Environmental proteomic analysis of anaerobic methane oxidizing systems
EMSL Project ID
19199
Abstract
Prokaryotic microorganisms represent the majority of living things on Earth. In many cases, interdependent constituents of this vast microbial biota play decisive roles in defining biogeochemical gradients that drive essential elemental cycles, including carbon, nitrogen and sulfur. Such cycles support the nutritional needs of all life forms and regulate global-scale atmospheric, terrestrial and oceanic processes. Understanding how metabolic networks link microbial activity within these cycles is a fundamental scientific problem. Because the vast majority of microbes in nature resist laboratory cultivation, we must develop and advance new tools and analytic methods to explore the wild metabolism of indigenous microbial groups at the community level. The anaerobic oxidation of methane (AOM) is a prime exemplar of the paradigm linking microbial activity to local and global-scale biogeochemical processes. AOM reduces methane flux from ocean to atmosphere, stimulates subsurface metabolism, and supports deep-sea microbial communities that derive energy from one of its by-products, hydrogen sulfide. Decades of geochemical research have led to chemical profiling of AOM in a variety of marine habitats. The phenomenon typically occurs at a boundary layer known as the sulfate-methane interface (SMI), characterized by the absence of oxygen, availability of methane and sulfate, and presence of dissolved inorganic carbon depleted in heavy carbon isotopes. Studies aimed at determining the biological component of AOM have identified uncultivated prokaryotic communities dominated by methanogen-related archaea (ANME-1 and ANME-2) and sulfate reducing bacteria (SRB). Recent application of cultivation-independent techniques to marine sediments associated with AOM have led to construction of environmental genomic maps encompassing the genetic potential of several ANME and SRB groups. These maps have enabled primary in silico reconstruction of specific enzymatic steps mediating AOM. We are now poised to validate this pathway based on analysis of expressed protein sequences.
This collaborative proposal seeks access to the EMSL user facility to detect and measure in situ protein expression profiles of uncultivated microbial populations associated with AOM. We will profile the environmental proteomic signature of ANME and SRB groups recovered from regions of the Northeastern Pacific Ocean and the Black Sea in order to compare gene expression under different geochemical conditions. The combined data set will simultaneously provide a robust detection method for gene products hypothesized to mediate the biological transformation of methane, and a validation mechanism for determining the accuracy of gene prediction models, including predicted hypothetic proteins, with supporting annotation. This work promises to open a previously unknown world of genomic and biochemical complexity defining the molecular basis of AOM. Given the profound impact of AOM on the environmental state of the biosphere today and throughout much of Earth’s history, the study of these mechanisms is highly relevant. The proposed research flows well with DOE energy and science strategic goals and with EMSL user themes of biological interactions and interfaces, and geochemistry and subsurface science. It is innovative, focusing on the development and application of novel methods to investigate gene expression in naturally occurring microbial groups, and it is interdisciplinary drawing on methods in environmental genomics, bioinformatics and mass spectrometry.
Project Details
Project type
Large-Scale EMSL Research
Start Date
2006-09-01
End Date
2009-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
19199_ASM2007