Leveraging the resilience of microbial communities to support stable ecosystems

Dr. Ashley Shade , Assistant Professor
Department of Microbiology & Molecular Genetics, Michigan State University

Microbial communities (or microbiomes) contain discrete populations of bacteria, archaea, fungi, and viruses that interact both with each other and with their local environment.  Environmental microbial communities act as both engines and engineers in ecosystems. They cycle important resources, and can alter the environment by transforming available resources by renovating their physical habitat and dispersing to colonize new territories. 

Many environmental microbiomes are among the most diverse on our planet, and soils in particular harbor tens of thousands of discrete microbial “species.”  The sheer taxonomic diversity of environmental microbial communities also suggests high functional diversity. Thus, one challenge faced by the researchers is to understand which of these many microbial species provide which important ecosystem functions and in what particular contexts. A second challenge is to understand the relationships between the systems-level functions that microbial communities provide and their taxonomic and functional diversity.

The researchers within the Shade lab want to understand microbiome resilience. Resilience is the capacity of a system to recover after its been altered by a disturbance. This is an important research pursuit because Earth’s ecosystems are faced with compounded disturbances associated with global climate change. These disturbances include stressors that are expected to accumulate and intensify over time, like rising temperatures and increased atmospheric carbon dioxide concentrations. They also include ephemeral but potentially intense events like droughts, hurricanes, and fires. Given this myriad of environmental changes, the Shade lab seeks to know if environmental microbial communities and the key functions they provide will remain stable.

The researchers intend to predict microbiome changes and manage those changes towards functional outcomes that will benefit the planet and humanity.  To achieve this, it is expected that they will need to learn how to harness environmental microbiomes to overcome the challenges presented by global climate change in agriculture and the energy industry. Understanding microbiome resilience is one key piece in this puzzle.

To understand community resilience, the Shade lab considers the extent of change after the disturbance, the rate and completeness of recovery to the pre-disturbance condition, and the potential for a system to move to an alternate stable state instead of recovering.  For microbial communities, understanding resilience also involves understanding the relationship between taxonomic diversity and community functions.  For example, it could be that microbial taxonomic diversity does not recover after a disturbance, but that functions recover due to redundancy in key traits among community members.

The Shade lab applies a multifaceted, integrated approach to understand microbial resilience.  This includes experiments in the field, lab, greenhouse, environmental chamber and within synthetic microbial communities.  The researchers use instrumentation and technology from Michigan State’s Genomics and Mass Spectrometry core facilities.  They combine large digital datasets, including microbial (meta)genome sequences, microbial and plant metabolites, in situ physical and chemical measurements, imaging and cell sorting.  With all of these different types of data and complementary approaches, the lab aims to gain a quantitative, systems-level understanding of microbiome resilience to various stressors.  Shade and others use compute resources at ICER to integrate and analyze their large datasets, and their trainees develop skills in data science in support of our research goals.  The Shade lab strives to make all of their data and code open access for the research community.  

The Shade lab currently has three major arms to their research program.  The first arm applies traditional ecological and macroecological theory to quantify microbiome resilience.  Here, they are focused particularly on how diversity reservoirs (rare and dormant microbes) contribute to resilience.  The researchers use the microbial communities inhabiting soils overlying the Centralia, Pennsylvania ongoing coal mine fire as a model of an ecosystem that is responding to a severe and unexpected disturbance.  The second arm aims to understand how the resilience of plant-associated microbiomes contributes to plant resilience.  The lab is part of the Great Lakes Bioenergy Research Center and they work collaboratively to support the growth of crops targeted for biofuel production on marginal lands.  The Shade lab is also part of the Plant Resilience Institute, and they work together with other PRI members to address fundamental questions to understand plant-microbe interactions as they relate to plant stress and global climate change.  The third arm aims to determine how the interactions among microbial populations contribute to community resilience.  For this research, the lab uses a synthetic community system in the laboratory to precisely control community diversity and environmental conditions, and to measure microbial interactions facilitated by extracellular molecules.   

The Shade lab expects that their research will provide fundamental insights into the resilience of environmental microbiomes, and will advance goals to predict microbiome responses and manage microbiome functional outcomes on our changing planet.