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Biology of FUNgi

Lecture 1Diversity of fungi

Fungus of the day - Saccharomyces cerevisae

Taxonomy: Phylum (subphylum) Ascomycota Order - Saccharomycetales Family - Saccharomycetaceae

Importance: Eukaryotic micro-organism (rapid generationtime), pet organism for genetics (relatively small genomesize, easy mutant selection, haploid and diploid buddingstages), marvel of a molecular biology tool (yac),ferments glucose (CO2 in bread, alcohol)

Related organisms: Candida albicans (human pathogen),Dekkera sp. (spontaneous fermentation for beer),Kluyveromyces sp. (strains that produce enzymesremoving lactose from milk products) S. cerevisae buds from

multiple locations andleave distinct buddingscars

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In the works today (objectives)

• We motivate ourselves by looking into howdiverse and abundant fungi are

• Then, we will sincerely attempt to confuseourselves with the fact how little we knowabout fungi

Fungi are everywhereInsects (1,000,000 species)and plants (250,000species) may be mostnumerous by record. Fungieasily take the third placewith 74,000 species.

Let’s build an argumentwhy fungi may actually bemore numerous than eitherof these groups.

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• In bacterial systems, as little as 1-5 % ofthe true, resident diversity is detected byconventional methods that rely ongrowing bacteria on pure culture media.

• Usually, direct molecular methods detectgreater diversity.

• Some of this diversity is often comprisedof “new organisms” which may representhigher taxa (phyla, divisions, orders).

How many species of fungi may exist?

Num

ber

of

bact

eria

Culturable Non-culturable + culturable

Detectedmolecularly

Detected bypure culturing

• Let’s look into a couple of potentialsources of fungal diversity

– In U.K., in an extensive botanical andmycological survey, it was estimatedthat for each species of plants there areca. 6 species of fungi

– 6 x 250,000 plants = 1,500,000 fungi– These studies focused on known

macroscopic and microscopic fungi,i.e. they may not have included all thatexist.

How many speciesof fungi may exist?

Num

ber

of

fung

i

Known Estimated total

Estimated taxa1.5 x 106

(5 x 105 – 9.9 x106)

Describedtaxa 7.4 x104

9.9 x106

5 x 105

Fungi are common endophytes ofplant root sand leaves

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• Let’s look into a couple of potentialsources of fungal diversity

– How about insects? Many flies carry asocial disease.

– If we assume that even half of theinsects (500,000) would have uniquefungi associated with them, we wouldarrive at some 500,000 fungal species.

How many speciesof fungi may exist?

Num

ber

of

fung

iKnown Estimated total

Estimated taxa1.5 x 106

(5 x 105 – 9.9 x106)

Describedtaxa 7.4 x104

9.9 x106

5 x 105

Laboulbenia spp are social diseasesof insects

• No matter how you look at it, numberof described taxa (74,000) is minusculeto estimated potential number offungal species 500,000 or 1,500,000.

• The number of estimated taxa varieswidely, but working hypothesis of 1.5 x106 has been proposed (Hawkswort,2001).

• This means that only ca. 5% ofexisting taxa are known and described.

• Are these estimates reasonable?

How many speciesof fungi may exist?

Num

ber

of

fung

i

Known Estimated total

Estimated taxa1.5 x 106

(5 x 105 – 9.9 x106)

Describedtaxa 7.4 x104

9.9 x106

5 x105

Laboulbenia spp are social diseasesof insects

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An Australian study on fungal diversity

• Collect truffles in southeastern Australia and recordnumber of species

• Let’s look why the trufflesare important

Chamonixia vittatispora -a basidiomycete truffle

Hydnoplicata whitei -an ascomycete truffle

Why are these truffles important – somemarsupials depend on truffles

Long-nosed potoroo (Potorous sp.)

Brown Bandicoot (Isoodon obesulus) Swamp wallaby (Wallabia sp.)

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Fungivory or mycophagy is not just a “down-under” anomaly

California red back vole (Clethrionomyscalifornicus) andnorthern flying squirrel (Glaucomyssabrinius) are North American examplesof fungivorous animals

So, animals eat truffles. What do the trufflesget in return?

Most truffles emit odors that animalsfind attractive

More rarely, the truffles mimic the foodsupply: Paurocystis pila and Weraroaerythrocephala mimic Podocarpus coneseaten by the kiwi-bird

Chamonixia vittatisporasmells like dog poop

Paurocystis pila andWeraroaerythrocephala looklike Podocarpus cones

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So, animals eat truffles. What do the trufflesget in return?

Animals that consume the trufflesunknowingly stratify the fungal spores intheir gut and disperse them with theirfeces

Some have developed clever aerialdispersal mechanisms

Elaphomyces sp.disperses aeriallyonce the sterileouter core is eaten

Mesophelliaceae are even moreclever than Elaphomyces spp.:animals need to get to the innersterile tissue through the sporemass

Predators candisperse spores evenlonger distances

In this Australian study...

• 209 different truffle species, only 57 species hadbeen previously described

• almost 75 % of all the species found were new orpreviously unrecorded

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• Study of Arrhenatherum roots; 7 of49 phylotypes 99% similar toGenBank rDNA sequences(Vandenkoornhuyse et al. 2002)

• In other words, 42 out of 49 detectedtaxa (85%) were novel as far asexisting sequence data goes.

• In this study, novel lineages (likenew BIG groups) were detected.

Non-culturable fungi?

• A study at Konza Prairie in Kansasconfirms the novel groups, new groupsnot detected in the previous studywere seen in the Prairie soil.

• In conclusion, there are a few possiblesources of new fungi that have notbeen detected as of now. The number74,000 seems an underestimate.

Locally, similar observations Soil_01_11.txtSoil_02_08.txtSoil_05_07.txtRoot_09_10.txtSoil_01_16.txtSoil_02_06.txtSoil_05_19.txtSoil_10_13.txtSoil_01_10_CHIMER.txt

Soil_05_12.txtSoil_07_02.txtSoil_05_09.txtSoil_01_01.txtEupenicillium_javanicum[U21298]Root_07_19.txtPenicillium_expansum[AF218786]

Soil_03_06.txtCapronia_pilosella[U42473]Root_03_20.txtCeramothyrium_linnaeae[AF022715]Soil_01_03.txtHalosarpheia_retorquens[AF050486]Petriella_setifera[U43908]Soil_03_13.txtRoot_01_12.txtFusarium_merismoides[AF141950]Soil_11_10.txtClaviceps_purpurea[AF281178]Neurospora_crassa[X04971]

Sordaria_fimicola[X69851]Soil_07_08.txtRoot_09_16.txtSoil_01_02.txtPhyllachora_graminis[AF064051]Root_11_11.txtSoil_01_14.txt

Soil_07_10.txtSoil_03_15.txtSoil_10_04.txtSoil_10_10.txtOphiostoma_stenoceras[M85054]Magnaporthe_grisea[AB026819]Root_03_17.txt

Soil_02_11.txtBlumeria_graminis[AB033476]Sphaerotheca_cucurbitae[AB033482]Byssoascus_striatosporus[AB015776]Oidiodendron_tenuissimum[AB015787]Pseudogymnoascus_roseus[AB015778]Root_09_15.txtBulgaria_inquinans[AJ224362]Scutellinia_scutellata[U53387]Soil_02_17.txtRoot_09_17.txtCaloscypha_fulgens[U53374]Root_09_20.txtRoot_10_03.txtSoil_03_05.txtRoot_02_08.txtLeptosphaeria_bicolor[U04202]

Alternaria_longissima[AF229511]Soil_01_19.txtRoot_02_05.txtSaccharomyces_cerevisae[Z75578]Torulaspora_delbrueckii[X98120]Candida_psychrophila[AB013528]Arxula_adeninivorans[AB018123]Soil_01_07.txtSoil_01_12.txt Root_01_13.txtRoot_01_18.txtRoot_01_02.txtLycoperdon_sp.[AF026619]

Entoloma_strictius[AF287832]Root_04_14.txtRoot_07_06.txtRoot_08_13.txtSoil_05_03.txtRoot_02_09.txtSoil_10_03.txt

Soil_02_19.txtSoil_07_09.txtSoil_07_19.txtSoil_10_11.txtTricholoma_myomyces[AF287841]Crucibulum_laeve[AF026624]Hygrophorus_sordidus[AF287834]

Inocybe_geophylla[AF287835]Root_06_02.txtSoil_07_07.txtSoil_09_13.txtRoot_06_06.txtClavaria_acuta[AF184180]Clavaria_zollingeri[AF184182]Soil_04_13.txtSoil_06_05.txtSoil_04_06.txt

Soil_10_19.txtRoot_01_14.txtBoletus_satanas[M94337]Paragyrodon_sphaerosporus[M90826]Xerocomus_chrysenteron[M94340]Rhizoctonia_solani[D85643]Thanatephorus_praticola[M92990]Auricularia_auricula-judae[L22254]Auricularia_polytricha[L22255]Root_01_11.txt

Tilletiopsis_fulvescens[D83189]Ustilago_hordei[U00973]Bensingtonia_phylladus[D38237]Soil_01_15.txtUredinopsis_intermedia[AB011018]Root_11_09.txtRoot_10_15.txt

Soil_05_18.txtNeolecta_vitellina[Z27393]Taphrina_deformans[U00971]Root_01_07.txtGigaspora_gigantea[Z14010]Scutellospora_pellucida[Z14012]Acaulospora_spinosa[Z14004]Glomus_proliferum[AF213462]Root_03_02.txtSoil_05_05.txtDissophora_decumbens[AF157133]Mortierella_alpina[AJ271630]Mortierella_wolfii[AF113425]Endogone_pisiformis[X58724]Spizellomyces_acuminatus[M59759]Corallochytrium_limacisporum[L42528]

Asc.

Bas.

Zyg.Chy.

Putative chimeric sequenceNon-chimeric sequence

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To sum up...

• We know of ca. 74,000 species. This is likely anunderestimate.

• Extrapolation methods estimate 500,000 to9,900,000 species.

• Arriving at a consensus of 1,500,000 speciesinvolved multiplication number of known plantswith estimated number of fungi associated withaverage plant species.

• Insects are a story of their own.