Should we do fruit-body inventories,
sequencing, or both?
Otso Ovaskainen
University of Helsinki
Outline of the talk
• Part I. What can we learn about fungal ecology with fruit-body
inventories?
• Part II. What can we learn about fungal ecology with sequencing?
• Part III. What can we learn about fungal ecology by combining
fruit-body inventories with sequencing?
Part I. What can we learn about fungal
ecology with fruit-body inventories?
fruit-bodies
resource patch
An example of fruit-body survey data
Data: 100,000 surveyed logs on 500 sites, includes 60,000 occurrences of 180 species
Data by Nórden, Penttilä, Siitonen, et al.
Resource use: species vary in their niche breath
Generalist: Asterodon ferroginosus
Most tree species and decay
classes, size and type of the tree do
not matter much
Specialist: Amylocystis lapponica
Spruce logs of decay class II-III,
large naturally downed logs
Nordén, J., Penttilä, R., Siitonen, J., Tomppo, E. and Ovaskainen, O. 2013. Specialist species of wood-inhabiting
fungi struggle while generalists thrive in fragmented boreal forests. Journal of Ecology 101, 701-712.
Threatened species are specialists that require connectivity
Let us survey the same
amount (200 logs of
standardized sizes and
qualities) of dead wood
in different forests.
How many species are to
be found?
Location:
Non-threatened
Threatened
fragmented
17.8
0.1
well-connected
18.5
1.1
Nordén, J., Penttilä, R., Siitonen, J., Tomppo, E. and Ovaskainen, O. 2013. Specialist species of wood-inhabiting
fungi struggle while generalists thrive in fragmented boreal forests. Journal of Ecology 101, 701-712.
Co-occurrence: some species pairs tend to occur
together, others avoid each other
these species like each other
these species avoid each other
Ovaskainen, O., Hottola, J. and Siitonen, J. 2010. Modeling species co-occurrence by multivariate
logistic regression generates new hypotheses on fungal interactions. Ecology 91, 2514-2521.
Fruit-body surveys reveal interesting patterns,
but tell only little about the underlying mechanisms
Why some species have responded negatively to
fragmentation but others not?
What life-history stages are influenced by fragmentation?
Are fungi dispersal limited, and do species differ in their
dispersal ability?
Why some species occur together and others not?
Part II. What can we learn about fungal
ecology with sequencing?
Dmitry Schigel and Jenni Hottola collecting sawdust samples with a drill
Veera Norros collecting spore
samples with a cyclone sampler
Sample -> DNA -> sequences
How do sequence data look like?
Sample 1
Sequence
1
Sequence
2
Sequence
10000
>FXCMJDV01EVR3Slength=271 xy=1885_0374 region=1
run=R_2009_06_11_14_00_39_CTGGTCATTTAGAGGAAGT
Sample 2
AAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGG
.
ATCATTAATGAAATTTATGACTGGGGTTGTCGCTGGCCTTTAAA
.
>FXCMJDV01EVR3Slength=271 xy=1885_0374 region=1
AACGGCATGTGCACGCCCCTTTCACTAATCCACACACACCTGT
.
run=R_2009_06_11_14_00_39_CTGGTCATTTAGAGGAAGT
GCACCTTCGCGGGGGCTCTTGGGAACCGACGCAAGTCGTAA
AAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGG
Sample 100
GTACCGGAGCTCGCGTCCCTTTACACACCCCTTTGTATGTCTTA
ATCATTAATGAAATTTATGACTGGGGTTGTCGCTGGCCTTTAAA
AGAATGTCTACTCGATGTAATAAAACGCATCTAATACA
AACGGCATGTGCACGCCCCTTTCACTAATCCACACACACCTGT
>FXCMJDV01EVR3Slength=271 xy=1885_0374 region=1
GCACCTTCGCGGGGGCTCTTGGGAACCGACGCAAGTCGTAA
>FXCMJDV01CK1BD length=245 xy=0942_2391 region=1 run=R_2009_06_11_14_00_39_CTGGTCATTTAGAGGAAGT
GTACCGGAGCTCGCGTCCCTTTACACACCCCTTTGTATGTCTTA
AAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGG
run=R_2009_06_11_14_00_39_TCCTCCGCTTATTGATATGC
AGAATGTCTACTCGATGTAATAAAACGCATCTAATACA
TTAAGTTCAGCGGGTATCCCTACCTGATCCGAGGTCAACCTGT ATCATTAATGAAATTTATGACTGGGGTTGTCGCTGGCCTTTAAA
AAAGATTGGGGGTTGCTGGCGGGCAACCGTAGGACCCTATAG AACGGCATGTGCACGCCCCTTTCACTAATCCACACACACCTGT
>FXCMJDV01CK1BD length=245GCACCTTCGCGGGGGCTCTTGGGAACCGACGCAAGTCGTAA
xy=0942_2391 region=1
CGAGGAGTATTACTACGCTAAGAGCCATGCGGCGCTGCCACT
run=R_2009_06_11_14_00_39_TCCTCCGCTTATTGATATGC
GCGTTTGAGGGCGGCAGAGTTGCCAGCCCCAAGACCACGCG GTACCGGAGCTCGCGTCCCTTTACACACCCCTTTGTATGTCTTA
TTAAGTTCAGCGGGTATCCCTACCTGATCCGAGGTCAACCTGT
AGAATGTCTACTCGATGTAATAAAACGCATCTAATACA
AGGCGTGATGTTGGTCATAATGACGCTCGAACAGGCATGCCC
AAAGATTGGGGGTTGCTGGCGGGCAACCGTAGGACCCTATAG
CGCGGAATACCACGG
CGAGGAGTATTACTACGCTAAGAGCCATGCGGCGCTGCCACT
>FXCMJDV01CK1BD length=245 xy=0942_2391 region=1
GCGTTTGAGGGCGGCAGAGTTGCCAGCCCCAAGACCACGCG
run=R_2009_06_11_14_00_39_TCCTCCGCTTATTGATATGC
.
AGGCGTGATGTTGGTCATAATGACGCTCGAACAGGCATGCCC
TTAAGTTCAGCGGGTATCCCTACCTGATCCGAGGTCAACCTGT
.
CGCGGAATACCACGG
AAAGATTGGGGGTTGCTGGCGGGCAACCGTAGGACCCTATAG
.
CGAGGAGTATTACTACGCTAAGAGCCATGCGGCGCTGCCACT
.
>FXCMJDV01CK1BD length=245 xy=0942_2391 region=1 GCGTTTGAGGGCGGCAGAGTTGCCAGCCCCAAGACCACGCG
.
AGGCGTGATGTTGGTCATAATGACGCTCGAACAGGCATGCCC
run=R_2009_06_11_14_00_39_TCCTCCGCTTATTGATATGC
.
TTAAGTTCAGCGGGTATCCCTACCTGATCCGAGGTCAACCTGT CGCGGAATACCACGG
AAAGATTGGGGGTTGCTGGCGGGCAACCGTAGGACCCTATAG
>FXCMJDV01CK1BD length=245. xy=0942_2391 region=1
CGAGGAGTATTACTACGCTAAGAGCCATGCGGCGCTGCCACT
run=R_2009_06_11_14_00_39_TCCTCCGCTTATTGATATGC
.
GCGTTTGAGGGCGGCAGAGTTGCCAGCCCCAAGACCACGCG
TTAAGTTCAGCGGGTATCCCTACCTGATCCGAGGTCAACCTGT
AGGCGTGATGTTGGTCATAATGACGCTCGAACAGGCATGCCC .
AAAGATTGGGGGTTGCTGGCGGGCAACCGTAGGACCCTATAG
CGCGGAATACCACGG
CGAGGAGTATTACTACGCTAAGAGCCATGCGGCGCTGCCACT
>FXCMJDV01CK1BD length=245 xy=0942_2391 region=1
OTUs = operational taxonomical units
TTTCCGTAGGTGAACCTGCGGAAGGATCATTAATGAATACAATTCGGTCGGCGGGAAGGAGGGGGAG
CTGTCGCTGGCCTTGTGGCATGTGCACGCTCTCTTTGGAACGTCGGTCGTCTTTCATATTTTCACCAGTG
CACCCAATGTAGGATGCCTCTCCTCCGGGAGGGGGGACCTATGTCTTTTTCAGACGCCCCCACAGTTTA
GAAAGTCTCAGAATGTTTACTATCGTCGAACCATGACTTCCAGGAGACGTGGGTCGGCGAGATAAAAG
TTATCACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAATTGCGATATG
TAATGTGAATTGCAGATCTACAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTGTTCCG
TTTCCGTAGGTGAACCTGCGGAAGGATCATTAATGAATACAATTCGGTCGGCGGGAAGGAGGGGGAG
AGGAGCATGCCTGTTTGAGTGTCAGTAAATTCTCAACCCCTCTCGATTAGCTTCGAGGGGGAGCTTGG
CTGTCGCTGGCCTTGTGGCATGTGCACGCTCTCTTTGGAACGTCGGTCGTCTTTCATATTTTCACCAGTG
ATAGTGGGGGCTGCCAGAGACCCAGACTTTGTTGTCTGGGACTTGGGCTCTCCTGAAATACATTGGCT
CACCCAATGTAGGATGCCTCTCCTCCGGGAGGGGGGACCTATGTCTTTTTCAGACGCCCCCACAGTTTA
TGCGATCGACTTTTTCGACTTTGCGCGACAAGGCTTTCGGCGTGATAATGATCGCCGTCTTCCGAAGCG
GAAAGTCTCAGAATGTTTACTATCGTCGAACCATGACTTCCAGGAGACGTGGGTCGGCGAGATAAAAG
CATGAACGGGAAGGGAAGGTCTCGTGCCTCCAACAATATGCGTCGACGGCAACGTCTTCCATCTTTTAT
TTATCACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAATTGCGATATG
TTTATGTTTGACCTCAAATCAGGTAGGACTACCCG
TAATGTGAATTGCAGATCTACAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTGTTCCG
TTTCCGTAGGTGAACCTGCGGAAGGATCATTAATGAATACAATTCGGTCGGCGGGAAGGAGGGGGAG
AGGAGCATGCCTGTTTGAGTGTCAGTAAATTCTCAACCCCTCTCGATTAGCTTCGAGGGGGAGCTTGG
CTGTCGCTGGCCTTGTGGCATGTGCACGCTCTCTTTGGAACGTCGGTCGTCTTTCATATTTTCACCAGTG
ATAGTGGGGGCTGCCAGAGACCCAGACTTTGTTGTCTGGGACTTGGGCTCTCCTGAAATACATTGGCT
CACCCAATGTAGGATGCCTCTCCTCCGGGAGGGGGGACCTATGTCTTTTTCAGACGCCCCCACAGTTTA
TGCGATCGACTTTTTCGACTTTGCGCGACAAGGCTTTCGGCGTGATAATGATCGCCGTCTTCCGAAGCG
GAAAGTCTCAGAATGTTTACTATCGTCGAACCATGACTTCCAGGAGACGTGGGTCGGCGAGATAAAAG
CATGAACGGGAAGGGAAGGTCTCGTGCCTCCAACAATATGCGTCGACGGCAACGTCTTCCATCTTTTAT
TTATCACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAATTGCGATATG
TTTATGTTTGACCTCAAATCAGGTAGGACTACCCG
TAATGTGAATTGCAGATCTACAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTGTTCCG
TTTCCGTAGGTGAACCTGCGGAAGGATCATTAATGAATACAATTCGGTCGGCGGGAAGGAGGGGGAG
AGGAGCATGCCTGTTTGAGTGTCAGTAAATTCTCAACCCCTCTCGATTAGCTTCGAGGGGGAGCTTGG
CTGTCGCTGGCCTTGTGGCATGTGCACGCTCTCTTTGGAACGTCGGTCGTCTTTCATATTTTCACCAGTG
ATAGTGGGGGCTGCCAGAGACCCAGACTTTGTTGTCTGGGACTTGGGCTCTCCTGAAATACATTGGCT
CACCCAATGTAGGATGCCTCTCCTCCGGGAGGGGGGACCTATGTCTTTTTCAGACGCCCCCACAGTTTA
TGCGATCGACTTTTTCGACTTTGCGCGACAAGGCTTTCGGCGTGATAATGATCGCCGTCTTCCGAAGCG
GAAAGTCTCAGAATGTTTACTATCGTCGAACCATGACTTCCAGGAGACGTGGGTCGGCGAGATAAAAG
CATGAACGGGAAGGGAAGGTCTCGTGCCTCCAACAATATGCGTCGACGGCAACGTCTTCCATCTTTTAT
TTATCACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAATTGCGATATG
TTTATGTTTGACCTCAAATCAGGTAGGACTACCCG
TAATGTGAATTGCAGATCTACAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTGTTCCG
TTTCCGTAGGTGAACCTGCGGAAGGATCATTAATGAATACAATTCGGTCGGCGGGAAGGAGGGGGAG
AGGAGCATGCCTGTTTGAGTGTCAGTAAATTCTCAACCCCTCTCGATTAGCTTCGAGGGGGAGCTTGG
CTGTCGCTGGCCTTGTGGCATGTGCACGCTCTCTTTGGAACGTCGGTCGTCTTTCATATTTTCACCAGTG
ATAGTGGGGGCTGCCAGAGACCCAGACTTTGTTGTCTGGGACTTGGGCTCTCCTGAAATACATTGGCT
CACCCAATGTAGGATGCCTCTCCTCCGGGAGGGGGGACCTATGTCTTTTTCAGACGCCCCCACAGTTTA
TGCGATCGACTTTTTCGACTTTGCGCGACAAGGCTTTCGGCGTGATAATGATCGCCGTCTTCCGAAGCG
GAAAGTCTCAGAATGTTTACTATCGTCGAACCATGACTTCCAGGAGACGTGGGTCGGCGAGATAAAAG
CATGAACGGGAAGGGAAGGTCTCGTGCCTCCAACAATATGCGTCGACGGCAACGTCTTCCATCTTTTAT
TTATCACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAATTGCGATATG
TTTATGTTTGACCTCAAATCAGGTAGGACTACCCG
TAATGTGAATTGCAGATCTACAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTGTTCCG
TTTCCGTAGGTGAACCTGCGGAAGGATCATTAATGAATACAATTCGGTCGGCGGGAAGGAGGGGGAG
AGGAGCATGCCTGTTTGAGTGTCAGTAAATTCTCAACCCCTCTCGATTAGCTTCGAGGGGGAGCTTGG
CTGTCGCTGGCCTTGTGGCATGTGCACGCTCTCTTTGGAACGTCGGTCGTCTTTCATATTTTCACCAGTG
ATAGTGGGGGCTGCCAGAGACCCAGACTTTGTTGTCTGGGACTTGGGCTCTCCTGAAATACATTGGCT
CACCCAATGTAGGATGCCTCTCCTCCGGGAGGGGGGACCTATGTCTTTTTCAGACGCCCCCACAGTTTA
TGCGATCGACTTTTTCGACTTTGCGCGACAAGGCTTTCGGCGTGATAATGATCGCCGTCTTCCGAAGCG
GAAAGTCTCAGAATGTTTACTATCGTCGAACCATGACTTCCAGGAGACGTGGGTCGGCGAGATAAAAG
CATGAACGGGAAGGGAAGGTCTCGTGCCTCCAACAATATGCGTCGACGGCAACGTCTTCCATCTTTTAT
TTATCACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAATTGCGATATG
TTTATGTTTGACCTCAAATCAGGTAGGACTACCCG
TAATGTGAATTGCAGATCTACAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTGTTCCG
AGGAGCATGCCTGTTTGAGTGTCAGTAAATTCTCAACCCCTCTCGATTAGCTTCGAGGGGGAGCTTGG
ATAGTGGGGGCTGCCAGAGACCCAGACTTTGTTGTCTGGGACTTGGGCTCTCCTGAAATACATTGGCT
TGCGATCGACTTTTTCGACTTTGCGCGACAAGGCTTTCGGCGTGATAATGATCGCCGTCTTCCGAAGCG
CATGAACGGGAAGGGAAGGTCTCGTGCCTCCAACAATATGCGTCGACGGCAACGTCTTCCATCTTTTAT
TTTATGTTTGACCTCAAATCAGGTAGGACTACCCG
OTU1
OTU2
OTU1
OTU3
OTU1
OTU2
Samples x OTUs -table
Example result: soil has greater fungal
diversity than dead wood
Number of OTUs
soil
wood
Decay class
Rajala, T. et al. (in preparation)
Example result: fungal communities in dead
wood approach gradually the soil community
Rajala, T. et al. (in preparation)
How can we move from OTUs to species?
TTTCCGTAGGTGAACCTGCGGAAGGATCATTAATGAATACAATTCGGTCGGCGGGAAGGAGGGGGAG
CTGTCGCTGGCCTTGTGGCATGTGCACGCTCTCTTTGGAACGTCGGTCGTCTTTCATATTTTCACCAGTG
CACCCAATGTAGGATGCCTCTCCTCCGGGAGGGGGGACCTATGTCTTTTTCAGACGCCCCCACAGTTTA
GAAAGTCTCAGAATGTTTACTATCGTCGAACCATGACTTCCAGGAGACGTGGGTCGGCGAGATAAAAG
TTATCACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAATTGCGATATG
TAATGTGAATTGCAGATCTACAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTGTTCCG
TTTCCGTAGGTGAACCTGCGGAAGGATCATTAATGAATACAATTCGGTCGGCGGGAAGGAGGGGGAG
AGGAGCATGCCTGTTTGAGTGTCAGTAAATTCTCAACCCCTCTCGATTAGCTTCGAGGGGGAGCTTGG
CTGTCGCTGGCCTTGTGGCATGTGCACGCTCTCTTTGGAACGTCGGTCGTCTTTCATATTTTCACCAGTG
ATAGTGGGGGCTGCCAGAGACCCAGACTTTGTTGTCTGGGACTTGGGCTCTCCTGAAATACATTGGCT
CACCCAATGTAGGATGCCTCTCCTCCGGGAGGGGGGACCTATGTCTTTTTCAGACGCCCCCACAGTTTA
TGCGATCGACTTTTTCGACTTTGCGCGACAAGGCTTTCGGCGTGATAATGATCGCCGTCTTCCGAAGCG
GAAAGTCTCAGAATGTTTACTATCGTCGAACCATGACTTCCAGGAGACGTGGGTCGGCGAGATAAAAG
CATGAACGGGAAGGGAAGGTCTCGTGCCTCCAACAATATGCGTCGACGGCAACGTCTTCCATCTTTTAT
TTATCACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAATTGCGATATG
TTTATGTTTGACCTCAAATCAGGTAGGACTACCCG
TAATGTGAATTGCAGATCTACAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTGTTCCG
TTTCCGTAGGTGAACCTGCGGAAGGATCATTAATGAATACAATTCGGTCGGCGGGAAGGAGGGGGAG
AGGAGCATGCCTGTTTGAGTGTCAGTAAATTCTCAACCCCTCTCGATTAGCTTCGAGGGGGAGCTTGG
CTGTCGCTGGCCTTGTGGCATGTGCACGCTCTCTTTGGAACGTCGGTCGTCTTTCATATTTTCACCAGTG
ATAGTGGGGGCTGCCAGAGACCCAGACTTTGTTGTCTGGGACTTGGGCTCTCCTGAAATACATTGGCT
CACCCAATGTAGGATGCCTCTCCTCCGGGAGGGGGGACCTATGTCTTTTTCAGACGCCCCCACAGTTTA
TGCGATCGACTTTTTCGACTTTGCGCGACAAGGCTTTCGGCGTGATAATGATCGCCGTCTTCCGAAGCG
GAAAGTCTCAGAATGTTTACTATCGTCGAACCATGACTTCCAGGAGACGTGGGTCGGCGAGATAAAAG
CATGAACGGGAAGGGAAGGTCTCGTGCCTCCAACAATATGCGTCGACGGCAACGTCTTCCATCTTTTAT
TTATCACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAATTGCGATATG
TTTATGTTTGACCTCAAATCAGGTAGGACTACCCG
TAATGTGAATTGCAGATCTACAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTGTTCCG
TTTCCGTAGGTGAACCTGCGGAAGGATCATTAATGAATACAATTCGGTCGGCGGGAAGGAGGGGGAG
AGGAGCATGCCTGTTTGAGTGTCAGTAAATTCTCAACCCCTCTCGATTAGCTTCGAGGGGGAGCTTGG
CTGTCGCTGGCCTTGTGGCATGTGCACGCTCTCTTTGGAACGTCGGTCGTCTTTCATATTTTCACCAGTG
ATAGTGGGGGCTGCCAGAGACCCAGACTTTGTTGTCTGGGACTTGGGCTCTCCTGAAATACATTGGCT
CACCCAATGTAGGATGCCTCTCCTCCGGGAGGGGGGACCTATGTCTTTTTCAGACGCCCCCACAGTTTA
TGCGATCGACTTTTTCGACTTTGCGCGACAAGGCTTTCGGCGTGATAATGATCGCCGTCTTCCGAAGCG
GAAAGTCTCAGAATGTTTACTATCGTCGAACCATGACTTCCAGGAGACGTGGGTCGGCGAGATAAAAG
CATGAACGGGAAGGGAAGGTCTCGTGCCTCCAACAATATGCGTCGACGGCAACGTCTTCCATCTTTTAT
TTATCACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAATTGCGATATG
TTTATGTTTGACCTCAAATCAGGTAGGACTACCCG
TAATGTGAATTGCAGATCTACAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTGTTCCG
TTTCCGTAGGTGAACCTGCGGAAGGATCATTAATGAATACAATTCGGTCGGCGGGAAGGAGGGGGAG
AGGAGCATGCCTGTTTGAGTGTCAGTAAATTCTCAACCCCTCTCGATTAGCTTCGAGGGGGAGCTTGG
CTGTCGCTGGCCTTGTGGCATGTGCACGCTCTCTTTGGAACGTCGGTCGTCTTTCATATTTTCACCAGTG
ATAGTGGGGGCTGCCAGAGACCCAGACTTTGTTGTCTGGGACTTGGGCTCTCCTGAAATACATTGGCT
CACCCAATGTAGGATGCCTCTCCTCCGGGAGGGGGGACCTATGTCTTTTTCAGACGCCCCCACAGTTTA
TGCGATCGACTTTTTCGACTTTGCGCGACAAGGCTTTCGGCGTGATAATGATCGCCGTCTTCCGAAGCG
GAAAGTCTCAGAATGTTTACTATCGTCGAACCATGACTTCCAGGAGACGTGGGTCGGCGAGATAAAAG
CATGAACGGGAAGGGAAGGTCTCGTGCCTCCAACAATATGCGTCGACGGCAACGTCTTCCATCTTTTAT
TTATCACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAATTGCGATATG
TTTATGTTTGACCTCAAATCAGGTAGGACTACCCG
TAATGTGAATTGCAGATCTACAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTGTTCCG
TTTCCGTAGGTGAACCTGCGGAAGGATCATTAATGAATACAATTCGGTCGGCGGGAAGGAGGGGGAG
AGGAGCATGCCTGTTTGAGTGTCAGTAAATTCTCAACCCCTCTCGATTAGCTTCGAGGGGGAGCTTGG
CTGTCGCTGGCCTTGTGGCATGTGCACGCTCTCTTTGGAACGTCGGTCGTCTTTCATATTTTCACCAGTG
ATAGTGGGGGCTGCCAGAGACCCAGACTTTGTTGTCTGGGACTTGGGCTCTCCTGAAATACATTGGCT
CACCCAATGTAGGATGCCTCTCCTCCGGGAGGGGGGACCTATGTCTTTTTCAGACGCCCCCACAGTTTA
TGCGATCGACTTTTTCGACTTTGCGCGACAAGGCTTTCGGCGTGATAATGATCGCCGTCTTCCGAAGCG
GAAAGTCTCAGAATGTTTACTATCGTCGAACCATGACTTCCAGGAGACGTGGGTCGGCGAGATAAAAG
CATGAACGGGAAGGGAAGGTCTCGTGCCTCCAACAATATGCGTCGACGGCAACGTCTTCCATCTTTTAT
TTATCACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAATTGCGATATG
TTTATGTTTGACCTCAAATCAGGTAGGACTACCCG
TAATGTGAATTGCAGATCTACAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTGTTCCG
AGGAGCATGCCTGTTTGAGTGTCAGTAAATTCTCAACCCCTCTCGATTAGCTTCGAGGGGGAGCTTGG
ATAGTGGGGGCTGCCAGAGACCCAGACTTTGTTGTCTGGGACTTGGGCTCTCCTGAAATACATTGGCT
TGCGATCGACTTTTTCGACTTTGCGCGACAAGGCTTTCGGCGTGATAATGATCGCCGTCTTCCGAAGCG
CATGAACGGGAAGGGAAGGTCTCGTGCCTCCAACAATATGCGTCGACGGCAACGTCTTCCATCTTTTAT
TTTATGTTTGACCTCAAATCAGGTAGGACTACCCG
Phellinus nigrolimitatus
Fomitopsis pinicola
...
...
...
...
Comparing environmental sequences
against a reference database
Reference database
query sequence
TTTCCGTAGGTGAACCTGCGGAAGGATCATTAATGAATACAATTCGGTCGGCGGGAAGGAGGGGGAG
CTGTCGCTGGCCTTGTGGCATGTGCACGCTCTCTTTGGAACGTCGGTCGTCTTTCATATTTTCACCAGTG
CACCCAATGTAGGATGCCTCTCCTCCGGGAGGGGGGACCTATGTCTTTTTCAGACGCCCCCACAGTTTA
GAAAGTCTCAGAATGTTTACTATCGTCGAACCATGACTTCCAGGAGACGTGGGTCGGCGAGATAAAAG
TTATCACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAATTGCGATATG
TAATGTGAATTGCAGATCTACAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTGTTCCG
AGGAGCATGCCTGTTTGAGTGTCAGTAAATTCTCAACCCCTCTCGATTAGCTTCGAGGGGGAGCTTGG
ATAGTGGGGGCTGCCAGAGACCCAGACTTTGTTGTCTGGGACTTGGGCTCTCCTGAAATACATTGGCT
TGCGATCGACTTTTTCGACTTTGCGCGACAAGGCTTTCGGCGTGATAATGATCGCCGTCTTCCGAAGCG
CATGAACGGGAAGGGAAGGTCTCGTGCCTCCAACAATATGCGTCGACGGCAACGTCTTCCATCTTTTAT
TTTATGTTTGACCTCAAATCAGGTAGGACTACCCG
best matching reference sequence
BLAST (basic local
alignment search tool)
Example result: identifying OTUs by
comparing to genbank
Rajala, T. et al. (in preparation)
Comparing environmental sequences
against a reference database
Reference database
query sequence
TTTCCGTAGGTGAACCTGCGGAAGGATCATTAATGAATACAATTCGGTCGGCGGGAAGGAGGGGGAG
CTGTCGCTGGCCTTGTGGCATGTGCACGCTCTCTTTGGAACGTCGGTCGTCTTTCATATTTTCACCAGTG
CACCCAATGTAGGATGCCTCTCCTCCGGGAGGGGGGACCTATGTCTTTTTCAGACGCCCCCACAGTTTA
GAAAGTCTCAGAATGTTTACTATCGTCGAACCATGACTTCCAGGAGACGTGGGTCGGCGAGATAAAAG
TTATCACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAATTGCGATATG
TAATGTGAATTGCAGATCTACAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTGTTCCG
AGGAGCATGCCTGTTTGAGTGTCAGTAAATTCTCAACCCCTCTCGATTAGCTTCGAGGGGGAGCTTGG
ATAGTGGGGGCTGCCAGAGACCCAGACTTTGTTGTCTGGGACTTGGGCTCTCCTGAAATACATTGGCT
TGCGATCGACTTTTTCGACTTTGCGCGACAAGGCTTTCGGCGTGATAATGATCGCCGTCTTCCGAAGCG
CATGAACGGGAAGGGAAGGTCTCGTGCCTCCAACAATATGCGTCGACGGCAACGTCTTCCATCTTTTAT
TTTATGTTTGACCTCAAATCAGGTAGGACTACCCG
best matching reference sequence
BLAST (basic local
alignment search tool)
How certain can we be that the
species behind the query sequence
is Cantharellus tubaeformis?
Two sources of error
How certain can we be that the best BLAST hit is the true species?
• The true species is not in the reference database
• The true species is not in the reference database but the
best hit went to another species (e.g. sister species or
mislabeled specimen)
Ovaskainen, O., Nokso-Koivisto, J., Hottola, J., Rajala, T., Pennanen, T., Ali-Kovero, H., Miettinen, O., Oinonen, P., Auvinen, P.,
Paulin, L., Larsson, K.-H. and Mäkipää, R. 2010. Identifying wood-inhabiting fungi with 454 sequencing - what is the probability
that BLAST gives the correct species? Fungal Ecology 3, 274-283.
Part III. What can we learn about fungal
ecology by combining fruit-body
inventories with sequencing?
Example study
Study design: 100 spruce logs sampled for sequencing and fruit-bodies
8m
basal
16 m
middle
• The logs represent evenly the decay classes I, II, III, IV
• All large in size (>20 cm diam, >20 m long)
Ovaskainen, O., Schigel, D., Ali-Kovero, H., Auvinen, P., Paulin, L., Nordén, B. and Nordén, J. 2013. Combining high-throughput
sequencing with fruit-body surveys reveals contrasting life-history strategies in fungi. The ISME Journal 7, 1696-1709.
The data in numbers
Environmental sequences. One third of
the 638,357 sequences identified with
90% confidence: 198 species.
Fruit-body surveys. 67 species.
Ovaskainen, O., Schigel, D., Ali-Kovero, H., Auvinen, P., Paulin, L., Nordén, B. and Nordén, J. 2013. Combining high-throughput
sequencing with fruit-body surveys reveals contrasting life-history strategies in fungi. The ISME Journal 7, 1696-1709.
Example pattern: Fomitopsis pinicola (a generalist)
prevalence
fruit body
abundance
mycelia
decay class
fruit body occurrence
fruit body abundance
decay class
relative mycelial abundance
relative mycelial abundance
mycelia
fruit body
abundance
prevalence
Example pattern: Phellinus nigrolimitatus (a specialist)
decay class
fruit body occurrence
fruit body abundance
decay class
relative mycelial abundance
relative mycelial abundance
In what sense are specialized species specialized?
A species may appear as specialist at the fruit-body stage because...
• Hypothesis I: ...it can colonize only certain kinds of logs (but fruit on any
kind of a log that it has colonized)
• Hypothesis II: ...it can fruit only on certain kinds of logs (but colonize any
kind of a log)
Support for hypothesis II: specialists have a low fruiting rate
time delay in fruiting
fruiting rate
Fruiting rate decreases with ecological specialization, partly
explained by the fact that specialized species show a long delay
from mycelial colonization until fruiting.
ecological specialisation
ecological specialisation
Ovaskainen, O., Schigel, D., Ali-Kovero, H., Auvinen, P., Paulin, L., Nordén, B. and Nordén, J. 2013. Combining high-throughput
sequencing with fruit-body surveys reveals contrasting life-history strategies in fungi. The ISME Journal 7, 1696-1709.
Conclusion
We should do both fruit-body inventories and sequencing
Taxonomical studies, field surveys, and laboratory studies
have largely followed their own traditions in fungal research.
New research approaches facilitated by high-throughput
sequencing are bringing these fields together.
Combining different sources of data helps to get a more
integrated picture