Structure and resilience of fungal communities in Alaskan boreal forest soils D. Lee Taylor Ian C. Herriott Jack W. McFarland Michael 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 successional UP3a, 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; Co-conspirators: fractions pooled within sites Jack McFarland Teresa Hollingsworth Roger Ruess Niall Lennon Chad Nusbaum
host preferences Dominants have strong Relative Proportion 10 12 0 2 4 6 8 Cortinarius collinitus Rhizoscyphus ericae Rhizoscyphus ericae Cortinarius cf. sani Russula laricina Phialophora sp. auri Urnula helvelloides Cortinarius vibratilis Piloderma olivaceu Trichophaea cf. hybr Black Spruce Distributions of 30 Dominant Taxa Candida tepae Amphinema byssoides Botryosphaeria corticis Early Deciduous Russula fellea Clitocybe lateritia Phialocephala fortinii Piloderma fallax Hebeloma bruchetii White Spruce Wilcoxina rehmii Tylospora asterophora Amphinema byssoides Hygrophorus olivaceoalbus Hydnellum cyanopodium Russula aeruginea Paraglomus occultum Inocybe flocculosa Hygrophorus pudorinus Russula persicina Candida tepae Piloderma sp. A18
NMS Ordination: UP and TKN black spruce sites, separate years Low year-year variation within a site
NMS Ordination: UP and TKN black spruce sites, years combined Upland Black spruce organic organic mineral
Tests for fungal community differentiation: multiple response permutation procedure 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 Upland + black spruce differ; horizons differ; year-year variation insignificant
NMS Ordination: UP only, years combined UP2 1) Strong structure by stage UP3 2) Greatest variation in early stage UP1
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 Lennon Chad Nusbaum D. Lee Taylor
NMS Ordination: Humic horizon 1) Seasons have different Spring communities 2) Summer most distinct Summer Fall Winter
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 Augustyn Scott Hillard Chad Nusbaum Jynene Black Teresa Hollingsworth Gary Laursen Michael Booth Sarah Hopkins Niall Lennon Dan Cardin Jason Hunt Jim Long József Geml Shawn Huston Mitali Patil Hope Gray Tom Marr Roger Ruess Ian Herriott Jack McFarland Ina Timling
Indicator species status among the 10 most frequent OTUs in the seasonal study Rank Indicator Species Blast ID 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
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)
25 Cortinarius flexipes 20 Number of Clones 15 10 5 0 250 Mineral Clones Cortinarius collinitus Organic Clones 200 Number of Clones 150 100 50 0 1 12 15 22 39 40 51 109 119 122 123 126 Black Spruce Site
Summary of Coring and Sequencing Efforts Study, Site Description Site Codes Col. Year Soil Horizons # of # of Clones DNAs Sequenced Soil Cores 2004-5 160 20 9216 White Spruce, seasonal study, UAF litter, humic, DNA mineral 2007 humic 1 2 4,224 White Spruce, seasonal study, UAF RNA-DNA 2004, 2005 organic, mineral 300 12 18048 Early successional upland UP1a, mixed forest UP1b, UP1c 2004, 2005 organic, mineral 300 12 12288 Mid-successional upland UP2a, mixed forest UP2b, UP2c 2004, 2005 organic, mineral 300 12 12288 Late successional upland UP3a, mixed forest UP3b, UP3c Dry acidic black spruce 2004, 2005 organic, mineral 100 4 9216 TKN0012 Dry acidic black spruce 2004, 2005 organic, mineral 100 4 9216 TKN0122 Dry acidic black spruce 2004, 2005 organic, mineral 100 4 9216 TKN0001 Moist acidic black spruce 2004, 2005 organic, mineral 100 4 9216 TKN0015 Moist acidic black spruce 2004, 2005 organic, mineral 100 4 9216 TKN0022 Moist acidic black spruce 2004, 2005 organic, mineral 100 4 9216 TKN0109 Dry nonacidic black spruce 2004, 2005 organic, mineral 100 4 9216 TKN0039 Dry nonacidic black spruce 2004, 2005 organic, mineral 100 4 9216 TKN0123 Dry nonacidic black spruce 2004, 2005 organic, mineral 100 4 9216 TKN0126 Moist nonacidic black spruce 2004, 2005 organic, mineral 100 4 9216 TKN0051 Moist nonacidic black spruce 2004, 2005 organic, mineral 100 4 9216 TKN0119 Moist nonacidic black spruce 2004, 2005 organic, mineral 100 4 9216 TKN0040 TOTALS 2160 90 162,432*
Study I: Fungal diversity in 0.25g of boreal forest soil Co-conspirators: Michael Booth Jack McFarland Ian Herriott Roger Ruess Niall Lennon Chad 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
Rank Abundance Plot, Core D8 2000 1800 1600 1400 1200 1000 800 600 400 200 0 OTU
D8 Species Accumulation Curve 350 Mao Tau 300 250 200 150 100 50 0 244 439.2 634.4 829.6 1025 1220 1415 1610 1806 2001 2196 2391 2586 2782 2977 3172 3367 3562 3758 3953 4148 4343 4538 4734 48.8 Number of Clones
Estimated Actual Number of Species 800 Chao 1 700 600 500 400 300 200 100 0 48.8 244 439.2 634.4 829.6 1025 1220 1415 1610 1806 2001 2196 2391 2586 2782 2977 3172 3367 3562 3758 3953 4148 4343 4538 4734 Number of Clones
Dominants from soil cores ~1m apart 2500 D8 2000 1500 H4 1000 500 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 OTU
0109M4&M5 Rarefaction Curves 350 300 250 200 M4 Mao Tau M5 Mao Tau M4&M5 Mau Tau M4&M5 Chao 1 150 100 We have not saturated within site/sample 50 diversity 0 0 500 1000 1500 2000 2500 Number of Clones
All Sites Rarefaction Curve 1400 1200 1000 800 Mao Tau Chao 1 600 We HAVE saturated overall 400 diversity across these sites (enough sequences) 200 0 0 5000 10000 15000 20000 25000 30000 Number of Clones
All Sites by Plot Rarefaction Curve 1400 1200 1000 800 Mao Tau Chao 1 600 400 More sites would 200 yield more species 0 0 5 10 15 20 25 Number of Plots
Ephemeral, clumped, large + small genets, appearance unpredictable Diverse, intermixed, clumped to over- dispersed ???
Soil Microbial Seasonal Dynamics Plot 70 M Q T 60 I J O 50 L H N P 40 S F 30 G B E D 20 A� C K 10 R 0 0 10 20 30 40 50 60 70 <--North South-->
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