, nematodes, viruses, bacteria and
fungi. These diseases can spread over wide geographic regions
with great consequences for national and international food
production and trade. Control methods can be performed to
prevent introduction, establishment or spread of the pathogens
and pests. In this context, the so-called quarantine organisms
are most important. In Europe, the European and Mediterra-
nean Plant Protection Organization (EPPO) is an intergov-
ernmental organization responsible for European cooperation
in plant health (see http://www.eppo.org/).
The diagnosis of the cause of the diseases is difficult and
requires extensive expertise and availability of a variety of
rapid and reliable detection methods. The problems and
challenges in this field are presented by Barba et al. (2010)
and illustrated by two examples (on Fusarium wilt of
banana and the sharka disease of stone fruits by the Plum pox
virus). Collections of plant pathogens are important to
preserve the variability of species in terms of pathogenicity,
virulence or metabolite and/or toxin production. Plant path-
ogen collections focused on plant health management (should)
provide a number of activities (Barba et al., 2010): (1) provide
reference material for diagnostics; (2) optimize and validate
protocols to detect plant pathogens; (3) screen crop for traits
that confer resistance to pathogens (here a role for national
reference centers seems more appropriate) using strains
endemic to the region; (4) perform analysis of the risk posed
410 L. Dijkshoorn et al. / Research in Microbiology 161 (2010) 407e413
by pathogenic strains. Identification of plant pathogens relies
first of all on national reference laboratories. If diagnosis
cannot be performed, collaboration with more advanced
laboratories should be sought. It is important that collections
house in their services advanced knowledge and expertise to
characterize plant pathogens and population variability and
develop appropriate tools for diagnosis and detection, to link
science to practical demands (Miller et al., 2009). Links
between collections are important for acquiring insight into
the variations of pathogens and develop appropriate tools for
their identification on a global scale.
6.4. Lactobacilli in food and feed production
Lactic acid bacteria form a heterogeneous group of bacteria
of great metabolic versatility which can be found in a variety
of ecological niches and which have been used for millennia in
food production. An overview of their taxonomy, diversity and
biotechnological applications is given by Giraffa et al. (2010).
Members of the genus Lactobacillus, the largest group of
lactobacilli, produce lactic acid by fermentation which causes
a rapid pH drop in raw material. Furthermore, they have
proteolytic activity and produce aroma compounds, bacterio-
cins and exopolysaccharides. Therefore, these organisms have
many applications in food preservation, as starters for dairy
fish, meat and vegetable fermentation, and in the production of
wine, beer and silage. They have also been proposed as pro-
biotics and microbial cell factories for the production of so-
called nutraceuticals, i.e. food or food products that provide
both health and medical benefits. Particular species, subspe-
cies or strains are used for specific purposes. For example,
Lactobacillus helveticus is used along with thermophilic lactic
acid bacteria in cheese manufacturing, while Lactobacillus
plantarum is used as silage inoculant. Genetic modification
and metabolic engineering are tools to obtain strains to be used
for special purposes (Giraffa et al., 2010). Exchange of isolates
between culture collections in different geographic areas may
extend the spectrum of useful strains for application in
biotechnology. Already, 25 sequenced genomes of Lactobacillus
species are in public databases, allowing functional genomics
studies to obtain insight into the metabolic potential of lacto-
bacilli. Results from these approaches are expected to reveal
characters of biotechnological importance. Next, strain collec-
tions can be screened for relevant markers and, hence, strains
selected for biotechnological applications (Siezen et al., 2004).
6.5. The preservation and distribution of yeasts
Like lactobacilli, the application of yeasts in fermentation
is related to the history of mankind (McGovern et al., 2004).
The applications of yeasts in the processing of food are
numerous and, globally, there is a wide diversity of yeasts
involved in these processes. Well-known examples of frequent
use of yeast fermentation are in bakeries, beverages, dairy
products and e.g. as protein, amino acid and vitamin sources in
animal feed (Daniel and Prasad, 2010). The global diversity of
yeasts in fermentation is largely unexplored, in particular in
Africa, Asia and Latin America, where fermentations are part
of traditional practices. Furthermore, many cultures used in
published studies of processing of staple food bases like cas-
sava have not been deposited with BRCs and are not available
to the biotechnical and scientific community (Daniel and
Prasad, 2010). Furthermore, a relatively small number of
well-documented species are widely used in food production,
as food additives and in agriculture. The role of BRCs to serve
as a repository and distribution center for yeasts is illustrated
by Daniel and Prasad (2010) who made an inventory of two
yeasts, the widely used Saccharomyces cerevisiae and
a specific beer brand using Dekkera bruxellensis. The high
number of cultures of S. cerevisiae in specialized and general
BRCs (w50,000 including 28,000 deletion mutants) empha-
sizes the biotechnological and economic importance of this
organism. The authors noted wide temporal gaps between
isolation, property description and eventual application of
strains, and they recommended long-term depositories.
7. New scientific challenges
7.1. Analysis of the microbial diversity in soil,
a metagenomics approach
The ocean and soil harbor the greatest microbial diversity on
the planet. It is generally estimated that less than 1% of the living
organisms on earth can be cultivated by current methods. The yet
unknown reservoir of microorganisms is expected to encompass
huge genetic and metabolic diversity. Analysis of this global
diversity with application of the most recent genomic and bio-
informatic approaches is a tremendous challenge. Benedetti and
Mocali (2010) have focused on the use of metagenomics to
study the entiregenome (the so-called metagenome) of soil biota
to discover novel species, genes and molecules relevant for
biotechnology and agricultural applications. An overview of the
most recent approaches in metagenomics is provided. The advent
of next-generation sequencing tools has considerably increased
the potential of metagenomics (Simon and Daniel, 2009).
Nevertheless, a number of obstacles have to be dealt with,
including the complexity of the microbial communities and the
difficulty in managing the large amount of genomic data
(Benedetti and Mocali, 2010).In response to the need to integrate
massive data sets of metagenomic information with biological
information, international genomic databases have been set up
which provide standardized data formats for simple retrieval and
computation by users. Although these initiatives are important
steps, Benedetti and Mocali (2010) plead for a combination of
scientific, technical, legal, institutional and normative efforts to
achieve an overall infrastructure linking microbial research with
genetic resources to explore the diversity and metabolic potential
of the soil biome.
7.2. Advances in extremophile research
Extremophilic organisms can inhabit ecosystems that are,
from a human perspective, extreme in the sense that these
systems have a very high or low pH, high or low temperature,
411L. Dijkshoorn et al. / Research in Microbiology 161 (2010) 407e413
high salinity, high pressure or combinations of these condi-
tions. These organisms can be found in the three domains of
life, Archaea, Bacteria and Eukarya, and are not only of
interest for their ability to live in particular extreme environ-
ments, like hot springs, but also for their biotechnological
potential. A well-documented example is the discovery of
Taq polymerase, the enzyme recovered from Thermus aqua-
ticus in a thermal spring (see also Staley et al., 2010) and so
successfully applied in the polymerase chain reaction. Isola-
tion of extremophiles and exploration of their biochemistry,
genetics and regulation of their metabolism to gain a better
understanding of their extremophilic life style is an important
area of research. Averhoff and Mu
¨ller (2010) discuss two
examples of adaptations of extremophiles to their environ-
ment. One example focuses on the molecular (regulatory)
basis of salt adaptation in halophiles upon exposure to
increasing osmolality, the other on the role of horizontal DNA
transfer as a means to adapt to extreme environments. The
authors argue that their findings have been obtained with pure
cultures and planktonic cells. Recent studies have revealed
that the organisms in nature live in biofilms, and gene
expression in biofilm-encapsulated cells is distinct from
planktonic cells. Further research will be focused on the
behavior of extremophiles and their interaction with the biotic
and abiotic environment. Altogether, research on extrem-
ophilic organisms, including their diversity and life style, is
a challenging field and, from the microbial commons and
biodiversity point of view, preservation of areas harbouring
these organisms is of great importance.
8. Final conclusions
There has been a dramatic increase in interest in commons
in the last 10e15 years, from traditional commons managing
the use of exhaustible natural resources by fixed numbers of
people within natural borders, to global information commons,
dealing with non-rival, non-excludible goods by a potentially
limitless number of unknown users. The emerging global
genetic resource commons fits somewhere in between, shifting
in the direction of information commons as digital-information
infrastructures which enable physically distributed commons
to be networked in virtual global pools.
As has been shown in the above review, the field of
microbial genetic resources is characterized by a strong and
lively commons-based innovation sector which has recently
been empowered by new digital means for distributed
collaborative research. Networking pools of genetic resources
in a global commons is needed to generate sufficient invest-
ment in the vast quantities of genetic resources that are
neglected because of their still unknown scientific and/or
unlikely commercial value. These neglected resources are the
building blocks for future scientific research and have enor-
mous value for sustaining biodiversity and local livelihoods.
However, the range of obstacles to full realization of the
new opportunities offered by global networking of genetic
resources is vast. This review discusses a set of measures that
are called for from a purely scientific perspective, such as
deposits upon publication or the deepening of common quality
management. Other major obstacles to be overcome are of
a legal, institutional and economic nature and are analyzed
systematically elsewhere (Dedeurwaerdere, 2006, 2010b;
Reichman, J.H., Dedeurwaerdere, T., and Uhlir, P.F., unpub-
lished data). The breadth of these obstacles shows the need for
appropriate organizational forms, legal arrangements and
social practices. These can help to better secure the global
microbial research community’s need to address issues of
common concern, such as global food security, global health,
biodiversity conservation and climate change. As discussed in
this paper, in response to these obstacles, governments, non-
profit organizations, global research communities and culture
collections have developed a range of initiatives for the
exchange of materials and information which have already
delivered important outcomes. The key issue is how to build
upon these incipient global microbial genetic resource
commons and place them on a solid scientific and institutional
basis.
Acknowledgements
Authors who contributed a paper to the Microbial Research
Commons special issue are gratefully acknowledged. The
authors gratefully acknowledge the financial support of the Food
and Agriculture Organization of the United Nations (PR 40621),
and Bioversity International (LoA 09/002) for organization of
the two expert workshops referred to in this introduction.
Further support for this research from the Belgian Science
Policy Division of the Ministry of Science under Grant IUAPVI/
06 and the support of the Sixth Framework Program in Research
and Development of the European Commission under Grant
RTD CIT3_513420 REFGOVare also acknowledged.
References
Averhoff, B., Mu
¨ller, V., 2010. Exploring research frontiers in microbiology:
recent advances in halophilic and thermophilic extremophiles. Res.
Microbiol. 161 (6), 506e514.
Barba, M., Van den Berg, I., Belisario, A., Feed, B., 2010. The need for culture
collections to support plant pathogen diagnostic networks. Res. Microbiol.
161 (6), 472e479.
Benedetti, A., Mocali, S., 2010. Exploring research frontiers in microbiology:
the challenge of metagenomics in soil microbiology. Res. Microbiol. 161
(6), 497e505.
Christensen, H., Bisgaard, M., Frederiksen, W., Mutters, R., Kuhnert, P.,
Olsen, J.E., 2001. Is characterization of a single isolate sufficient for valid
publication of a new genus or species? Proposal to modify recommenda-
tion 30b of the bacteriological code (1990 revision). Int. J. Syst. Evol.
Microbiol. 51, 2221e2225.
Daniel, H.-M., Prasad, G.S., 2010. The role of culture collections as an
interface between providers and users: the example of yeasts. Res.
Microbiol. 161 (6), 488e496.
Dawyndt, P., Dedeurwaerdere, T., Swings, J., 2006. Exploring and exploiting
microbiological commons: contributions of bioinformatics and intellectual
property rights in sharing biological information. Introduction to the special
issue on the microbiological commons. Int. Soc. Sci. J. 188, 249e258.
Dawyndt, P., Vancanneyt, M., De Meyer, H., Swings, J., 2005. Knowledge
accumulation and resolution of data inconsistencies during the integration
of microbial information sources. IEEE Trans. Knowledge Data Eng. 17,
1111e1126.
412 L. Dijkshoorn et al. / Research in Microbiology 161 (2010) 407e413
Dedeurwaerdere, T., 2006. The institutional economics of sharing biological
information. Int. Soc. Sci. J. 188, 351e368.
Dedeurwaerdere, T., 2010a. Global microbial commons: institutional chal-
lenges for the global exchange and distribution of microorganisms in the
life sciences. Res. Microbiol. 161 (6), 414e421.
Dedeurwaerdere, T., 2010b. Self-governance and international regulation of
the global microbial commons: introduction to the special issue on the
microbial commons. Int. J. Commons 4, 390e403.
Dedeurwaerdere, T., Iglesias, M., Weiland, S., Halewood, M., 2009. Use and
Exchange of Microbial Genetic Resources Relevant for Food and Agricul-
ture. Background Study Paper No. 46. Commission on Genetic Resources for
Food and Agriculture, Rome. On line at: www.fao.org/nr/cgrfa.
Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U., Ball, L.A. (Eds.),
2005. Virus Taxonomy, Eighth Report of the International Committee on
Taxonomy of Viruses. Elsevier Academic Press, Amsterdam.
Fravel, D.R., 2005. Commercialization and implementation of biocontrol.
Annu.Rev. Phytophathol 43, 337e359.
Giraffa, G., Chanishvili, N., Widyastuti, Y., 2010. Importance of lactobacilli in
food and feed biotechnology. Res. Microbiol. 161 (6), 480e487.
Goris, J., Konstantinidis, K.T., Klappenbach, J.A., Coenye, T., Vandamme, P.,
Tiedje, J.M., 2007. DNAeDNA hybridizationvalues and their relationship to
whole-genome sequencesimilarities. Int. J. Syst. Evol. Microbiol. 57, 81e91.
Hess, C., Ostrom, E., 2006. Understanding Knowledge as a Commons: from
Theory to Practice. MIT Press, Cambridge, MA, p. 4.
Hibbett, D.S., Binder, M., Bischoff, J.F., Blackwell, M., Cannon, P.F.,
Eriksson, O.E., Huhndorf, S., James, T., et al., 2007. A higher-level
phylogenetic classification of the Fungi. Mycol. Res. 111, 509e547.
Ho
¨fte, M., Altier, N., 2010. Fluorescent pseudomonads as biocontrol agents
for sustainable agricultural systems. Res. Microbiol. 161 (6), 464e471.
Janssens, D., Arahl, D.R., Bizet, C., Garay, E., 2010. The role of public bio-
logical resource centers in providing a basic infrastructure for microbial
research. Res. Microbiol. 161 (6), 422e429.
Konstantinidis, K.T., Tiedje, J.M., 2005. Genomic insights that advance the species
definition for prokaryotes. Proc. Natl. Acad. Sci. USA 102, 2567e2572.
Kurtzman, C.P., Fell, J.W., Boekhout, T. The Yeasts, a Taxonomic Study, fifth
ed. Elsevier, Amsterdam, in press.
Lindstro
¨m, K., Murwira, M., Willems, A., Altier, N., 2010. The biodiversity of
beneficial microbeehost mutualism: the cae of rhizobia. Res. Microbiol.
161 (6), 453e463.
Lutzoni,F., Kauff, F., Cox, C.J., Mclaughlin, D.,Gail, C., Bryn,D., Mahajabeen,P.,
David, H., et al., 2004. Assembling the fungal tree of life: progress, classifi-
cation, and evolution of subcellular traits. Am. J. Bot. 91, 1446e1480.
McGovern, P.E., Zhang, J.H., Tang, J.G., Zhang, Z.Q., Hall, G.R., Moreau, R.
A., Nunez, A., Butrym, E.D., et al., 2004. Fermented beverages of pre- and
proto-historic China. Proc. Natl. Acad. Sci. USA 101, 17593e17598.
Miller, S.A., Beed, F.D., Harmon, C.L., 2009. Plant disease diagnostic capa-
bilities and networks. Annu. Rev. Phytopathol. 47, 15e38.
Moore, E.R.B., Mihaylova, S.A., Vandamme, P., Krichevsky, M.I.,
Dijkshoorn, L., 2010. Microbial systematics and taxonomy: relevance for
a microbial commons. Res. Microbiol. 161 (6), 430e438.
OECD, 2001. Biological Resource Centres: Underpinning the Future of Life
Sciences and Biotechnology. In: Science and Technology Series. Organi-
zation for Economic Cooperation and Development, Paris.
Siezen, R.J., van Enckevort, F.H., Kleerebezem, M., Teusink, B., 2004.
Genome data mining of lactic acid bacteria: the impact of bioinformatics.
Curr. Opin. Biotechnol. 15, 105e115.
Simon, C., Daniel, R., 2009. Achievements and new knowledge unraveled by
metagenomic approaches. Appl. Microbiol. Biotechnol. 85, 265e276.
Stackebrandt, E., Frederiksen, W., Garrity, G.M., Grimont, P.A., Kampfer, P.,
Maiden, M.C., Nesme, X., Rossello-Mora, R., Swings, J., Truper, H.G.,
Vauterin, L., Ward, A.C., Whitman, W.B., 2002. Report of the ad hoc
committee for the re-evaluation of the species definition in bacteriology.
Int. J. Syst. Evol. Microbiol. 52, 1043e1047.
Staley, J.T., 2006. The bacterial species dilemma and the genomicephyloge-
netic species concept. Phil. Trans. R. Soc. 361, 1899e1909.
Staley, J.T., FitzGerald, K., Fuerst, J.A., Dijkshoorn, L., 2010. Microbiological
material exchanges among scientists. Res. Microbiol. 161 (6), 446e452.
Stalpers, J., Kracht, M., Janssens, D., Deley, J., Vandertoorn, J., Smith, J.,
Clause, D., Hippe, H., 1990. Structuring data for storage and retrieval of
information on bacteria in MINE, the Microbial Information Network
Europe. Syst. Appl. Microbiol. 13, 92e103.
Tindall, B.J., Rosello
´-Mora, R., Busse, H.-J., Ludwig, W., Ka
¨mpfer, P., 2010.
Notes on the characterization of prokaryote strains for taxonomic
purposes. Int. J. Syst. Evol. Microbiol. 60, 249e266.
Verslyppe, B., Kottmann, R., De Smeta, W., De Baets, B., De Vos, P.,
Dawyndt, P., 2010. Microbiological Common Language (MCL): a stan-
dard for electronic information exchange in the microbial commons. Res.
Microbiol. 161 (6), 439e445.
Wayne, L.G., et al., 1987. Report of the ad hoc committee on reconcilliation
of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37,
463e464.
Vandamme, P., Pot, B., Gillis, M., De Vos, P., Kersters, K., Swings, J., 1996.
Polyphasic taxonomy, a consensus approach to bacterial systematics.
Microbiol. Rev. 60, 407e438.
413L. Dijkshoorn et al. / Research in Microbiology 161 (2010) 407e413
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