Microbial metaomics discussion group this week: metatranscriptomics and biogeography

A visiting student at my lab Lea Benedicte Skov Hansen will be leading our “metaomics” discussion group this week.  We will be discussing a combination of metatranscriptomics and biogeography and the papers of the week are:

Metatranscriptomics paper:

Microbial community gene expression in ocean surface waters. Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW, Delong EF. Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3805-10. Epub 2008 Mar 3.

Some related papers of potential interest from DeLong

• Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyre.
• Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea.
• Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean.
• Microbial metatranscriptomics in a permanent marine oxygen minimum zone.
• Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities.

We are also discussing:

Drivers of bacterial beta-diversity depend on spatial scale. Martiny JB, Eisen JA, Penn K, Allison SD, Horner-Devine MC.
Proc Natl Acad Sci U S A. 108(19):7850-4.  (NOTE I am an author on this one – but the meat of the ideas/work was done by Jen Martiny, Claire Horner-Devine and others).

Related papers of possible interest by Jen Martiny and Claire Horner-Divine include:

• Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems.
• Patterns of fungal diversity and composition along a salinity gradient.
• The biogeography of ammonia-oxidizing bacterial communities in soil.
• Phylogenetic clustering and overdispersion in bacterial communities.
• Microbial biogeography: putting microorganisms on the map.
• An ecological perspective on bacterial biodiversity.
• A taxa-area relationship for bacteria.
• A comparison of taxon co-occurrence patterns for macro- and microorganisms.

Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis View all posts by Jonathan Eisen