Research

Google Scholar Profile for a full list of published work.

Methodology:  I use environmental genomics, culturing, and biogeochemical assays to understand soils chemistry, microbial communities, and their function (e.g. nutrient cycling and symbioses).  My work is empowered by both traditional lab techniques and computational biology.  I generate ecological insights through a combination of experimental approaches (e.g. laboratory microcosms, bioassays, plot-scale manipulations) and observational field studies (e.g. successional chronosequences).

Projects:  

Community Assembly

What are the controls on how microbes assemble into particular communities with particular functions?   I am interested in how the assembly of microbes through succession may drive the development of ecosystem structure and function. My research in microbial community assembly centers around the use of deglaciated forefields and post-fire landscapes to understand the controls on microbial community assembly through succession.    My work examines how, when, and where nutrients, biotic interactions, and microbial traits may be predictive microbial community assembly and drive ecosystems to have particular functions. 

Example Work:

Knelman JE, Schmidt SK, Lynch RC, Darcy JL, Castle SC, Cleveland CC, Nemergut DR. Nutrient addition dramatically accelerates microbial community succession. PloS one. 2014.

Nemergut DR, Knelman JE, Ferrenberg S, Bilinski T, Melbourne B, Jiang L, Violle C, Darcy JL, Prest T, Schmidt SK, Townsend AR. Decreases in average bacterial community rRNA operon copy number during succession. The ISME journal. 2015.

Knelman JE, Nemergut DR. Changes in community assembly may shift the relationship between biodiversity and ecosystem function. Frontiers in microbiology. 2014.

Nemergut DR, Schmidt SK, Fukami T, O'Neill SP, Bilinski TM, Stanish LF, Knelman JE, Darcy JL, Lynch RC, Wickey P, Ferrenberg S. Patterns and processes of microbial community assembly. Microbiology and Molecular Biology Reviews. 2013.

Plant-microbe mutualism and ecosystem development

How do microbial symbioses facilitate plant health, growth, and competition in stressful environments?  In past work I have sought to understand how plants interact with specific microbes to colonize and survive in low nutrient, poorly developed soils.  In addition, I have used microbial culturing techniques and a model grass system to better understand mutualism that improve plant growth under nutrient limited conditions.  My postdoctoral work focused on developing an experimental bioassay in which a reduced complexity microbial community (with cultures of all community members)  would reproducibly colonize a model grass root under experimental conditions.  This bioassay systems facilitates an experimental approach to studying many aspects of plant-bacterial mutualism including the underlying plant genomic effect on microbial communities and how different environmental conditions may impact plant-microbe mutualism. 

 Example Work:

Knelman JE, Graham EB, Prevéy JS, Robeson MS, Kelly P, Hood E, Schmidt SK. Interspecific Plant Interactions Reflected in Soil Bacterial Community Structure and Nitrogen Cycling in Primary Succession. Frontiers in microbiology. 2018.

Knelman JE, Legg TM, O’Neill SP, Washenberger CL, González A, Cleveland CC, Nemergut DR. Bacterial community structure and function change in association with colonizer plants during early primary succession in a glacier forefield. Soil Biology and Biochemistry. 2012.

Plant community-soil feedbacks in the context of climatic changes.

Microbes can help or deter plants from growing, and plants can influence which microbes are abundant in the soils.  In this way microbes influence aboveground plant community composition and plants influence microbial mediated biogeochemistry (the cycling of C, N, P, S, Fe, etc.). My research seeks to understand the connection between soil microbes and plant communities particularly in high latitude and elevation environments that are prone to ongoing climatic changes.  As plant communities respond to climate change, shifts in community composition can feedback on microbial communities with implications for soil dynamics, ecosystem function, and global climate (e.g. C cycling).  My work in plant-microbe interactions looks at how shifts in plant communities in response to climatic changes (precipitation, temperature, nitrogen deposition) may influence microbes and related biogeochemistry.  

Example work:

Yuan X, Knelman JE, Gasarch E, Wang D, Nemergut DR, Seastedt TR. Plant community and soil chemistry responses to long‐term nitrogen inputs drive changes in alpine bacterial communities. Ecology. 2016.

de Mesquita CP**, Knelman JE**, King AJ, Farrer EC, Porazinska DL, Schmidt SK, Suding KN. Plant colonization of moss-dominated soils in the alpine: Microbial and biogeochemical implications. Soil Biology and Biochemistry. 2017.

Yuan X, Knelman JE, Wang D, Goebl A, Gasarch E, Seastedt TR. Patterns of soil bacterial richness and composition tied to plant richness, soil nitrogen, and soil acidity in alpine tundra. Arctic, Antarctic, and Alpine Research. 2017.

Soil responses and microbial recovery from wildfire disturbance

With climatic changes driving increased frequency and intensity of wildfires in the Intermountain West, understanding forest ecosystem dynamics and recovery in the wake of such disturbance is dependent upon responses of soil microbial communities and the biogeochemistry they mediate (e.g. C, N, and P cycling).  My work seeks to build insights into the controls on microbial community composition and function after fires.  My work has examined both how shifts in nutrient pools as well as revegetation processes may influence post fire soil succession, or recovery.  Current research projects are also examining how multiple disturbances may impact forest ecosystems and soil microbial community structure and function.

Example Work:

Knelman JE, Graham EB, Trahan NA, Schmidt SK, Nemergut DR. Fire severity shapes plant colonization effects on bacterial community structure, microbial biomass, and soil enzyme activity in secondary succession of a burned forest. Soil Biology and Biochemistry. 2015 Nov 30;90:161-8.

Knelman JE, Schmidt SK, Garayburu-Caruso V, Kumar S, Graham EB. Multiple, compounding disturbances in a forest ecosystem: fire increases susceptibility of soil edaphic properties, bacterial community structure, and function to change with extreme precipitation event. Soil Systems. 2019 Jun;3(2):40.

Knelman JE, Graham EB, Ferrenberg S, Lecoeuvre A, Labrado A, Darcy JL, Nemergut DR, Schmidt SK. Rapid shifts in soil nutrients and decomposition enzyme activity in early succession following forest fire. Forests. 2017 Sep 15;8(9):347.

Ecosystem structure-function relationships

At the core of my research is understanding the connection between microbial community structure and function.  Across diverse ecosystems, quantifying this relationship helps to understand and predict biogeochemistry and how various environmental factors may influence ecological processes.  I have extended this general research approach to a variety of systems in collaboration with other scientists.  For example, I have helped with work that focuses on factors that control microbial cycling of Mercury in wetlands and waterways of the economically and socially important St. Louis River Estuary, Minnesota.  In other cases, I have helped with work to understand how the structure of Baboon and Vervet Monkey gut microbiomes may interact with parasite loads.   I am always excited to extend my perspective in microbial ecology and microbial biogeochemistry via productive collaborations with other scientists.