October 2–4, 2013

Program

Wednesday, October 2

7:00 am Trillium II

Continental breakfast

8:00 am – 12:30 pm Trillium II

Optional data analysis training session: KBase (2 hrs) and MG-RAST (2.5 hrs)

Session 1 KBase (2 hrs)

The DOE Systems Biology Knowledgebase (KBase) is a next generation platform for Systems Biology and Bioinformatics. KBase provides a number of workflows (genomic analyses, metagenomic analyses, RNAseq, GWAS, etc.) all integrated into a single platform with a single programmer’s interface.

Prerequisites: A laptop with virtual box (recent version), some programming knowledge (e.g. Perl, Python), unix command line knowledge

Intended audience: Advanced users of bioinformatics and genomics

Session 2 MG-RAST (2.5 hrs)

MG-RAST is 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.

Prerequisites: A laptop with virtual box (recent version), some general computer knowledge, some R knowledge (beginners’ level) and some statistics background will help you follow this tutorial.

Intended audience: Users of metagenomic data who want to perform more in-depth analyses.

12:00  Sorrell II

Lunch

1:00  Trillium II

Welcome & Introduction

1:20–5:00  Trillium II

Session I: Microbial community structure and function

1:20     Invited: Genomic signatures of ecological trade-offs in microbial communities

Stuart E. Jones

1:40     Invited: Cross-site response of soil microbial community composition and function to elevated nutrient inputs

Jonathan W. Leff, Noah Fierer

2:00     The merlot microbiome: a multi ‘omic approach

Iratxe Zarraonaindia, Sarah M. Owens, Sean M. Gibbons, Jarrad T. Hampton-Marcell, Kristin West, Sita Shimire, Gilles Martin, Safiyh Taghavi, Daniel van der Lelie, Jack A. Gilbert

2:20    Discussion

2:50    Break

3:20     Shifts in functional gene capacity parallel shifts in microbial composition with tropical forest recovery

A. Peyton Smith, Erika Marin-Spiotta, Teri Balser

3:40     The Earth Microbiome Project: Microbial ecology of exotic plant invasions

Sean M. Gibbons, Jai Rideout, Antonio Gonzalez, Emmanuel Prestat, J. Gregory Caporaso, Rob Knight, Janet Jansson, Ylva Lekberg, Dan Mummey, Philip W. Ramsey, Maureen L. Coleman, Jack A. Gilbert

4:00     Scaling microbial ecosystems at the National Ecological Observatory Network

Jacob Parnell

4:20     Do we need to understand microbial community structure to predict ecosystem function?

Diana Nemergut, Emily Graham

4:40     Discussion

5:30–7:00 pm   Cyperus I-II (cash bar)

Posters I

7:00–9:00 pm Trillium I
Keynote session with dinner

Traits-based approaches to soil microbial ecology

Jay Lennon

Thursday, October 3

7:00  Sorrell II

Continental breakfast

8:30–12:00  Trillium II

Session II: Metaproteomic and metagenomic analysis

8:30     Invited: Mass spectrometry-based proteogenomic approaches reveal insight into the activities and functions of soil microbial communities

Robert Hettich, Ritiin Sharma, Xiaoxin Liu, Karuna Chourey, Chongle Pan, Richard Giannone

8:50     Efficient and unbiased extraction and quantification of soil proteins – the first step to characterization

Siobhán Staunton, Priscila Jorge-Araujo, Laurie Amenc, Sonia Hem, Véronique Santoni, Hervé Quiquampoix

9:10     Invited: Development of advanced measurement capabilities for global and targeted metaproteomics analyses

SJ Callister, MS Lipton, AT Wright, CD Nicora, MJ Wilkins, BL LaMarche, RD Smith, AE Konopka

9:30    Discussion

10:00   Break

10:30   Invited: Microbial drivers of biogeochemical cycling

Kirsten Hofmockel, Adina Chuang Howe, Ryan Williams, Elizabeth Bach, Folker Meyer

10:50   Soil microbial community responses to warming as revealed by metagenomics and metatranscriptomics

Eric R. Johnston, Chengwei Luo, Luis M. Rodriguez-R, Liyou Wu, Lei Cheng, Kai Xue, Qichao Tu, Ye Deng, Sherry A. Rebecca, Dejun Li, Zhili He, Yiqi Luo, Edward A.G. Schuur, James M. Tiedje, Jizhong Zhou, Konstantinos T. Konstantinidis

11:10   Invited: Using the PhyloFacts Encyclopedia to analyze metagenome data

Lee Ann McCue

11:30   Discussion

12:00  Sorrell II

Lunch

2:00–5:00  Trillium II

Session III: Identifying novel function from sequence data

2:00     Invited: Identifying enzymes from metagenomes

Elizabeth Edwards, Alexander Yakunin, Emma Master, Robyn Goacher, Alexei Savchenko, Shuiquan Tang, Xiaoming Liang, Charles Mims, Ana Popovic, Tran Hai, Anatoli Tchigvintsev, Greg Brown

2:20     Ca. Nitrososphaera evergladensis reveals metabolic versatility of soil thaumarchaeotal group 1.1b

Kateryna V. Zhalnina, Raquel Dias, Michael T. Leonard, Patricia Dorr de Quadros, William G. Farmerie, Samira H. Daroub, Eric W. Triplett

2:40     Invited: Exploitation of unculturable eukaryotic enzymes by a metatranscriptomics approach

Nobutada Kimura

3:00    Discussion

3:30    Break

4:00     Invited: Digging into the hidden riches of soil and sediment functions

Sara Sjöling

4:20     Microbial ecology of aromatics-polluted environments: Linking metabolic activity with specific taxa and functional genes

Ondrej Uhlik, Jiri Wald, Michal Strejcek, Lucie Musilova, Miluse Hroudova, Jakub Ridl, Tomas Macek

4:40     Metagenomic analysis of chlorine cycling in arctic tundra soils

Jaime E. Zlamal, Elizabeth A. Dinsdale, David A. Lipson

5:00    Discussion

5:30–7:00 pm Cyperus I-II (cash bar)

Posters II

Dinner on your own

Friday, October 4

7:00  Sorrell II

Continental breakfast

8:30–12:00 Trillium II

Session IV: Decomposition and N cycling

8:30     Invited: Do gene abundances in DNA or mRNA predict rates of corresponding processes?

Jennifer D. Rocca, Matthew D. Wallenstein

8:50     Ecology of fungi and bacteria on plant litter: expanded role for bacterial decomposition?

Petr Baldrian, Rubén López-Mondéjar, Salvador Lladó-Fernández, Martina Štursová, Jana Vořišková, Vojtěch Tláska, Vendula Brabcová

9:10     Functional gene patterns may explain priming in soil litter decomposition

Shengjing Shi, Donald J. Herman, Zhili He, Jizhong Zhou, Mary K. Firestone

9:30    Discussion

10:00   Break

10:30   Chronic atmospheric N deposition alters the composition and function of saprotrophic soil bacteria

Zachary Freedman, Donald R. Zak

10:50   Nitrification and nitrogen mineralization in an agricultural system with contrasting nitrogen sources

Jeanette Norton, Yang Ouyang, John Stark, Jennifer Reeve, Mussie Habteselassie

11:10   Detecting nitrous oxide reductase (nosZ) genes in soil metagenomes: method development, temporal patterns and implications for the nitrogen cycle

Luis Orellana, Allana Welsh, Joanne Chee-Sanford, Robert Sanford, Steven Higgins, Frank Löffler, Konstantinos Konstantinidis

11:30   Discussion

12:00 Closing remarks/Adjourn

12:00 Sorrell II

Lunch

1:30–4:30 pm     Concurrent optional sessions

QIIME tutorial and Enzymes in the Environment/TerraGenome RCN workshop

QIIME     Trillium II

This tutorial covers a full QIIME workflow using Illumina sequencing data. This tutorial is intended to be quick to run, and as such, uses only a subset of a full Illumina Genome Analyzer II (GAIIx) run. We’ll make use of the 12_10 release of the Greengenes reference OTUs. You can always find a link to the latest version of the reference OTUs on the QIIME resources page. The tutorial can be accessed here.

Prerequisites: Laptop with a web browser.

Intended audience: Beginning to intermediate users of QIIME for 16S-based microbial community analysis

 

Enzymes in the Environment and TerraGenome Research Coordination Networks Joint Workshop

Cyperus I-II

Participants in this workshop will discuss recent advances in using ‘omics approaches to enhance our understanding of microbial function and the ecology of enzymes in soils. The aim is to develop an agenda for future research in this area by identifying challenges and opportunities for growth. The workshop will feature focused small group discussions that will then be synthesized for the full group to efficiently work towards a consensus viewpoint that incorporates input from all participants.  We envision this synthesis resulting in an opinion piece to be submitted to a peer-reviewed journal.

Intended audience: Those interested in critically examining the current use of ‘omics and shaping the future role of ‘omics in addressing microbial function and enzymes in soil ecosystems. Workshop participants will be selected from all applicants to ensure a practical workshop size that includes diverse expertise and experience.

Posters     Cyperus I-II

Posters

Session I: Odd-numbered titles

Session II: Even-numbered titles

All posters may remain displayed through Thursday evening. Please remove posters by Friday morning.

Metagenomic insight into elemental cycles

1. Integrating omics to understand soil C cycling responses to precipitation variation
Robert L. Hettich, Maude M. David, Emmanuel Prestat, Lydia H. Zeglin, Peter J. Bottomley, Janet K. Jansson, Ari Jumpponen, Charles W. Rice, Susannah G. Tringe, Nathan C. VerBerkmoes, David D. Myrold

2. Co-occurrence of microbial carbon cycling genes reveals diverse communities with similar functional capacity
Ryan J. Williams, Adina C. Howe, Kirsten S. Hofmockel

3. The genetic potential of microbial depolymerization of SPRUCE peatland in Marcell Experimental Forest, MN
Fan Yang, Xueju Lin, Joel E. Kostka, Kirsten S. Hofmockel

4. Integrated metagenomic and NMR spectroscopic analysis of carbon metabolism and nutrient acquisition (N, P) in an ombrotrophic peatland
Xueju Lin, Malak M. Tfaily, Stefan Green, Jessica M. Steinweg, Patrick Chanton, Jeff P. Chanton, William Cooper, Christopher Schadt, Paul Hanson, Joel E. Kostka

5. Diversity of NrfA in agricultural soils with depth, position in the field, season and soil type reveals varying populations capable of mediating dissimilatory nitrate reduction to ammonia (DNRA)
Allana Welsh, Joanne Chee-Sanford, Lynn Connor, Frank Loffler, Robert Sanford

6. Analysis of typical- and atypical-nitrous oxide reductase (nosZ) genes in two contrasting agricultural soils
Joanne Chee-Sanford, Ryan Riessen, Allana Welsh, Lynn Connor, Robert Sanford

7. Soil microbial community composition as an indicator of agroecosystem N2O emissions
David S. Duncan, Kelsea A. Jewell, David A. Williams, Garret Suen, Randall D. Jackson

8. Microbial nitrogen cycling potential is driven towards ammonium production during polyaromatic hydrocarbon pollution in marine sediments
Nicole M. Scott, Olivia U. Mason, Matthias Hess, Janet K. Jansson,Jack A. Gilbert

9. Proposed methodology for investigating plant-microbe controls on nitrogen priming in an agroecosystem
Amanda B. Daly, A. Stuart Grandy

Microbial community structure and function

10. How do warming and grazing affect soil bacterial diversity in the Mongolian steppe?
Aurora MacRae-Crerar, Pierre Liancourt, Laura A. Spence, Bazartseren Boldgiv, Daniel S. Song, Jack A. Gilbert, Sarah M. Owens, Jarrad Hampton-Marcell, Brendan Hodkinson, Brenda B. Casper, Peter S. Petraitis

11. Influence of environmental gradients on soil microbial communities in a polar desert
Kevin Geyer, Adam Altrichter, Tina Takacs-Vesbach, Mike Gooseff, Jeb Barrett

12. Spatial diversity of sediment bacteria, an approach using GIS and 16S rRNA gene sequence profiling: The case of Chilika Lake
Jean-Sébastien Beaulne, Samir Mishra, Sébastien Cecillon, Vishakha Raina, Gurdeep Rastogi, Ajit Pattnaik, Mrutyunjay Suar, Timothy M. Vogel

13. Soil bacterial community shifts in response to the altered ecology of a tussock dominated permafrost ecosystem
Michael P. Ricketts, Miquel A. Gonzalez-Meler

14. Microbial community shifts as an effect of 1 year of experimental warming in permafrost and temperate soils revealed by metagenomics
Eric R. Johnston, Chengwei Luo, Luis M. Rodriguez-R, Liyou Wu, Zhili He, Edward A.G. Schuur, Jizhong Zhou, and Konstantinos T. Konstantinidis

15. Metagenomic analyses of microbial communities in Canadian high arctic active Layers and permafrost following long term thawing
A. Chauhan, A. Layton, M.C.Y. Lau, T. Vishnivetskaya, S. Pfiffner, D. Williams, T. Phelps, B. Stackhouse, K. Chourey, R.L.Hettich, L. Whyte, N. Mykytczuk, T.C. Onstott

16. Viable methanogens in the McMurdo Dry Valleys permafrost
Kirill Krivushin, Tatiana Vishnivetskaya, Viktoria Shcherbakova, Elizaveta Rivkina

17. Identifying novel pathways for anaerobic microbial oxidation of methane
Edward J. O’Loughlin, Dionysios A. Antonopoulos, Kenneth M. Kemner, Jason Koval, Sarah L. O’Brien, Sarah Owens

18. Deconstructing a microbial community degrading plant material in a wet, tropical forest soil
Dara Goodheart, Jincai Ma, Whendee L. Silver, Terry C. Hazen, Jizhong Zhou, and Mary K. Firestone

19. Identifying bacterial populations potentially integral to anaerobic soil disinfestation
Jason C. Hong, Kendall J. Martin, Nancy Kokalis-Burelle, David M. Butler, Erin N. Rosskopf

20. The power of soil microbes: Evaluation of the performance of terrestrial microbial fuel cells as a function of incubation temperature
Robyn A. Barbato, Karen L. Foley, Jorge A. Toro-Zapata, Elizabeth Kamb, Charles M. Reynolds

Plant-microbe interactions

21. Changes in the soil bacterial communities in a cedar plantation invaded by moso bamboo
Yu-Te Lin, Sen-Lin Tang, Chung-Wen Pai, William B. Whitman, David C. Coleman, Chih-Yu Chiu

22. Biogeochemical processes controlling soil carbon storage in conventional and cover-crop-enhanced row crop agro-ecosystems
Britton Hildebrandt, Alexandra N. Kravchenko, Terence L. Marsh

23. Bacterial diversity in the rice fields in south of Brazil
Michele Pittol, Lisa M. Durso, Victor Hugo Valiati, Lidia Mariana Fiuza

24. Effects of plant treatment on soil bacterial and actinomycete communities
Laura Felice, Sheri Huerd, Ruth Dill-Macky, Nicholas Jordan, Linda Kinkel

25. Digging out the decomposer community from soil metagenomic data
Emily E. Curd, Thomas B. Smith, Huiying Li

26. Plant species-specific stoichiometry influences on the rhizosphere microbiome in a semi-arid grassland ecosystem
Colin W. Bell, Yolima Carrillo, Claudia M. Boot, Elise Pendall, Matthew D. Wallenstein

27. Mycorrhizal fungal community structure along an elevational gradient
Jeremiah A. Henning, Quentin D. Read, Nathan J. Sanders, Aimée T. Classen

28. The impact of Pseudomoas fluorescens strains on aspen growth during phosphorus and nitrogen limitation
Shalaka Desai, Pater Larsen, Jonathan Cumming, Frank Collart

29. Mediation of stress-induced root exudation by mycorrhizal fungi
Jonathan Cumming, Shalaka Desai, Dhiraj Naik, Ernie Smith

Computational concepts and method development

30. Ribosomal Database Project: tools for gene-targeted metagenomics
Jordan A. Fish, Qiong Wang, Benli Chai, Yanni Sun, James M. Tiedje, James R. Cole

31. ZovaSeq: Next-Gen sequencing data analysis for quick microbial identification
Robert T. Yamamoto, Matthew Kidd, Daniel Sphar, Andreia Maer

32. Targeted metagenomics: Functional diversity through sequence capture
Lokeshwaran Manoharan, Sandeep Kushwaha, Dag Ahrén, Katarina Hedlund

33. Evaluation of metatranscriptomic investigations in an agricultural soil
Aaron Garoutte, Jim Tiedje, Adina Howe

34. Integrating evolutionary history into metagenomic understanding
Pamela Weisenhorn, Fangfang Xia, Janaka Edirisinghe, and Chris Henry

35. Modeling the responses of mycorrhizal helper bacteria Pseudomonas to plant root exudates using deep sequencing transcriptomic data
Peter E. Larsen, Shalaka Desai, Sara Zerbs, Frank R. Collart

36. Genome reconstruction of soil ammonia-oxidizing archaeon from metagenomeRaquel Dias, Kateryna V. Zhalnina, Michael T. Leonard, Patricia Dorr de Quadros, William G. Farmerie, Samira H. Daroub, Eric W. Tripplett

37. Functional metagenomics for enhanced bioplastics production through bacterial chromosome engineeringJiujun Cheng, John Heil, Trevor Charles

38. Metabolic pathways of Pseudomonas fluroescens ICT in the perspective of groundwater bioremediationIva Sakmaryová, Alena Ševcu, Petr Baldrian, Alica Chroňáková

39. Synchrotron approaches to analyze carbon chemistry in soil samples
K. M. Kemner, B. Mishra, E. J. O’Loughlin, M. Balasubramanian, R. Gordon, J. Jastrow,  V. Bailey, C. Jacobsen, R. Reininger

40. Detection of antibiotic resistance, virulence factor and pathogen-associated sequences in plasmid metagenomes from municipal biosolids
Elizabeth Bent, Crystal M. McCall, Marc Habash, Kari Dunfield

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