Publications

AA Pratama, G Dominguez-Huerta, JM Wainaina, B Bolduc, F Tian, J Ellenbogen, J Guo, EMERGE Field Team, EMERGE Coordinators, JH Kuhn, KC Wrighton, AA Zayed, MB Sullivan. RNA virus ecogenomics along a subarctic permafrost thaw gradient. 2025. bioRxiv

J Guo, S Aroney, G Dominguez-Huerta, D Smith, D Vik, C Owusu Ansah, AA Pratama, S Solonenko, F Tian, C Howard-Varona, Z Zhong, A Fofana, G Smith, SB Hodgkins, D Cronin, EMERGE Field Teams 2010-2019, EMERGE Coordinators, BJ Woodcroft, GW Tyson, VI Rich, MB Sullivan, S Roux, SC Bagby. Mobile genetic elements that shape microbial diversity and functions in thawing permafrost soils. 2025. bioRxiv

[18] OM Pérez-Carrascal, AA Pratama, MB Sullivan, K Küsel. Unveiling plasmid diversity and functionality in pristine groundwater. 2025. Environ. Microbiome. 20(1): 1-21.

[17] CL Sun†, AA Pratama†, MC Gazitúa, D Cronin, BB McGivern, JM Wainaina, DR Vik, AA Zayed, B Bolduc, IsoGenie Project Field Teams 2010-2017, the IsoGenie and EMERGE Projects Coordinators, KC Wrighton, VI Rich, MB Sullivan. Virus ecology and 7-year temporal dynamics across a permafrost thaw gradient. 2024. Environmental Microbiology. 26(8): e16665 | † contributed equally

[16] D Vik, B Bolduc, S Roux, CL Sun, AA Pratama, M Krupovic, MB Sullivan. MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets. 2023. ISME comm. 3 (1), 87. 

[15] M Yan*, AA Pratama, S Somasundaram, Z Li, Y Jiang, MB Sullivan, Z Yu. Interrogating the viral dark matter of the rumen ecosystem with a global virome database. 2023. Nature Comm. 14 (1), 5254 | * former graduate student | Media coverage: Center of Microbiome Science Ohio State University

[14] G Dominguez-Huerta†, AA Zayed, JM Wainaina†, J Guo, F Tian, AA Pratama, B Bolduc, M Mohssen, O Zablocki, E Pelletier, E Delage, A Alberti, JM Aury, Q Carradec, C Da Silva, K Labadie, J Poulain, Tara Oceans Coordinators §, C Bowler, D Eveillard, L Guidi, E Karsenti, JH Kuhn, H Ogata, P Wincker, A Culley, S Chaffron, MB Sullivan. Diversity and ecological footprint of Global Ocean RNA viruses. 2022. Science 376 (6598), 1202-1208 | † contributed equally | Media coverage: The Ohio State News, News medical, Science daily

[13] AA. Zayed†, JM. Wainaina†, G Dominguez-Huerta†, E Pelletier, J Guo, M Mohssen, F Tian, AA Pratama, B Bolduc, O Zablocki, D Cronin, L Solden, E Delage, A Alberti, JM Aury, Q Carradec, C da Silva, K Labadie, J Poulain, HJ Ruscheweyh, G Salazar, E Shatoff, Tara Oceans Coordinators, R Bundschuh, K Fredrick, LS Kubatko, S Chaffron, Al Culley, S Sunagawa, JH Kuhn, P Wincker, MB Sullivan. 2022. Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome. 2022. Science 376 (6589), 156-162 | † contributed equally | Media coverages: Science highlight; The Conversation and The Scientist

[12] J Guo, B Bolduc, AA Zayed, A Varsani, G Dominguez-Huerta, TO Delmont, AA Pratama, MC Gazitúa, D Vik, MB Sullivan, S Roux. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. 2021. Microbiome 9, 1-13. 

[11] AA Pratama, B Bolduc, AA Zayed, ZP Zhong, J Guo, DR Vik, MC Gazitúa, JM Wainaina, SR, MB Sullivan. 2021. Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation. 2021. PeerJ 9: e11447 | Top 5 most viewed Bioinformatics, Microbiology and Virology article published in 2021 in PeerJ journal

[10] AA Pratama, J Terpstra*, ALM de Oliveria, JF Salles. The role of rhizosphere bacteriophages in plant health. 2020. Trends in Microbiology 28 (9), 709-718 | * former graduate student | Media coverage: Phys.org and EurekAlert! AAAS

[9] AA Pratama, DJ Jiménez, Q Chen, B Bunk, C Spröer, J Overmann, JD van Elsas. Delineation of a Subgroup of the Genus Paraburkholderia, Including P. terrae DSM 17804T, P. hospita DSM 17164T, and Four Soil-Isolated Fungiphiles, Reveals Remarkable Genomic and Ecological Features—Proposal for the Definition of a P. hospita Species Cluster. 2023. Genome biology and evolution 12 (4), 325-344

[8] AA Pratama and JD van Elsas. Gene mobility in microbiomes of the mycosphere and mycorrhizosphere–role of plasmids and bacteriophages. 2019. FEMS microbiology ecology 95 (5): fiz053

[7] AA Pratama, JD van Elsas. The viruses in soil-potential roles, activities, and impacts. 2019. Modern soil microbiology (third edition). Tylor&Francis: New York

[6] JD van Elsas, AA Pratama, WL de Araujoand JT Trevors. Microbial interactions in soil. 2019. Modern soil microbiology (third edition). Tylor&Francis: New York

[5] AA Pratama, JD Van Elsas. The ‘neglected’soil virome–potential role and impact. 2018. Trends in Microbiology 26 (8), 649-662

[4] AA Pratama, M Chaib De Mares, JD Van Elsas. Evolutionary History of Bacteriophages in the Genus Paraburkholderia. 2018. Frontiers in microbiology 9, 835

[3] AA Pratama, IU Haq, R Nazir, M Chaib De Mares, JD van Elsas. Draft genome sequences of three fungal-interactive Paraburkholderia terrae strains, BS007, BS110 and BS437. 2017. Standards in Genomic Sciences 12, 1-14

[2] AA Pratama, JD van Elsas. A novel inducible prophage from the mycosphere inhabitant Paraburkholderia terrae BS437. 2017. Scientific Reports 7 (1), 9156

[1] Obeng*, AA Pratama, JD van Elsas. The significance of mutualistic phages for bacterial ecology and evolution. 2016. Trends in microbiology 24 (6), 440-449 | * former graduate student