A microbial perspective

By Kelly S Ramirez

This past winter went by in a hurry. Workshops, data analysis and proposals, combined with a few weekend trips resulted in surprise and slight panic when I realized on Monday that it was already April 1st. We all tend to get caught up in work and our daily lives, and I sometimes question if I make enough time to appreciate the science I work on.

Currently, I am working on a project surveying the biodiversity in the soil in Central Park NYC. We are examining all the life- bacteria, archaea and eukaryotes -in the soils of Central Park, and this is one project where I really do appreciate the underlying science. To survey the organisms in the soil we sequence genes from DNA extracted from each soil sample (16S rRNA genes for bacteria and archaea, and 18S rRNA genes for eukaryotes). These genes are like an organisms fingerprint, they are highly conserved and relative long, and can therefore give us not only knowledge about what each organisms is but also place it in a phylogenetic context: how it is evolutionarily related to other organisms.

This fundamental method, the use of the small-subunit ribosomal RNA genes to identify and place organisms into a phylogenetic context, was developed, by Carl Woese. Woese and his colleague George Fox published on their findings in 1977  and ultimately changed biology (1). Pace et al (2) provide a clear, insightful overview of the impressive work, that is really worth a read.

Briefly, the work by Woese and Fox had two major impacts on science. First, it established that life is tritrophic; that there are three domains of life- Eukaryotes (humans, animals, plants for example), Bacteria, and Archaea:

You may remember from your own education learning about the six kingdoms. However, with the development and use of ribosomal RNA, Woese identified that all life could be related and placed into one of these three domains. This revelation was especially relevant to the microbial world, where prior to this work, life was described as Eukarya and Prokarya (previously known as Monera). This work established that bacteria and archaea were two separate domains of life and the term prokarya was obsolete.

Second, Woese’s work changed how the microscopic world was studied. Before this, culture based methods were used to identify the ‘unseen’ microbes in an environment. Culturing methods are limited though as the majority (>90%) of microorganisms cannot be cultured. Instead, by sequencing genes from the DNA extracted out of a given sample, we are able to get a much better snap-shot of all the organisms present.

I was introduced to Woese’s work my first year of graduate school in a Microbial Ecology class taught by Dr. Norman Pace of CU-Boulder. Norm was a postdoc at the University of Illinois with Woese. Norm is an excellent teacher. His class discussed techniques and progress being made in the field of microbial ecology, the Tree of Life and most memorably, the fact that “Prokaryote’ is obsolete terminology.

The lessons of Norm’s class were inspired by the work that Woese, Fox, himself and others did. Their work laid the groundwork and established the framework for microbial ecology as we approach it today, and that I am using in my own project on Central Park. From Norm’s course and the story of Woese, I learned more than microbial ecology or that the relationships between organisms can be explained succinctly through a three domain system; I learned to appreciate the amazingness of life with a microbial perspective.

What perspective do you use to appreciate your own work?

In honor of Carl Woese, who died December 30, 2012.

REFERENCES:

1. Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proc Natl Acad Sci USA 74:5088–5090.

2. Pace NR et al. 2012. Phylogeny and beyond: Scienti!c, historical, and conceptual significance of the first tree of life. PNAS: 109:4 (1011-1018) http://www.pnas.org/content/early/2012/01/13/1109716109

A great read by Rob Dunn: http://www.robrdunn.com/2012/12/chapter-8-grafting-the-tree-of-life/

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