October 21-23, 2015


Download the full program for the agenda, abstracts, and participant list! Please note: to save paper, we will only be distributing hard copies of the agenda.

Full program PDF: 7th_ArgonneSoils2015_FullProgram


Tuesday, October 20

Optional data analysis tutorials (separate registration required)

8:00 Breakfast and registration

9:00-12:00 MG-RAST and downstream analysis

12:00 Lunch

1:00-5:00  Microbial community analysis

The MG-RAST team will present a half-day tutorial on MG-RAST, a web-based analysis and integration platform for metagenomic data with over 80,000 data sets (http://metagenomics.anl.gov). This tutorial will briefly introduce the MG-RAST pipeline and the web interface and focus on using the MG-RAST API for analysis. The majority of the tutorial will focus on using R (a statistical language) to analyze metagenomic data after processing with MG-RAST.

Martin Hartmann will present a half-day tutorial devoted to analysis of microbial community sequence data. This lecture-style lesson will cover quality control, OTU clustering, and taxonomic classification of amplicon reads with substantial time for questions and discussion. No prior experience is required.

Wednesday, October 21

7:30 Registration
Continental breakfast

8:15 Introduction & announcements

Session I: The Underexplored Biosphere

Ecological and evolutionary insight into the persistence of soil bacteria
Jay T. Lennon, Stuart E. Jones

Phylogenetic distribution of resuscitation genes in soil microbes
Fan Yang, Stuart E. Jones, Jay T. Lennon, Adina Howe

Moleculo hybrid synthetic long reads reconstruct full genomes from the rare biosphere with functional potential elucidated by high resolution mass spectrometry
Richard Allen White III, Eric M. Bottos, Taniya Roy Chowdhury, Carrie D. Nicora, Kristin Burnum-Johnson, Lee Ann McCue, Erin Baker, Janet K. Jansson

Uncovering Earth’s virome
David Paez-Espino, Alexander D. Thomas, Emiley Eloe-Fadrosh, Marcel Huntemann, Amrita Pati, Edward Rubin, Natalia N. Ivanova, Nikos C. Kyrpides

Moldy dark matter: Inferring the taxonomic and funcational diversity of soil fungi through a combined meta-‘omic strategy
J.R. Herr

Soil, lateral gene transfer, and hybrid genomes—Invited
Robert G. Beiko

10:40 Break

Session II: Breakthroughs in Informatics

Accurate detection and quantification of target genes in shotgun metagenomes: Method development and application to the nitrogen cycle genes
Luis H. Orellana, Luis M. Rodriguez-R, Kostas T. Konstantinidis

Hunting down frame shifts: Processing amplicon data of biphenyl and benzoate dioxygenase genes
Michal Strejcek, Tomas Macek, Ondrej Uhlik

RefSoil: Continuous progress in reference soil database
Jinlyung Choi, Erick Cardenas, Ryan Williams, Adina Howe


12:15 Lunch

1:30 Posters I

Session III: Frozen(ish) Soils

Soil microbial communities as sentinels of environmental change—Invited
Martin Hartmann

Control of boreal forest soil decomposition processes by plant secondary compounds
Mary-Cathrine Leewis, Mary Beth Leigh

Serving as a glimpse into the past, Alaskan paleosols harbor unique microbial diversity
Robyn A. Barbato, Natalia Vinas, Robert Jones, Karen Foley, Thomas Douglas, Julie Esdale, Edward Perkins

The genetic potential for siderophore-mediated dissimilatory iron reduction in arctic soil microbial communities
Archana J. Srinivas, Elizabeth A. Dinsdale, David A. Lipson

Frozen in time? Microbial strategies for survival and carbon metabolism over geologic time in a Pleistocene permafrost chronosequence
Rachel Mackelprang, Thomas A. Douglas, Mark P. Waldrop


Group photo

5:00 Mixer – cash bar

6:30 Plenary session – Keynote talk and buffet dinner

What do ‘omics do best?
David D. Myrold

Thursday, October 22

7:30 Continental breakfast

Session IV: Microbial members of the ecosystem

Identifying biotic and abiotic factors controlling methane emissions in a freshwater wetland—Invited
Kelly Wrighton

Composition of bacterial communities tracks salinity and flooding gradients
Pamela Weisenhorn, Jack A. Gilbert, Loretta Battaglia

Soil bacterial and fungal community dynamics during conversion of Conservation Reserve Program (CRP) fields to cropping systems
Mamatha Kakarla, Jennifer Moore-Kucera, Lisa Fultz, Chenhui Li, Veronica Acosta-Martinez, Jon Zak, Kameswara Rao Kottapalli

Diverse carbon utilization from field collected rhizosphere soils using paired metagenomic and metatranscriptomic approaches
Aaron Garoutte, Jim Tiedje

10:00 Break

Using critical zone observatories to understand how microbial community structure changes with elevation
Chelsea Carey, Stephen C. Hart, Clifford Riebe, Sarah Aciego, Molly Blakowski, Emma Aronson

The importance of dispersal in microbial communities—Invited
Kabir G. Peay

11:10 Break

Session V: If a tree falls in the forest, do the microbes respond?

Forest harvesting affects the soil microbial diversity of nitrogen- and carbon-cycling genes: A study of five ecozones across North America
Erick Cardenas, Kendra Maas, Luis Orellana, Kostas T. Konstantinidis, William W. Mohn

Structure and activity of denitrifier communities in biochar-amended soil and their impact on N2O emissions
Johannes Harter, Ivan Guzman Bustamante, Stefanie Kühfuß, Reiner Ruser, Reinhard Well, Oliver Spott, Mohamed El-Hadidi, Daniel Huson, Andreas Kappler, Sebastian Behrens

Stable isotope probing reveals long-term impacts of timber harvesting on cellulolytic soil community
Roland Wilhelm, Erick Cardenas, Hilary Leung, András Szeitz, Lionel D. Jensen, William Mohn

Linking ecosystem processes to individual microbes in forest soils
Petr Badrian, Salvador Lladó-Fernández, Rubén López-Mondéjar, Tomás Vetrovsky, Adina Chuang, Howe, Katharina Riedel, Lucia Zifcáková


1:00 Lunch

2:00 Posters II

Session VI: Microbes in a changing world

Soil microbial community responses to warming as revealed by comparative metagenomics—Invited
Eric Johnston, Chengwei Luo, Luis M. Rodriguez-R, Liyou Wu, Shi Zhou, Kai Xue, Zhili He, Mengting Maggie Yuan, Yiqi Luo, Edward A.G. Schuur, James R. Cole, James M. Tiedje, Jizhong Zhou, Kostas Konstantinidis

Increased soil C storage under anthropogenic N deposition: lignocellulolytic baterial ascendance in a fungal world
Zachary B. Freedman, Rima A. Upchurch, Donald R. Zak, Lauren C. Cline

Changes in microbial community structure and function in response to long-term N addition as revealed by soil metaproteomics—Invited
Katharina M. Keiblinger, Stefan J. Forstner, Stefanie Kloss, Stephan Fuchs, Kathrin Riedel, Martin H. Gerzabek, Sophie Zechmeister-Boltenstern

Methylotrophy and archaeal heterotrophy dominate processing of sub-root soil carbon
Cristina N. Butterfield, Zhou Li, Peter Andeer, Susan Spaulding, Trent Northen, Brian C. Thomas, Chongle Pan, Robert Hettich, K. Blake Suttle, Susannah Tringe, Jillian F. Banfield

Why is it so difficult to incorporate metagenomics into traditional soil models? —Invited
Kathe Todd-Brown

5:40 Discussion

6:00 Dinner on your own

Friday, October 23

7:30 Continental breakfast

Session VII: Breakthroughs at the bench

Single cell genomics: From science fiction to mainstream microbiology—Invited
Ramunas Stepanauskas

BacEx segregates microbial DNA from eukaryotic DNA “clutter” allowing for more efficient microbiome sequencing
Robert T. Yamamoto, Allyn Forsyth

Deconstructed PCR: Improved library preparation tools for high throughput amplicon sequencing
Stefan J. Green, Ankur Naqib

Advanced proteomic approaches to soil microbe characterization—Invited
Mary S. Lipton, Carrie D. Nicora, Thomas O Metz, Erin Baker, Richard A. White III, Taniya Roy Chowdhury, Eric M. Bottos, Jennifer E. Kyle, Colin J. Brislawn, Kristin E. Burnum-Johnson, Samuel Payne, Chris Whidbey, Natalie C. Sadler, Janet K. Jansson


10:20 Break

Session VIII: Co-occurrence and interactions among microbes

Microbial Soil Community Responses to Extreme Disturbance: Insights from the Ongoing Subterranean Centralia Coal Mine Fire —Invited
Ashley Shade

Investigating microbial co-occurrence patterns based on metagenomic compositional data
Yuguang Ban, Lingling An, Hongmei Jiang

Elucidating microbial interactions that drive decomposition through a co-occurrence framework
Ryan J. Williams, Kirsten S. Hofmockel, Adina Howe

Modeling the Pseudomonas fluorescens sulfur regulome
Sarah Zerbs, Peter Korajczyk, Frank R. Collart, Philippe Noirot, Peter E. Larsen

Molecular mechanisms of a plant-fungus-bacterial community interaction
Shalaka Shinde, Sarah Zerbs, Peter E. Larsen, Jonathan R. Cumming, Frank R. Collart, Steve J. Callister, Philippe Noirot

Rhizosphere versus endosphere bacterial microbiomes: How much do they overlap?
Marketa Polivkova, Lucie Musilova, Michal Strejcek, Jachym Suman, Tomas Macek, Ondrej Uhlik


1:15 Adjourn



Session I: Titles with odd numbers

Session II: Titles with even numbers
1. High resolution DNA stable isotope probing reveals that root exudate addition to soil changes the identity of the microbes that degrade cellulose but not the rate of degradation
Ashley N. Campbell, Charles Pepe-Ranney, Anh Vinh T. Nguyen, and Daniel H. Buckley

2. Capturing the spatial variability of microbial communities within agricultural soils
Sarah Castle, Jessica Gutknecht, Linda Kinkel, Carl Rosen, Michael Sadowsky, Deborah Samac

3. Plant-microbe interactions: The Populus atlas
Melissa Cregger, Miranda Crouch, Zamin Yang, Dale Pelletier, Rytas Vilgalys, Chris Schadt

4. Effect of a changing in the aboveground plant community on the soil physicochemical properties and microbial community
Marie Duhamel, Kabir Peay

5. Multi-year functional soil metagenomic characterization of cellulosic bioenergy feedstock production systems
DS Duncan, JM Tiejde, GP Robertson, RD Jackson

6. Microbial community arsenic tolerance and the fate of arsenic in soil
Taylor K Dunivin, John Chodkowski, Jackson Sorensen, Ashley Shade

7. Niche and neutral community dynamics in parallelized aerobic, single carbon-source enrichment cultures
Theodore M. Flynn, Jason C. Koval, Kenneth M. Kemner, Dionysios A. Antonopoulos

8. Salinity effects in soil microbial communities, enzyme activity and carbon biogeochemistry in tidal freshwater wetlands
Georgios Giannopoulos, Dong Yoon Lee, Olivia De Meo, Scott Neubauer, Bonnie Brown, Rima Franklin

9. Metagenomics and physiology based analysis of bacterial communities from differently managed agricultural soils
Timothy Gsell and Craig Sweet

10. Study of seasonal variation of desert keratinophilic fungi
P. Hamm, R. C. Mueller, J. Belnap, C. R. Kuske, A. Porras-Alfaro

11. Biogeography and metabolism of dominant bacterial populations in tundra soils
Eric R. Johnston, Luis M. Rodriguez-R, Liyou Wu, Zhili He, Edward A.G. Schuur, Yiqi Luo, James M. Tiedje, Jizhong Zhou, and Konstantinos T. Konstantinidis

12. Manipulating soil temperature and moisture to uncover microbial community trends for modelling purposes
Robert M Jones, Karen L Foley, Charles M Reynolds, Robyn A Barbato

13. Meta- and isolate- genomic analyses of grassland soil microbial communities
Ulas Karaoz, Heejung Cho, Kateryna Zhalnina, Mary Firestone, Eoin Brodie

14. Understanding microbial community responses and limitations to the SPRUCE deep peat heat experiment
Laurel Kluber, Samantha Allen, J. Nicholas Hendershot, Paul Hanson, Christopher Schadt

15. Plant response to various phosphorus sources under nutrient limitation
Peter Korajczyk, Shalaka Shinde, Sarah Zerbs, Frank R. Collart, Philippe Noirot

16. The influences of thorny bamboo growth on the bacterial community in badland soils
Yu-Te Lin and Chih-Yu Chiu

17. Metagenomic and comparative analysis in agricultural and mining soils in Guanajuato, Mexico
María Elena López-Pérez, Gabriela Ana Zanor, María Cristina del Rincón-Castro

18. Soil bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta
Xiaofei Lyu, Junbao Yu, Bin Ma, Scott Chang

19. Microbial ecology of restored floodplains
Christopher W Marshall, Sarah L O’Brien, Kenneth M Kemner, Edward J O’Loughlin, Neil R Gottel, Silvia Alvarez Clare, Aaron A Best, Theodore M Flynn, and Jack A Gilbert

20. Spatio-temporal dynamics of Phymatotrichopsis root rot disease in alfalfa hay production fields
Chakradhar Mattupalli, Casey Curtsinger, Corey A. Moffet, James K. Rogers, Carolyn A. Young

21. Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms
Kyle Meyer, Ann Klein, Jorge Rodrigues, Klaus Nüsslein, James M. Tiedje, Titus Brown and Brendan J.M. Bohannan

22. Proteomics of soil and sediment: Protein identification by de novo sequencing of mass spectra complements traditional database searching
Samuel Miller, Adriana Rizzo, Jacob Waldbauer

23. BAC Sudoku sequencing strategy for in silico screening of large-insert soil metagenomic libraries
Scott Monsma, Jinglie Zhou, Alinne Pereira, Blaine Pfeifer, Timothy Bugni, Scott R. Santos, Megan Niebauer, Erin Ferguson, Ron Godiska, ChengCang Wu, David Mead, and Mark R. Liles

24. Bacterial and archaeal ammonia oxidizers are reduced by increasing timber harvest intensity in surface and subsurface soils of the western Gulf Coastal Plain
Ryan M. Mushinski, Thomas W. Boutton, and Terry J. Gentry

25. Distribution of fungi in arid microenvironments and their potential role on plant growth
Cedric Ndinga Muniania, Katrina Sandona, Jayne Belnap, Cheryl R. Kuske, Andrea Porras-Alfaro

26. Agricultural nitrogen management affects response to ammonium and ammonia oxidizer communities
Jeanette Norton, Yan Ouyang, John Stark, Mussie Habteselassie

27. Identifying microbial habitats in soil using quantum dots and x-ray fluorescence microtomography
Sarah L. O’Brien, Matthew D. Whiteside, Deirdre Sholto-Douglas, Alice Dohnalkova, Daniel Durall, Doga Gursoy, Melanie D. Jones, Libor Kovarik, Barry Lai, Christian Roehrig, Shane Sullivan, Stefan Vogt, Kenneth Kemner

28. Effects of soluble electron shuttles on microbial Fe(III) reduction and methanogenesis in wetland sediments
Edward J. O’Loughlin, Margaret F. Sladek, Dionysios A. Antonopoulos, Theodore M. Flynn, Jason C. Koval, Christopher W. Marshall, and Kenneth M. Kemner

29. Exploring Verrucomicrobia populations in grassland soil using Moleculo
Sarah M. Owens, William L. Trimble, Sarah L. O’Brien, Stephanie M. Greenwald, Dionysios A. Antonopoulos, and Folker Meyer

30. The role of environmental and genetic factors in shaping the microbiome of a highly olfactory bird species
Douglas S. Pearce, Brian Hoover, Gabrielle A. Nevitt and Kathryn Docherty

31. Comparative analysis of metatranscriptomes provide insights of microbial communities under warming conditions
William Rodriguez, Lauren Alteio, Grace Pold, Linda van Diepen, Serita Frey, Jerry Melillo, Kristen DeAngelis, Jeffrey Blanchard

32. Nicotiana roots recruit rare rhizosphere taxa as major root-inhabiting microbes
Muhammad Saleem, Audrey D. Law, Luke A. Moe

33. Fungal community diversity in long-term biochar amended forest soils
Jessica Sarauer, Amy Ross-Davis, Mark Coleman

34. Discovering thermophilic diversity in temperate soils affected by a subterranean coal fire
Jackson Sorensen, Sang-Hoon Lee, Ashley Shade

35. The effects farming practices on fungal communities associated with Glycine max (soybeans)
Terri Tobias, Sara Dean, Winthrop Phippen, Joel Gruver, Andrea Porras-Alfaro

36. Heavy metal tolerant fungal community analysis from temperate pine forest soil using Illumina sequencing
Terry Torres Cruz, Cedar Hesse, Cheryl Kuske, Andrea Porras-Alfaro

37. The diversity of metagenomes in MG-RAST
William L. Trimble, Travis Harrison, Jared Bischof, Kevin P. Keegan, Folker Meyer

38. Who’s on first? Bacterial and fungal colonization of fresh soil minerals
Thea Whitman, Rachel Neurath, Ping Zhang, Tong Yuan, Joe Zhou, Peter Weber, Jennifer Pett-Ridge, Mary Firestone

39. Soil microbial community composition affects the weed suppression potential of green manures
Anthony Yannerell, Yi Lou

40. How does microbial community composition and function change in ageing primary boreal forest ecosystems?
Stephanie A. Yarwood, Tamara Walsky, Mona N. Högberg

41. Identifying Pseudomonas fluorescens genetic resources for metabolism of diverse sulfur nutrients
Sarah Zerbs, Peter Korajczyk, Frank R. Collart, Philippe Noirot, and Peter E. Larsen

42. Active, Near-Surface Methanogens Contribute to Greater Methane Emissions in Exposed Mud Flats in a Freshwater Wetland
J. C. Angle, A. B. Narrowe, M. A. Jackson, G. J. Smith, M. D. Johnston, K. C. Stefanik, D. N. Marcus, R.A. Daly, R. T. McVeety, M. J. Wilkins, C. S. Miller, and K.C. Wrighton

43. Peatland microbial community responses to plant functional group, water table and peat depth
L.J. Lamit, J.T. Lennon, E.A. Lilleskov

44. The Effect of Root Exudate 7,4′-dihydroxyflavone and Naringenin on Soil Bacterial Community Structure
Márton Szoboszlay, Alison White-Monsant, Luke A. Moe

45. Terrestrial Influences on Airborne Microbial Communities
Kathryn M. Docherty, Kristina M. Lemmer, Rebecca L. Hale

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