(Badgley lab members are bolded; Brian’s Google Scholar page can be accessed here.)


Luo S, Waller L, Badgley BD, He Z, Young EB (2020) Effects of bacterial inoculation and nitrogen loading on bacterial-algal consortium composition and functions in an integrated photobioelectrochemical system. Sci Total Environ 716:137135. (Link)


Badgley BD, Steele MK, Cappellin C, Burger J, Jian J, Neher TP, Orentas M, Wagner R (2019) Fecal indicator dynamics at the watershed scale: variable relationships with land use, season, and water chemistry. Sc Total Environ 697:134113. (Link)

Wepking C, Badgley BD, Barrett JE, Knowlton KF, Lucas JM, Minick KJ, Ray P, Shawver S, Strickland MS (2019) Prolonged exposure to manure from livestock‐administered antibiotics decreases ecosystem carbon‐use efficiency and alters nitrogen cycling. Ecol Lett 22:2067-2076. (Link)

Strickland MS, Thomason WE, Yamada S, Franklin J, Minick K, Badgley BD (2019) Short-term effects of covercrops on belowground structure and function across actively managed farms. Agrosystems Geosci Environ 2(1). (Link)

Medina D, Hughey MC, Walke JB, Becker MH, Pontarelli K, Sun S, Badgley BD, Belden LK (2019) Amphibian skin fungal communities vary across host species and do not correlate with infection by a pathogenic fungus. Environ Microbiol 21:2905-2920. (Link)

Weiskerger CJ, Brandão J, Ahmed W, Aslan A, Avolio L, Badgley BD, … & Jordao L (2019) Impacts of a changing earth on microbial dynamics and human health risks in the continuum between beach water and sand. Water Res 162:456-470. (Link)

Sun S, Badgley BD (2019) Changes in microbial functional genes within the soil metagenome during forest ecosystem restoration. Soil Biol Biochem 135:163-172. (Link)

Vander Vorste R, Timpano AJ, Cappellin C, Badgley BD, Zipper CE, Schoenholtz SH (2019) Microbial and macroinvertebrate communities, but not leaf decomposition, change along a mining‐induced salinity gradient. Freshw Biol 64:671-684. (Link)


Stewart RD, Jian J, Gyawali AJ, Thomason WE, Badgley BD, Reiter MS, Strickland MS (2018) What We Talk about When We Talk about Soil Health. Agricultural & Environmental Letters3(1). (Link)

Blaszczak JR, Steele MK, Badgley BD, Heffernan JB, Hobbie SE, Morse JL, … & Groffman PM (2018) Sediment chemistry of urban stormwater ponds and controls on denitrification. Ecosphere, 9: e02318. (Link)

Waller LJ, Evanylo GK, Krometis LAH, Strickland MS, Wynn-Thompson T,  Badgley BD (2018) Engineered and Environmental Controls of Microbial Denitrification in Established Bioretention Cells. Environmental science & technology, 52: 5358-5366. (Link)


Sun S, Li S, Avera B, Strahm BD, Badgley BD (2017) Soil bacterial and fungal communities show distinct recovery patterns during forest ecosystem restoration. Applied and Environmental Microbiology 83:e00966-17. (Link)

#Yuan H, #Sun S, Abu-Reesh IM, Badgley BD,  He Z (2017) Unraveling and Reconstructing the Nexus of Salinity, Electricity, and Microbial Ecology for Bioelectrochemical Desalination. Environmental Science & Technology, 51: 12672-12682. (Link)

(#co-first authors)

Li X, Sun S, Yuan H, Badgley BD, He Z (2017) Mainstream upflow nitritation-anammox system with hybrid anaerobic pretreatment: Long-term performance and microbial community dynamics. Water Research. (Link)

Garner E, Benitez R, von Wagoner E, Sawyer R, Schaberg E, Hession WC, Krometis LAH, Badgley BD, Pruden, A (2017) Stormwater loadings of antibiotic resistance genes in an urban stream. Water Research, 123:144-152. (Link)

Cantor J, Krometis LA, Sarver E, Cook N, Badgley BD (2017) Tracking the downstream impacts of inadequate sanitation in central Appalachia. Journal of Water and Health, wh2017005. (Link)

Willard LL, Wynn-Thompson T, Krometis LAH, Neher TP, Badgley BD (2017) Does it pay to be mature? Evaluation of bioretention cell performance seven years post construction. Journal of Environmental Engineering, 04017041. (Link)

Wepking C, Avera B, Badgley BD, Barrett JE, Franklin J, Knowlton KF, Ray PP, Smitherman C, Strickland MS (2017) Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities. Proceedings of the Royal Society B 284:20162233. (Link)


Young S, Nayak B, Sun S, Badgley BD, Rohr J, Harwood VJ (2016) Vancomycin resistant enterococci and changes in bacterial community structure associated with a residential sewage spill. Applied and Environmental Microbiology, 82:5653-5660. (Link)

Li X, Sun S, Badgley BD, He Z (2016) Long-term performance and microbial community characterization of an osmotic anammox system for removing reverse-fluxed ammonium. Bioresource Technology, 211:628-635. (Link)

Li X, Sun S, Badgley BD, Sung S, Zhang H, He Z (2016) Nitrogen removal by granular nitritation – anammox in an upflow membrane-aerated biofilm reactor. Water Research, 94:23-31. (Link)


Liao H, Krometis LA, Hession WC, Benitez R, Sawyer R, Schaberg E, Von Wagoner E, Badgley BD (2015) Storm loads of culturable and molecular fecal indicators in an inland urban stream. Science of the Total Environment, 530:347-356. (Link)

Hunolt AE, Maguire RO, Ogejo JA, Badgley BD, Frame WH, Reiter MS, (2015) Multiple applications of sodium bisulfate to broiler litter affect ammonia release and litter properties. Journal of Environmental Quality, 44(6):1903-1910. (Link)


Liao H, Krometis LA, Hession WC, House LL, Kline K, Badgley BD (2014) Hydrometeorological and physicochemical drivers of fecal indicator bacteria in urban stream bottom sediments. Journal of Environmental Quality, 43:2034-2043. (Link)

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. Journal of Environmental Quality, 43:1013-1023. (Link)

#Scholz F, #Badgley BD, Sadowsky MJ, Kaplan DH (2014) Immune mediated shaping of microflora community composition depends on barrier site. PLoS One 9:e84019. (Link)
(#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 Microbiology Reviews 38:1-40. (Link)


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 Research, 47:6839-6848. (Link)

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 evaluations of the performance of Catellicoccus marimammalium PCR assays developed to target gull fecal sources. Water Research, 47:6883-6896. (Link)

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 Research, 47:6862-6872. (Link)

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. Marine Ecology Progress Series, 494:231-240. (Link)

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 Biology, 14:R17. (Link)

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


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. Journal of Great Lakes Research, 38:390-395. (Link)


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. Applied and Environmental Microbiology, 77:5050-5055. (Link)

Badgley BD, Thomas FIM, Harwood VJ (2011) Quantifying environmental reservoirs of fecal indicator bacteria associated with sediment and submerged aquatic vegetation. Environmental Microbiology, 13:932-942. (Link)


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. colipopulations in Lake Michigan. Water Research, 45:721-731. (Link)

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 Research, 44:5857-5866. (Link)

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


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

Badgley BD, Lipschultz F, Sebens KP (2006) Nitrate uptake by the reef coral Diploria strigosa: effects of concentration, water flow, and irradiance. Marine Biology, 149:327-338. (Link)