Dr. Brian Badgley

Crop & Soil Environmental Sciences

Research in my lab focuses on environmental microbiology and microbial ecology, with two particular interests. First, we are interested in elucidating the ecological roles of microbial populations and communities in natural systems.  Microbes mediate many important processes at the ecosystem and global scales, yet approximately 99% of all microbes are not culturable, meaning we know little or nothing about their distribution or role in the environment. Second, we are interested in the fate of particular microorganisms in the environment, such as pathogens, water quality indicators, or biodegraders. Even though these organisms may be relatively low in abundance, they are still highly significant, particularly from an applied perspective, and it is important to understand their survival and transport through ecosystems. By combining new methods in genomics and metagenomics with traditional culture based techniques we can seek to gain new insights into these important questions in a variety of habitats. We also strive to conduct highly collaborative and interdisciplinary projects, working with a variety of colleagues from ecosystem ecology, agriculture, chemistry, engineering, and public health.

Examples of some of the studies in which we are currently involved include:

  • Patterns in microbial diversity and community structure in a variety of habitats, including reclaimed mine soils, agricultural and forest soils, stream waters and sediments, ballast water in cargo ships, and the surface of mouse skin.
  • The impact of storm events on sediment resuspension and microbial transport in stream ecosystems.
  • The effect of diversity on ecological function in soil microbial communities.

Email         Lab Website


Recent Publications

Guentzel KS, Hondzo M, Badgley BD, Finlay JC, Sadowsky MJ, Kozarek JL, Sotiropolous F (2014) Measurement and modeling of denitrification in sand-bed streams of varying land use. J Environ Qual 43:1013-1023.

Scholz F, Badgley BD, Sadowsky MJ, Kaplan DH (2014) Immune mediated shaping of microflora community composition depends on barrier site. PLoS One 9:e84019.
(#co-first authors)

Harwood VJ, Staley C, Badgley BD, Borges K, Korajkic A. (2014) Microbial source tracking markers for detection of human sewage and fecal contamination in environmental waters: relationships to pathogens and human health outcomes. FEMS Mirobiol Rev 38:1-40.

Ebentier DL, Hanley KT, Cao Y, Badgley BD, Boehm AB, Ervin JS, Goodwin KD, Gourmelon M, Griffith JF, Holden PA, Kelty CA, Lozach S, McGee C, Peed LA, Raith M, Ryu H, Sadowsky MJ, Scott EA, Santo Domingo J, Schriewer A, Sinigalliano CD, Shanks OC, Van De Werfhorst LC, Wang D, Wuertz S, Jay JA (2013) Evaluation of the repeatability and reproducibility of a suite of qPCR-based microbial source tracking methods. Water Res 47:6839-6848.

Sinigalliano CD, Ervin J, Van De Werfhorst LC, Wang D, Wanless D, Bartkowiak J, Layton B, Raith M, Schriewer A, Badgley BD, Lee C, Goodwin KD, Lee J, Boehm AB, Noble R, Holden PA, Jay J, Wuertz S, Byappanahalli M, Whitman R, Sadowsky MJ, Meijer WG, Ballesté E, Gourmelon M, Griffith J, Ryu H, Santo Domingo JW (2013) Multi-laboratory assessment on the performance of PCR assays targeting Catellicoccus marimammalium for microbial source tracking of coastal birds. Water Res47:6883-6896.

Cao Y, Van De Werfhorst LC, Dubinsky EA, Badgley BD, Sadowsky MJ, Andersen GL, Griffith JF, Holden PA (2013) Evaluation of molecular community analysis methods for discerning fecal sources and human waste. Water Res 47:6862-6872.

Thomas FIM, Kregting LT, Badgley BD, Donahue MJ, Yund PO (2013) Fertilization in a sea urchin is not only a water column process: effects of water flow on fertilization near a spawing female. Mar Ecol Prog Ser 494:231-240.

Sugawara M, Epstein B, Badgley BD, Unno T, Xu L, Reese J, Gyaneshwar P, Denny R, Mudge J, Bharti AK, Farmer AD, May GD, Woodward JE, Medigue C, Vallenet D, Lajus A, Rouy Z, Martinez-Vax B, Tiffin P, Young ND, Sadowsky MJ (2013) Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies. Genome Biol 14:R17.

Ran Q, Badgley BD, Dillon N, Dunny GM, Sadowsky MJ (2013) Occurrence, genetic diversity, and persistence of enterococci in a Lake Superior watershed. Appl Environ Microbiol 79:3067-3075.

Badgley BD, Ferguson J, Hou Z, Sadowsky MJ (2012) A model laboratory system to study the synergistic interaction and growth of environmental Escherichia coli with macrophytic green algae. J Great Lakes Res 38:390-395.

Nayak BS, Badgley BD, Harwood VJ (2011) Comparison of genotypic and phylogenetic relationships of environmental Enterococcus isolates by BOX-PCR typing and 16S rRNA gene sequencing. Appl Environ Microbiol 77:5050-5055.

Badgley BD, Thomas FIM, Harwood VJ (2011) Quantifying environmental reservoirs of fecal indicator bacteria associated with sediment and submerged aquatic vegetation. Environ Microbiol13:932-942.

Badgley BD, Ferguson J, Vanden Heuvel A, Kleinheinz GT, McDermott CM, Sandrin TR, Kinzelman J, Junion EA, Byappanahalli MN, Whitman RL, Sadowsky MJ (2010) Multi- scale temporal and spatial variation in genotypic composition of Cladophora-borne E. coli populations in Lake Michigan. Water Res 45:721-731.

Badgley BD, Nayak BS, Harwood VJ (2010) The importance of sediment and submerged aquatic vegetation as potential habitats for persistent strains of enterococci in a subtropical watershed. Water Res 44:5857-5866.

Badgley BD, Thomas FIM, Harwood VJ (2010) The effects of submerged aquatic vegetation on the persistence of environmental populations of Enterococcus spp. Environ Microbiol 12:1271-1281.

Korajcik A, Badgley BD, Brownell MJ, Harwood VJ (2009) Application of microbial source tracking methods in a Gulf of Mexico field setting. J Appl Microbiol 107:1518-1527.