MBL Micro-Eco Discussion Group, Fall 2009
September 24, Show and tell (new grants)
Joe Vallino and Julie Huber
Jessica Mark Welch and colleagues
October 8 & 15, David Mark Welch
Tour of errors associated with (but not necessarily caused by) pyrosequencing, and how 454 informatics gurus are investigating and dealing with those errors.
Reading:
Victor Kunin, Anna Engelbrektson, Howard Ochman and Philip Hugenholtz. (2009) Wrinkles in the rare biosphere: pyrosequencing errors lead to artificial inflation of diversity estimates. Environmental Microbiology (in press).
Supplementary papers:
Quince C, Lanzen A, Curtis TP, et al. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. NATURE METHODS Volume: 6 Issue: 9 Pages: 639-U27
Reeder J, Knight R (2009) The 'rare biosphere': a reality check. NATURE METHODS Volume: 6 Issue: 9 Pages: 636-637
Oct. 22, Zoe Cardon
Lauber CL, Hamady M, Knight R, et al. (2009) Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale. APPLIED AND ENVIRONMENTAL MICROBIOLOGY Volume: 75 Issue: 15 Pages: 5111-5120
Also mentioned:
Vogel TM, Simonet P, Jansson JK, et al. (2009) TerraGenome: a consortium for the sequencing of a soil metagenome. NATURE REVIEWS MICROBIOLOGY Volume: 7 Issue: 4 Pages: 252-252
And in response to this terragenome announcement, a little disagreement about where resources should be directed when trying to understand soil function and diversity...
Singh BK, Campbell CD, Sorenson SJ, et al. (2009) Soil genomics. NATURE REVIEWS MICROBIOLOGY Volume: 7 Issue: 10
Baveye PC (2009) To sequence or not to sequence the whole-soil metagenome? NATURE REVIEWS MICROBIOLOGY Volume: 7 Issue: 10
And Vogel et al's response to these responses...
Vogel TM, Hirsch PR, Simonet P, et al. (2009) Advantages of the metagenomic approach for soil exploration: reply from Vogel et al. NATURE REVIEWS MICROBIOLOGY Volume: 7 Issue: 10
Oct. 29 More show and tell (more new grants)
Jeremy Rich, Anne Giblin, and Joe Vallino
Anton Post
Nov. 5 Emelia DeForce
Report on a soil metagenomics/MG-RAST workshop she attended a few weeks ago, and discussion of the Vogel et al. metagenome paper (and responses) briefly mentioned Oct. 22.
Nov. 12 Laura Williams
Laura brought this paper up at the end of our discussion Nov. 5, as an example of functional characterization of microbes using culture-independent sampling.
Sommer MOA, Dantas G, and Church GM (2009) Functional characterization of the antibiotic resistance reservoir in the human microflora. Science 325: 1128.
Nov. 19 Gretta Serres
A "reverse ecology" paper:
Elhanan Borenstein, Martin Kupiec, Marcus W. Feldman, and Eytan Ruppin (2008)Large-scale reconstruction and phylogenetic analysis of metabolic environments. PNAS 105:14482–14487
Nov. 16 HAPPY THANKSGIVING!
Dec. 3 Phil Neal
Dagmar Woebken, Bernhard M. Fuchs, Marcel M. M. Kuypers, and Rudolf Amann (2007) Potential Interactions of Particle-Associated Anammox Bacteria with Bacterial and Archaeal Partners in the Namibian Upwelling System. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 73: 4648–4657
Dec. 10 Linda Amaral Zettler and Sheri Simmons
Gregory J Dick, Anders F Andersson, Brett J Baker, Sheri L Simmons, Brian C Thomas, A Pepper Yelton and Jillian F Banfield (2009) Community-wide analysis of microbial genome sequence signatures. Genome Biology 10(8),R85
