{"46232":{"#nid":"46232","#data":{"type":"news","title":"Systems Biology Reveals Diversity in Key Environmental Cleanup Microbe","body":[{"value":"\u003Cp\u003EResearchers have completed the first thorough, system-level assessment of the diversity of an environmentally important family of microbes known as \u003Cem\u003EShewanella\u003C\/em\u003E. Microbes belonging to that genus frequently participate in bioremediation by confining and cleaning up contaminated areas in the environment.\u003C\/p\u003E\n\u003Cp\u003EThe 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 \u003Cem\u003EShewanella\u003C\/em\u003E. They believe the study results will help researchers choose the best \u003Cem\u003EShewanella\u003C\/em\u003E strain for bioremediation projects based on each site\u0027s environmental conditions and contaminants.\n\u003C\/p\u003E\n\u003Cp\u003EThe 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 \u003Cem\u003EProceedings of the National Academy of Sciences\u003C\/em\u003E. This research was supported by the U.S. Department of Energy through the Shewanella Federation consortium and the Proteomics Application project.\n\u003C\/p\u003E\n\u003Cp\u003ESimilar to a human breathing in oxygen and exhaling carbon dioxide, many \u003Cem\u003EShewanella\u003C\/em\u003E microbes have the ability to \u0022inhale\u0022 certain metals and compounds and convert them to an altered state, which is typically much less toxic. This ability makes \u003Cem\u003EShewanella\u003C\/em\u003E very important for the environment and bioremediation, but selecting the best strain for a particular project has been a challenge.\n\u003C\/p\u003E\n\u003Cp\u003E\u0022If you look at different strains of \u003Cem\u003EShewanella\u003C\/em\u003E 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 \u003Cem\u003EShewanella\u003C\/em\u003E bacteria are very similar, if not identical, but that is not true,\u0022 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 Georgia Tech School of Biology, led the research team in analyzing the data.\u003C\/p\u003E\n\u003Cp\u003EUsing 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. \n\u003C\/p\u003E\n\u003Cp\u003EBy comparing the 10 \u003Cem\u003EShewanella\u003C\/em\u003E genomes, which were sequenced at the Department of Energy\u0027s 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. \n\u003C\/p\u003E\n\u003Cp\u003E\u0022These findings suggest that similarity in gene regulation and expression constitutes an important factor for determining phenotypic similarity or dissimilarity among the very closely related \u003Cem\u003EShewanella\u003C\/em\u003E genomes,\u0022 noted Konstantinidis. \u0022They 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.\u0022\n\u003C\/p\u003E\n\u003Cp\u003EUpon 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 \u003Cem\u003EShewanella\u003C\/em\u003E 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.\u003C\/p\u003E\n\u003Cp\u003EThe most rapidly changing individual functions in the \u003Cem\u003EShewanellae\u003C\/em\u003E were related to \u0022breathing\u0022 metals and sensing mechanisms, which represent the first line of adaptive response to different environmental conditions. \u003Cem\u003EShewanella\u003C\/em\u003E 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.\n\u003C\/p\u003E\n\u003Cp\u003E\u0022Let\u0027s say you have a strain of \u003Cem\u003EShewanella\u003C\/em\u003E that is unable to convert uranium dissolved in contaminated groundwater to a form incapable of dissolving in water,\u0022 explained Konstantinidis. \u0022If 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.\u0022\n\u003C\/p\u003E\n\u003Cp\u003EThis adaptability of bacteria is remarkable, but requires further study in the bioremediation arena, since it frequently underlies the emergence of new bacterial strains. Konstantinidis\u0027 team at Georgia Tech is currently investigating communities of these \u003Cem\u003EShewanella\u003C\/em\u003E 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. \n\u003C\/p\u003E\n\u003Cp\u003EOngoing studies should broaden the researchers\u0027 understanding of the relationship between genotype, phenotype, environment and evolution, he said.\n\u003C\/p\u003E\n\u003Cp\u003E\u003Cstrong\u003EResearch News \u0026amp; Publications Office\u003Cbr \/\u003E\nGeorgia Institute of Technology\u003Cbr \/\u003E\n75 Fifth Street, N.W., Suite 100\u003Cbr \/\u003E\nAtlanta, Georgia  30308  USA\n\u003C\/strong\u003E\u003C\/p\u003E\n\u003Cp\u003EMedia Relations Contacts: Abby Vogel (404-385-3364); E-mail: (\u003Ca href=\u0022mailto:avogel@gatech.edu\u0022\u003Eavogel@gatech.edu\u003C\/a\u003E) or John Toon (404-894-6986); E-mail: (\u003Ca href=\u0022mailto:jtoon@gatech.edu\u0022\u003Ejtoon@gatech.edu\u003C\/a\u003E).\n\u003C\/p\u003E\n\u003Cp\u003E\u003Cstrong\u003EWriter:\u003C\/strong\u003E Abby Vogel\u003C\/p\u003E","summary":null,"format":"limited_html"}],"field_subtitle":"","field_summary":[{"value":"Researchers analyzed the gene sequences, proteins expressed and physiology of 10 strains of bioremediation microbes called Shewanella. Results showed surprising diversity not seen using traditional microbiology approaches.","format":"limited_html"}],"field_summary_sentence":[{"value":"Diversity found in family of key environmental cleanup microbes"}],"uid":"27206","created_gmt":"2009-08-31 00:00:00","changed_gmt":"2016-10-08 03:03:14","author":"Abby Vogel Robinson","boilerplate_text":"","field_publication":"","field_article_url":"","dateline":{"date":"2009-08-31T00:00:00-04:00","iso_date":"2009-08-31T00:00:00-04:00","tz":"America\/New_York"},"extras":[],"hg_media":{"46233":{"id":"46233","type":"image","title":"Kostas Konstantinidis","body":null,"created":"1449174358","gmt_created":"2015-12-03 20:25:58","changed":"1475894412","gmt_changed":"2016-10-08 02:40:12","alt":"Kostas Konstantinidis","file":{"fid":"101033","name":"tvl34376.jpg","image_path":"\/sites\/default\/files\/images\/tvl34376_0.jpg","image_full_path":"http:\/\/hg.gatech.edu\/\/sites\/default\/files\/images\/tvl34376_0.jpg","mime":"image\/jpeg","size":1316218,"path_740":"http:\/\/hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/tvl34376_0.jpg?itok=yD2Znd-j"}},"46234":{"id":"46234","type":"image","title":"Kostas Konstantinidis Shewanella","body":null,"created":"1449174358","gmt_created":"2015-12-03 20:25:58","changed":"1475894412","gmt_changed":"2016-10-08 02:40:12","alt":"Kostas Konstantinidis Shewanella","file":{"fid":"101034","name":"tkv34376.jpg","image_path":"\/sites\/default\/files\/images\/tkv34376_0.jpg","image_full_path":"http:\/\/hg.gatech.edu\/\/sites\/default\/files\/images\/tkv34376_0.jpg","mime":"image\/jpeg","size":885919,"path_740":"http:\/\/hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/tkv34376_0.jpg?itok=xWiOB3HY"}},"46235":{"id":"46235","type":"image","title":"Kostas Konstantinidis Shewanella","body":null,"created":"1449174358","gmt_created":"2015-12-03 20:25:58","changed":"1475894412","gmt_changed":"2016-10-08 02:40:12","alt":"Kostas Konstantinidis Shewanella","file":{"fid":"101035","name":"twi34376.jpg","image_path":"\/sites\/default\/files\/images\/twi34376_0.jpg","image_full_path":"http:\/\/hg.gatech.edu\/\/sites\/default\/files\/images\/twi34376_0.jpg","mime":"image\/jpeg","size":1704188,"path_740":"http:\/\/hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/twi34376_0.jpg?itok=cz6b6UcG"}}},"media_ids":["46233","46234","46235"],"related_links":[{"url":"http:\/\/www.ce.gatech.edu\/fac_staff\/faculty-listing\/research-interests\/?active_id=ktk3","title":"Kostas Konstantinidis"},{"url":"http:\/\/www.ce.gatech.edu\/","title":"School of Civil and Environmental Engineering"},{"url":"http:\/\/www.biology.gatech.edu\/","title":"School of Biology"}],"groups":[{"id":"1188","name":"Research Horizons"}],"categories":[{"id":"145","name":"Engineering"},{"id":"154","name":"Environment"},{"id":"146","name":"Life Sciences and Biology"},{"id":"135","name":"Research"}],"keywords":[{"id":"7077","name":"bacteria"},{"id":"7081","name":"bioremediation"},{"id":"4320","name":"ecology"},{"id":"807","name":"environment"},{"id":"3028","name":"evolution"},{"id":"7084","name":"genomic"},{"id":"7086","name":"genotype"},{"id":"7082","name":"metal"},{"id":"7078","name":"microbe"},{"id":"5696","name":"Microbiology"},{"id":"7079","name":"microorganism"},{"id":"7087","name":"phenotype"},{"id":"7085","name":"proteomic"},{"id":"7083","name":"remediation"},{"id":"170842","name":"Shewanella"},{"id":"167402","name":"Systems Biology"}],"core_research_areas":[],"news_room_topics":[],"event_categories":[],"invited_audience":[],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[{"value":"\u003Cstrong\u003EAbby Vogel\u003C\/strong\u003E\u003Cbr \/\u003EResearch News and Publications\u003Cbr \/\u003E\u003Ca href=\u0022http:\/\/www.gatech.edu\/contact\/index.html?id=avogel6\u0022\u003EContact Abby Vogel\u003C\/a\u003E\u003Cbr \/\u003E\u003Cstrong\u003E404-385-3364\u003C\/strong\u003E","format":"limited_html"}],"email":["avogel@gatech.edu"],"slides":[],"orientation":[],"userdata":""}}}