IEP: Deconstructing bacterial community biomass stoichiometry one cell at a time

Colorado State University, Fort Collins CO

Investigators

Abstract

Over the last ten years our ability to uncover the complexity of the living world has increased in leaps and bounds largely due to our ability to read the genetic sequence of microorganisms that cannot be grown in the laboratory. This plethora of information has revealed a diversity of environmental microorganisms beyond our wildest estimates. Microbes that live in virtually all environments are responsible for maintaining the ecosystem services that are vital for all life on earth. However, even with advances in understanding of microbial biodiversity we still have very little ability to link the presence of a given microorganism to the task it is performing. This research addresses that gap by developing and applying new tools to understand which molecules (proteins, nucleic acids, lipids) and how much of certain elements (e.g. nitrogen and phosphorus) are contained within living cells in the environment without having to grow them separately in the laboratory. More importantly, the proposed research provides an opportunity to link the information on genetic biodiversity with molecular and element composition of cells growing in the environment (i.e. without culturing). These approaches will allow us to began to make inferences on how microorganisms partition limiting resources under different conditions and how they alter availability of limiting nutrients to other organisms. Inferences from this will improve our understanding of fundamental constraints of life on earth and the role of biodiversity in maintaining the ecosystem processes essential for all living organisms. The PI proposes to apply existing ecological theory (Ecological Stoichiometry) to natural microbial communities using novel molecular and single-cell techniques to address pressing questions in environmental microbiology. He has proposed to couple analyses of Raman microspectroscopy (which allows for analysis of macromolecular content of single cells) with xray microanalysis (which allows for analysis of elemental composition of single cells) with in situ hybridization (e.g. FISH or EL-FISH, which allows for phylogenetic identification of cells visualized in both eplifluorescence (Raman MS) and transmission electron (XRMA) microscopy). Each method is established for use in environmental microbiology however the synthesis of molecular microbiology with single cell approaches to extend the application of ecological theory provides a unique and novel approach to understanding the controls and constraints on an important ecosystem parameter (microbial community stoichiometry). While microorganisms are exceptionally important to the functioning of all ecosystems our ability to understand how they influences even the most basic ecosystem function (e.g. CO2 release) is limited by the exceptional complexity of the genetic and metabolic diversity inherent in natural microbial communities. Sequencing microbial genes directly extracted from the environment has dramatically increased our understanding of the breadth and depth of microbial diversity in the environment. However, information on phylogenetic structure of a community often comes unaccompanied with any additional information on that organism's physiology or phenotype. This project will use new empirical tools to track the response of natural microbial communities to nutrient additions from the relative abundance of macromolecules through changes in phylogenetic structure to the elemental composition of the whole community. The research will advance the current understanding of how complex microbial communities alter fundamental ecosystem processes (i.e. nutrient cycling). While this project focuses on aquatic planktonic communities, because it is rooted in microbial physiology and ecological theory the results should be applicable to analysis of microbial communities from a wide range of ecosystems.