Source: UNIVERSITY OF CALIFORNIA, BERKELEY submitted to
ECOLOGICAL INVESTIGATIONS OF FUNGAL MYCORRHIZAL AND SAPROBIC COMMUNITIES
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
0218569
Grant No.
(N/A)
Project No.
CA-B-MIC-0008-H
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Oct 1, 2009
Project End Date
Sep 30, 2014
Grant Year
(N/A)
Project Director
Bruns, T.
Recipient Organization
UNIVERSITY OF CALIFORNIA, BERKELEY
(N/A)
BERKELEY,CA 94720
Performing Department
Microbial Biology
Non Technical Summary
Research in my lab during the next five-year will continue to focus on fungal community ecology. The major changes are the advance into genomics, and expansion into saprobic fungi (i.e., those that decay dead material) in an addition to the work on mycorrhizal fungi (those that are mutualists with plant roots) communities. Genomics work will be focused on completing the sequencing and assembly of the genome of the mycorrhizal fungus Rhizopogon salebrosus. This will be done in collaboration the Joint Genome Institute, and it will open up many opportunities to better understand the interaction between pines and their fungal symbionts. Work on the mycorrhizal community ecology will focus on understanding the observed partitioning of species in time and space. Prior studies have shown that there is a temporal succession of fungal species, and we hypothesize that this is driven by differences among species in spore dispersal and spore behavior. A spatial patterning of species has also been observed in which a subset of species are found primarily at the edge of the root system. We hypothesize that this is cause by differences in competitive strategies that are overlaid on a gradient of root densities. We will test both hypotheses with a combination of field sampling and manipulative laboratory experiments. This work will provide a better understanding of the relationship between species richness and functional parameters of the community, and may lead to improved management of pinaceous ecosystems. Two types of saprobic fungal communities will be studied: those associated with indoor environments, and those associated with decay of bioenergy crop grass residues. The indoor air fungal communities are of interest because of their involvement with human allergies, and the bioenergy crop communities are of interest as source of novel enzymes for biofuel production. High throughput DNA sequence analyses will be used in both communities to characterize the fungal species present. Fungal cultures derived from the bioenergy crops will be screened for their enzymatic capacity to breakdown lignified cellulose. The field of fungal ecology has been driven in large part by the development of molecular tools for rapid identification. The methodologies have advanced quickly in this field, but the infrastructure for sequence-based identification has lagged behind. Specifically, the primary sequence database (NCBI) has accumulated a large number of misidentified and under-identified sequences, and these lead to additional misidentifications. In addition tools are not yet available for rapid, accurate classification of fungi by sequences. We are addressing these problems by assembling a consortium of researchers to accurately annotate fungal gene sequences used for identification and to use these curated sequences to set up an automatic classifier. The above work will advance the field through peer-reviewed publications, training of students and postdocs, and community-wide collaborative efforts directed at improved scientific infrastructure. The work will also have practical applications in forestry, indoor air quality, and biofuel production.
Animal Health Component
(N/A)
Research Effort Categories
Basic
(N/A)
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
1020612107030%
1020612110230%
2060612110210%
2060680110210%
7230410110210%
2014020104010%
Knowledge Area
102 - Soil, Plant, Water, Nutrient Relationships; 201 - Plant Genome, Genetics, and Genetic Mechanisms; 206 - Basic Plant Biology; 723 - Hazards to Human Health and Safety;

Subject Of Investigation
0612 - Conifer forests of the West; 0680 - Other products of the forest; 0410 - Air; 4020 - Fungi;

Field Of Science
1070 - Ecology; 1102 - Mycology; 1040 - Molecular biology;
Goals / Objectives
1) To obtain a complete genome sequence of Rhizopogon salebrosus. 2) To measure aerial spore dispersal of key ectomycorrhizal fungi. 3) To examine the effect of root density on ectomycorrhizal community structure. 4) To characterize the species components of key saprobic fungal communities. 5) To coordinate development of software tools for rapid sequence classification and species level identification. Completing the sequence of R. salebrosus (1) will be done in conjunction with the Joint Genome Institute, and a consortium of collaborators. The immediate outcome of this work is that it will facilitate comparative genomics among ectomycorrhizal fungi and lead to a better understanding of the biochemical diversity of these organisms. Insight into the evolutionary pattern of this critical symbiosis is also an expected outcome. Understanding the pattern of aerial spore dispersal (2) and the effects of host root density on mycorrhizal community structure (3) will lead to a functional understanding of the classic spatial and temporal patterns that have been well documented in ectomycorrhizal communities. This knowledge will be useful for reforestation or for production of high-value edible fungi such as Boletus edulis, Matsutake, or Cantharellus. The key saprobic communities we are targeting (4) include those that are present in buildings and those that are involved with cell wall degradation of grasses used for biofuel production. In the case of indoor air fungi, we expect our results to tie in directly with the concerns about allergies and "sick buildings", and in the case of saprobic communities our work will contribute a wealth of enzymes for use in production of biofuels. The coordination of software tools to facilitate fungal identification from sequence is an ongoing project with the Fungal Environmental Sampling and Informatics Network (FESIN). We expect our first product to be curation of the GenBank sequences used for identification (e.g. ITS, LSU, SSU). Our initial work on this lead to a open letter to Science that was signed by 257 scientists (Bidartondo et al 2008, Science 319:1616) and called for third-party annotation of sequences . We are now progressing toward rules for such annotations, and creation of a third-party database where this can be done.
Project Methods
We are working with the Joint Genome Institute to complete the genome sequencing for R. salebrosus. Our role is to provide high quality total genomic DNA, and total RNA from several different conditions. The nucleic acids will be extracted by standard methods. To examine aerial spore dispersal we have placed sample stations and bait seedling at 16 locations in Pt. Reyes National Seashore. We will use sequence analysis of the Internal Transcribed Spacer (ITS) region to identify the fungal spores captured and the fungi that successfully colonize the seedlings. In addition we will establish inoculation curves for key species using the methods we have already employed with Rhizopogon (Bruns et al. New Phytol. 2009, 181:463-470), and we will determine spore dispersal curves from individual mushrooms using short-range sampling onto microscope slides. The effect of root density on mycorrhizal community structure will be tested with a combination of field sampling and manipulative growth chamber experiments. Saprobic community structure will be analyzed by sequence analysis of the ITS and LSU. This will be facilitated by high-throughput pyrosequencing (Roesch et al. 2007 Isme J. 1:283-290, Hudson 2008, Mol Ecol. Res. 8:3-17).

Progress 10/01/09 to 09/30/14

Outputs
Target Audience: The target audience for this work includes scientists, particularly ecologists and mycologists that study community ecology, mycorrhizal ecology, dispersal, fungal biology or fungal taxonomy. There is also outreach and coordination with amateur or citizen science groups of mycologists, and some interaction with National forest and National park managers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? The people listed below received training in the lab during this period. This included technical training on molecular methods, field sampling methods, and software use. The training related to oral and written desemination of scientific results. Dr. Sara Bronco postdoctoral associate Dr. Rachel Adams postdoctoral associate Akiko Carver Resident Graduate student Dr. Abdul Razaq visiting graduate student (Pakistan) Sydney Glassman Resident Graduate student Lisa Rosenthal Undergraduate (now graduated) Noah Gardner Undergraduate Judy Chung Technician Angela DiRocco undergraduate student How have the results been disseminated to communities of interest? The results in this reporting period have been desseminated to the scientific community primarily through the eight publications listed under products and discussed above under accomplishments. A total of 17 talks were given by the the PI, two postdocs and one of the graduate students at scientific meetings and departmental seminars, and 4 additional talks were given to public citizen science groups. In addition the text for three websites for the joint genome institute (JGI) were written by the PI, and the underlying genomic data were made possible through the DNA and RNA that we supplied JGI. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Accomplishments in this final year addressed all five goals. For goal 2 a second paper on spore dispersal of basidiomycota was published (Peay & Bruns 2014). This work showed spore dispersal of particular species is highly predictable, and spatially restricted, while many others exhibited highly stochastic spatial/temporal patterns. These patterns had direct effects on pine seeding colonization. The continental pattern of ectomycorrhizal fungi associated with pines was also documented for the first time (Talbot et al. 2014). These two papers coupled with the published work previously reported for this project provide compelling evidence that dispersal limitation is an important process even for wind-dispersed fungi with massive spore production. The effect of root density of ectomycorrhizal communities (goal 3) turned out to be barely detectable (Branco et al 2013), yet an effect on saprotrophic communities was unexpectedly found. The work also resulted in methodological improvements in a technique used to assay actively growing fungi. Three papers on saprotrophic fungal communities (Adams et al 2013 a, b, 2014) revealed new aspects of saprotrophic fungal communities in housed. This work showed that most fungi found on indoor surfaces are derived from outdoors and are not likely to be actively growing of the surfaces. This pattern even extended to human skin surfaces, which surprisingly were found to be dominated by fungi "collected" from the outdoor environment. Drains were one of the few exceptions where unique fungal communities were resident. No significant effect of room use on fungal communities was found. Indoor fungal communities were also found to have a long residence time, and unique community components were shown to linger in rooms for months or perhaps years. In contrast indoor bacterial communities were different between rooms, and the human signature of these communities was obvious. This human input helped distinguish indoor from outdoor bacterial communities. The curation of fungal sequence databases is a pivotal step toward goal 5 that was addressed in the Ceja-Navarro et al. 2014 paper. The results of this work made sequence identification of ectomycorrhizal fungi much more accurate and efficient. In coordination with the Joint Genome Institute a draft genome of Rhizopogon salebrosus was completed. Problems with obtaining high quality DNA slowed this work down, but in the final year of project goal 1 was finally achieved. As reported last year, we had also managed to help complete two other genomes of other ectomycorrhizal fungi while we worked out the problems with R. salebrosus.

Publications

  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Bates ST, Ahrendt S, Bik HM, Bruns TD, Caporaso JG, Cole J, Dwan M. Meeting Report: Fungal ITS Workshop 2013. Standards in genomic sciences 8 (1): 118
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Branco S, Bruns TD, Singleton I. 2013. Fungi at a small scale: spatial zonation of fungal assemblages around single trees. PLoS One 8(10) e78295
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Ceja-Navarro, J.A., N.H. Nguyen, U. Karaoz, S.R. Gross, D.J. Herman, G.L. Andersen, T.D. Bruns, J. Pett-Ridge, M. Blackwell, and E.L. Brodie, Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of Odontotaenius disjunctus. Isme Journal, 2014. 8(1): p. 6-18.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Koljalg, U., R.H. Nilsson, K. Abarenkov, L. Tedersoo, A.F.S. Taylor, M. Bahram, S.T. Bates, T.D. Bruns, J. Bengtsson-Palme, T.M. Callaghan, B. Douglas, T. Drenkhan, U. Eberhardt, M. Duenas, T. Grebenc, G.W. Griffith, M. Hartmann, P.M. Kirk, P. Kohout, E. Larsson, B.D. Lindahl, R. Luecking, M.P. Martin, P.B. Matheny, N.H. Nguyen, T. Niskanen, J. Oja, K.G. Peay, U. Peintner, M. Peterson, K. Poldmaa, L. Saag, I. Saar, A. Schuessler, J.A. Scott, C. Senes, M.E. Smith, A. Suija, D.L. Taylor, M.T. Telleria, M. Weiss, and K.H. Larsson, Towards a unified paradigm for sequence-based identification of fungi. Mol. Ecol. 2013. 22(21): p. 5271-5277.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Adams, R.I., M. Miletto, J.W. Taylor, and T.D. Bruns, The Diversity and Distribution of Fungi on Residential Surfaces. Plos One, 2013. 8(11).
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Adams, R.I., A.S. Amend, J.W. Taylor, and T.D. Bruns, A Unique Signal Distorts the Perception of Species Richness and Composition in High-Throughput Sequencing Surveys of Microbial Communities: a Case Study of Fungi in Indoor Dust. Microbial Ecology, 2013. 66(4): p. 735-741.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Adams R.I., Miletto M, Lindow S.E., Taylor J.W., TD Bruns. 2014. Airborne Bacterial Communities in Residences: Similarities and Differences with Fungi. PloS One 9 (3), e91283
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Talbot J.M., Bruns T.B., Taylor J.W., Smith D.P., Branco S., Glassman S.I., Erlandson S., Vilgalys R., Liao H-L., Smith M, and Peay K.G. 2014. Endemism and functional convergence across the North American soil mycobiome. Proc. Natl. Acad. Sc. (USA). 111 (17), 6341-6346
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Peay KG, TD Bruns. 2014. Spore dispersal of basidiomycete fungi at the landscape scale is driven by stochastic and deterministic processes and generates variability in plantfungal interactions. New Phytol. 204 (1), 180-191


Progress 01/01/13 to 09/30/13

Outputs
Target Audience: The target audience for this work includes scientists, particularly ecologists and mycologists that study community ecology, mycorrhizal ecology, dispersal, fungal biology or fungal taxonomy. There is also outreach and coordination with amateur or citizen science groups of mycologists, and some interaction with National forest and National park managers. In the 9 month reporting period talks were given by Bruns at two scientific meeting and two meetings of amateur mycologists * The North American Mycoflora Project. Alberta Mycological Society, Annual Foray, Castle Rock, Alberta, Aug 30, 2013. *Synthesizing Pattern and Process of Microbial Ecology in the Built Environment – the experimental road forward. Sloan Foundation Microbial Ecology of Built Environment Conferences, Boulder Co. May 24, 2013 * Toward a global view of fungal biodiversity: challenges and opportunities. Keynote talk, Opening of IDIV Center for Biodiversity, Leipzig Germany, April 19, 2013 * The North American Mycoflora Project. Sonoma Mycological Association Camp January 20, 2013. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? The following people received training in the lab during this period Dr. Yu Liang Visiting scholar (China) Dr. Sara Bronco postdoctoral associate Dr. Rachel Adams postdoctoral associate Dr. Sobia Ilyas visiting graduate student (Pakistan) Dr. Abdul Razaq visiting graduate student (Pakistan) Sydney Glassman Resident Graduate student Dr. Nhu Nguyen Resident Graduate student (now graduated) Judy Chung undergraduate student Lisa Rosenthal undergraduate student Benjamin Araki undergraduate student The postdoctoral associates honed their writing and analytical skills. The graduate students learned technical skills in high-throughput sequence, and bioinformatics and were guide through the process of proposal, manuscript, and dissertation writing. Ngu Nguyen completed his PhD and moved on successfully to a postdoctoral position at the University of Minnesota. Undergraduates learned basic lab skills, field-sampling skills, and were involved with directed studies. Liang Yu, a visiting scholar, gained insight into the US scientific system and improved his writing and speaking skills. The two Pakistani students learned sequence and statistical analyses and were able to complete their degrees within a few months of returning home. How have the results been disseminated to communities of interest? The primarily mode of dissemination to the scientific community was through publication. Talks from PI were also presented at two scientific meetings: *Synthesizing Pattern and Process of Microbial Ecology in the Built Environment – the experimental road forward. Sloan Foundation Microbial Ecology of Built Environment Conferences, Boulder Co. May 24, 2013 * Toward a global view of fungal biodiversity: challenges and opportunities. Keynote talk, Opening of IDIV Center for Biodiversity, Leipzig Germany, April 19, 2013 Outreach to citizen science groups included two talks: * The North American Mycoflora Project. Sonoma Mycological Association Camp January 20, 2013. * The North American Mycoflora Project. Alberta Mycological Society, Annual Foray, Castle Rock, Alberta, Aug 30, 2013. What do you plan to do during the next reporting period to accomplish the goals? Fieldwork in the Rim Fire area will be targeted at understanding mycorrhizal dispersal (goal 2), and the analyses of data collected last summer will also contribute to this goal. Work on saprobic fungal communities (goal 4) in building is ongoing, and some of the work has moved into a model chamber study. Several papers in this area will be published in the next period. A major collaborative paper on the sequence database curation will be published in the next year (goal 5).

Impacts
What was accomplished under these goals? The draft genome of two mycorrhizal fungi, Suillus brevipes and Wilcoxina mikolae, were completed by work in our lab in coordination with JGI. A number of important results were reported in the five publications listed above as products. In Schecter and Bruns (2013) we show that serpentine soil chemistry is a major determinant of arbuscular mycorrhizal (AM) community. Previously it was known that the AM community differed between serpentine and non-serpentine soil, but it was unclear whether this was driven by the differences in host plants found in these soils or by the soil chemistry itself. We separated these two effects by using a common garden design where plants, and AM inoculum were controlled. In the Wong and Bruns (2013) paper we present a new way to germinated seeds of the mycoheterotrophic plant Pterospora amdromedea. This is a plant with an unusual biology in that it is a non-photosynthetic parasite of mycorrhizal fungi. Prior work from our lab had shown that mycelium of its host fungi induce seed germination, while non-host fungi lack that ability. In the latest paper we show that we can germinate a much higher percentage of seeds with a simple gibberellic acid treatment than can be achieved with its host fungus. This is important because the low germination rate had inhibited the study of this plant, which is a rare and endangered plant in the Lake States region. Two papers contributed to the our knowledge of saprobic fungal communities. In the Kerekes et al. 2013 paper we examined the determinants of fungal species composition and richness in tropical tree litter communities, and found, unexpectedly, that long-term nutrient additions increased rather than decreased fungal richness. Individual nutrients have more subtle effects, but all combinations of nutrients that contained increased phosphorus had a similar composition of fungi. In the Adams et al. 2013 paper we show that the primary determinant of fungal composition in houses is outdoor air, and differences in fungal composition between houses is related to dispersal limitation. This work is important because most fungal work in buildings has been focused on buildings where water problems have caused mold problems. When we look at “healthy buildings” instead, we see that the outdoor environment is the overwhelming source of fungi in the air. The short distance (<0.5 km) over which we saw dispersal limitation was a novel finding that has major implications for fungal community ecology. In addition we developed an inexpensive way to monitor fungal composition of the air over month long periods. This is likely to be used extensively by indoor air researcher.

Publications

  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Schecter, S.P. and T. D. Bruns. 2013. A Common Garden Test of Host-Symbiont Specificity Supports a Dominant Role for Soil Type in Determining AMF Assemblage Structure in Collinsia sparsiflora. PLOS ONE 8 (2), e55507
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Wong, V.l. and T.D. Bruns 2013. Gibberellic acid induces asymbiotic germination of the obligate mycoheterotroph Pterospora andromedea (Ericaceae). Madro�o 60: 186192
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Kerekes J.F., Kaspari M., Stevenson B., Nilsson H., Hartmann M., Amend A., Bruns, T. D. 2013. Nutrient enrichment increased species richness of leaf litter fungal assemblages in a tropical forest. Mol. Ecol. 22: 2827-2838
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Nguyen N. N., Kerekes J.F., Vellinga E.C. and Bruns T.D. 2013 Synonymy of Suillus imitatus, the imitator of two species within the S. caerulescens/ponderosus complex. Mycotaxon 112: 389-398
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Adams, RI, Meletto M, Taylor JW, Bruns TD 2013. Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. ISME 1-12


Progress 01/01/12 to 12/31/12

Outputs
OUTPUTS: Five peer-reviewed journal articles(24-28), three non-peer reviewed articles (29-30), and a website were produced during the last year. In addition Bruns gave three lectures at scientific meetings (Max Planck biodiversity symposium; North American Mycoflora conference, Citizen Science Conference, UC Davis), one lecture to a government agency (National Park Service, Washington DC), two departmental seminars (Univ. Oregon, Eugene; Chicago Botanical Gardens), and one lecture to the general public (UC Berkeley homecoming). Fieldwork continued on the NSF funded Dimensions of Biodiversity project; this included field sampling in Florida, Mississippi, California, and Oregon, and from this work we have assembled the data necessary for several papers. PARTICIPANTS: Participants include the following: PhD students Nhu Nguyen, Sydney Glassman; Postdoctoral Researchers Sara Branco and Rachel Adams; Technician Tim Szaro. TARGET AUDIENCES: The target audiences for this work are 1) academic researchers in the areas of ecology and systematics 2) forest land managers, including the National Park Service, and 3) amateur plant and mushroom groups. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
The published work during this period was important for the following reasons. 1) We demonstrated different roles for mycorrhizal and saprophytic fungi in the breakdown and release of nutrients in litter versus mineral soil (Talbot et al 2012). 2) We showed that contrary to what had been stated in the literature, plants that are parasites on arbuscular mycorrhizal fungi do not target a narrow set of these fungi (Merckx et al 2012). 3) We found that the observed differences in community structure of arbuscular mycorrhizal fungi is driven more by soil chemistry than by plant genetic (Schechter & Bruns 2012). 4) We discovered that propagules of ectomycorrhizal fungi can live at least six years under natural soil conditions, and several species that exhibited this longevity were not expected to do so (Nguyen et al 2012). 5) We measured spore dispersal of ectomycorrhizal fungi directly via qPCR and high-throughput sequence analysis and indirectly via pine seedling bioassays, and we showed that these different measures are congruent. Furthermore we showed that ectomycorrhizal spore dispersal is limited within distances of less that a kilometer from a forest edge (Peay et al 2012). Bruns organized the first meeting of North American mycoflora project. This resulted in two papers (Bruns 2012 & Bruns & Beug 2012), a website, and momentum toward this goal. The mycoflora project is important because we currently have very poor knowledge of fungi we have in North America, and very little information on their ranges, habitats, and hosts. The goal of this project is to set up a framework for collecting and assembling this information for our native fungi.

Publications

  • Peay KG, Shubert M, Nguyen NH and Bruns TD. 2012 Measuring ectomycorrhizal fungal dispersal: macroecological patterns driven by microscopic propagules. Mol. Ecol. 21 (16): 4122-4136
  • Bruns TD 2012. The North American Mycoflora project-the first steps on a long journey New Phytol. 196 (4), 972-974
  • Bruns TD and Desjardin DE 2011 Spongiforma squarepantsii. What's in a name and what's the underlying biology Mushroom the Journal 107 (vol. 28): 55-56, 58-59.
  • Bruns TD and Beug MW 2012. Working toward a North American Mycoflora for Macrofungi. McIlvainea (on line journal of American Amateur Mycology) http://namyco.org/publications/mcilvainea/v21/Toward_NA_Mycoflora.htm l
  • Talbot JM, Bruns TD, Smith DP, Branco S, Glassman SI, Erlandson S, Vilgalys R, Peay KG 2012. Independent roles of ectomycorrhizal and saprotrophic communities in soil organic matter decomposition. Soil Biol. Biochem. (in Press)
  • Merckx VSFT, Janssens SB, Hynson NA, Specht CD, Bruns TD; Smets EF 2012. Mycoheterotrophic interactions are not limited to a narrow phylogenetic range of arbuscular mycorrhizal fungi. Mol. Ecol. 21:1524-1532
  • Schecter SP and TD Bruns 2012. Edaphic sorting drives arbuscular mycorrhizal fungal community assembly in a serpentine/non-serpentine mosaic landscape, Ecosphere 3 (5) pp. art42
  • Nguyen NH, Hynson NA, and Bruns TD. Stayin' Alive: survival of mycorrhizal fungal propagules from six-year-old forest soil. 2012. Fungal Ecology 5: 741-746


Progress 01/01/11 to 12/31/11

Outputs
OUTPUTS: Five peer reviewed journal papers and six non-reviewed articles were published during the review period. In addition Bruns presented six research talks and one outreach talk at Scientific meetings (Mycol. Soc. Amer., Symbiosis workshop), invited departmental seminars (Universidad del Turabo, Puerto Rico; UC Davis (2), Univ Mich.) and at a public venue (Yosemite Forum). Two graduate students (Val Wong, and Jennifer Kerkes) completed their PhD degrees. Work also started on new five-year NSF funded project that is focused on survey the dimensions of diversity of ectomycorrhizal communities across North America. As part of this work six sites were sampled in pinaceous forest in Alaska, California, and North Carolina. The first results from this work are just now being analyzed. PARTICIPANTS: Participants include the following: PhD students Sydney Glassman, Jennifer Kerekes, Nhu Nguyen, and Valarie Wong; Postdoctoral associates: Sara Branco and Prachand Shrestha; Technician: Tim Szaro. TARGET AUDIENCES: The target audiences for this work are 1) academic researchers in the areas of ecology and systematics 2) forest land managers, including the National Park Service, and 3) amateur plant and mushroom groups. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The published work during this period was important because it 1) set standards for reporting on high-throughput sequence data in ecological studies (Nilisson et al 2011); 2) surveyed the fungi that breakdown energy crops in nature and found many that have superior degradation abilities to Trichoderma, the most widely used source of cellulases in the bioenergy industry (Shresha et al 2011); 3) laid out a new theory to explain a widely observed spatial pattern in the succession of ectomycorrhizal fungi (Peay et al 2011); 4) reviewed the complex pattern of fungal associations in mycorrhizal parasitic plants (Hynson and Bruns 2010); and 5) described a new, bizarre, species of mycorrhizal fungus (Desjardin et al 2011). In addition the set of six "Presidents Corner" essays (Bruns, inoculum articles), helped steer the field of mycology in this country and generated interest in starting work on a North American Mycoloflora.

Publications

  • Nilsson, RH, Tedersoo, L, Lindahl,BD, Kjoller,R, Carlsen, T, Quince, C, Abarenkov, K, Pennanen, T, Stenlid, J, Bruns, T, Larsson, KH, Koljalg, U, Kauserud, H. 2011. Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities New Phytol. 191(2): 314-318
  • Bruns T.D. 2011. Working toward a North American Mycobiota for macrofungi: what is stopping us Inoculum News Letter to the Mycological Society of America 62:1-3.
  • Bruns T.D. 2011. Expanding Faculty Positions in Mycology. Inoculum News Letter to the Mycological Society of America 62(3):1-3.
  • Bruns T.D. 2011. Why is Mycology a small field And how can we expand it Inoculum News Letter to the Mycological Society of America 62(2):2-4.
  • Bruns T.D. 2011. Meet and Eat Grants: where is our next meal going to come from. Inoculum News Letter to the Mycological Society of America 62(1):4-5.
  • Bruns T.D. and Dickie I. 2010. Point: counter point: why fungi are (not) microbes. Inoculum News Letter to the Mycological Society of America 61(6):8-11.
  • Bruns T.D. and Dickie I. 2010. IMC9: What a meeting! Inoculum News Letter to the Mycological Society of America 61(5):8-11.
  • Shrestha, P, Szaro, TM, Bruns, TD, Taylor, JW 2011. Systematic search for cultivable fungi that best deconstruct cell walls of Miscanthus and sugarcane in the field. Applied and Environmental Microbiology, 77: 5490-5504.
  • Desjardin, D.E., Peay,K.G., Bruns, T.D. 2011. Spongiforma squarepantsii, a new species of gasteroid bolete from Borneo. Mycologia 103: 1119-1123.
  • Peay, K. G., P. G. Kennedy, and T. D. Bruns. 2011. Rethinking ectomycorrhizal succession: are root density and hyphal exploration types drivers of spatial and temporal zonation Fungal ecology 4:233-240.
  • Hynson, N. A. and Bruns, T.D. 2010. Fungal hosts for mycoheterotrophic plants: a nonexclusive, but highly selective club. New Phytol. 185:598-601.


Progress 01/01/10 to 12/31/10

Outputs
OUTPUTS: Five peer-reviewed research papers were published in 2010, and four research talks were presented by Bruns at the Mycological Society of America, the International Mycological Congress, Harvard University, and Middlebury University. Two PhD students, Shannon Schechter and Nicholas Rosenstock, completed their degrees and moved on to postdoctoral positions, and two postdoctoral associates, Anthony Amend and Kabir Peay, completed their work and went on to a second postdoctoral position and a faculty position, respectively. The ongoing work in the lab has shifted toward metagenomic analysis of both mycorrhizal and saprobic fungal communities. These new tools are greatly enhancing our ability to dissect fungal communities. . We have also initiated a fungal survey of Yosemite National Park using members of the trained public and university researchers, and we are continuing a similar survey of Pt Reyes National Seashore. In the first year of the Yosemite survey we have more than doubled the number of fungi known from the park, and have found that the mycoflora of Yosemite is very distinct from that of Pt. Reyes National Seashore. PARTICIPANTS: Participants include the following: PhD students Sydney Glassman, Jennifer Kerekes, Nhu Nguyen, Shannon Peters, Nicholas Rosenstock, and Valarie Wong; Postdoctoral associates: Anthony Amend and Kabir Peay; Technician: Tim Szaro. TARGET AUDIENCES: The target audiences for this work are 1) academic researchers in the areas of ecology and systematics 2) forest land managers, including the National Park Service, and 3) amateur plant and mushroom groups. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The published work during this period showed that: 1) the ectomycorrhizal (EM) community is strongly shaped by soil type in tropical dipterocarp forests (Peay et al. 2010a); 2) dispersal limitation is important even within a few kilometers of a forest edge (Peay et al. 2010b); 3) fungi present in the indoor environment are more diverse than expected and have unique global distribution patterns (Amend et al 2010a), 4) tropical mycoheterotrophic plants differ in the way they interact with mycorrhizal fungi from temperate mycoheterotrophs (Merckx 2010); and 5) high throughput sequence analysis produces highly distorted views of fungal absolute abundance but a rough semi-quantitative metric for individual fungi (Amend et al 2010b),. The first two results are important because they contribute to our understanding of the community structure of ectomycorrhizal fungi. The finding of dispersal limitation is particularly important because it was not expected, and it means that forest expansion will often be limited by fungal inoculum. The third result is important because the diversity of indoor fungi was found to be highest in the temperate zones and lowest in the tropics; this is the reverse of diversity patterns for most other organisms. The work on quantifying the biases of high-throughput sequence is important because the method is widely used without regard to the underlying biases. This work was the first to used spiked quantities of known fungi to examine error rate.

Publications

  • Peay, K. G., Kennedy, P. G., Davies, S. J., Tan, S. & Bruns, T. D. 2010a. Potential link between plant and fungal distributions in a dipterocarp rainforest: community and phylogenetic structure of tropical ectomycorrhizal fungi across a plant and soil ecotone. New Phytol. 185, 529-542.
  • Peay, K. G., Garbelotto, M. and Bruns, T. D. 2010b. Evidence of dispersal limitation in soil microorganisms: Isolation reduces species richness on mycorrhizal tree islands. Ecology 91: 3631-3640.
  • Amend A.S., Seifert, K.A., Samson, R., and Bruns T.D. 2010a. Indoor Fungal Assemblages are Geographically Patterned and More Diverse in Temperate Zones than the Tropics. Proc. Nat. Acad. Sc. 107(31): 13748-13753
  • Merckx, V. Stockel, M., Fleischmann, A., Bruns, T. D., Gebauer. G. 2010. 15N and 13C natural abundance of two mycoheterotrophic and a putative partially mycoheterotrophic species associated with arbuscular mycorrhizal fungi. 2010. New Phytol. 188 (2): 590-596
  • Amend, A., Seifert, K., Bruns, T.D. 2010b. Quantifying microbial communities with 454 pyrosequencing: Does read abundance count Mol. Ecol. (in press, doi: 10.1111/j.1365-294X.2010.04898.x)


Progress 10/01/09 to 12/31/09

Outputs
OUTPUTS: Seven peer-reviewed scientific papers were published during the start of this new project. In addition Dr. Bruns presented a talk at the Third International Barcode of Life Conference in Mexico City, and a talk to the Mycological Society of Los Angles. New work was started on quantifying airborne spore dispersal of ectomycorrhizal fungi. This work depended on high-throughput DNA sequencing and quantitative PCR coupled with pine seedling bioassays. The results from this work show that species composition of fungal spores changes in relationship to distance from a forest border, and that inoculum of all fungi becomes limiting for seedling establishment beyond a kilometer from a forest edge. PARTICIPANTS: The following PhD students are worked on these parts of project: Nhu Nguyen works on spore establishment and bacterial interactions in ectomycorrhizal communities; Jennifer Kerekes worked on structure of saprophytic fungal communities; Nicole Hynson worked on mycoheterotrophic and mixotrophic members of the Pyrolaceae; Nicholas Rosenstock worked on effects of cat ion depletion on ectomycorrhizal community structure; Valerie Wong; Shannon Schecter worked on arbuscular mycorrhizal communities and plant adaptation to serpentine soil. The following Postdoctoral researchers are working on these parts of the project: Kabir Peay worked on spore dispersal and establishment patterns in ectomycorrhizal communities. TARGET AUDIENCES: Much of work contributes to basic science and our target audience for this would be ecologists, microbiologist, mycologists, and foresters. In addition we have had long-term interactions with Park Service at Pt. Reyes National Seashore and have advised them on fungal issues many times. We also conduct public outreach through the local mushroom clubs such as the Bay Area Mycological Society, the Mycological Society of San Francisco, and the Sonoma Mycological Association. Members of the lab have given talks at all of these in the past year, and the Bay Area Mycological Society meets on the Berkeley campus. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
The published work from this project demonstrated that spores of Rhizopogon are capable of retaining their viability in the soil for many years (1). This is interesting because Rhizopogon species often dominate the colonization of pine seedlings in postfire and post-logging settings. Our work also showed that soil heating intensity and ash inputs fire can change the composition of the ectomycorrhizal (EM) community that colonized seedlings (2,3). This result has important implications for postfire dynamics of EM fungal communities. Continued work on competitive interaction among EM fungi showed that "priority effects" are the dominant factor in early spore colonizers. Essentially, the fungus that arrives first can prevent others from colonizing. Stable isotopes were used to show that Pyrola aphylla is a true mycoheterotrophic plant (5). That is to say it receives its carbon from surrounding plants via a shared mycorrhizal fungus. This is significant because it is the first plant in the family to show such behavior. The structures of saprobic fungal communities are addressed in publication 6; this area of research is poorly developed relative to EM fungal communities, but has great potential for novel findings. Suillus quiescens was described as a new EM fungal species. This is the most common species of Suillus on Santa Cruz Island, and sequence-based identification showed that it has a much wider range in California and Oregon.

Publications

  • Bruns T. D., Peay, K. G., Boynton P. J., Lisa C. Grubisha, L. C., Hynson, N. A., Nhu H. Nguyen, N. H., Rosenstock, N. P. 2009. Inoculum potential of Rhizopogon spores increased with time over the first four years of a 99-year spore burial experiment. New Phytol. 181:463-470.
  • Peay, K G., Garbelotto, M., and Bruns, T. D. 2009. Spore heat resistance plays an important role in disturbance-mediated assemblage shift of ectomycorrhizal fungi colonizing Pinus muricata seedlings. J. Ecol. 97:537-547.
  • Peay, K.G., Bruns, T. D. and Garbelotto, M. 2009. Testing the ecological stability of ectomycorrhizal symbiosis: effects of heat, ash and mycorrhizal colonization on Pinus muricata seedling performance. Plant Soil 330:291-302.
  • Kennedy, P. G. Peay, K.G. and Bruns T.D. 2009. Root tip competition among ectomycorrhizal fungi: are priority effects a rule or an exception Ecology 90:2098-2107.
  • Hynson, N.A., Preiss, K., Gebauer, G. and Bruns. T.D. 2009. Isotopic evidence of full and partial myco-heterotrophy in the plant tribe Pyroleae (Ericaceae). New Phytol. 182:719-726.
  • Robinson C. H., Szaro, T. M, Izzo, A. D., Anderson, I. C., Parkin, P. I., Bruns, T. D. 2009. Spatial distribution of Fungal Communities in a coastal Grassland Soil. Soil Biology & Biochem. 41:414-416.
  • Bruns, T. D., Grubisha, L. C. Trappe, J.M., Kerekes J., Vellinga, L. C. 2009. Suillus quiescens, a new species commonly found in the spore bank in California and Oregon. Mycologia 102(2): 438-446.