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Hot Topic Origins Origin & Evolution of Life Rethinking Species
 
Rethinking Species
Based on a American Society for Microbiology news release
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Origin & Evolution of Life
Posted:   04/05/07

Summary: Microbiologists are rethinking the ways in which they define and classify microbial species. Studying microbes and understanding how they are related to one another throughout evolutionary time is important in determining how life originated on our planet.

 

In the past, much of what we knew about microbes was based on information gathered from single organisms cultured in laboratories. However, many kinds of microbes cannot be cultured with known methods.
Credit: Pacific Northwest National Laboratory

Until a decade ago, scientists categorized microorganisms almost exclusively by their physical characteristics: how they looked, what they ate, and the by-products they produced. With the advent of genomic sequencing and genetic analysis in the 1990s, our understanding of the relationships between different microorganisms fundamentally changed. In light of this new knowledge, what exactly is the definition of a microbial species, and how should microbiologists be categorizing microorganisms? These questions are the focus of a new report released by the American Academy of Microbiology (AAM) entitled "Reconciling Microbial Systematics and Genomics."

"It is clear that the current system for designating microbial species is somewhat functional, but inadequate in many ways. It is unclear whether this system should be replaced or renovated," says Richard Roberts of New England Biolabs, one of the authors of the report.

The report is the result of a colloquium convened by the AAM in September 2006. Participants with expertise in microbial taxonomy, systematics, ecology, physiology and other areas described the history of microbial taxonomy, the state of the field today, and how work in the field should proceed in the future. The report is a record of their comments and recommendations. The results of the report are important to astrobiologists, whose interest in microbial life stems from the fact that microbes were the first form of life to develop on our planet. Microbes can also live in some of the most inhospitable environments on Earth, and if life has ever existed on other planets in the Solar System it would most likely resemble microbial life.

These close-up images, taken by an electron microscope, reveal tiny one-cell organisms called halophiles and methanogens. Halophiles get their name from living in salty environments and methanogens produce methane as a metabolic product.
Credit: Maryland Astrobiology Consortium, NASA and STScI

In the late 1800s, in order to make sense of the vast diversity of microbiological organisms, microbial taxonomists developed a system of placing microorganisms into categories in which each organism was granted a "genus" and "species" designation. At the time, physical (or phenotypic) properties were the only means of describing microorganisms, so the system was based on measurable and observable characteristics of the organisms, not genetic traits.

In the late 20th century, molecular biology uncovered the genetic relationships between microorganisms, and some of the secrets of microbes that had yet to be cultured in the lab (and hence phenotypically characterized) were revealed.

"Much of this new knowledge was incorporated into species descriptions, but difficulties in classification persisted and novel issues arose," says Roberts. "Conflicts exist between phenotypic and phylogenetic information, the means for classifying non-cultured microbes are limited under the current paradigm, and microbial species do not always demonstrate the phenotypic or genetic cohesiveness expected of them. For these reasons and others it has become clear that the species classification framework in use today is not capable of fully portraying and organizing microbial diversity."

A New Domain : In the late 1970s, Dr. Carl Woese spearheaded a study of evolutionary relationships among prokaryotes. Instead of physical characters, he relied on RNA sequences to determine how closely related these microbes were. He discovered that the prokaryotes were actually composed of two very different groups -- the Bacteria and a newly recognized group that he called Archaea. Each of these groups is as different from the other as they are from eukaryotes. These three groups are now recognized as three distinct domains of life.
Credit: Berkeley

The report contains an in-depth review of the myriad issues and conflicts involved in the classification of microbes in the post-genomic era, including a discussion on the definition of the term "species." It ends with a set of specific recommendations including, but not limited to:

-The establishment of a subcommittee within the International Committee on Systematics of Prokaryotes to consider a paradigm shift in the species definition.

-The need for more thorough study of the mechanisms of speciation before a more meaningful and practical species theory can be developed.

-The need for more comprehensive and systematic data to uncover whether microorganisms are organized into robust, definable, biologically meaningful clusters that adhere to the concept of species.

-The acquisition of draft-quality genome sequences for all type strains to help advance the integration of genomic information into our understanding of microbial diversity and enable researchers to map phenotypes to genomes.


Related Web Sites

The Structure of Origins
Microbes, Microbes Everywhere
Ordering Genes
Primordial Stone Soup
Intimate Strangers: Unseen Life on Earth (PBS)
Diversity in the Air
A Shadow Biosphere


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