Navigation Links
Hidden diversity in key environmental cleanup microbes found by systems biology assessment
Date:8/31/2009

Researchers have completed the first thorough, system-level assessment of the diversity of an environmentally important genus of microbes known as Shewanella. Microbes belonging to that genus frequently participate in bioremediation by confining and cleaning up contaminated areas in the environment.

The team of researchers from the Georgia Institute of Technology, Michigan State University and the Pacific Northwest National Laboratory analyzed the gene sequences, proteins expressed and physiology of 10 strains of Shewanella. They believe the study results will help researchers choose the best Shewanella strain for bioremediation projects based on each site's environmental conditions and contaminants.

The findings, which further advance the understanding of the enormous microbial biodiversity that exists on the planet, appear in the early online issue of the journal Proceedings of the National Academy of Sciences. This research was supported by the U.S. Department of Energy through the Shewanella Federation consortium and the Proteomics Application project.

Similar to a human breathing in oxygen and exhaling carbon dioxide, many Shewanella microbes have the ability to "inhale" certain metals and compounds and convert them to an altered state, which is typically much less toxic. This ability makes Shewanella very important for the environment and bioremediation, but selecting the best strain for a particular project has been a challenge.

"If you look at different strains of Shewanella under a microscope or you look at their ribosomal genes, which are routinely used to identify newly isolated strains of bacteria, they look identical. Thus, traditional microbiological approaches would suggest that the physiology and phenotype of these Shewanella bacteria are very similar, if not identical, but that is not true," explained Kostas Konstantinidis, an assistant professor in the Georgia Tech School of Civil and Environmental Engineering. Konstantinidis, who also holds a joint appointment in the School of Biology, led the research team in analyzing the data.

Using the traditional method for determining interrelatedness between microbial strains -- sequencing of the 16S ribosomal gene -- the researchers determined that the 10 strains belonged to the same genus. However, the technique was unable to distinguish between most of the strains or define general properties that would allow the researchers to differentiate one strain from another. To do that, they turned to genomic and whole-cell proteomic data.

By comparing the 10 Shewanella genomes, which were sequenced at the Department of Energy's Joint Genome Institute, the research team found that while some of the strains shared 98 percent of the same genes, other strains only shared 70 percent. Out of the almost 10,000 protein-coding genes in the 10 strains, nearly half -- 48 percent -- of the genes were strain-specific, and the differences in expressed proteins were consistently larger than their differences at the gene content level.

"These findings suggest that similarity in gene regulation and expression constitutes an important factor for determining phenotypic similarity or dissimilarity among the very closely related Shewanella genomes," noted Konstantinidis. "They also indicate that it might be time to start replacing the traditional microbiology approaches for identifying and classifying new species with genomics- or proteomics-based methods."

Upon further analysis, the researchers found that the genetic differences between strains frequently reflected environmental or ecological adaptation and specialization, which had also substantially altered the global metabolic and regulatory networks in some of the strains. The Shewanella organisms in the study appeared to gain most of their new functions by acquiring groups of genes as mobile genetic islands, selecting islands carrying ecologically important genes and losing ecologically unimportant genes.

The most rapidly changing individual functions in the Shewanellae were related to "breathing" metals and sensing mechanisms, which represent the first line of adaptive response to different environmental conditions. Shewanella bacteria live in environments that range from deep subsurface sandstone to marine sediment and from freshwater to saltwater. All but one of the strains was able to reduce several metals and metalloids. That one exception had undertaken a unique evolution resulting in an inability to exploit strictly anaerobic habitats.

"Let's say you have a strain of Shewanella that is unable to convert uranium dissolved in contaminated groundwater to a form incapable of dissolving in water," explained Konstantinidis. "If you put that strain in an environment that contains high concentrations of uranium, that microbe is likely to acquire the genes that accept uranium from a nearby strain, in turn preventing uranium from spreading as the groundwater flows."

This adaptability of bacteria is remarkable, but requires further study in the bioremediation arena, since it frequently underlies the emergence of new bacterial strains. Konstantinidis' team at Georgia Tech is currently investigating communities of these Shewanella strains in their natural environments to advance understanding of the influence of the environment on the evolution of the bacterial genome and identify the key genes in the genome that respond to specific environmental stimuli or conditions, such as the presence of heavy metals.

Ongoing studies should broaden the researchers' understanding of the relationship between genotype, phenotype, environment and evolution, he said.


'/>"/>

Contact: Abby Vogel
avogel@gatech.edu
404-385-3364
Georgia Institute of Technology Research News
Source:Eurekalert  

Related biology technology :

1. Jazz Pharmaceuticals to Present at Natixis Bleichroeders Hidden Gems Conference
2. Advanced Life Sciences to Present at Natixis Bleichroeder Hidden Gems Conference
3. Kendle to Present at the Natixis Bleichroeder Hidden Gems Conference
4. Biodel Inc. to Present at Natixis Bleichroeder Hidden Gems Conference on October 8, 2007
5. Iomai CEO to Speak at Natixis Bleichroeder Hidden Gems Conference on Monday
6. diaDexus, Inc. and Living Heart Foundation Offer the PLAC(R) Test to Detect Hidden Risk for Heart Attack and Stroke in Retired NFL Players
7. Nektar Therapeutics President and CEO Howard W. Robin to Present at Natixis Bleichroeder Second Annual Hidden Gems Conference in New York City
8. Arena Pharmaceuticals to Present at the Natixis Bleichroeder Second Annual Hidden Gems Conference
9. Pharmasset to Present at the Natixis Bleichroeder Hidden Gems Conference on Monday, October 13th
10. Transcept Pharmaceuticals, Inc. to Present at the Natixis Bleichroeder Second Annual Hidden Gems Conference
11. Kaiser Permanente to Host 30th Annual Diversity Conference
Post Your Comments:
*Name:
*Comment:
*Email:
Related Image:
Hidden diversity in key environmental cleanup microbes found by systems biology assessment
(Date:10/11/2017)... ... October 11, 2017 , ... ... its endogenous context, enabling overexpression experiments and avoiding the use of exogenous expression ... guides is transformative for performing systematic gain-of-function studies. , This complement to ...
(Date:10/11/2017)... ... 11, 2017 , ... ComplianceOnline’s Medical Device Summit is back for its 4th ... in San Francisco, CA. The Summit brings together current and former FDA office bearers, ... and government officials from around the world to address key issues in device compliance, ...
(Date:10/11/2017)... 11, 2017  VMS BioMarketing, a leading provider of patient ... Clinical Nurse Educator (CNE) network, which will launch this week. ... among health care professionals to enhance the patient care experience ... and other health care professionals to help women who have ... ...
(Date:10/11/2017)... ... October 11, 2017 , ... Disappearing forests and increased emissions are the ... million people each year. Especially those living in larger cities are affected by air ... one of the most pollution-affected countries globally - decided to take action. , “I ...
Breaking Biology Technology:
(Date:8/23/2017)... -- The general public,s help is being enlisted in what,s thought to be ... on the human body –and are believed to affect health.  ... The Microbiome Immunity Project is the largest study ... gut. The project's goal is to help advance scientific knowledge of the ... ...
(Date:6/14/2017)... IBM ) is introducing several innovative partner startups at VivaTech ... startups and global businesses, taking place in Paris ... will showcase the solutions they have built with IBM Watson ... France is one of the most dynamic ... in the number of startups created between 2012 and 2015*, ...
(Date:4/24/2017)... 2017 Janice Kephart , former ... Strategy Partners, LLP (IdSP) , today issues the ... Trump,s March 6, 2017 Executive Order: Protecting ... can be instilled with greater confidence, enabling the ... refugee applications are suspended by until at least ...
Breaking Biology News(10 mins):