Plant Microbe-Interfaces Aim 1

Characterizing host drivers of the Populus microbiome

Over the course of the next 3 years, we will (1) produce the first comprehensive description of the diversity of bacterial and fungal associates that is explicitly linked to the genomic composition and phenotypic variation in the host plant, Populus; (2) gain an improved understanding of host genomic, phenotypic, and environmental factors that influence this diversity and relate this to function where possible through improved metaomic approaches; and (3) generate a catalog of host candidate genes for further molecular characterization. Additionally, we will create the most extensive and representative culture collection of microbial associates ofPopulus worldwide. This catalog will allow us to pursue further studies on the mechanisms underlying these interkingdom relationships and community assembly.

Aim 1 Tasks

Figure: Overview of the subtasks in Aim 1.

Aim 1 Related Publications

Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types.
Neil R. Gottel,Hector F. Castro,Marily Kerley,Zamin Yang,Dale A. Pelletier,Mircea Podar,Tatiana Karpinets,Ed Uberbacher,Gerald A. Tuskan,Rytas Vilgalys,Mitchel J. Doktycz,Christopher W. Schadt
Appl Environ Microbiol. 2011 Sep;77(17):5934-44. doi: 10.1128/AEM.05255-11. Epub 2011 Jul 15.
Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome.
Brendan P. Hodkinson, Neil R. Gottel, Christopher W. Schadt and François Lutzoni
Environ Microbiol. 2012 Jan;14(1):147-61. doi: 10.1111/j.1462-2920.2011.02560.x. Epub 2011 Sep 12.
Biosynthesis and emission of insect-induced methyl salicylate and methyl benzoate from rice.
Nan Zhao,Ju Guan,Jean-Luc Ferrer,Nancy Engle,Mawsheng Chern,Pamela Ronald,Timothy J. Tschaplinski,Feng Chen
Plant Physiol Biochem. 2010 Apr;48(4):279-87. doi: 10.1016/j.plaphy.2010.01.023. Epub 2010 Feb 8.
Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments
Florence Wisniewski-Dyé,Kirill Borizak,Gurusahai Khalsa-Moyers,Gladys Alexandre,Leonid O. Sukharnikov,Kristin Wuichet,Gregory B. Hurst,W. Hayes McDonald,Jon S. Robertson,Valérie Barbe,Alexandra Calteau,Zoé Rouy,Sophie Mangenot,Claire Prignet-Combaret,Philippe Normand,Michaël Boyer,Patricia Siguier,Yves Dessaux,Claudine Elmerich,Guy Condemine,Ganisan Kirshnen,Ivan Kennedy,andrew H. Paterson,Vicotr González,Patrick Mavingui,Igor B. Zhulin
PLoS Genetics 7(12): e1002430
New North American truffles (Tuber spp.) and their ectomycorrhizal associations
Guevara G, Bonito G, Trappe JM, Cázares E, Williams G, Healy RA, Schadt CW, and Vilgalys R
Mycologia 2013 105:194-209
Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoides
Steven D. Brown, Sagar M. Utturkar, Dawn M. Klingeman, Courtney M. Johnson, Stanton L. Martin, Miriam L. Land, Tse-Yuan S. Lu, Christopher W. Schadt, Mitchel J. Doktycz and Dale A. Pelletier
J. Bacteriol. November 2012 vol. 194 no. 21 5991-5993
System-wide Studies of N-Lysine Acetylation in Rhodopseudomonas palustris Reveal Substrate Specificity of Protein Acetyltransferases
Heidi A. Crosby, Dale A. Pelletier, Gregory B. Hurst, and Jorge C. Escalante-Semerena
The Journal of Biological Chemistry, 287, 15590-15601.
Draft Genome Sequence of Rhizobium sp. Strain PDO1-076, a Bacterium Isolated from Populus deltoides
Steve Brown, Tse-Yuan Lu, Sagar Utturkar, Chris Schadt, Mitch Doktycz, Dale Pelletier
Journal of Bacteriology 2012, 194(9): 2383-2384 DOI: 10.1128/JB.00198-12
Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap Velos
Zhou Li, Rachel M. Adams, Karuna Chourey, Gregory Blake Hurst, Robert L. Hettich, and Chongle Pan
Journal of Proteome Research 2012, 11 (3), pp 1582-1590
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities
Shakya M, Quince C, Campbell JH, Yang ZK, Schadt CW, Podar M.
Enivronmental Microbiology (2013), 15(6): 1882-1899
Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche
Emmanuelle Morin,Annegret Kohler,Adam R. Baker,Marie Foulongne-Oriol,Vincent Lombard,Laszlo G. Nagy,Robin A. Ohm,Aleksandrina Patyshakuliyeva,Annick Brun,Andrea L. Aerts,Andrew M. Bailey,Christophe Billette,Pedro M. Coutinho,Greg Deaking,Harshavardhan Doddapaneni,Dimitrios Floudas,Jane Grimwood,Kristina Hildén,Ursula Kües,Kurt M. LaButti,Alla Lapidus,Erika A. Lindquist,Susan M. Lucas,Claude Murat,Robert W. Riley,Asaf A. Salamov,Jeremy Schmutz,Venkataramanan Subramanian,Han A.B. Wösten,Jianping Xu,Daniel C. Eastwood,Gary D. Foster,Anton S.M. Sonnenberg,Dan Cullen,Ronald P. de Vries,Taina Lundell,David S. Hibbett,Bernard Henrissat,Kerry S. Burton,Richard W. Kerrigan,Michael P. Challen,Igor V. Grigoriev,Francis Martin
PNAS USA 109(43): 17501-17506 Correction: 110(10) 4146-4148
A Multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees.
Migun Shakya, Neil Gottel, Hector Castro, Zamin K. Yang, Lee Gunter,Jessy Labbé,Wellington Muchero,Gregory Bonito,Rytas Vilgalys,Gerald A. Tuskan,Mircea Podar,Christopher W. Schadt
PLoS ONE, DOI: 10.1371/journal.pone.0076382
Atomic Force Microscope Controlled Topographical Imaging and Proximal Probe Thermal Desorption/Ionization Mass Spectrometry Imaging
Olga S. Ovchinnikova, Kevin Kjoller, Gregory B. Hurst, Dale A. Pelletier, and Gary J. Van Berkel
Analytical Chemistry DOI: 10.1021/ac4026576
Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia
Steven D. Brown,Shilpa Nagaraju,Sgar Utturkar,Sashini De Tissera,Simón Segovia,Wayne Michell,Miriam L. Land,Asela Dassanayake,Michael Köpke
Biotechnology for Biofuels 2014, 7:40
Transgenic American chestnuts show enhanced blight resistance and transmit the trait to T1 progeny.
Andrew E. Newhouse,Linda D. Polin-Guigan,Kathleen A. Baier,Kristia E.R. Valletta,William H. Rottmann,Timothy J. Tschaplinski,Charles A. Maynard,William A. Powell
Plant Science, DOI: 10.1016/j.plantsci.2014.04.004
Towards a holistic understanding of the beneficial interactions across the Populus microbiome
Stéphane Hacquard,Christopher W. Schadt
New Phytologist, doi: 10.1111/nph.13133
Leaf endophytes and Populus genotype affect severity of damage from the necrotrophic leaf pathogen, Drepanopeziza populi
Posy E. Busby,Naupaka Zimmerman,David J. Weston,Sara S. Jawdy,Jos Houbraken,George Newcombe
Ecosphere 4(10):125.
Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants
Gregory Bonito,Hannah Reynolds,Michael S. Robeson,Jessica Nelson,Brendan P. Hodkinson,Gerald Tuskan,Christopher W. Schadt,Rytas Vilgalys
Molecular Ecology (2014) 23, 3356–3370
Prospects and challenges for fungal metatranscriptomics of complex communities
Cheryl R. Kuske,Cedar N. Hesse,Jean F. Challacombe,Daniel Cullen,Joshua R. Herr,Rebecca C. Mueller,Adrian Tsang,Rytas Vilgalys
Fungal Ecology 14: 133-137 April 2015