On-going research projects

Improved detection and quantification of antibiotic resistant genes and organisms in the environment


The global spread of antimicrobial-resistant (AMR) organisms and spread of AMR-associated genes poses a serious threat to the safety of our food and public health while being responsible for increased hospitalization and mortality of both humans and production animals. The release of AMR genes and organisms and microbes in the environment from agricultural sources is considered a serious threat but little is known about their persistence and spread in the environment. Current risk assessment models cannot adequately characterize and quantify the proliferation of resistance. We are developing a sequence-based approach that will provide considerably improved detection and quantification of antibiotic resistant genes including greater breadth in the numbers of genes that can be detected, the identify of microorganisms carrying these genes, and the likely association of these genes with transfer mechanisms (Diversity of Antibiotic Resistance Genes and Transfer Elements - Quantitative Monitoring, DARTE-QM). By demonstrating this approach in both laboratory model systems and the field, we hope to identify critical control points that may be sensitive to mitigation of emergence, spread, and persistence of resistance in the environment. Synergistic with this effort, we also are studying the occurrence and transport of antibiotics, antibiotic-resistant bacteria (ARB), and antibiotic resistance genes (ARG) in tile-drained agricultural fields that receive manure application. We will determine the effect of manure application timing, tillage, and patterns of rainfall/drainage on the persistence and losses of antibiotics, ARB, and ARG in soil and drainage water and determine the effects of alternative manure treatment and storage on the persistence of antibiotics, ARB, and ARG in manure.

This effort is a fantastic collaboration with Iowa State University (Michelle Soupir), the USDA (Heather Allen and Tom Moorman), and Grinnell College (Shannon Hinsa).

Understanding ecosystem services: What are the microbial drivers of soil health in bioenergy crops?

COBS site

Using a data-driven and integrated modeling framework, we collaborate with researchers who will develop the predictive capability to determine which feedstock combinations, regions and land types, market conditions, and bioproducts have the potential to support the ecologically and economically sustainable displacement of fossil fuels. Soils represent the most challenging ecosystem for microbial studies because of its extraordinary high diversity and structural complexity. Similar to their role in our gut systems, microbial communities drive nutrient cycling in the soil. In particular, our area of emphasis will be to obtain a mechanistic understanding of the plant, soil, microbe, and climate interactions that underlie the productivity and ecosystem services of different feedstocks.

This project is funded by the DOE and is part of the Center for Advanced Bioenergy and Bioproducts Innovation.

Understanding the dimensions of biodiversity: What is the scope and role of life on Earth?


Despite centuries of discovery, most of our planet’s biodiversity remains unknown. The scale of the unknown diversity on Earth is especially troubling given the rapid and permanent loss of biodiversity across the globe. As part of the NSF Dimensions of Biodiversity campaign, we hope to describe and understand the scope and role of life on Earth. The goal of this project is to study the ecology of microorganisms that are found in floral nectar. The results will be used to understand how the following three dimensions of biodiversity affect one another: genetic diversity of the most common species of nectar-colonizing yeast; species diversity of the bacteria that also colonize nectar; and functional diversity of the yeast and bacteria in their effects on the chemical characteristics of nectar and the consequences for pollination success and seed production. Although focused on a specific group of microorganisms, the primary research question addressed in this project is a general one: what are the factors that determine which “alternative stable state” is realized? Ecosystems are said to be in alternative stable states when final community membership depends on the order and timing in which species arrive. By regarding floral microbial communities as miniature ecosystems, the investigators will consider interactions among the three biodiversity dimensions as a factor that influences alternative stable states. Ecological researchers usually assume that the regional pool of species that supplies immigrants to local communities is stable and unaffected by local communities. This project will relax this commonly held, but unrealistic assumption by asking the following specific questions in tandem: how the regional diversity of nectar-colonizing microbes is modified by the seasonal timing of flowering; how local microbial diversity within flowers is shaped by hummingbird-assisted dispersal from the regional species pool; and how local microbial diversity in turn affects regional diversity by altering hummingbird-assisted dispersal. This study will help to understand biodiversity as both a cause and consequence of alternative stable states.

This project is funded by the NSF and is in collaboration with the Fukami lab, led by Tadashi Fukami, at Standford University.

Understanding environmental health and productivity: How can we use microbial indicators to assess ecosystem services and disturbances?


We use a systems approach to identify genetic and environmental factors controlling the occurrence of harmful algal blooms (HABs) in Iowa’s recreational lakes. We hypothesize that HAB ecology and cyanotoxin production are the predictable result of environmental factors, that the underlying genetic markers for cyanotoxin production are taxonomically controlled, and that incipient cyanotoxin-degrading microbes are present during HABs. The proposed research aims to test these hypotheses through development of monitoring and predictive tools to target future cyanotoxin monitoring and mitigation to the highest-risk recreational waters. The following objectives will be accomplished: conduct an integrated meta-analysis of physicochemical parameters and microbiome analyses of Iowa’s HAB-impacted recreational waters to develop a predictive model of HAB occurrence; develop scalable tools that can be used to rapidly monitor HABs and identify when additional cyanotoxin monitoring is necessary; identify emerging cyanotoxins within Iowa’s lakes and determine the freshwater HAB species linked to these toxins and the genetic systems that control toxin production; and identify and evaluate novel toxin-degraders for the mitigation of HAB cyanotoxins.

This project is funded by the EPA and is in collaboration with Kaoru Ikuma and Elizabeth Swanner at Iowa State University.

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