October 1–3, 2014


Wednesday, October 1

7:30–9:00      Registration & continental breakfast

9:00–9:30      Introduction & announcements

Session I         Mining for function

Chris Schadt, moderator


What drives soil community structure?
James Tiedje


Mining soil aggregate metagenomes for ecologically relevant extracellular enzymes
Ryan J. Williams, Adina Howe, Kirsten S. Hofmockel


A metagenomic approach to assess microbial halogenation and dehalogenation potential in soil
Pascal Weigold, Mohamed El-Hadidi, Andreas Kappler, Daniel H. Huson, Sebastian Behrens




Metagenomic and metagenetic approaches to enhanced anaerobic reductive dechlorination of polychlorinated biphenyls: linking structure and function
Sebastien Cecillon, Timothy M. Vogel


Describing diversity and mining of ring hydroxylating dioxygenase genes from soil metagenomes: Achievements and challenges
Ondrej Uhlik, Michal Strejcek, Jachym Suman, Jan Capek, Jiri Wald, Tomas Macek


Opportunities to contribute to a community soil databasse
Adina Howe

12:15              Lunch

1:30–3:00      Posters I

Session II        Climate change

Kirsten Hofmockel, moderator


Soil microbial oligotrophs respond to long-term warming in temperate forest soils
Kristen M. DeAngelis, Grace Pold, Linda van Diepen, William Rodriguez, Jeffrey Blanchard, Jerry Melillo, Serita Frey


Integration of metagenomic and biogeochemical data from soil subjected to a climate shift
Vanessa L. Bailey, Nancy J. Hess, Lee Ann McCue


Advancing the ‘omics toolkit to study the effects of experimental warming in Midwestern and Alaskan soil microbial communities
Eric R. Johnston, Chengwei Luo, Luis M. Rodriguez-R, Liyou Wu, Zhili He, Edward A.G. Schuur, Jizhong Zhou, Yiqi Luo, James M. Tiedje, Konstantinos T. Konstantinidis


Omics reveals microbial life in frozen permafrost and climate change impacts
Janet K. Jansson

4:40                Discussion

5:00                Mixer – cash bar

6:30                Plenary session – Keynote talk and buffet dinner

What are soil ‘omic analyses telling us?

Mary K. Firestone

Thursday, October 2

7:30–8:30      Continental breakfast

Session III      Nitrogen Cycle

Jennifer Moore-Kucera, moderator


Linking microbial diversity and ecosystem functioning: The nitrogen cycle example
Laurent Philippot


Linking nitrogen cycle effects of experimental warming to altered nutrient processing
Grace Pold, William Rodriguez-Reillo, Jeffrey Blanchard, Jerry Melillo, Serita Frey, Linda van Diepen, Kristen M. DeAngelis


Process and communities of ammonia oxidizers in an agricultural soil
Jeanette Norton, Yang Ouyang, John Stark, Jennifer Reeve, Mussie Habteselassie


Seasonal and spatial changes in nitrogen cycle potential in Midwestern agricultural soils as revealed by metagenomics
Luis Orellana, Joanne Chee-Sanford, Robert Sanford, Frank Loffler, Kirsti Ritalahti, Konstantinos Konstantinidis

10:00              Break

Session IV       Genomes!

Bob Hettich, moderator


A robust statistical framework for reconstructing genomes from metagenomic data
Dongwan D. Kang, Jeff Froula, Rob Egan, Zhong Wang


Recovering individual genomes from a complex metagenome using MaxBin, a novel binning algorithm
Yu-Wei Wu, Stephanie A. Eichorst, Susannah G. Tringe, Blake A. Simmons, Steven W. Singer


Genome-based comparative analyses of Antarctic and temperate species of Paenibacillus
Melissa Dsouza, Michael W. Taylor, Susan J. Turner, Jackie Aislabie


Predicting Pseudomonads’ ecological roles in the rhizosphere using machine learning and ‘omics computational modeling
Peter E. Larsen, Frank R. Collart, Yang Dai

12:00              Lunch & Learn  Sponsored by Pacific Biosciences

Applications of Single Molecule, Real-Time (SMRT) Sequencing in Metagenomics
Dr. Richard J. Hall, Senior Scientist, Pacific Biosciences

1:30–3:00       Posters II

Session V     Making sense of sequences

Gretta Serres, moderator


Rapid and accurate metagenome read characterization using a hierarchical suite of unique signatures
Patrick Chain


A Bayesian hierarchical approach for estimating microbial community composition and diversity assessed using two sets of primers via polymerase chain reaction
Nels G. Johnson, Akihiro Koyama, Colleen T. Webb, Joseph C. von Fischer


Deconstructing the polymerase chain reaction: A new method to reduce bias associated with primer degeneracies and mismatches
Stefan J. Green, Raghavee Venkatramanan

4:10                Break


Ask not “did I get it all” but rather “how much did I get?”
William L. Trimble, Luis Rodriguez-Rojas, Travis Harrison, Kostas Konstantinidis, Folker Meyer


Evaluating metatranscriptome from agricultural soil: A benchmarking study
A. Garoutte, E. Cardenas, J. Tiedje, A. Howe


Fast metagenome analysis
Daniel Huson

5:50                Discussion

6:00–7:30      Optional breakout sessions – cash bar

Session A: Q & A for DNA extraction and library preparation

Session B: Opportunities to contribute to a community soil database

Session C: Brainstorming priorities for continuing ‘omics research

Any meeting participant is welcome to lead an additional breakout session on any ‘omics-related topic. Contact Sarah O’Brien if you would like to arrange a session in advance. Last-minute ideas will also be accommodated.


Dinner on your own


Friday, October 3

7:30–9:00      Continental breakfast

Session VI       Trends in space and time

Tim Vogel, moderator


Large scale spatial analysis of bacterial communities in sediments (Chilika Lake), the role of physico-chemical parameters, spatial distance, land cover, and extreme events
Jean-Sebastien Beaulne, Sebastien Cecillon, Mrutyunjay Suar, Timothy M. Vogel


The importance of time and space: Temporal variability over-shadows the effects of warming and grazing on soil bacterial communities in the steppe of northern Mongolia
Aurora MacRae-Crerar, Eric R. Johnston, Pierre Liancourt, Laura A. Spence, Bazartseren Boldgiv, Daniel S. Song, Jack A. Gilbert, Sarah M. Owens, Jarrad Hampton-Marcell, Brenda B. Casper, Peter S. Petraitis


Bacterial biogeography of the rare Charitable Research Reserve
Brent Seuradge, Michael Hall, Maren Oelbermann, Josh Neufeld


Soil habitat connectivity has contrasting impacts on bacterial and fungal diversity
Alexandra B. Wolf, George A. Kowalchuk

10:20              Break

Session VII     Plants and microbes

Dave Myrold, moderator


Microbial activity in the soil is regulated by the seasonal changes of tree activity in a temperate forest
Petr Baldrian, Lucia Zifcakova, Salvador Llado-Fernandez, Tomas Vetrovsky, Jana Voriskova, Adina Chuang Howe, Katharina Riedel, Stefan Fuchs, Ruben Lopez-Modejar


Microbial community structure and functional potential associated with four boreal forest vegetation types
Mary-Cathrine Leewis, D. Lee Taylor, Mary Beth Leigh


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

11:50              Discussion

12:15              Adjourn


Friday afternoon

1:30 – 5:00PM

Automating things with the shell (Will Trimble)

Optional tutorial on introducing the shell and shell automation with bio-relevant examples for those interested.

Introducing the Shell (What is going on?); Files and Directories (cd, ls); Creating Things (mv, rm, cp); Pipes and Filters; Loops (for); Shell Scripts (Doing Stuff); Finding Things (find, grep)

For a more detailed agenda and additional resources please see the link below:



Saturday October 4

Turquoise Room (second floor Tower – same building as main hotel rooms)

7:30–9:00AM             Continental breakfast

9:00AM – 5:00PM     Data analysis training workshop (additional registration required); lunch included



Introduction (Adina Howe)


MEGAN (Daniel Huson)


MG-RAST interface (Folker Meyer)

12:30-1:30             Lunch


KBase – metabolic models for metagenomes


Cloud computing to do more I (instances and similarity searching) (Will Trimble)


Cloud computing to do more II (pipelines) (Will Trimble)



MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project. MEGAN is suitable not only for DNA reads (metagenome data), but for RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and 16S rRNA data (amplicon sequencing) as well.


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


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.



Session I: Titles with odd numbers

Session II: Titles with even numbers

1.       Influence of nutrient availability on greenhouse gas emissions and microbial community composition in a lowland tropical rainforest

Silvia Alvarez-Clare, Edward J. O’Loughlin, Theodore M. Flynn, Dionysios A. Antonopoulos

2.       Soil temperature and moisture effects on soil respiration and microbial community abundance in four soils

Robyn A. Barbato, Karen L. Foley, Charles M. Reynolds

3.       Analysis and comparison of metagenomes from six North American forests : Giants on shoulders of giants

Erick Cardenas, Kendra Maas, Steven Hallam, William W. Mohn

4.       Predicting N2O emissions using soil microbial community composition

David S. Duncan, Kelsea A. Jewell, Lawrence G. Oates, Garret Suen, Randall D. Jackson

5.       Coupled metagenomic and chemical analyses of degrading fungal necromass and implications for microbial contributions to soil organic matter

Louise M. Egerton-Warburton, Benjamin S.T. Morgan, Jeremy Schultz, Kathryn M. Schreiner, Neal E. Blair

6.       Community level physiological profiling of diverse environments reveals functional and taxonomic diversity within aerobic, single carbon-source enrichments

Theodore M. Flynn, Jason C. Koval, Stephanie M. Moormann, Sarah M. Owens, Sarah L. O’Brien, Silvia Alvarez-Clare, Edward J. O’Loughlin, Kenneth M. Kemner, Dionysios A. Antonopoulos

7.       Dispersal limitation and environmental filtering of bacterial communities along a long-term glacial chronosequence

Zachary Freedman, Donald R. Zak

8.       Is the regulation of nitrogen fixation in tropical legumes controlled phylogenetically or function of the symbiont identity?

Maria G. Gei, Martijn Slot, Jennifer S. Powers

9.       Soil bacterial composition dynamics across a Conservation Reserve Program (CRP) chronosequence in the Texas High Plains region using Illumina MiSeq paired-end sequencing

Mamatha Kakarla, Jennifer Moore-Kucera, Lisa Fultz, Chenhui Li, Veronica Acosta-Martinez, Jon Zak, Kameswara Rao Kottapalli

10.   Informed selection of analyses applied to deep sequencing data; AMETHST the analysis method selection tool

K.P. Keegan, W. Gerlach, I. Zarraonaindia, S.L. O’Brien, E. Glass, S. Gibbons, W. Trimble, M. Mühling, I. Joint, K. Tait, J. Shaw,  J.A. Gilbert, F. Meyer

11.   BAC Sudoku sequencing of a soil metagenomic library for secondary metabolite pathways

Brendan Keough, Megan Niebauer, Amanda Krerowicz, Jinglie Zhou, Scott Santos, Mark Liles, Xing-Cong Li, Blaine Pfeifer, David Mead, Scott Monsma

12.   Ecological impact assessment of a biostimulation site on remediation of tetrachloroethylene by metagenomic approaches

Nobutada Kimura, Saori Watahiki, Atsushi Yamazoe, Yuji Sekiguchi, Naohiro Noda, Yo Takahata, Hideaki Nojiri, Masao Fukuda

13.   Methanotroph community composition controls sensitivity of methane uptake to increased ammonium contents in grassland soils across the US Great Plains

Akihiro Koyama, Nels G. Johnson, Evan Rosenlieb, Colleen T. Webb, Joseph C. von Fischer

14.   Observed GC bias in metagenomic cosmid libraries may be due to selection against transcriptionally active fragments in E. coli

Kathy N. Lam, Trevor C. Charles

15.   Do cedar and bamboo plantations alter structure and diversity of soil bacterial community in subtropical mountain?

Yu-Te Lin, William B. Whitman, David C. Coleman, Chih-Yu Chiu

16.   Changes of soil bacterial communities in bamboo plantations at different elevations

Yu-Te Lin, Shiang-Yun Shi, William B. Whitman, David C. Coleman, Sen-Lin Tangand, Chih-Yu Chiu

17.   Microbial communities and carbon dynamics across a depth profile of organic and conventionally managed agricultural systems in the Mid-Atlantic region

Jude Maul, Glade Dlott, Dietrich Schmidt, Michel Cavigelli, Jeffery Buyer, Stephanie Yarwood

18.   Nanoliter qPCR platform for highly parallel, quantitative assessment of reductive dehalogenase genes and populations of dehalogenating microorganisms in complex environments

Koshlan Mayer-Blackwell, Mohammad F. Azizian, Christina Machak, Elena Vitale, Giovanna Carpani, Francesca de Ferra, Lewis Semprini, Alfred M. Spormann

19.   MaxRebo: hidden Markov model-driven metagenomics data analysis

Lee Ann McCue, Darren Curtis, Aaron Phillips

20.   Characterization of depth-related changes in structural and functional microbial community associated with arsenic reduction in soil profile of Northen Utah

Babur S. Mirza, Xianyu Meng, Darwin L. Sorenson, R. Ryan Dupont, Joan E. Mclean

21.   High efficiency long insert mate pair library preparation for NGS platforms

Amanda Krerowicz, Scott Monsma, David Mead, Svetlana Jasinovica, Erin Ferguson, Michael J. Lodes

22.   High-throughput sequencing reveals diverse fungal communities associated with lignin decomposition in seasonally dry forests of the Yucatan Peninsula

Benjamin Morgan, Louise Egerton-Warburton

23.   Global change stressors affect the relationship between standing and active fungal communities

Eric W. Morrison, Serita D. Frey, Linda T.A. van Diepen, Anne Pringle

24.   Diversity of bacteria associated with natural vegetation of long-term PCB-contaminated soil

Lucie Musilova, Eglantina Lopez Echartea, Tomas Macek, Ondrej Uhlik

25.   Development and Decline of Microbial Communities Associated with Ectomycorrhizal Mats

David D. Myrold, Jed E. Cappellazzi, Jane E. Smith, Peter J. Bottomley

26.   Response of soil bacterial communities to tree girdling after elevated CO2 exposure

Sarah L. O’Brien, Eric R. Johnston, Kevin P. Keegan, Colleen M. Iversen, Richard J. Norby, Jeffrey M. Warren, Dionysios A. Antonopoulos

27.   Effects of 2-chloro-6-methylpyridine concentration on microbial community development during aerobic methane oxidation

Edward J. O’Loughlin, Theodore M. Flynn, Jason C. Koval, Sarah M. Owens, Kirsti Arend, Dionysios A. Antonopoulos

28.   Soil sample size affects fungal and bacterial community structure and richness values obtained from amplicon sequencing

C. Ryan Penton, Vadakattu Gupta, Julian Yu, James Tiedje

29.   The Earth Microbiome Project goes underground

Dorota L. Porazinska, Gail Ackermann, Jose A. Navas-Molina, Rob Knight

30.   Deciphering the roles of host innate immunity in shaping the structure and assembly cues of leaf surface microbiota

Bharath Prithiviraj, Aaron McCrary, Yingqing Guo, Myoung-Hwan Chi, Kelly Craven, Dilip Shah

31.   Predicted relative metabolic turnover using metagenomic data from Harvard Forest warming experiment

William Rodriguez, Jeffrey Blanchard, Grace Pold, Kristen DeAngelis, Serita Frey, Linda van Diepen, Jerry Melillo

32.   Chronic nitrogen deposition affects the active bacteria in a northern hardwood forest

Karl J. Romanowicz, Zachary B. Freedman, Donald R. Zak

33.   Microbial metabolic succession in oil contaminated sediments during the Deepwater Horizon Oil Spill in the Gulf of Mexico (GoM)

Nicole M. Scott, Tingting Yang, Adam Robbins-Pianka, Jarrad Hampton-Marcell, Sarah M. Owens, Andreas P. Teske, Jack A. Gilbert

34.   Expanding the definition of Myxobacteria by reconstructing genomes of uncultivated populations from terrestrial environments

Steven W. Singer, Yu-Wei Wu, Yung-Hsu-Tang, Blake A. Simmons

35.   Does chronic nitrogen deposition alter the functional potential of soil microbial communities in northern hardwood forests?

Rima A. Upchurch, Zachary B. Freedman, Karl J. Romanowicz, Donald R. Zak

36.   Fungal resources at RDP

Qiong Wang, Benli Chai, Vinita Deshpande, Paul Greenfield, Michael Charleston, Andrea Porras-Alfaro, Cheryl R. Kuske, Nai Tran-Dinh, David Midgley, James M. Tiedje, James R. Cole

37.   Understanding cultivar-specificity and soil determinants of the Cannabis microbiome

Max E. Winston, Jarrad Hampton-Marcell, Iratxe Zarraonaindia, Sarah M. Owens, Corrie S. Moreau, Jack A. Gilbert, Josh Hartsel, Suzanne J. Kennedy, S.M. Gibbons

38.   Microbial cellulose utilization at the aggregate scale

Alexandra B. Wolf, Adina Howe, Kirsten S. Hofmockel

39.   MaxBin: recovering individual genomes from complex metagenomes using an expectation-maximization algorithm

Yu-Wei Wu, Stephanie A. Eichorst, Susannah G. Tringe, Blake A. Simmons, Steven W. Singer

40.   Using the concept of informative genomic segment to investigate microbial diversity of metagenomics sample

Qingpeng Zhang, C. Titus Brown

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