Phone: (352) 374-5930

1600-1700 SW 23rd Drive
Gainesville, FL 32608

Research Group Site

Adam Rivers has experience applying a range of microbiome and metagenomics methods to diverse microbial systems. As head of the metagenome program at the Joint Genome Institute, he oversaw the sequencing and analysis of 1500 metagenomes/metatranscriptomes and 10,000 amplicon samples annually for approximately 150 different users. He implemented process improvements for amplicon and viral sequencing and conducted research applying machine learning methods to viral metagenomics. Prior to that he worked on the bacterial metatranscriptomics, transciptomics and genomics of marine bacteria. Projects included determining the metabolic response of bacteria to the Deepwater Horizon oil spill and discovering small RNA’s through transcriptome sequencing.  He joined GBRU in early 2017.

• Projects

  Applied Agricultural Genomics and Bioinformatics Research In-House Appropriated (D)   Accession Number:434717

  Developing a Cyberinformatic Platform for the Rapid Identification of Salmonella Outbreak Strains Using Population Metagenomics and Machine Learning Interagency Reimbursable Agreement (I)   Accession Number:436487

  Bioinformatics and Application Development Non-Assistance Cooperative Agreement (S)   Accession Number:438896

  Development of Tn-Seq Methods for the Functional Characterization of Bacteria Non-Assistance Cooperative Agreement (S)   Accession Number:433541

  Sex Determination of Eggs by High-speed Volatile Compound Mass Spectrometry and Machine Learning Trust Fund Cooperative Agreement (T)   Accession Number:436241

• Publications

  • (Clicking on the reprint icon will take you to the publication reprint.)
  • Harnessing AI to transform agriculture and inform agricultural research-(Peer Reviewed Journal)
    Peters, D.C., Rivers, A.R., Hatfield, J.L., Lemay, D.G., Liu, S.Y., Basso, B. 2020. Harnessing AI to transform agriculture and inform agricultural research. IEEE IT Professional. 22(3):16-21. https://doi.org/10.1109/MITP.2020.2986124.
    
  • Under-the-radar dengue virus infections in natural populations of aedes aegypti mosquitoes-(Peer Reviewed Journal)
    Boyles, S., Mavian, C., Finol, E., Ukhanova, M., Stephenson, C., Hamerlinck, G., Kang, S., Baumgartner, C., Geesey, M., Rivers, A.R. 2020. Under-the-radar dengue virus infections in natural populations of aedes aegypti mosquitoes. mSphere. 5(2):e00316-20. https://doi.org/10.1128/mSphere.00316-20.
    
  • AI down on the farm-(Peer Reviewed Journal)
    Sudduth, K.A., Woodward Greene, M.J., Penning, B., Locke, M.A., Rivers, A.R., Veum, K.S. 2020. AI down on the farm. IEEE IT Professional. 22(3):22-26. https://doi.org/10.1109/MITP.2020.2986104.
    
  • Rice plant biomass traits influencing rhizosphere soil microbial community composition-(Proceedings)
    Fernandez-Baca, C., Rivers, A.R., Maul, J.E., Kim, W., McClung, A.M., Roberts, D.P., Barnaby, J.Y. 2020. Rice plant biomass traits influencing rhizosphere soil microbial community composition. Proceedings of Rice Technical Working Group Meeting, February 24-27, 2020, Orange Beach, Alabama. p 65. Electronic Publication.
    
  • QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science-(Peer Reviewed Journal)
    Bolyen, E., Rideout, J., Dillon, M., Bokulich, N., Abnet, C., Al-Ghalith, G., Alexander, H., Alm, E., Arumugam, M., Asnicar, F., Rivers, A.R. 2019. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. Nature Biotechnology. https://doi.org/10.1038/s41587-019-0209-9.
    
  • Rice soil microbiome interactions with plant growth characteristics and methane emissions-(Abstract Only)
    Fernandez-Baca, C.P., Rivers, A.R., Maul, J.E., Kim, W., Yarwood, S.A., Roberts, D.P., McClung, A.M., Barnaby, J.Y. 2019. Rice soil microbiome interactions with plant growth characteristics and methane emissions. American Society for Microbiology.
    
  • Nine new RNA viruses associated with the fire ant Solenopsis invicta from its native range-(Peer Reviewed Journal)
    Valles, S.M., Rivers, A.R. 2019. Nine new RNA viruses associated with the fire ant Solenopsis invicta from its native range. Virus Genes. https://doi.org/10.1007/s11262-019-01652-4.
    
  • ITSxpress: software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis-(Peer Reviewed Journal)
    Rivers, A.R., Weber, K.C., Gardner, T.G., Liu, S., Armstrong, S. 2018. ITSxpress: software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis. F1000Research. 7:1418. https://doi.org/10.12688/f1000research.15704.1.
    
  • A metagenomics study of the corn kernel and silk microbiome following infection with aflatoxigenic and non-aflatoxigenic Aspergillus flavus strains-(Abstract Only)
    
    
  • Profiles of rhizosphere soil microbial composition affecting methane emissions-(Abstract Only)
    Barnaby, J.Y., Kim, W., Rivers, A.R., McClung, A.M., Maul, J.E. 2018. Profiles of rhizosphere soil microbial composition affecting methane emissions. 5th International Rice Conference Abstract. Available: http://ricecongress2018.irri.org/sites/default/files/Profiles%20of%20Rhizosphere%20soil%20microbial%20composition%20affecting%20methane%20emmissions.pdf.
    
  • Understanding the physiological and molecular mechanisms of rice-microbial interactions that produce methane-(Abstract Only)
    Woojae, K., Liem, B., Chun, J., McClung, A.M., Adviento-Borbe, A.A., Rivers, A.R., Pinson, S.R., Maul, J.E., Reddy, V., Barnaby, J.Y. 2018. Understanding the physiological and molecular mechanisms of rice-microbial interactions that produce methane. 29th Annual Beltsville Poster Day Book, pg 33.
    
  • Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea -(Peer Reviewed Journal)
    Bowers, R.M., Kyrpides, N.C., Stepanauskas, R., Harmon-Smith, M., Schulz, F., Doud, D., Reddy, T.K., Jarett, J., Rivers, A.R., Eloe-Fadrosh, E.A., Tringe, S.G., Ivanova, N., Copeland, A., Clum, A., Becraft, E.D., Malmstrom, R.R., Birren, B., Schriml, L., Podar, M., Bork, P., Weinstock, G.W., Banfield, .F., Garrity, G.M., Hugenholtz, P., Parks, D.H., Tyson, G.W., Rinke, C., Dodsworth, J.A., Yooseph, S., Sutton, G., Yilmaz, P., Glöckner, F.O., Meyer, F., Gilbert, J.A., Nelson, W.C., Hallam, S.J., Jungbluth, S.P., Ettema, T.J., Tighe, S., Konstantinidis, K.T., Liu, W., Baker, B.J., Rattei, T., Eisen, J.A., Hedlund, B., Mcmahon, K.D., Fierer, N., Knight, R., Finn, R., Karsch-Mizrachi, I., Eren, A.M., Woyke, T. 2017. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology. 35, 725–731. doi:10.1038/nbt.3893.
    
  • Patterns and drivers of fungal community depth stratification in Sphagnum peat -(Peer Reviewed Journal)
    Lamit, L.J., Romanowicz, K.J., Potvin, L.R., Rivers, A.R., Singh, K., Lennon, J.T., Tringe, S., Kane, E.S., Lilleskov, E.A. 2017. Patterns and drivers of fungal community depth stratification in Sphagnum peat. FEMS Microbiology Ecology. https://doi: 10.1093/femsec/fix082.
    

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