Roni Pasi (undergrad researcher) counts mycorrhizal colonization at root interestions of different crop species.

Microbes play important roles in sustainable food production and nutrient cycling, yet we lack some basic ecological knowledge about this group of organisms and their interactions with crop plant and forest communities.   As an ecologist, who works with mutualistic, saprotrophic, and pathogenic microbes, I study microbes and the plants they interact with in forests and in agricultural fields from molecular, physiological, community, and ecosystem-scale perspectives.


In order to successfully design sustainable, diverse cropping rotations, it is critical to understand the interactions between the crop plant community and soil microbes.

1. Cropping System Diversity and Management Effects on Mycorrhizal Fungi

Maintaining active arbuscular mycorrhizal (AM) fungal hyphae in cropping systems can allow for:

  • rapid seedling colonization
  • better early plant growth and nutrient uptake
  • improvements to soil structure.

In the NESARE Sustainable Dairy Cropping Systems project at The Pennsylvania State University, we are evaluating the effects of preceding crop type and system management on AM fungal colonization, early plant growth, and nutrient uptake.

2. Interactions by the Fungal Pathogen, Verticillium dahliae, with Crop Plant Hosts

Potato with Verticillium wilt symptoms at a farm in PA.
Potato with Verticillium wilt symptoms at a PA farm.

Yields for hundreds of vegetable crop species worldwide are greatly reduced by the soil-borne plant-fungal pathogen, V. dahliae, due to a disease known as Verticillium wilt. After colonizing plant roots and invading plant vascular tissues, V. dahliae causes wilting, and upon death of the plant, produces long-lived fungal structures, called microsclerotia, that persist in soil for up to ten years. Verticillium wilt management outcomes using crop rotational strategies have been variable, most likely because the pathogen can colonize some plants without causing wilting symptoms, but while still producing fungal inoculum. Many of these “asymptomatic” host plants that are colonized by this pathogen are also frequently used in crop rotations with susceptible host crops (Malcolm et al. 2013, Phytopathology) in efforts to control the wilting disease.   Since plant pathologists often overlook plants lacking symptoms but still potentially hosting pathogen populations, we may be missing valuable information about fungal-plant interactions, fungal genetic diversity, and persistence of an important portion of soil-borne fungal pathogen populations.


1. Microbial Feedbacks with Climate Change: An Ecophysiological Perspective

Rather than treating soil as a “black box”, understanding how different soil microbial communities regulate ecosystem processes will help scientists make better predictions regarding future climatic changes. Through my research, I identify key members of the microbial community using molecular tools and explore how different microbial species influence nutrient cycling, including the decomposability of their tissues, which impacts the size of the soil organic carbon pool, and their short and long-term temperature-respiration responses, which influences the amount of carbon dioxide returning to the atmosphere under different temperature regimes. In the past, we found that the composition of the microbial community might influence the rate at which that community decomposes or respires carbon dioxide into the atmosphere. For example, if microbial species that dominate a community decompose more slowly, that particular community will have a different effect on the size of the soil organic carbon pool than a community dominated by species with different traits, highlighting the importance of linking microbial species with ecosystem functions.

2. Effects of Crop Rotation Composition and Management on Nitrous Oxide Emissions

Me, measuring N2O release over manure injection slits for the NESARE project at Penn State.
Me, measuring nitrous oxide release over manure injection slits in a corn field.

Nitrous oxide emissions, a potent greenhouse gas, are effected by management of fertilizer, animal and plant manures, and crop residues in different crop rotation designs.  Currently, in Penn State’s NESARE Dairy Cropping System Project, we are evaluating a variety of crop rotation factors on nitrous oxide emissions.  I have also modeled nitrous oxide emissions for different dairy cropping systems using the Farm Energy Analysis Tool (FEAT).   In the future, better linking crop rotation management, nitrous oxide emissions, and microbial communities could be quite interesting.

Future: Please contact me if you find any of these research topics interesting or if you have other ideas for exploring questions surrounding plant-microbial effects on ecosystem functions.


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