Memorandum submitted by the Society for
General Microbiology
ABOUT THE
SOCIETY FOR
GENERAL MICROBIOLOGY
The Society for General Microbiology (SGM) was
founded in 1944/1945 and is now the largest microbiological society
in Europe. It has over 5000 members of whom 75 per cent are in
the UK. The remainder are located in more than 60 countries throughout
the world. Most members are qualified to PhD; MB ChB or equivalent
level. There are 1000 postgraduate student members and 450 schools
are corporate members.
The Society provides a common meeting ground
for scientists working in academic centres and in a number of
fields with applications in microbiology, such as medicine, dentistry,
veterinary medicine, pharmaceuticals, numerous industries, agriculture,
food and beverages, the environment and education. The main activities
of the Society are organizing scientific conferences, publishing
learned journals, promoting microbiology education and careers,
and promoting understanding of the importance of microbiology
to government, the media and the general public.
The Society is governed by a Council of 24 comprising
appointed officers and representatives elected by the membership.
Its headquarters office has a staff of more than 30 and an annual
turnover in excess of £3.5m.
SYSTEMATICS AND
TAXONOMY OF
MICRO-ORGANISMS:
MORE DIFFERENCES
UNDER THE
SUN THAN
MEET THE
EYE
The science of microbiology covers a great diversity
of life forms: disease-related molecular structures such as prions
and viruses; archaea, bacteria, fungi, protozoa and microscopic
algae. Microbiology is important because:
— Microbes represent a greater proportion
of the biomass on the planet than plants and animals combined,
and exist in a wider range of environments, such as deep within
the Earth's crust, where plants and animals are absent.
— Microbes are crucial in a number
of processes affecting all life on Earth: the cause and control
of disease; fertility of soils and aquatic environments; nutrient,
gas and mineral cycling; fermentation; biodegradation of waste
materials and dead biomass; food and drink production; bioprocessing
steps in drug and antibiotic production, and molecular biotechnology.
Life on this planet would grind to a halt without micro-organisms.
Extend this to "derived prokaryotes" and we have mitochondria
and chloroplasts as essential components of eukaryotic cells.
— Changes in microbial-influenced processes
such as CO2 and CH4 cycling will potentially play significant
or dominant roles in determining the effects of climate change.
An examination of the systematics and taxonomy
of microbes provides a number of fascinating contrasts with the
state of knowledge and development for plants and animals. Because
plants and animals are visually and practically so much more accessible,
and have inherent attractiveness to amateur enthusiasts, the general
public and indeed the entertainment industry, they have been studied
far more than the Earth's microbes. It's easier, and to many more
pleasant, to do it with the butterflies and buttercups, than it
is with the bugs (in the microbiological rather than entomological
sense of the word). And for a number of reasons, it has been easier
to develop systematic research and theory with the larger organisms.
However, given the importance of microbes in controlling global
processes, and the fact that they have been doing so for 3.5 billion
years, this is an imbalance that should be considered when allocating
resources to future research.
Some key contrasts between the systematics of
microbes and other organisms are now listed. Most of these refer
to prokaryotic microbes (Archaea and Bacteria),
but many of the points made are relevant to the numerous types
of eukaryotic micro-organisms, especially the diverse groups encompassed
by the term "fungi". The viruses are another world of
complexity and diversity in their own right,
— The number of prokaryotic species
isolated, described and validly named within the rules of the
International Code of Nomenclature of Prokaryotes, currently
ca 7,000, is vastly smaller than the numbers of species known
for plants and animals. For example, more than 1,000,000 species
of insect have been described and named; more than 20,000 orchids.
— However, the number of prokaryotic
species remaining to be discovered is immense. Modern methods
of DNA analysis (eg "gene dredging") indicate that probably
99 per cent or more of prokaryotic species are out there, probably
doing very important things in their ecosystems, but as yet uncharacterized.
In contrast, it is likely that for many well-studied groups of
plants and animals, the majority of existing species have already
been described.
— Many of these unknown prokaryotic
organisms form lineages containing no named or well-studied member.
Many of these groups would be at the level of order or higher
in animal or plant taxonomy: there is at least one lineage (the
Korarchaea) equivalent to Kingdom level containing no known cultivar.
— The overall biological diversity
of the micro-organisms (prokaryotic plus eukaryotic), as measured
by molecular methods, is immensely greater than that of the higher
plants and animals. See for example the three domain model for
the universal tree of life, pioneered by Carl Woese, where higher
plants and animals represent small, recent branches.
— The "species" concept for
prokaryotes is quite different from that for plants and animals,
and much more a matter of debate. If the current pragmatic definitions
of prokaryotic "species" such as Escherichia coli,
based on DNA hybridization were applied to animals, then arguably
all of the Insecta would be in a single species, as would
humans, chimpanzees and lemurs in another.
— Characterization and naming the as
yet undescribed species of prokaryotes is hindered by the fact
that many of them can be difficult to isolate and grow in pure
culture for further study; indeed many may only grow in complex
communities with other organisms and substrates. Their existence
can be detected, and biodiversity quantified, by sequencing techniques,
but there is a major block in moving them up to the next stage
of taxonomic description and systematic analysis.
— Morphological diversity of Prokaryotes
is very limited, compared with that of Eukaryotes. This has perhaps
led to an anthropocentric perception that the Prokaryotes are
less interesting. However, the physiological and metabolic diversity
of the Prokaryotes far exceeds that of the plant and animal worlds.
The physiology of plants and animals is mainly limited by oxygenic
photosynthesis and aerobic respiration respectively, whereas a
tremendous metabolic diversity is found in the different groups
of bacteria. They include aerobic and anaerobic chemo-organotrophs,
able to degrade just about any naturally occurring organic compound
on Earth, different types of photoauxotrophs (oxygenic as well
as anoxygenic) and photoheterotrophs, and chemolithotrophs that
obtain their energy from the oxidation of reduced inorganic compounds.
— Descriptions and names of new species
of plants and animals are published in hundreds of journals, which
has lead to much fragmentation and duplication. In contrast, the
great majority of new prokaryotic species are published in a single
journal, the International Journal of Systematic and Evolutionary
Microbiology (IJSEM). Furthermore, where new prokaryotic species
are published in other journals, the names of the new species
must be validated by publication in IJSEM, with checks
that rules for description of new species and deposit in culture
collections have been complied with. The title is formally owned
by the International Committee on Systematics of Prokaryotes.
IJSEM is published by the Society for General Microbiology
on behalf of ICSP, as a service to the international prokaryotic
and microbial eukaryotic systematics community. It should be recognised
that the journal's highly experienced editorial staff make a major
contribution to the quality and consistency of descriptions of
new taxa, and that this is ultimately funded from income to the
journal from institutional subscriptions. The journal currently
operates at close to break-even point financially, although when
SGM took it over as publisher it made a significant loss. Current
moves by major research funders such as NIH, the Wellcome Trust
and Research Councils UK, to require journals to make articles
"open access" at the time of publication for work they
have funded, sometimes in exchange of an author-side payment,
could impact adversely on journals such as IJSEM, where
authors generally do not have sufficient grant funding to support
such author-side payments.
RESPONSES TO
SPECIFIC QUESTIONS
RAISED BY
THE INQUIRY
1. What is the state of systematics research
and taxonomy in the UK?
As a central resource, IJSEM provides
a ready source of accurate statistical information about the level
of prokaryotic systematics research in the UK. In the years 2000-2002,
some 8-9 per cent of papers had corresponding authors from the
UK. By 2007 this had fallen to 2 per cent. Examination of the
January 2008 issue of IJSEM showed that only two papers
describing new species came from UK laboratories. Perhaps more
notably, of the 55 papers describing new taxa emanating from laboratories
overseas, not a single one had a UK co-author.
The message is quite clear, that the number
of active prokaryotic taxonomists in UK institutions is declining.
Specifically, two very active (and internationally renowned) university
groups have been lost in recent years, one due to retirement of
the group leader, and one due to the group being disbanded because
of suspected RAE pressures.
A professor of systematic bacteriology at another
UK university comments:
"A fair number of eminent prokaryotic systematists
based in the UK are contributors to the world's most highly respected
reference text upon the subject—Bergey's Manual of Systematic
Bacteriology (publishing between 2001 and 2009); this demonstrates
considerable UK interest and expertise in the field, a field that
is much better regulated in terms of its proposal of new taxa
and emendations, and its regulation of nomenclature, than are
other areas of biology.
However, few young bacteriologists working within
systematics at present will be able to contribute to subsequent
editions of the Manual, or to other works or bodies in
this field, because the emphasis in training now has to be upon
techniques to be learned, rather than upon the organisms that
they may be applied to, and so the long-term study of a genus
or species for its own sake appears to be a thing of the past;
we therefore no longer have a generation of prokaryote systematists
growing up with the knowledge and experience of individual groups
of organisms. This is not just a problem for the UK, but it is
acutely felt here on account of many years of underfunding. As
a result, publications from UK scientists are dwindling at an
alarming rate. Most students working on systematics in my laboratory
are from overseas, often from outside the EU, and all my funding
comes from outside the UK.
This loss of expertise is a most worrying matter,
as the UK will lose what little presence it has in what is now
becoming a more widely appreciated field—for example, a
systematic approach to Mycobacterium tuberculosis and its
relatives, and an understanding of these organisms' relationships,
has a key role in our progress in understanding and controlling
tuberculosis. Knowing how to diagnose and treat the individual
patient has never been enough, and currently this shortcoming
is repeatedly emphasised. In addition to natural diseases, we
also now have major concerns over biosecurity and bioterrorism,
where this increasing need for prokaryote systematists also applies."
2. What is the role of systematics and taxonomy||.how
do they contribute to research areas such as biodiversity, ecosystem
services and climate change?
The importance of microorganisms in the biodiversity
and ecological stability of this planet is undisputed and acknowledged
by acclaimed zoologists such as E.O.Wilson. We know very little
about the prokaryote species diversity within the UK and we know
virtually nothing about their roles on maintaining habitats favourable
for plant and animal communities. The fact that they are not visible
does not mean that they do not play a crucial role. Recent work
in agricultural areas, for example, indicates how the compacting
of soil can be monitored by the change in the microflora in favour
of anaerobes. Changes in the way fields are fertilised will also
cause changes in the microflora and influence the plant and animal
communities.
Changes in microbial communities and their activities
are likely to be critical in Earth responses to climate change.
Examples include CO2 fixation by phytoplankton, release of fixed
CO2 from soils by microbial activity, and release of methane.
Studies of all of these processes depend on an understanding of
what microbial communities are involved.
3. Does the way in which systematics research
is organized and coordinated best meet the needs of the user community?
The recommendations by the UK government in
the last report do not seem to have done anything for the acute
problems in prokaryote systematics. Supplying extra funding to
specialist units does not solve the problem in prokaryote systematics,
because such units currently do not exist in prokaryote systematics.
There are no equivalents to the NHM, RBG Kew or the RBG Edinburgh
in the area of prokaryotes. Equally well there are far too few
scientists active in either universities or other research establishment
with an appreciation/experience in prokaryote systematics to provide
an effective lobby for prokaryote systematics within the UK. The
situation in other European countries varies from marginally better
to significantly worse.
4. What level of funding would be needed to
meet the need for taxonomic information? Who should be supplying
it?
Prokaryotic systematics has different requirements
in terms of infrastructure and funding to those perceived as important
in botany and zoology. As such, solutions tailored to meet the
needs of botany and zoology do not solve problems in prokaryotic
systematics.
It is perceived that the current UK Research
Assessment Exercise has led to a concentration on a smaller number
of areas of research that can be published in high impact factor
journals, to the detriment of those engaged in long-term scholarship
in specialized fields. UK research funders should recognize the
value of systematics and taxonomy, which apart from their own
scientific merit, underpin so many other research areas.
The long-term financial stability of culture
collections is critical not only for microbial systematics and
taxonomy, but also for their service to wider areas of research
and industry. There has been long-term failure to invest properly,
which has endangered the quality of the service on offer, and
failure to appreciate the underlying value of systematics. One
may cite the recent issues concerning the use of the wrong cell
lines in cancer research as examples of inadequately maintained
and verified primary biological material in research institutions/universities,
and the dangers of uncoupling from important secondary information.
The costs associated with maintaining verified collections are
often seen as being too high, but are negligible when compared
with the costs associated with entire research programmes based
on incorrect biological material."
5. How does funding in other countries compare?
Again, IJSEM provides some interesting
statistics. The number of papers published from South Korea increased
from 10—15 in 2000—2002, to 140 published in 2007.
This was the result of a major research programme funded by the
Korean Government to discover and characterize new bacterial species
in Korean environments. There have also been significant increases
in papers published from China, Japan and India.
6. What impacts have developments in DNA sequencing,
genomics and other new technologies had on systematics research?
These developments have revolutionised the science
of prokaryotic systematics. New and relatively inexpensive sequencing
and related technology has increased the rate of characterization
of new taxa, and the molecular approach has led to radical new
thinking about the structure of the tree of life, and the early
evolution of life on Earth. In some ways, a gap is opening up,
in that the other taxonomic information required as part of the
description of new species has still to be collected, accurately,
and this is more dependent on experienced "wise heads"
than on automated technology.
Nowhere is the gap more clearly shown that where
"gene dredging" can indicate millions of new bacterial
species in particular environments, but where completing proper
taxonomic descriptions for all but a few would be an enormous
task.
The use of gene-based systems has helped to
crystallise our appreciation of prokaryote diversity, but it has
not solved the problem alone. Co-relation with other data was
a significant factor some 30 years ago and provided a widely based
system, with a greater chance of it being stable on the long-term.
The availability of full genomes potentially opens the way to
understanding individual strains completely. However, we already
know that transcriptomics and proteomics are already necessary
to complement this area. Other topics will follow, that require
an in-depth appreciation of cellular structure, function and organisation.
Genomics alone cannot achieve this goal.
7. Does the way in which taxonomic data is
collected, managed and maintained best meet the needs of the user
community? What is the state of local and national recording schemes?
Prokaryote diversity is rarely tackled at this
level, although there is no reason why this should not be the
case.
8. What is the role of the major regional
museums and collections?
We know of no microbial taxonomy being undertaken
in any regional museum and no prokaryotic taxonomy in any museum.
The role of the culture collections is crucial to disseminate
strains and provide continuity between short-term research projects
in (typically university) research laboratories.
The major collections in the UK continue to
be hit by reductions in financial support. As such their contribution
to taxonomy hit an all time low some years ago, from which they
have not been able to recover. One should also qualify the fact
that "major" in terms of collections of micro-organisms
in the UK means no more than 10 staff (often significantly less).
9. What progress has been made in development
of a web-based taxonomy?
The internet plays an increasingly important
role in microbial systematics given the central role that molecular
data play. Major culture collections also make their catalogues
web-accessible and some journals (notably those of the SGM and
the American Society for Microbiology) make their journals open
access after a one-year commercial period. SGM is currently providing
funding for the entire back archive of IJSEM and its predecessors,
back to 1946, to be digitized and made freely available to all
on the internet.
There are microbial components to initiatives
such as the Tree of Life <http://www.tolweb.org> but there
is no co-ordinated push to develop a web-based taxonomy. Prokaryote
systematics is largely defined by Bergey's Manual <http://www.bergeys.org>
which is published by a Trust whose income is derived from sales
of the resulting books. There is no obvious business model to
transfer this resource to the web as current academic web servers
(including JANET in the UK) currently prohibit advertising to
generate a replacement revenue stream.
Prokaryote taxonomy and nomenclature has played
a pioneering role in a number of web-based areas, dating back
to the late 1960s. mid 1970s, largely without any significant
funding and dependant upon one or two dedicated individuals. However,
much of this was done in the past and due to the current flood
of data cannot continue on this basis. The pioneering work has
included:
— the compulsory registration of all
new names and combinations from 1.1.1980
— the setting up of web based sites
reflecting the registered names as well as indication of synonymies,
location of type material, etc., such as
http://www.dsmz.de/microorganisms/main.php?contentleft_id=14
http://www.taxonomicoutline.org/
http://www.bacterio.cict.fr/ This excellent website,
a listing of bacterial names with standing in nomenclature, was
set up and is maintained by Jean Euz
by, who also pioneered the listing of names and taxonomic
opinions on the web. It is hosted and supported by SGM through
IJSEM.
— The IJSEM serves as the central
registry for all names and a current project (Names 4 Life) will
attempt to extract taxonomically relevant information from the
manuscripts submitted using a markup language. Further and more
rapid progress in this area of prokaryote systematics is largely
hampered by lack of funding to meet the needs of the end users,
who are microbiologically orientated and are currently not served
by initiatives such as GBIF, EoL, GTI, etc.
— SGM is a supporter and research partner
in the Names4Life project.
Online catalogues for the major collections,
listing their holdings, have been implemented rapidly in the early
to mid-1990s and data set standardisation tackled early on among
European collections via the MINE project. The European collections
have also pioneered close co-operation, which has resulted in
the CABRI and EBRCN projects.
On a global scale the establishment of the World
Data Centre (WDC) and World Federation for Culture Collections
(WFCC) have played pioneering roles in listing and linking the
global culture collection community, which were also closely tied
to the International Committee on the Systematics of Prokaryotes,
all of which are now web-based.
The prokaryotic community invented the registration
of names and have shown that (within limits) it works. It was
set up without major funding and continues to operate on this
basis, but the failure to invest in the system could eventually
result it its demise.
10. What needs to be done to ensure that web-based
taxonomy is of high quality, reliable and user-friendly?
A web-based taxonomy depends on the availability
of experts, both in the way the Code works and in the way taxonomic
information is handled. The number of Code experts world-wide
has always been small in prokaryote systematics, but at present
there are 3 active experts, all of whom are between 50-60 and
none are resident in the UK. Without experts in the relevant areas
a web-based system cannot fulfil a long-term function. This is
evident in web-based systems that do not draw on the available
expertise and are starting to swamp the accurate sites with contradictory
and inaccurate information. The lack of scientists trained in
this area also has a major impact on the role of peer review of
the original articles. The effect is a dangerous spiral where
inaccurate information can be perpetuated and added to because
expertise is lacking to evaluate the original work properly.
11. How does the taxonomic community engage
with the non-taxonomic community? What role do field studies play?
In the sense of field studies as undertaken
in botany and zoology, microbiology often takes a different approach.
However, even clone libraries and metagenomic studies require
an underlying taxonomy on which to base their identification.
Given the vast number of prokaryote taxa that have yet to be described
one is often left with vague identifications that rely solely
on per cent sequence similarities of the 16S rDNA gene, with little
to no information on what the organisms is, nor what it is actually
doing in the environment:
12. What are the number and ages of trained
taxonomists working in UK universities and other organizations?
"Can't answer this one, but does one need
more than two hands to count them!"
See also comments on other questions.
13. What is the state of training and education
in systematics and taxonomy? Are there gaps in capacity? Are the
numbers in training enough to meet current and future needs?
In order to teach systematics or taxonomy an
important pre-requisite is that one should have at least some
training in that area oneself. Traditionally there have been very
few centres in the UK where such qualified staff could be found.
However, their students have rarely found suitable positions in
UK establishments, with the consequence that as these experts
retire they are leaving a vacuum. The consequences are that with
the short term lack of interest in systematics/taxonomy there
is no perceived need for such trained individuals. However, discussions
are already underway that highlight that there is a desperate
need for experts that understand and appreciate where the current
deficits are. If the present decline continues one need not consider
the future, because there will not be one.
CONCLUSION
Prokaryote systematics has always been a poor
relation to botanical and zoological systematics—no David
Attenborough-type programmes on television or radio, or glossy
magazine articles, are devoted to the microbes, and no member
of the public or any politician is likely to be aware of this
fundamental part of the biosphere on a day-to-day basis. Who will
weep when a bacterium becomes extinct, and how will we know that
it has happened? Does the average biologist—or politician—appreciate
the fact that our body harbours ten to 100 times more microbial
cells than our own human cells, or that the healthy development
of the human gut is highly dependant upon an amazing consortium
of microorganisms that may be composed of as many as 800 different
species?
The public perception of bacteria is little
better than the ill-informed and demeaning media and advertising
images that "all germs are bad", or, at best, that there
are "good" and "bad" bacteria. As part of
the overall drive to improve the nation's health, some better
understanding than this is vital, and bacterial systematics and
taxonomy is a fundamental part of any such educational advance;
without it, it is akin to attempting to teach a language without
a vocabulary. And again, don't forget the amazing diversity of
viruses.
The last House of Lords Science and Technology
Committee report did not address the viral and prokaryote systematics
and taxonomy issue adequately; it is a matter that needs to be
addressed specifically, because its moribund state will not be
resolved by measures that consider only the larger forms of life.
Indeed, a holistic approach that considers each special part of
the biosphere is the approach that is most likely to be efficient
and effective in terms of conservation and human knowledge.
4 February 2008
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