Overview
Soils contain tens of thousands of different microbial populations, and these microbes provide critical functions to ecosystems, including supporting plant health, making nutrients available, and modulating the exchange of gases with the atmosphere. Thus, these communities are front-line players in determining how ecosystems respond to stress. It is of societal importance to understand how soil microbial communities respond to stress so that we can manage them to be resilient and stable in the critical functions they provide. To better understand soil microbial responses to a large and unnatural stress, this award leveraged the ongoing underground coal seam fire in Centralia, Pennsylvania, USA, that ignited accidentally in 1962. The Centralia heat gradient enabled a long-term investigation of soil microbial community responses to and recovery from stress.

Intellectual Merit
This award advanced the understanding of how complex microbial communities respond to and recover from environmental stress. Soil microbial communities shifted starkly in their compositions in response to the heat and recovered gradually as the soils cooled. The communities in heated soils had traits and likely functions adapted to the stress, including relatively smaller genomes and specialized metabolisms. Together, experimental and field results showed that bacterial populations sensitive to the heat later re-established in the soil by dispersal or by persisting in an inactive state, likely to gain protection during the stress. Experimental results showed that interactions among different bacterial populations can also influence how a community responds to stress: a population’s functions can change depending on which other populations were present and whether their interactions were positive or negative. In addition, this award supported the targeted investigation of how several microbial genes responded to heat stress, including arsenic and antibiotic resistance genes, which encode functions relevant to human and animal health and can be exchanged among different microbial populations. Generally, these genes changed with stress intensity, which was attributed to concordant changes in the microbial populations present rather than gene exchange.  

This award has broadly advanced ecological understanding of the consequences of microbial biodiversity for community stress response and ecosystem functions. It has highlighted the importance and consequences of microbial inactivation and re-activation to support community transitions during stress and their eventual resilience towards a recovered state. It has also advanced the understanding of how reservoirs of inactive microbial biodiversity can accumulate during and after a disturbance, with consequences for a community’s recovery potential. These specific findings have provoked new directions of research.

This work resulted in 23 peer-reviewed scientific papers, three doctoral dissertations, and over a thousand publicly available data products actively used by scientists (e.g., for gene and pathway mining), including DNA sequences, metabolite profiles, code for computational data analysis, and a public reference database of soil bacterial genomes linked to plasmids. Significant results were communicated via 21 posters and talks at approximately 19 scientific conferences and 18 invited university or institutional seminars. The media covered the award’s research results at least six times.  

Broader Impacts
This award benefited society by advancing understanding of the mechanisms that support resilient soil microbial communities, with broad relevance for understanding how to predict and manage soil health in natural and agricultural ecosystems. It further advanced societal goals of open and reproducible science by making data and educational products publicly available. The scientific community is using the rich sequencing data generated as part of this award to discover microbial pathways that may be useful for developing new products or drugs.  

It also produced several educational products established at Michigan State University and MSU’s Kellogg Biological Station. These efforts included a five-year, annually-delivered training workshop on big data analysis and computing that reached 132 domestic and international learners. It also produced publicly available learning materials for the microbiology and ecology undergraduate classroom, including team-based active learning exercises, video lectures, and specific learning objectives aligned to content and assessments.

The award supported the scientific workforce training of three Ph.D. students, one MSc. student, four post-doctoral scholars, three teaching fellows, one technician, over 30 undergraduate researchers, and two visiting international scholars. These project personnel developed quantitative skills in data analysis, computing, ecology, microbiology, molecular biology, soil science, experimental design, and responsible conduct of research, including societal values of open and reproducible science. All graduate students contributing to this award’s work are currently employed in science-relevant public or private sector positions. It supported a Ph.D. internship in the private sector with a start-up company and allowed the PI to engage in science communication training at Michigan State.   

Last Modified: 02/19/2025
Modified by: Ashley L Shade