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Published manuscripts/Pre-Prints 
  • Vilardi, K, Cotto, I, Bachman, M., Parson, M., Klaus, S., Wilson, C., Bott, C.B., Pinto, A.J. (2023) Co-occurrence, and cooperation between comammox and anammox bacteria in full-scale attached growth municipal wastewater treatment system. Environmental Science & Technology. 57(12): 5013-5023. DOI: 10.1021/acs.est.2c09223
  • Gabrielli, M., Dai, Z., Delafont, V., Timmers, P., van der Wielen, P., Antonelli, M., and Pinto, A.J. (2023). Identifying eukaryotes in drinking water metagenomes and factors influencing their biogeography.  Environmental Science & Technology. 57, 3645-3660. DOI: 10.1021/acs.est.2c09010
  • Vosloo, S., Huo, L. , Chauhan, U., Cotto, I., Gincley, B., Vilardi, K., Yoon, B., Pieper, K.J., Stubbins, A., and Pinto, A.J. (2023) Systematic recovery of building plumbing-associated microbial communities after extended periods of altered water demand during the COVID-19 pandemic. Environmental Science & Technology 57(8): 3248-3259. DOI: 10.1021/acs.est.2c07333
  • Parallel deployment of passive and automated samplers in a university campus for surveillance and variant profiling of SARS-CoV-2 in sewage reveals the usefulness of the former. Science of the Total Environment. 866, 161101. DOI: 10.1016/j.scitotenv.2022.161101
  •  Cotto, I., Vilardi, K.J. , Huo, L. , Fogarty, E.C., Khunjar, W., Wilson, C., De Clippeleir, H., Gilmore, K., Bailey, E., Lucker, S., Pinto, A.J. (2023). Low diversity and microdiversity of comammox bacteria in wastewater systems suggests wastewater-specific adaptation within the Ca. Nitrospira nitrosa cluster. Water Research. 229(1): 119497. DOI: 10.1016/j.watres.2022.119497. 
  • Hegarty, B., Dai, Z., Raskin, L., Pinto, A.J., Wigginton, W., Duhaime, M. (2022)  A snapshot of the global drinking water virome: diversity and metabolic potential vary with residual disinfectant use. Water Research. 118484. DOI: 10.1016.j.watres.2022.118484.
  • Vilardi, K., Cotto, I., Sevillano-Rivera, M., Dai, Z., Anderson, C.L. and Pinto, A.J. (2022) Comammox Nitrospira bacteria outnumber canonical nitrifiers irrespective of electron donor mode and availability in biofiltration systems. FEMS Microbiology Ecology. 98(4). DOI: 10.1093/femsec/fiac032.
  • Birnbaum, D.P., Vilardi, K.J., Anderson.C.L., Pinto, A.J. and Joshi, N.  (2021) A simple, affinity-based method for concentration viruses from wastewater using engineered curli fibers. ACS EST: Water. DOI: 10.1021/acsestwater.1c00208.
  • Sevillano, M.C., Vosloo, S., Cotto, I., Dai, Z., Jiang, T., Santana, J.M.S, Pagilla, I.Y., Rosario-Pabon, Z., Vega, C.V., Cordero, J.F., Alshawabkeh, A., Gu, Z.A., Pinto, A.J. (2021). Spatial-temporal targeted and non-targeted surveys to assess microbiological composition of drinking water in Puerto Rico following Hurricane Maria. Water Research X. Water Research X. 13(1): 100123.  DOI: 10/1016.j.wroa.2021.100123.
  • Srinivasan, V. N., Li, G., Wang, D., Tooker, N. B., Dai, Z., Onnis-Hayden, A., Pinto, A.J., Gu, A. Z. (2021). Oligotyping and Genome-Resolved Metagenomics Reveal Distinct Candidatus Accumulibacter Communities in Full-Scale Side-Stream versus Conventional Enhanced Biological Phosphorus Removal (EBPR) Configurations. Water Research. 206(1) 117725. DOI: 10.1016/j.watres.2021.117725. 
  • Vosloo, S., Huo. L., Anderson, C.L., Dai, Z., Sevillano, M. Pinto.A.J. (2021) Evaluating de novo assembly and binning strategies for time-series drinking water metagenomes. Microbiology Spectrum. 9 (3) e01434-21. DOI: 10.11128/Spectrum.01434-21
  • McDaniel, E.A, Wahl, S.A, Ishii, S., Pinto, A., Ziels, R., Nielsen, P.H., McMahon, K.D., Williams, R.B.H. (2021) Prospects for multi-omics in the microbial ecology of water engineering. Water Research. 205, 117608 DOI: 10.1016/j.watres.2021.117608
  • Potgieter, S., Dai, Z., Havenga, M., Vosloo, S., Sigudu, M., Pinto, A.J., Venter, S. (2021) Reproducible microbial community dynamics of two drinking water systems with similar source waters.  ACS EST Water. 1(7): 1617-1627. DOI: 10.1021/acsestwater.1c00093
  • Sloan, W.T., Nnaji, C.F., Lunn, M., Curtis, T.P., Colloms, S.D., Couto, J.M., Pinto, A.J., Connelly, S., Rosser, S.J. (2021). Drift dynamics in microbial communities and effective community size. Environmental Microbiology. 23(5): 2473-2483. DOI: 10.1111/1462‐2920.15453
  • Martin, R.M., Moniruzzaman, M., Stark, G.F., Gann, E.R., Derminio, D.S., Wei, B., Hellwefer, F.L., Pinto, A.J., Boyer, G., Wilhelm, S.W. (2020). Episodic decrease in temperature increases mcy gene transcription and cellular microcystin in continuous cultures of Microcystis aeruginosa PCC 7806. Frontiers in Microbiology. 11:3081. DOI: 10.3389/fmcib.2020.601864.
  • Sevillano, M.C. , Dai, Z. , Calus, S.T. , Bautista de los Santos, Q.M. , Eren, A.M., Ijaz, U.I., van der Wielen, P., and Pinto.A.J. (2020). Differential prevalence and host association of antimicrobial resistance traits in disinfected and non-disinfected drinking water systems. Science of the Total Environment. 749:141451. DOI: 10.1016/j.scitotenv.2020.141451.
  • Lin Y, Sevillano-Rivera M.C., Jiang T, Li G, Cotto I, Vosloo S, Carpenter CMG, Larese-Casanova P, Giese RW, Helbling DE, Padilla IY, Rosario-Pabón Z, Vélez Vega C, Cordero JF, Alshawabkeh AN, Pinto A, Gu AZ. (2020) Impact of Hurricane Maria on Drinking Water Quality in Puerto Rico. Environmental Science & Technology. 54(15):9495-509. DOI: 10.1021/acs.est.0c01655.
  • Potgieter, S.C. , Dai, Z. , Venter, S.N., Sigudu, M., and Pinto, A.J. (2020) Microbial nitrogen metabolism in chloraminated drinking water reservoirs. mSphere. 5:e002724-20. DOI: 10.1128/mSphere.00274-20.
  • Dai, Z. , Sevillano, M.C., Calus,.S.T.  , Bautista de los Santos, Q.M. , Eren, A.M., Ijaz, U.I., van der Wielen, P., and Pinto.A.J. (2020). Disinfection systematically impacts the drinking water microbiome. Microbiome. 8: 42. DOI:10.1186/s40148-020-00813-0
  • Cotto, I, Dai, Z, Huo, L, Anderson, C.L, Vilardi, K.J. , Ijaz, U.Z., Khunjar, W, Wilson, C., De Clippeleir, H., Gilmore, K., Bailey, E., Pinto, A.J. (2020) Long solids retention times and attached growth phase favor prevalence of comammox bacteria in nitrogen removal systems. Water Research. 169:115268. DOI: 10.1016/j.wateres.2019.11528
  • Chen, L., Pinto, A.J., Alshawabkeh, AN (2019) Activated carbon as a cathode for water disinfection through the Electron Fenton process. Catalysts. 9(7): 601. DOI: 10.3390/catal907601.
  • Kirtis, M.J., Emelko, M., and Pinto, A.J. (2019) Applying biotechnology for drinking water biofiltration: advancing science and practice. Current Opinion in Biotechnology. 57:197-204. DOI: 10.1016/j.copbio.2019.05.009
  • Hull N., Ling F., Pinto A.J., Albertsen, M., Jang H.G., Hong, PY., Konstantinidis, K.T., LeChevallier, M., Colwell, R.R., and Liu, W.T. (2019) Drinking water microbiome project: Is it time? Trends in Microbiology. 27(8): P670-677. DOI: 10.1016/j.tim.2019.03.011
  • Bradley, I., Sevillano-Rivera, M., Pinto, A.J., and Guest, J.S. (2019) Impact of solids residence time on community structure and nutrient dynamics of mixed phototrophic wastewater treatment systems. Water Research. 150 (1): 271-282. DOI: 10.1016/j.watres.2018.11.065
  • Fedders, A.C., DeBellis, J.L., Bradley, I.M., Sevillano-Rivera, M.C., Pinto, A.J., and Guest, J.S. (2018) Comparable nutrient uptake across diel cycles by three phototrophic communities. Environmental Science and Technology. 53(1): 390-400. DOI: 10.1021/acs.est.8b05874.
  • Calus, S.T. , Ijaz, U.I, and Pinto, A.J. (2018) NanoAmpli-Seq: A workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform. Gigascience. 7(12): giy140 DOI: 10.1093/gigascience/giy160
  • Potgieter, S. , Pinto, A.J., Sigudu, M., du Preez , H., Ncube, E, Venter, S. (2018) Long-term spatial and temporal microbial community dynamics in a large-scale drinking water distribution system with multiple disinfectant regimes. Water Research. 139: 406-419. DOI: 10.1016/j.watres.2018.03.077
  • Liu, G., Zhang, U., van der Mark, E., Knezev, A., Pinto, A.J., van den Bogert, B., Liu, W.T., van der Meer, W., and Medema, G. (2018) Assessing the origin of bacteria in tap water and distribution system in an unchlorinated drinking water system by SourceTracker using microbial community fingerprints. Water Research. 138: 86-96. DOI: 10.1016/j.watres.2018.03.043
  • De Vriese, J., Pinto, A.J., Sloan, W.T., and Ijaz, U.I. (2018) The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool. Microbiome. 6: 63. DOI: 10.1186/s40168-018-0449-9
  • Chao, L., Olivares, C., Pinto, A.J., Lauderdale, C., Brown, J., Selbes, M., and Karanfil, T., (2017) The control of disinfection by-products and their precursors in biologically active filtration processes. Water Research. 124: 63-653. DOI: 10.1016/j.waterres.2017.07.080
  • Chia-Chen, W., Ghosh, S., Martin, K., Pinto, A.J., Denef, V.J., Olson, T.M., and Love, N.G. (2017) The microbial colonization of activated carbon block point-of-use (PoU) filters with and without chlorinated phenol disinfection byproducts. Environmental Science: Water Research and Technology. 3: 830-843. DOI: 10.1039/C7EW00134G
  • Sismaet, H.J., Pinto, A.J., and Goluch, E.D. (2017) Electrochemical sensors for identifying pyocyanin production in clinical Pseudomonas aeruginosa isolates. Biosensors and Bioelectronics. 97: 65-69. DOI: 10.1016/j.bios.2017.05.042
  • Marcus, D.N, Pinto, A.J., Anantharaman, K, Ruberg, S., Kramer, E., Raskin, L., and Dick, G. (2017) Diverse manganese (II)-oxidizing bacteria are prevalent in drinking water. Environmental Microbiology Reports. 9: 120-128. DOI: 10.1111/1758-2229.12508
  • Bradley, I., Pinto, A.J., and Guest, J.S. (2016) Design and evaluation of Illumina MiSeq compatible primers for the 18S rRNA gene for improved characterization of mixed microalgal communities.  Applied and Environmental Microbiology. 82(19): 5878-5891. DOI: 10.1128/AEM.01630-16
  • Bautista, Q.M. , Schroeder, J., Sevillano, M.C.R, Sungthong, R., Ijaz, U., Sloan, W.T., and Pinto, A.J. (2016) Drinking water microbial communities across disinfection strategies – a meta-analysis. (accepted). Environmental Science: Water Research and Technology. 2: 631-644. DOI: 10.1039/C6EW00030D
  • Clancy, T.M., Smith, A., Reddy, R., Pinto, A.J., Hayes, K., and Raskin, L. (2016) Anaerobic microbial community response to methanogenic inhibitors 2-bromoethanosulfonate and propionic acid. Microbiology Open. 5: 537-550. DOI: 10.1002/mbo3.349
  • Pinto A.J., Sharp, J.O., Yoder, M.J., and Almstrand, R. (2016): Draft genome of two novel Acidimicrobiaceae from an acid mine drainage biofilm metagenome. Genome Announcements. 4: e01563-15. DOI: 10.1128/genomeA.01563-15.
  • Almstrand, R., Pinto, A.J., Figueroa, L.A., and Sharp, J.O. (2016): Draft genome of a novel Desulfobacteraceae member from a sulfate-reducing bioreactor metagenome. Genome Announcements. 4: e01540-15. DOI: 10.1128/genomeA.01540-15.
  • Bautista, Q.M., Blakemore, O., Schroeder, J., Moses, J., Haffey, M., Sloan, W., and Pinto, A.J. (2016): The impact of sampling, PCR, and sequencing replication on discerning changes in drinking water bacterial community over diurnal time-scales. Water Research. 90: 216-224. DOI: 10.1016/j.watres.2015.12.010.
  • Pinto, A.J., Marcus, D.N., Ijaz, U.Z., Bautista, Q.M. , Dick, G.J. and Raskin, L. (2015): Metagenomic evidence for the presence of comammox Nitrospira-like bacteria in a drinking water system mSphere J. 1: e00054-15. DOI: 10.1128/mSphere.00051-15. (Note: Featured in Science Magazine, DOI: 10.1126/science.aad9839)
  • Schroeder, J., Lunn, M., Pinto, A.J., Raskin, L., and Sloan, W.T. (2015): Probabilistic models to describe the dynamics of  migrating microbial communities. PLoS One, 10: e0117221. DOI: 10.1371/journal.pone.0117221.
  • Pinto, A.J., Schroeder, J., Lunn, M., Sloan, W.T., and Raskin, L. (2014): Spatial-temporal survey and occupancy-abundance modeling to predict bacteria community dynamics in the drinking water microbiome. mBio J. 5: e01135-14. DOI: 10.1128/mBio.01135-14.
  • Chiao, T.C., Clancy, T., Pinto, A.J., Xi, C., and Raskin, L. (2014): Differential resistance of drinking water bacterial populations to monochloramine disinfection, Environmental Science & Technology. 48: 4038-4047.  DOI: 10.1021/es4055725.
  • Pinto, A.J. and Raskin, L. (2012): PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets PLoS One. 7: e43093. DOI: 10.1371/journal.pone.0043093. (Note: Recommended article by F1000 Prime. DOI: 10.3410/f.718417056.393498737)
  • Pinto, A.J., Xi, C., and Raskin, L. (2012): Bacterial community structure in the drinking water microbiome is governed by filtration processes  Environmental Science & Technology. 46: 8851-8859.   DOI: 10.1021/es302042t. (Note: Press release issued by American Chemical Society and featured in The Scientist and The New Scientist magazines).
  • Pinto, A.J., and Love, N.G. (2012): Bioreactor function under perturbation scenarios is affected by interactions between bacteria and protozoa  Environmental Science & Technology. 45: 7558-7566. DOI: 10.1021/es301220f.
  • Pinto, A.J., Guest, J., Love, N., Shaw, A., Fairey, A., Iler, P., Earle, J., Shellenbarger, D., Barker, D (2007): Testing corrective action strategies to mitigate the impact of toxic shock events in activated sludge systems Water Practice, 1: 1-11. DOI: 10.2175/193317707X256973. 
Pre-prints
  • Dowdell, K., Greenwald, H., Joshi, S., Grimard-Conea, M., Pitell, S., Song, Y., Ley, C., Kennedy, L.C., Vosloo, S.*, Huo, L.*, Haig, S-J., Hamilton, K., Nelson, K., Pinto, A.J., Prevost, M., Proctor, C., Raskin, L., Whelton, A.J., Garner, E., Pieper, K.J., and Rhoads, W.J. (2022). Legionella pneumophila occurrence in reduced-occupancy buildings in 11 cities during the COVID-19 pandemic. medRxiv preprint: DOI: 10.1101/2022.06.28.22277022  
Technical reports
  • Pinto, A.J., Cotto, I., Khunjar, W., Wilson, C., DeClippelier, H. (2021) Estimating the comammox contribution to ammonia oxidation in nitrogen removal systems. Water Research Foundation Report 4884.
  • Zhang, Y., Edwards, M., Pinto, A.J., Love, N., Camper, A., Rahman, M., and Baribeau, H. (2010) Effect of Nitrification on Corrosion in the Distribution System. American Water Research Foundation.
  • T2.  Love, N.G., Pinto A.J., Guest, J.S., Hardin S.C., and Shaw, A. (2009) Determining and Assessing Corrective Action strategies for Treatment Plants Exposed to Chemical Toxins. Water Environment Research Foundation. Project number: 04-CTS-11S