Structure and resilience of fungal communities in Alaskan boreal forest soils

D. Lee TaylorIan C. HerriottJack W. McFarlandMichael G. Booth

Photographer: Roger Ruess

Summary of Three Fungal Community Structure Studies

I. Two broad surveys, 1) UP and 2) TKN black

spruce sites

a. Inter-annual variation

b. Successional dynamics

II. 3) Intra-annual variation, single spruce site

III. Conclusions

Coupling Diversity with Function: Metagenomics of Boreal Forest Fungi USDA-NSF Microbial Genome Sequencing Program, 2003-2007

Goals• Fill out sequence space for Alaskan fungi

- Sporocarps

- Soil DNA

• Determine how to adequately sample fungi in soil

• Characterize fungal community structure within the BNZ

LTER site across time space and time

BNZ Upland “UP” Core Sites; Interior Alaska Black Spruce TKN Sites

Upland• 9 sites: UP1a, b, c - early successional

UP2a, b, c - mid successionalUP3a, b, c - late successional

Black spruce• 12 sites: - 3 dry, acidic

- 3 wet, acidic- 3 dry, non-acidic- 3 wet, non-acidic

• Sampled same locations in 2004, 2005• 50 cores per site/sampling date, 2100 cores total• Cores divided into organic and mineral fractions;

fractions pooled within sites Co-conspirators:Jack McFarlandTeresa HollingsworthRoger RuessNiall LennonChad Nusbaum

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Black Spruce Early Deciduous White Spruce

Distributions of 30 Dominant TaxaDominants have strong host preferences

NMS Ordination: UP and TKN black spruce sites,separate years

Low year-year variation within a site

Black spruceUpland

organic

mineral

organic

NMS Ordination: UP and TKN black spruce sites,years combined

Factor Effect size, A Significance, p Horizon (Mineral vs. Organic) 0.03074992 < 0.00000001 Stand (Upland vs black spruce) 0.06293753 < 0.00000001 Year -0.00067788 0.57493865

Tests for fungal community differentiation:multiple response permutation procedure

Upland + black spruce differ; horizons differ; year-year variation insignificant

UP1

UP2

UP3

NMS Ordination: UP only, years combined

1) Strong structure by stage

2) Greatest variation in early stage

Community dissimilarities by successional stage

Greatest variation in early succession

F = 4.17, p = 0.036

Summary of Three Fungal Community Structure Studies

I. Broad surveys, UP and TKN black spruce

sites

a. Inter-annual variation

b. Successional dynamics

II. Intra-annual variation, single spruce site

III. Conclusions

Part 2: Seasonal Dynamics?

• Sampled 1 site (white/black spruce) : August ‘04, October ‘04, February ‘05 and May ‘05

• cores into: Litter, Humic, Mineral• 10 pooled cores per sampling date• ~9500 clones analyzed Ian Herriott

Niall LennonChad NusbaumD. Lee Taylor

FallSummer

Winter

Spring

NMS Ordination: Humic horizon

1) Seasons have different communities

2) Summer most distinct

Summary of Three Fungal Community Structure Studies

I. Broad surveys, 1) UP and 2) TKN black

spruce sites

a. Inter-annual variation - resilence

b. Successional dynamics - strong habitat

and horizon prefs, most variable early

II. 3) Intra-annual variation - detectable

dynamics

III. Conclusions

Funding Sources and Supporting Agencies

Thanks!

Michelle AugustynJynene Black Michael Booth Dan Cardin József Geml Hope GrayIan Herriott

Scott HillardTeresa Hollingsworth Sarah Hopkins Jason HuntShawn HustonTom MarrJack McFarland

Chad NusbaumGary LaursenNiall LennonJim LongMitali PatilRoger RuessIna Timling

Indicator Species Blast ID Rank

Abundance Indicator of Ecology Subphylum Family Seasonal indicator species in the Humic Horizon

Tricholoma orirubens 1 Winter ECM Agaricomycotina Tricholomataceae

Piloderma lanatum 4 Spring ECM Agaricomycotina Atheliaceae

Orbilia auricolor 6 Summer Sap Pezizomycotina Orbiliaceae

Piloderma lanatum 7 Summer ECM Agaricomycotina Atheliaceae

Cortinarius erythrinus 8 Spring ECM Agaricomycotina Cortinariaceae Seasonal indicator species in the Mineral Horizon

Tricholoma orirubens 1 Summer ECM Agaricomycotina Tricholomataceae

Piloderma lanatum 4 Summer ECM Agaricomycotina Atheliaceae

Cortinarius erythrinus 8 Summer ECM Agaricomycotina Cortinariaceae

Orbilia auricolor 10 Spring Sap Pezizomycotina Orbiliaceae

Indicator species status among the 10 most frequent OTUs in the seasonal study

Take-Home Messages:

- Inter-annual stability of communities (resilience)

- Extreme structure by soil horizon

- Divergence in horizon preferences among closely

related taxa (fine niche-partitioning => lower

resilience)

- Detectable seasonal shifts in structure (resilience)

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Mineral Clones

Organic ClonesCortinarius collinitus

Cortinarius flexipes

Black Spruce Site

Study, Site Description Site Codes Col. Year Soil Horizons # of Soil Cores

# of DNAs

Clones Sequenced

White Spruce, seasonal study, DNA

UAF 2004-5 litter, humic, mineral

160 20 9216

White Spruce, seasonal study, RNA-DNA

UAF 2007 humic 1 2 4,224

Early successional upland mixed forest

UP1a, UP1b, UP1c

2004, 2005 organic, mineral 300 12 18048

Mid-successional upland mixed forest

UP2a, UP2b, UP2c

2004, 2005 organic, mineral 300 12 12288

Late successional upland mixed forest

UP3a, UP3b, UP3c

2004, 2005 organic, mineral 300 12 12288

Dry acidic black spruce TKN0012 2004, 2005 organic, mineral 100 4 9216 Dry acidic black spruce TKN0122 2004, 2005 organic, mineral 100 4 9216 Dry acidic black spruce TKN0001 2004, 2005 organic, mineral 100 4 9216 Moist acidic black spruce TKN0015 2004, 2005 organic, mineral 100 4 9216 Moist acidic black spruce TKN0022 2004, 2005 organic, mineral 100 4 9216 Moist acidic black spruce TKN0109 2004, 2005 organic, mineral 100 4 9216 Dry nonacidic black spruce TKN0039 2004, 2005 organic, mineral 100 4 9216 Dry nonacidic black spruce TKN0123 2004, 2005 organic, mineral 100 4 9216 Dry nonacidic black spruce TKN0126 2004, 2005 organic, mineral 100 4 9216 Moist nonacidic black spruce TKN0051 2004, 2005 organic, mineral 100 4 9216 Moist nonacidic black spruce TKN0119 2004, 2005 organic, mineral 100 4 9216 Moist nonacidic black spruce TKN0040 2004, 2005 organic, mineral 100 4 9216 TOTALS 2160 90 162,432*

Summary of Coring and Sequencing Efforts

Study I: Fungal diversity in 0.25g of boreal forest soil

Co-conspirators:Michael BoothJack McFarlandIan HerriottRoger RuessNiall LennonChad Nusbaum

Summary Stats

• Total clones sequenced 17664• Too short, >2% Ns, non-fungal or ITS missing 8209

• Chimeras identified 258• Clones remaining 9197

• D8 - final sequences 4880- OTUs 276- Singleton OTUs 162

• H4 - final sequences 4317- OTUs 218 - Singleton OTUs 105

• Combined OTUs 433• Shared D8-H4 OTUs 60

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Rank Abundance Plot, Core D8

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D8 Species Accumulation Curve

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Estimated Actual Number of Species

Dominants from soil cores ~1m apart

D8

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0109M4&M5 Rarefaction Curves

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We have not saturated within site/sample diversity

All Sites Rarefaction Curve

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We HAVE saturated overall diversity across these sites (enough sequences)

All Sites by Plot Rarefaction Curve

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More sites would yield more species

Ephemeral, clumped, large + small genets, appearance unpredictable

Diverse, intermixed, clumped to over-dispersed

???

Soil Microbial Seasonal Dynamics Plot

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