Microbial Meta-omics and Ecosystem Function

Spring Semester 2011



Date  Topic Discussion Leader Readings (* = primary reading)
1/14/2011 Organizational meeting    Guidelines for discussion and Suggested Topics



Introductory Readings: Microbes, Biogeochemistry, and "Environmental Genomics" (presentation)
     We will focus on Falkowski et al, which gives an overview of microbially-driven biogeochemistry and the evolution of the redox chemisty of life.

Scott Saleska / Virginia Rich

Falkowski, P.G., Fenchel, T. & Delong, E.F. 2008. The microbial
engines that drive Earth’s biogeochemical cycles. Science




Introductory Readings: Microbes, Biogeochemistry, and "Environmental Genomics"
     Vandenkoornhuyse et al, provide a more in-depth review of the science of 'environmental genomics' and how it is advancing this field (note the glossary of terms at the end of the text, which can be the start of the glossary that we assemble over the time of the course).
     I'll give an overview of microbial links to biogeochemistry (presentation here), and then we will discuss environmental genomics through the scaffold of the Vandenkoornhuyse review.(presentation here)

Virginia Rich

Vandenkoornhuyse, P., et al. 2010. Integration of molecular
functions at the ecosystemic level: breakthroughs and future goals of
environmental genomics and post-genomics, Ecology Letters
(includes supplementary info Box 1 and Box 2)




No meeting this week





Isotopes as tracers of biogeochemical processes
We will survey this voluminous field via the classic review by Farquhar et al (~2,000 citations!) of carbon isotope discrimination in photosynthesis. This provides an introduction to terms and concepts, and as well as an overview of its main topic. Supplemental papers are posted for reference on use of isotopes as tracers of other biogeochemical cycles (N2O, CH4, water), which you may read at you leisure or cite in the discussion.


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]

Stein and Yung. 2003. Production, isotopic composition, and
atmospheric fate of biologically produced N2O.
Chanton et al. 2004. Carbon and Hydrogen Isotopic Effects in Microbial
CH4 from Terrestrial Environments



No meeting    



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
Waters off the Chilean Coast, Science, 330: 1375-1378

Walsh et al., 2009, Metagenome of a Versatile Chemolithoautotroph
from Expanding Oceanic Dead Zones, Science, 326: 578-582.



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
monooxygenase operon from soil by combining stable isotope probing
and metagenomic analysis, Environmental Microbiology

Wooley et al 2010, A primer on metagenomics,
PLOS Computational Biology (for reference)

More recent papers in this series
Dumont et al, 2011, DNA-, rRNA- and mRNA-based stable
isotope probing of aerobic methanotrophs in lake sediment
Environmental Microbiology
Chen, Dumont, et al. 2008. Revealing the uncultivated majority:
combining DNA stable-isotope probing, multiple displacement
amplification and metagenomic analyses of uncultivated
Methylocystis in acidic peatlands, Env. Microbiology

An interesting-looking paper that we decided was too
technical/methods oriented:
Gianolis, et al., 2009. Quantifying environmental adaptation of
metabolic pathways in metagenomics, Proc. Nat. Acad. Sci



No meeting    


Spring Break    



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.
      NOTE: there is a consistent typographical error in Freitag et al (2010): wherever it refers to "gene:transcript abundance ratios" (e.g. y-axis labels in Fig. 1, or the heading on page 161), it actually of course means the inverse, i.e., "transcript:gene abundance ratios". (because genes per transcript wouldn't actually make much biological sense).

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
Functional Gene Transcriptional Activity in a Peat Soil.
Appl. Env. Microbiology

Freitag et al., 2010. Links between methane flux and
transcriptional activities of methanogens and methane oxidizers
in a blanket peat bog FEMS Microbiol Ecol, 73: 157–165.

A related line of work using controlled lab incubations:

Hendrickson et al., 2007. Functionally distinct genes regulated by
hydrogen limitation and growth rate in methanogenic Archaea, PNAS.
Xia et al. 2008. Quantitative proteomics of nutrient limitation in
the hydrogenotrophic methanogen Methanococcus maripaludis,
BMC Microbiology



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
changes in soil redox potential status, Envir. Microbiology.



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
isotope probing of aerobic methanotrophs in lake sediment
Environmental Microbiology
Dumont et al 2010, Supplement



No meeting (Joost defense)    



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
global change at community and ecosystem scales, Global Change

Marquez et al (2007) A Virus in a Fungus in a Plant: Three-Way
Symbiosis Required for Thermal Tolerance, Science


(started 18 January 2011)
Copyright © 2011