Microorganisms inhabit almost every imaginable environment on Earth, playing integral roles in various ecosystem processes. Microbiomes, collections of microbes in specific habitats, change significantly from place to place and over time. Although rapid advances in genetic technologies have revolutionized our understanding of microbiomes, the rules governing microbiome function are yet to be learned. Research to understand these mechanisms in natural ecosystems can be difficult due to their open nature and extremely high diversity. Adequately capturing this complexity results in a need for extremely large datasets over long time scales. By contrast to open natural systems, engineered anaerobic digesters (ADs) are enclosed systems with controlled environments. AD systems are used globally for waste treatment and represent the largest engineering application of microbial biotechnology. As such, AD systems provide an ideal model system for understanding the rules governing microbiome function because of their microbial diversity, environmental significance, and the ability to control the environment. The goal of this research is to identify the rules controlling microbiome dynamics in ADs that can be used for other microbial ecosystems. This study will provide fundamental knowledge critical to predicting microbiome behavior in engineered and natural microbial ecosystems. Benefits to society resulting from this project will include improved science-based management of microbial ecosystems in both engineered and natural systems. Additional benefits include the training of the next generation of microbiome professionals with broad interdisciplinary expertise and skills to understand and control microbiome dynamics.

The overall goal of this project is to identify general ecological rules governing microbiome dynamics in different ecosystems with a focus on ADs as model microbial ecosystems. This will be achieved by examining whether general rules exist for species-area relationships as are known to exist in ecology. The four fundamental ecological processes of selection, dispersal, diversification, and drift will serve as a general theory to explain how microbial communities in microbiomes are assembled across space and time. Specific research objectives to achieve this goal include the following tasks: 1) Laboratory AD systems will be used to determine the short- (< 1 year) and long-term (>15 years) stability of microbiome biodiversity, structure, and function in responses to various environmental changes; 2) Advanced statistical tools will be used to elucidate underlying community assembly mechanisms in AD systems; 3) Novel mathematical approaches will be developed to detect the transient dynamics of AD microbiomes in response to environmental perturbations; and 4) Novel metagenomics-enabled anaerobic digestion models will be developed to provide effective frameworks for predicting and manipulating the dynamics of AD systems for desired functions. Resulting rules describing AD microbiome dynamics will be tested for their utility in describing other microbiomes from a variety of habitats including soils, marine, lacustrine, groundwater, gut, and other engineered systems. Cross-disciplinary training and workforce development will be achieved through research, training, and workshops to meet future needs for microbiome professionals.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

National Science Foundation (NSF)
Emerging Frontiers (EF)
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Karl Rockne
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University of Florida
United States
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