HOME SYLLABUS
SCHEDULE OF READINGS
Date | Topic | Discussion Leader | Readings (* = primary reading) |
1/14/2011 | Organizational meeting | Guidelines for discussion and Suggested Topics | |
1 1/21/2011 |
Introductory Readings: Microbes, Biogeochemistry, and "Environmental Genomics" (presentation) |
Scott Saleska / Virginia Rich |
Falkowski, P.G., Fenchel, T. & Delong, E.F. 2008. The microbial
|
2 1/28/2011 |
Introductory Readings: Microbes, Biogeochemistry, and "Environmental Genomics" |
Virginia Rich |
Vandenkoornhuyse, P., et al. 2010. Integration of molecular |
3 2/4/2011 |
No meeting this week |
|
|
4 2/11/2011 |
Isotopes as tracers of biogeochemical processes |
Scott Saleska | Farquhar, Ehleringer, and Hubick. 1989. Carbon Isotope discrimination and Photosynthesis. [N.B. OK, in retrospect, this was probably too plant oriented for this group. Sorry! -SS] Supplemental: |
5 2/18/2011 |
No meeting | ||
6 2/25/2011 |
Biogeochemistry and metagenomics of Oxygen minimum zones (OMZ) in coastal oceans Canfield et al (2010) is on the biogeochemistry associated with OMZs off of the Chilean Coast and will be the main focus of our discussion. Walsh et al (2009) is for skimming and is on SUP05 bacteria and their potential role in biogeochemical cycles in OMZs based on metagenomic analysis. |
Bonnie Hurwitz | Canfield et al. 2010, A Cryptic Sulfur Cycle in Oxygen-Minimum–Zone Walsh et al., 2009, Metagenome of a Versatile Chemolithoautotroph |
7 3/4 |
We will focus on a methods paper (Dumont et al., 2006) that used isotopically-labeled methane (13CH4) to identify (from the label) the DNA of uncultivated organisms that were engaged in methanotrophic metabolism, followed by metagenomics. Also posted here are some follow up papers from the same group (Chen et al., 2008, Dumont et al., 2011) pursuing this work with more recent methods. (also a primer on metagenomics: Wooley et al., 2010, and an alternate paper from a completely different area, Gianolis, et al 2009, that we decided not to discuss at this time) |
Brandon Iker | Dumont et al. 2006, Identification of a complete methane Background More recent papers in this series An interesting-looking paper that we decided was too |
8 3/11 |
No meeting | ||
3/18 |
Spring Break | ||
9 3/25 |
We will focus on two papers, Freitag & Prosser (2009) and Freitag et al. (2010), which investigate the link between methane fluxes, genes, and gene transcripts. Freitag et al (2010) in particular is interesting because it attempts to complete the link molecular information about transcribed genes and ecosystem-scale fluxes. Also posted here (but not for reading this week) are a couple of other related papers from John Leigh's lab that use lab incubations and limiting factors (e.g. H2) to control the rate of methanogenesis while examining transcripts (Hendrickson et al) or proteins (Xia et al) related to methane production. |
Carrie McCalley | Freitag & Prosser. 2009. Correlation of Methane Production and A related line of work using controlled lab incubations: Hendrickson et al., 2007. Functionally distinct genes regulated by |
10 4/1 |
This paper reports on incubations conducted through fluctuating redox conditions (while sampling active communities through RNA:DNA ratios) to assess how well adapted different communities are to fluctuating conditions. | group | DeAngelis et al., 2010. Microbial communities acclimate to recurring |
11 4/8 |
We will contiune the line of reading started in Brandon's previous presentation. This time, they apply the method developed there (stable isotope probing combined with metagenomics) to look at methanotrophs in a lake sediment environment. | Brandon Iker |
Dumont et al, 2011,
DNA-, rRNA- and mRNA-based stable |
12 4/15 |
No meeting (Joost defense) | ||
13 4/22 |
We will discuss plant-microbe interactions, and how those interactions mediate plant function or ability to live in extreme environments. The primary paper is Antoninka et al but please also skim the short & sweet Marquez et al Science paper, a cool story, Loren wants to see what the group thinks about whether endophytes could possibly affect plants' responses to climate change. | Loren Albert | Antoninka et al (2009). Linking above- and belowground responses to Marquez et al (2007) A Virus in a Fungus in a Plant: Three-Way |
(started 18 January 2011)
Copyright © 2011