The Spatial and Chemical Diversity of a Model Microbial Ecosystem by a Combination of Metabolomics and NMR Imaging
EMSL Project ID
39997
Abstract
Mixed microbial communities drive many key biogeochemical processes, but the mechanisms by which microbial species interact, as well as and the relationship between these interactions and community function is poorly understood. Many studies of microbial communities rely on analysis of community DNA, RNA, or protein sequences, and are often conducted on large (> 1 cm3) samples. These analyses cannot address two important sources of diversity in microbial ecosystems: (i) the fine-scale (<1 mm) spatial diversity of community structure and function, and (ii) the chemical diversity in small molecule metabolites. We propose to study these two sources of diversity in a model microbial community biofilm through the use of EMSL's advanced NMR and mass spectrometry facilities. Our model community grows in highly acidic (pH < 1.0) iron-rich acid mine drainage solutions. Previous studies of community biofilms have revealed a heterogeneous distribution of member species and the presence of a variety of metabolites of novel composition. The heterogeneous distribution of community members' cells throughout our model microbial community suggests that community metabolic activity is also heterogeneously distributed, but we additionally hypothesize that spatial diversity exists even in regions of biofilm dominated by single species. To test this hypothesis, we plan to study gradients in the concentrations of organic small molecules in living biofilm. This experiment relies on EMSL's capability for NMR imaging as well as our group's capability to culture representative mixed microbial communities in the laboratory. EMSL's NMR imaging technology can measure the concentrations of hydrogen-containing metabolites at concentrations as low as 1 mM in voxels less than 200 nL in size.
Initial accurate-mass liquid chromatography-mass spectrometry has indicated the presence of many molecular species not represented in metabolite databases, highlighting the chemical diversity inherent in the AMD biofilms. EMSL's high-resolution NMR and FT-ICR capabilities will enable us to identify many more metabolites. Initial targets for analysis will be organic molecules present in the acidic, iron-rich culture medium, and a class of unusual monoacyl phosphoethanolamine lipids identified in our initial LC-MS2 metabolomics studies. Because the phosphoethanolamine lipids comprise several isomers which were not resolved in our initial analyses, we want to make use of EMSL's ion mobility mass spectrometer to help resolve these isomers, as well as studying these phospholipids by 31P NMR. Additionally, our ability to grow representative AMD biofilm communities in the lab has allowed us to introduce stable isotopic labels. High-resolution, heteronuclear NMR studies of metabolomic extracts of isotopically labeled AMD biofilm will permit unparalleled assessment of the metabolomic inventory of this model ecosystem.
Together, this study will help define the spatial scales at which community members interact, and the chemical means by which they do so.
Project Details
Project type
Large-Scale EMSL Research
Start Date
2010-10-01
End Date
2012-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members