Publications

Publications

You can find an updated list of publications at Ryan Ziels’ Google Scholar profile.

Published manuscripts and pre-prints

2023

  • McDaniel, E.A., Scarborough, M., Mulat, D.G., Lin, X., Sampara, P.S., Olson, H.M., Young, R.P., Eder, E.K., Attah, I.K., Markillie, L.M. and Hoyt, D.W., Lipton M.S., Hallam, S.J, Ziels, R.M. (2023). Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium. The ISME Journal, pp.1-14. https://doi.org/10.1038/s41396-023-01542-6
  • Vyshenska, D.*, Sampara, P.*, Singh, K., Tomatsu, A., Kauffman, W.B., Nuccio, E., Blazewicz, S.J., Pett-Ridge, J., Varghese, N., Kellom, M. and Clum, A., Riley, R., Roux, S., Eloe-Fadrosh, E., Ziels, R.M.**, Malmstrom, R.**, (2023). A standardized quantitative analysis strategy for stable isotope probing metagenomics. mSystems. e01280-2 (* and ** These authors contributed equally) https://doi.org/10.1128/msystems.01280-22
  • Bowes, Devin A., et al. “Structured ethical review for wastewater-based testing in support of public health.” Environmental science & technology 57.35 (2023): 12969-12980. https://doi.org/10.1021/acs.est.3c04529
  • Qiu, Y., Noonan, A.J., Dofher, K., Koch, M., Kieft, B., Lin, X., Ziels, R.M. and Hallam, S.J., (2023). Complete Genome Sequence of Phormidium yuhuli AB48, Isolated from an Industrial Photobioreactor Environment. Microbiology Resource Announcements, 12(2), pp.e00759-22. https://doi.org/10.1128/mra.00759-22
  • Lin, X., Waring, K., Tyson, J. and Ziels, R.M, (2023). High-accuracy meets high-throughput for microbiome profiling with near full-length 16S rRNA amplicon sequencing on the Nanopore platform. bioRxiv, pp.2023-06. https://doi.org/10.1101/2023.06.19.544637

2022

  • Sampara, P., Luo, Y., Lin, X., & Ziels, R.M. (2022). Integrating Genome-Resolved Metagenomics with Trait-Based Process Modeling to Determine Biokinetics of Distinct Nitrifying Communities within Activated Sludge. Environmental Science & Technology. https://doi.org/10.1021/acs.est.2c02081
  • Gagliano, M. C.*, Sampara, P.*, Plugge, C. M., Temmink, H., Sudmalis, D., & Ziels, R.M. (2022). Functional Insights of Salinity Stress-Related Pathways in Metagenome-Resolved Methanothrix Genomes. Applied and Environmental Microbiology, e02449-21. (* Shared first authorship) https://doi.org/10.1128/aem.02449-21
  • Ahmed, W., Bivins, A., Metcalfe, S., Smith, W.J., Ziels, R.M., Korajkic, A., McMinn, B., Graber, T.E. and Simpson, S.L., (2022). RT-qPCR and ATOPlex sequencing for the sensitive detection of SARS-CoV-2 RNA for wastewater surveillance. Water Research, p.118621. https://doi.org/10.1016/j.watres.2022.118621
  • Holohan, B. C., Duarte, M. S., Szabo-Corbacho, M. A., Cavaleiro, A. J., Salvador, A. F., Pereira, M. A., Ziels, R. M., Frijters, C. T., Pacheco-Ruiz, S., Carballa, M., Sousa, D. Z., Stams, A. J. M, O’Flaherty, V., van Lier, J. B., and Madalena Alves, M., (2022). Principles, Advances, and Perspectives of Anaerobic Digestion of Lipids. Environmental Science & Technology. 56(8), pp.4749-4775. https://doi.org/10.1021/acs.est.1c08722
  • Ahmed, W., Bivins, A., Smith, W.J., Metcalfe, S., Stephens, M., Jennison, A.V., Moore, F.A., Bourke, J., Schlebusch, S., McMahon, J., Hewitson, G., Nguyen S., Barcelon, J., Jackson, G., Mueller, J., Ehret, J., Hosegood, I., Tian, W., Wang, H., Yang, L., Bertsch, P., Tynan, J., Thomas, K. V., Bibby, K., Graber, T. E., Ziels, R. M., Simpson, S.L., (2022). Detection of the Omicron (B.1.1.529) Variant of SARS-CoV-2 in Aircraft Wastewater. Science of the Total Environment. 820, pp.153171 https://doi.org/10.1016/j.scitotenv.2022.153171

2021

  • Madill, M. B. W.*, Luo, Y.*, Sampara, P., Ziels, R.M., (2021). Activity-Based Cell Sorting Reveals Resistance of Functionally Degenerate Nitrospira during a Press Disturbance in Nitrifying Activated Sludge. mSystems, 6(4), pp.e00712-21 (* Shared first authorship). https://doi.org/10.1128/mSystems.00712-21
  • Lin, X., Glier, M., Kuchinski, K., Mierlo, T. R.-V., McVea, D., Tyson, J. R., Prystajecky, N., Ziels, R.M., (2021). Assessing Multiplex Tiling PCR Sequencing Approaches for Detecting Genomic Variants of SARS-CoV-2 in Municipal Wastewater. mSystems, 6(5), pp.e01068-21. https://doi.org/10.1128/mSystems.01068-21
  • McDaniel, E. A., Wahl, S. A., Ishii, S., Pinto, A., Ziels, R. M., 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, pp.117608. https://doi.org/10.1016/j.watres.2021.117608
  • Wei, S. Stensel, H. D., Ziels, R. M., Herrera, S., Lee, P. H., Winkler, M. K. H., (2021). Partitioning of nutrient removal contribution between granules and flocs in a hybrid granular activated sludge system. Water Research, 203, pp.117514 https://doi.org/10.1016/j.watres.2021.117514
  • Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N., Schulz, F., Wu, D., Paez-Espino, D., Chen, I.M., Huntemann, M., Palaniappan, K., Ladau, J., Mukherjee, S., Reddy, TBK., Nielsen, T., Kirton, E., Faria, J.P, Edirisinghe, J.N., Henry, C.S., Jungbluth, S.P., Chivian, D., Dehal, P., Wood-Charlson, E.M., Arkin, A.P., Tringe, S.G., Visel, A., IMG/M Data Consortium*, Woyke, T., Mouncey, N.J., Ivanova, N.N, Kyrpides, N.C., Eloe-Fadrosh, E.A., (2021). “A genomic catalog of Earth’s microbiomes.” Nature biotechnology, 39(4) pp.499-509. https://doi.org/10.1038/s41587-020-0718-6
  • Karst, S. M.*, Ziels, R. M.*, Kirkegaard, R.H., Sørensen, E. A., McDonald, D., Zhu, Q., Knight, R. and Albertsen, M., (2021). Enabling high-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing. Nature Methods. 18,pp.165-169. (* Shared first authorship) https://doi.org/10.1038/s41592-020-01041-y

2020

  • Campanaro, S., Treu, L., Rodriguez-R, L. M., Kovalovszki, A., Ziels, R. M., Maus, I., Zhu, X., Kougias, P. G., Basile, A., Luo, G. and Schlüter, A., (2020). New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters. Biotechnology for biofuels, 13(1), pp.1-18. https://doi.org/10.1186/s13068-020-01679-y

2019

  • Ziels, R. M., Nobu, M. K., Sousa, D. Z., (2019). Elucidating syntrophic butyrate-degrading populations in anaerobic digesters using stable isotope-informed genome-resolved metagenomics. mSystems, 4(4), pp.e00159-19.
  • Baldwin S., Taylor JC., Ziels R. M., (2019). Genome-resolved metagenomics links microbial dynamics to failure and recovery of a bioreactor removing nitrate and selenate from mine-influenced water. Biochemical Engineering Journal, 151, pp.107297.
  • Cogert K., Ziels R. M., Winkler M., (2019). Reducing Cost and Environmental Impact of Wastewater Treatment with Denitrifying Methanotrophs, Anammox, and Mainstream Anaerobic Treatment” Environmental Science and Technology. 53(21), pp.12935-12944

2018

  • Ziels, R. M., Svensson B. H., Sundberg C., Larsson M., Karlsson A., Yekta S. S., (2018). Microbial rRNA gene expression and co-occurrence profiles associate with biokinetics and elemental composition in full-scale anaerobic digesters. Microbial Biotechnology, 11(4), pp.694-709
  • Ziels, R. M., Sousa, D. Z., Stensel, H. D., Beck, D. A., (2018). DNA-SIP based genome-centric metagenomics identifies key long-chain fatty acid-degrading populations in anaerobic digesters with different feeding frequencies. The ISME Journal. 12(1), pp.112-123

2017

  • Ziels, R. M., Beck, D. A., Stensel, H. D., (2017). Long-chain fatty acid feeding frequency in anaerobic codigestion impacts syntrophic community structure and biokinetics. Water Research. 117, pp.218-229
  • Björn, A., Yekta, S. S., Ziels, R. M., Gustafsson, K., Svensson, B. H., Karlsson, A., (2017). Feasibility of OFMSW co-digestion with sewage sludge for increasing biogas production at wastewater treatment plants. Euro-Mediterranean Journal for Environmental Integration. 1(2).
  • Yekta S., Ziels R. M., Björn A., Skyllberg U., Ejlertsson J., Karlsson A., Svedlund M., Wilen M., Svensson B.H., (2017). Importance of sulfide interaction with iron as regulator of the microbial community in biogas reactors and its effect on methanogenesis, volatile fatty acids turnover, and syntrophic long-chain fatty acids degradation. Journal of Bioscience and Bioengineering. 123(5), pp.597-605.

2016

  •  Ziels, R. M., Karlsson, A., Beck, D. A. C., Ejlertsson, J., Yekta S., Bjorn A., Stensel, H. D., Svensson, B. H.,(2016). Microbial community adaptation influences long-chain fatty acid conversion during anaerobic codigestion of fats, oils, and grease with municipal sludge. Water Research. 103, pp.372-382

2015

  •  Ziels, R. M., Beck, D. A. C., Marti, M., Gough, H. L., Stensel, H. D., Svensson, B.H.,(2015). Monitoring the dynamics of syntrophic β-oxidizing bacteria during anaerobic degradation of oleic acid. FEMS Microbiology Ecology. 91(4). pp.5028
  •  Lust, M. J., Ziels, R. M., Strand, S. E., Gough, H. L., Stensel, H. D., (2015). Biodegradation kinetics of 17α -ethinylestradiol in activated sludge treatment processes. Environmental Engineering Science. 32(7). pp.637-646

2014

  •  Ziels, R. M., Lust, M. J., Gough, H. L., Strand, S. E., & Stensel, H. D., (2014). Influence of Bioselector Processes on 17α-Ethinylestradiol Biodegradation in Activated Sludge Wastewater Treatment Systems. Environmental science & technology, 48(11). pp.6160-6167