BE/GEN-EN: Analysis of Factors Determining the Ecological Function and Resilience of Microbial Communities

University Of California-Berkeley, Berkeley CA

Investigators

Abstract

Abstract Environmental chemistry is largely controlled by the interplay between microbial activity and geochemistry. The complex nature of most communities in natural systems makes it difficult to unravel the specific mechanisms of this interaction. A compounding factor is that most microorganisms have not been isolated, and thus their biochemistry and actual roles in geochemical cycling are largely unknown. This project will study a community at the level of its metabolic network in order to develop and test ecological models for community resilience and function. The approximately five member community is derived from a subsurface extreme acid mine drainage (AMD) site within an ore body. The environmental geochemistry is simple because the ore deposit is ~95% pyrite (FeS2), and receives minimal inputs of fixed carbon and nitrogen. Energy is supplied to autotrophs from only two sources: aerobic iron and sulfur oxidation. These and other characteristics make the system tractable to bioreactor experiments and modeling that can document ecosystem structure and function. Two groups of hypotheses based on established ecological principles will be tested. First, microorganisms responsible for nitrogen fixation and oxidation of elemental sulfur are hypothesized to be keystone species because their impact on the community is disproportionate to their abundance. Perturbation studies will be used to test this hypothesis. Second, iron-oxidizing organisms are hypothesized to be adapted to higher pH conditions. Microbes colonize pyrite surfaces, and through a series of species succession events, lead to a climax community at an optimal low pH (facilitative succession). The identity and metabolic characteristics of early to late colonizers in bioreactor communities will be determined in a series of eight washout-perturbation treatments in order to test this hypothesis. The central product of this study will be a genome-enabled elucidation of the metabolic pathways that regulate and determine survival of individual species and the community. Genome data and gene expression will be analyzed to identify and monitor activity of genes responsible for oxidation of ferrous iron (the primary sulfide oxidant) and sulfur (the key acid generating reaction), and CO2 and nitrogen fixation. Metaphysiological trophic models will be developed to describe the system and test hypotheses. This modeling technique is particularly adept at handling non-linearities in complex systems. Outcomes will include the first tests of ecological theories of succession and species interactions with genetic-level resolution, and students trained in the development of new approaches to ecology.