Marine Fungal Diversity and Bioprospecting 2.5 Collection, Isolation, and Identification of Fungi 21
Part A | 2.5
Table 2.1 Key to the classes of fungi
S. No. Major classes
Key characters
1.
Zygomycetes
Hyphal filaments, usually one-celled, rarely septate usually multinucleate; aquatic species propagating by zoospores, terrestrial species by zoospores, conidia, or conidia-like sporangia; sex cells when
present forming oospores or zygospores
2.
Phycomycetes
Hyphal filaments, when present, multicellular, cell with one, two, or several nuclei, without zoospores,
with or without sporangia, usually with conidia; sexual reproduction absent or culminating in the
formation of asci or basidia
2a.
Ascomycetes
Sexual spores born in asci
2b.
Basidiomyctes
Sexual spores born in basidia
2c.
Fungi imperfecti
(Deuteromycetes)
Without a sexual stage in the life cycle, or with sexual stage rare or obscure; spores born on conidiophores, which may produced at random, in clusters, or within pycnidia
lationships but is rather a convenient scheme which
hinders exploration of marine fungi that might produce
microbial metabolites for therapeutic use. This necessitates the careful identification and selection of species
unique to a particular host before the high-throughput
screening of metabolites for desired industrial applications. Therefore, taxonomy of fungi is a formidable
challenge for most applications.
Fungal taxonomy is a dynamic, progressive discipline that consequently requires changes in nomenclature. The baseline of traditional fungal taxonomy and
nomenclature is morphological criteria or their phenotypes. Numerous alternative approaches have been
developed, including nutritional and physiological studies, serologic tests, secondary metabolites, and fatty
acids. Although some of these are very useful for
identifying poorly differentiated fungi such as yeast
and black yeast, in most cases they are only complementary tools of morphological data. The fungus
as a whole comprises a teleomorph (sexual state)
and one or more anamorphs (asexual states). Traditional fungal classification is possible when the fungus
is at its teleomorphic stage (asexual spore morphology also helps); however, the snag occurs in cases
of fungi where only the anamorphic stage is available. The dual modality of fungal propagation, i. e.,
sexual and asexual, has led to a dual nomenclature. The anamorph and the teleomorph generally develop at different times and on different substrates.
Species identification by morphological traits is often problematic because mycelial pigmentation, and
the shape and size of conidia, which are unstable
and highly dependent on the composition of media and environmental conditions. Further, subspecies
level of identification is usually based upon pathogenic
or physiological race reactions on a set of differential cultivars [2.74]. These processes of identification
of fungi are time consuming, labor intensive, and
subject to varying environmental or cultural growth
conditions during the experiments [2.75], and also
lead to inappropriate and unreliable application of
species [2.76].
Thus methods are needed to distinguish between
closely related species that occur in different habitats.
Hence, molecular techniques for fungal identification
and to investigate genetic variability within species
have been increasingly used during the last decade.
Molecular techniques based on polymerase chain reaction (PCR) have been used as a tool in genetic mapping,
molecular taxonomy, evolutionary studies, and diagnosis of several fungal diseases [2.77, 78].
Differentiation of the Fusarium species/subspecies
based on comparison of deoxyribonucleic acid (DNA)
sequences of the ribosomal DNA (rDNA) and internal transcribed spacer (ITS) regions have been reported [2.79, 80]. The sequenced rDNA region of F.
oxysporum (Accession no. JX 840353) isolated from
sediments of mangroves along the southeast Indian
coast covered the 18S ribosomal ribonucleic acid
(rRNA) gene, partial sequence; internal transcribed
spacer1; the 5.8S ribosomal RNA gene and ITS2; complete sequences; and the 28S ribosomal RNA gene,
partial sequence. In the constructed phylogenetic tree,
the strains F. oxysporum (GU205817), F. oxysporum
(EF495237), F. oxysporum (EF495230), and Fusarium
sp., (JF429684) have 98% similarity with the isolated strain F. oxysporum (JX 840353) [2.55] and 97%
similarity with Fusarium sp., (GU973787). Genotypic
identification of the 18S ribosomal RNA gene of endophytic Fusarium sp. isolated from leaves of Rhizophora
annamalayana has been analyzed (accession number
JN681281) and the fungus was found to be the closest
homolog to Fusarium moniliforme [2.34]. Ribosomal
RNA genes (rDNA) possess characteristics that are suit-
Part A | 2.5
Table 2.1 Key to the classes of fungi
S. No. Major classes
Key characters
1.
Zygomycetes
Hyphal filaments, usually one-celled, rarely septate usually multinucleate; aquatic species propagating by zoospores, terrestrial species by zoospores, conidia, or conidia-like sporangia; sex cells when
present forming oospores or zygospores
2.
Phycomycetes
Hyphal filaments, when present, multicellular, cell with one, two, or several nuclei, without zoospores,
with or without sporangia, usually with conidia; sexual reproduction absent or culminating in the
formation of asci or basidia
2a.
Ascomycetes
Sexual spores born in asci
2b.
Basidiomyctes
Sexual spores born in basidia
2c.
Fungi imperfecti
(Deuteromycetes)
Without a sexual stage in the life cycle, or with sexual stage rare or obscure; spores born on conidiophores, which may produced at random, in clusters, or within pycnidia
lationships but is rather a convenient scheme which
hinders exploration of marine fungi that might produce
microbial metabolites for therapeutic use. This necessitates the careful identification and selection of species
unique to a particular host before the high-throughput
screening of metabolites for desired industrial applications. Therefore, taxonomy of fungi is a formidable
challenge for most applications.
Fungal taxonomy is a dynamic, progressive discipline that consequently requires changes in nomenclature. The baseline of traditional fungal taxonomy and
nomenclature is morphological criteria or their phenotypes. Numerous alternative approaches have been
developed, including nutritional and physiological studies, serologic tests, secondary metabolites, and fatty
acids. Although some of these are very useful for
identifying poorly differentiated fungi such as yeast
and black yeast, in most cases they are only complementary tools of morphological data. The fungus
as a whole comprises a teleomorph (sexual state)
and one or more anamorphs (asexual states). Traditional fungal classification is possible when the fungus
is at its teleomorphic stage (asexual spore morphology also helps); however, the snag occurs in cases
of fungi where only the anamorphic stage is available. The dual modality of fungal propagation, i. e.,
sexual and asexual, has led to a dual nomenclature. The anamorph and the teleomorph generally develop at different times and on different substrates.
Species identification by morphological traits is often problematic because mycelial pigmentation, and
the shape and size of conidia, which are unstable
and highly dependent on the composition of media and environmental conditions. Further, subspecies
level of identification is usually based upon pathogenic
or physiological race reactions on a set of differential cultivars [2.74]. These processes of identification
of fungi are time consuming, labor intensive, and
subject to varying environmental or cultural growth
conditions during the experiments [2.75], and also
lead to inappropriate and unreliable application of
species [2.76].
Thus methods are needed to distinguish between
closely related species that occur in different habitats.
Hence, molecular techniques for fungal identification
and to investigate genetic variability within species
have been increasingly used during the last decade.
Molecular techniques based on polymerase chain reaction (PCR) have been used as a tool in genetic mapping,
molecular taxonomy, evolutionary studies, and diagnosis of several fungal diseases [2.77, 78].
Differentiation of the Fusarium species/subspecies
based on comparison of deoxyribonucleic acid (DNA)
sequences of the ribosomal DNA (rDNA) and internal transcribed spacer (ITS) regions have been reported [2.79, 80]. The sequenced rDNA region of F.
oxysporum (Accession no. JX 840353) isolated from
sediments of mangroves along the southeast Indian
coast covered the 18S ribosomal ribonucleic acid
(rRNA) gene, partial sequence; internal transcribed
spacer1; the 5.8S ribosomal RNA gene and ITS2; complete sequences; and the 28S ribosomal RNA gene,
partial sequence. In the constructed phylogenetic tree,
the strains F. oxysporum (GU205817), F. oxysporum
(EF495237), F. oxysporum (EF495230), and Fusarium
sp., (JF429684) have 98% similarity with the isolated strain F. oxysporum (JX 840353) [2.55] and 97%
similarity with Fusarium sp., (GU973787). Genotypic
identification of the 18S ribosomal RNA gene of endophytic Fusarium sp. isolated from leaves of Rhizophora
annamalayana has been analyzed (accession number
JN681281) and the fungus was found to be the closest
homolog to Fusarium moniliforme [2.34]. Ribosomal
RNA genes (rDNA) possess characteristics that are suit-