Associate Research Scientist
p: 508 289 7388
f: 508 457 4727
Dr. Margrethe Serres is a microbiologist by training. She is a Track II scientist in the JBPC at the MBL. Her current work focuses on understanding the functional make up of microbes and how this relates to their evolutionary history and the environments they inhabit. Her work is computational in nature. She uses pathway genome databases to curate microbial genome sequences and predict metabolic pathways using inputs from the literature, sequence-based analyses, and omics datasets; transcriptomes, proteomes, and metabolomes. Dr. Serres has been involved in the functional characterization of model organisms including Escherichia coli K-12 and Shewanella oneidensis MR-1. Her research interests also include functions encoded by protein families, linking their repertoire to metabolic capabilities and possibly novel metabolisms. Dr. Serres is using cross genome comparisons to detect differences in genome-encoded functions linked to evolutionary history and environmental adaptation. Together with collaborators she compared members of the genus Shewanella and identified functional categories differing in their degree of conservation across an evolutionary gradient. Her research has also included relating Shewanella genotypes to phenotypic traits, including growth on different C, N, P and S sources. More recently Dr. Serres has applied her genome analyses to microbes that co-exist either in laboratory grown cultures or in natural environments. She is searching selected genome sequences for activities related to the exchange of metabolites between microbes and their environment and to the establishment of microbial consortia. Dr. Serres has collaborated for several years with research groups linked to research efforts at the Pacific Northwest National Lab (Shewanella Federation, Biological Systems Interaction FSFA). She has received her funding from DOE.
Genome annotation and analysis.
My research includes collecting and predicting functions encoded by microbial genomes. We make use of sequence similarity, protein domain content, protein family membership, and genome context to infer gene product functions. Our annotation efforts emphasize the use of similarity to experimentally based functions. We also make use of omics based data for our predictions (i.e. gene and protein expression data, mutant analysis, promoter predictions). The annotations are captured in Pathway Genome Databases of the BioCyc type. These databases are further used as a framework for analyzing functional compositions and for genome comparisons. We have worked on the annotation of the model organism Shewanella oneidensis MR-1, a microbe with unique respiratory capabilities and of importance in biogeochemical cycles. We have also been involved in the annotation of 20 additional members of the Shewanella genus. More recently our annotation work includes the annotation of Synechococcus genomes and genome sequences from environmental isolates
Ecophysiological adaptations and speciation of Shewanella.
Members of the Shewanella genus occupy a variety of ecological niches including lakes, rivers, oceans, sediments, and terrestrial sub-surfaces. This suggests a high degree of physiological variety and the existence of several ecotypes. Diversity among Shewanella strains has been detected in metabolic processes (i.e. use of metals and radionuclides for respiration, carbohydrate degradation) and environmental sensing and signaling. Also, the Shewanellae are believed to play an important role in the biogeochemical cycles of C, N and S in redox interfaces of marine environments. We are interested in identifying genome signatures and functions that can be linked to adaptation of Shewanella to its various ecological niches. Our goal is to better understand how speciation and ecology relate to observed genotypes and phenotypes. We are also interested in the effect of lateral gene transfer on the current functional repertoire of organisms. Genes believed to be obtained through lateral transfer have been identified in theShewanella genome sequences. We are in the process of analyzing these sequences and their potential impact on ecological fitness.
We are using our annotation efforts and genome analyses to better understand how organisms interact with one another and with their environment. In collaboration with microbiologist at the Biological Division of the Pacific Northwest National Lab we are studying interactions between heterotrophs and autotrophs in co-cultures and in selected environments.
Protein families: a means to study functional diversity and metabolic capabilities.
My research interests also involve studying protein families both as a means to understand functional diversity and to link this diversity to metabolic capabilities and environmental adaptations. We are using protein groups for cross genome comparisons with the goal of relating family differences to functional capacity.