identification using rapid screening techniques
and objectives (1)
Filamentous fungi constitute an economically important group of micro-organisms,
primarily due to the wide variety of secondary metabolites they produce.
Many species have been identified and are routinely used in fermentation
technology and the food industry. Others are known to be agents of disease
in animals and plants. Species identified to date constitute a mere 1%
of all existing species. With an expansion in the use of genetically modified
organisms in the food and medical industries, an improved understanding
of fungal diversity is essential. It will enable development of rapid
and efficient screening techniques for studying fungal populations, will
aid in the identification of new species and will allow for the development
of specific probes which can be used to study "problematic"
and consolidate the current status of fungal identification, we initiated
a workshop, inviting international experts on mycology and molecular taxonomy,
with the aim of designing recommendations for fungal identification within
the European scientific and industrial communities.
(1) This project was a direct follow-on from EC project:
Assessment of methodology for the fast design of fungal DNA probes
and PCR tags (Concerted action BIOT-CT91-0301).
Approach and methodology
The "Fungal Identification Techniques" workshop was held in
Barcelona from April 5th-8th, 1995. Forty-three
scientists from academia and industry participated, coming from Spain,
Italy, Greece, Germany, Holland, England, Ireland, Sweden, Denmark and
the USA. A total of 31 talks were given, along with two round-table discussions
on "Fungal Identification Techniques Current Status"
and "Fungal Identification Techniques Application to Complex
Samples". All speakers contributed a paper to the proceedings of
the meeting, which have been published together with the recommendations
of the project group.
Main findings and outcome
One clear outcome of the workshop was that the requirements for fungal
identification are dependent on both the field of application and the
use of research (i.e. whether the aim is to improve human health, economise,
expand current knowledge of biology, or for financial gain).
In the food and fermentation industries, fungal identification requirements
can be separated into two main areas. Firstly, the detection of spoilage
and toxic organisms, (which is more often a functional detection than
an actual species identification), and secondly, to ensure quality control
of fermentation isolates, where identification is more differentiated
than simply identifying the species level.
Fungal identification in the pharmaceutical industry is necessary at a
level beyond that of species identification. This is to enable correct
naming prior to patenting, to ensure quality control of fungal products,
and to carry out efficient screening programmes, risk evaluations and
In the domain of human pathology, rapid fungal detection is more important
than precise species identification. Nonetheless, species identification
is crucial for the development of specific diagnostic kits. Furthermore,
very few relevant species have been identified, however with an increasing
number of immuno-compromised patients, a large number of novel species
are likely to become relevant.
In plant pathology, detection is substantially more complex than simply
identifying a species. This is due to the development by plant pathogens
of host range specificity, based on pathogenicity factors. Good identification
techniques are essential for the prevention of disease spread, particularly
with respect to quarantine regulations.
The overriding problem in the domain of ecology, is the lack of quantitative
and qualitative data describing the fungal population. This raises two
principal issues: firstly, that some organisms are non-culturable and
secondly, that some of the culturable fungi cannot be named using traditional
criteria, as they only produce mycelia under laboratory conditions.
This workshop was particularly informative, showing that a large number
of fungi have been, and continue to be incorrectly identified. It also
highlighted a clear need to train more classical taxonomists in both classical
skills and in the use of molecular techniques. In addition, a multidisciplinary
approach is necessary for correct fungal classification and consequent
fungal identification. The most promising approach for "fast"
nomenclature appears to be the use of ribosomal sequences. Furthermore,
some techniques, such as immunological methods and fatty acid profiles,
are best suited for detection or identification at a higher (i.e. genus)
level. It was also concluded that a concerted effort is required to ensure
that DNA sequences are made available through public databases, and that
a specific fungal database would be extremely useful. This research is
likely to be of benefit where genetically modified filamentous fungi are
used in industrial applications, such as when rapid identification of
potentially useful fungi is needed for quality control of mixed starter
cultures and detection of food pathogens.
Rossen L., Frisvad J.C., Dawson M.T. and Rubio V. (eds.), Proceedings
from the Workshop on Fungal Identification Techniques, Barcelona,
April 1995. Published by the European Commission, ISBN 92-827-5677-7.
of the project
September 1994 - September 1996
The workshop "Fungal Identification Techniques", Barcelona,
Universidad Autónoma de Madrid (ES)
Technical University of Denmark
University College Galway (IE)