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Most recent updates can be found on PubMed or Google Scholar



CA Martinez-Gutierrez, JC Uyeda, FO Aylward. A timeline of bacterial and archaeal diversification in the ocean. eLife, 2023, In press.

M Moniruzzaman, MP Erazo Garcia, R Farzad, AD Ha, A Jivaji, S Karki, U Sheyn, J Stanton, B Minch, D Stephens, DC Hancks, RAL Rodrigues, JS Abrahao, A Vardi, FO Aylward. Virologs, viral mimicry, and virocell metabolism: the expanding scale of cellular functions encoded in the complex genomes of giant viruses. FEMS Microbiology Reviews, 2023; 5;47(5):fuad053.


M Moniruzzaman & FO Aylward. Endogenous DNA viruses take center stage in eukaryotic genome evolution. PNAS, 120 (21) e2305212120.

TB Machado, AC Picorelli, BL de Azevedo, IL de Aquino, VF Queiroz, RA Rodrigues, ... FO Aylward, LE Del-Bem, JS Abrahão. Gene duplication as a major force driving the genome expansion in some giant viruses. Journal of Virology, 2023; e01309-23.

FO Aylward, JS Abrahão, CPD Brussaard, MG Fischer, M Moniruzzaman, H Ogata, CA Suttle. Taxonomic update for giant viruses in the order Imitervirales (phylum Nucleocytoviricota). Archives of Virology, 2023; 168(11):283.

J Niemeyer, L Fischer , FO Aylward, M Schroda. Analysis of Viral Promoters for Transgene Expression and of the Effect of 5′-UTRs on Alternative Translational Start Sites in Chlamydomonas. Genes, 2023; 14(4):948.


AD Ha, M Moniruzzaman, & FO Aylward. Assessing the biogeography of marine giant viruses in four oceanic transects. ISME communications, 2023; 3(1), 43.


SS Tithi, FO Aylward, RV Jensen, L Zhang. FastViromeExplorer-Novel: Recovering Draft Genomes of Novel Viruses and Phages in Metagenomic Data. Journal of Computational Biology, 2023; 30(4):


R Farzad, AD Ha, FO Aylward. Diversity and genomics of giant viruses in the North Pacific Subtropical Gyre.  Frontiers in Microbiology, 2022; 13:1021923.

M Moniruzzaman, MP Erazo-Garcia, FO Aylward. Giant Endogenous Viruses contribute to intra-strain genomic variability in the unicellular green alga Chlamydmonas reinahrdtii. Virus Evolution, 2022, 8(2):veac102.

FO Aylward & M Moniruzzaman. Viral Complexity. Biomolecules, 2022, 12(8):1061.

CA Martinez-Gutierrez & FO Aylward. Genome size distributions in bacteria and archaea are strongly linked to phylogeny at broad phylogenetic scales. PLOS Genetics, 2022, 18(5):e1010220.

AR Weinheimer & FO Aylward. Infection strategy and biogeography distinguish cosmopolitan groups of jumbo bacteriophages. The ISME Journal, 2022, 16: 1657–1667. 



FO Aylward, M Moniruzzaman, AD Ha, EV Koonin. A phylogenomic framework for charting the diversity and evolution of giant viruses. PLOS Biology, 2021, 19(10). 

CA Martinez-Gutierrez & FO Aylward. Phylogenetic signal, congruence, and uncertainty across bacteria and archaea. Molecular Biology and Evolution, 2021, 38(12).

AD Ha, M Moniruzzaman, FO Aylward. High transcriptional activity and diverse functional repertoires of hundreds of fiant viruses in a coastal marine system. mSystems, 2021, 6(4).

ED Osburn, BD Badgley, BD Strahm, FO Aylward, JE Barrett. Emergent properties of microbial communities drive accelerated biogeochemical cycling in disturbed temperate forestsEcology, 2021, 102(12).

ED Osburn, FO Aylward, JE Barrett. Historical land use has long-term effects on microbial community assembly processes in forest soilsISME Communications. 2021, 1(48).

S Karki, M Moniruzzaman, FO Aylward. Comparative genomics and environmental distribution of large dsDNA viruses in the family Asfarviridae. Frontiers in Microbiology, 2021, 12:657471.

FO Aylward, M Moniruzzaman. ViralRecall—A flexible command-line tool for the detection of giant virus signatures in ‘omic data. Viruses, 2021, 13(2):150.


M Moniruzzaman, AR Weinheimer, CA Martinez-Gutierrez, FO Aylward. Widespread endogenization of giant viruses shapes genomes of green algae. Nature, 2020. 

FO Aylward. The Coevolutionary history of the microbial planet. Crystal Ball perspective for Environmental Microbiology Reports, 2020.

AR Weinheimer & FO Aylward. A distinct lineage of Caudovirales that encodes a deeply-branching multi-subunit RNA Polymerase. Nature Communications, 2020, 11(1): 1-9.

FO Aylward, AE Santoro. Heterotrophic thaumarchaea with small genomes are widespread in the dark ocean. mSystems, 2020, 5:e00415-20.

M Moniruzzaman, CA Martinez-Gutierrez, AR Weinheimer, FO Aylward. Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses. Nature Communications, 2020, 11(1): 1-11. 

AM Linz, FO Aylward, S Bertilsson, KM McMahon. Time-series metatranscriptomes reveal conserved patterns between phototrophic and heterotrophic microbes in diverse freshwater systems. Limnology and Oceanography, 2020, 65:101-112.


CA Martinez-Gutierrez & FO Aylward. Strong purifying selection is associated with genome streamlining in epipelagic Marinimicrobia. Genome Biology and Evolution, 2019, 11 (10), 2887-2894.

ED Osburn, SG McBride, FO Aylward, BD Badgley, BD Strahm, JD Knoepp, JE Barrett. Soil bacterial and fungal communities exhibit distinct long-term responses to disturbance in temperate forests. Frontiers in Microbiology, 2019, 10.

BC Kolody, JP McCrow, L Zeigler Allen, FO Aylward, KM Fontanez, A Moustafa, M Moniruzzaman, FP Chavez, CA Scholin, EE Allen, AZ Worden, EF Delong, AE Allen. Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection. ISME J., 2019, 13(11): 2817-2833.

MJ Harke, KR Frischkorn, ST Haley, FO Aylward, JP Zehr, ST Dyhrman. Periodic and coordinated gene expression between a diazotroph and its diatom host. ISME J., 2019, 13(1): 118-131.


EW Getz, SS Tithi, L Zhang, FO Aylward. Parallel evolution of genome streamlining and cellular bioenergetics across the marine radiation of a bacterial phylum. mBio, 20189:e01089-18.

SS Tithi, FO Aylward, RV Jensen, L Zhang. FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data. PeerJ, 2018, 6:e4227 


Luo E, FO Aylward, DR Mende, EF DeLong. Bacteriophage distributions and temporal variability in the ocean’s interior. mBio, 2017, 8(6):e01903-17.

FO Aylward, D Boeuf, DR Mende, EM Wood-Charlson, A Vislova, JM Eppley, AE Romano, EF DeLong. Diel cycling and long-term persistence of viruses in the ocean’s euphotic zone. Proceedings of the National Academy of Sciences, USA, 2017, 114(43): 11446-11451.

DR Mende*, J Bryant*, FO Aylward*, JM Eppley, TN Nielsen, DM Karl, EF DeLong. Environmental drivers of a microbial genomic transition zone in the ocean’s interior. Nature Microbiology, 2017, 2(10): 1367.

ST Wilson*, FO Aylward*, F Ribalet, B Barone, JR Casey, PE Connell, JM Eppley, S Ferrón, JN Fitzsimmons, CT Hayes, AE Romano, KA Turk-Kubo, A Vislova, EV Armbrust, DA Caron, MJ Church, JP Zehr, DM Karl, EF DeLong. Coordinated regulation of growth, activity and transcription in natural populations of the unicellular nitrogen-fixing cyanobacterium Crocosphaera. Nature Microbiology, 2017, 2(9): 118.

EA Gontang, FO Aylward, C Carlos, TG del Rio, M Chovatia, A Fern, C-C Lo, SA Malfatti, SG Tringe, CR Currie, R Kolter. Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach. PLOS ONE, 2017, 12(5): e0177189.


DR Mende, FO Aylward, JM Eppley, TN Nielsen, EF DeLong. Improving environmental genomes via integration of metagenomic and single-cell assemblies. Frontiers in Microbiology, 2016, 7:e143.

JA Bryant, FO Aylward, JM Eppley, DM Karl, MJ Church, EF DeLong. The influence of wind and solar radiation on microbial community diversity in the North Pacific Subtropical Gyre. The ISME Journal, 2016, 10(6):1308-1322.


FO Aylward, JM Eppley, JM Smith, FP Chavez, CA Scholin, EF DeLong. Microbial community transcriptional networks are conserved across all three domains at ocean basin scales. Proceedings of the National Academy of Sciences, USA, 2015; 112(17): 5443-5448.

[Highlighted in a PNAS commentary by AF Haas and F Rohwer]

MA Spero, FO Aylward, CR Currie, TJ Donohue. Phylogenomic analysis and predicted physiological role of the proton-translocating NADH:quinone oxidoreductase (complex I) across Bacteria. mBio, 2015; 5(6): e02077-14.

FO Aylward, L Khadempour, DM Tremmel, BR McDonald, CD Nicora, S Wu, RJ Moore, DJ Orton, ME Monroe, PD Piehowski, SO Purvine, RD Smith, MS Lipton, KE Burnum-Johnson, CR Currie. Enrichment and broad representation of plant biomass-degrading enzymes in the specialized hyphal swellings of Leucoagaricus gongylophorus, the fungal symbiont of leaf-cutter ants. PLOS ONE, 2015; 10(8): e0134752.


FO Aylward, G Suen, PHW Biedermann, AS Adams, JJ Scott, SA Malfatti, T Glavina del Rio, SG Tringe, M Poulsen, KF Raffa, KD Klepzig, CR Currie. Convergent bacterial microbiotas in the fungal agricultural systems of insects. mBio, 2014; 5(6): e02077-14.

EL Huang, FO Aylward, Y-M Kim, B-JM Webb-Robertson, CD Nicora, Z Hu, T Metz, MS Lipton, RD Smith, CR Currie, KE Burnum-Johnson. The Fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation. Environmental Microbiology Reports, 2014; 6(4): 389-395.


FO Aylward, KE Burnum, SG Tringe, C Teiling, DM Tremmel, J Moeller, JJ Scott, KW Barry, CD Nicora, PD Piehowski, S Malfatti, SO Purvine, LA Goodwin, RD Smith, GM Weinstock, NM Gerardo, G Suen, MS Lipton, CR Currie. Leucoagaricus gongylophorus produces diverse lignocellulases for the degradation of recalcitrant plant polymers in the fungus gardens of leaf-cutter ants. Applied and Environmental Microbiology, 2013; 79(12): 3770-3778.

FO Aylward, BR McDonald, SM Adams, A Valenzuela, RA Schmidt, LA Goodwin, T Woyke, CR Currie, G Suen, M Poulsen. Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities. Applied and Environmental Microbiology, 2013; 79(12): 3724-3733.

AS Adams, FO Aylward, SM Adams, N Erbilgin, BH Aukema, CR Currie, G Suen, and KF Raffa. Mountain pine beetles colonizing historical, transitional, and naïve host trees are associated with a community of terpenoid-degrading bacteria. Applied and Environmental Microbiology, 2013; 79(11): 3468-3475.

MR Christopherson, G Suen, S Bramhacharya, KA Jewell, FO Aylward, D Mead, PJ Brumm. The genome sequences of Cellulomonas fimi and “Cellvibrio gilvus” reveal the cellulolytic strategies of two facultative anaerobes, transfer of “Cellvibrio gilvus” to the genus Cellulomonas, and proposal of Cellulomonas gilvus sp. nov. PLOS ONE, 2013; 8(1): e53954.

FO Aylward, DM Tremmel, DC Bruce, P Chain, A Chen, KW Davenport, C Detter, CS Han, J Han, M Huntemann, NN Ivanova, NC Kyrpides, V Markowitz, K Mavrommatis, M Nolan, I Pagani, A Pati, S Pitluck, C-L Wei, LA Goodwin, T Woyke, CR Currie. Complete genome of Enterobacteriaceae bacterium sp. strain FGI 57, a strain associated with leaf-cutter ant fungus gardens. Genome Announcements, 2013; 1(2): e00239-12

FO Aylward, DM Tremmel, GJ Starrett, DC Bruce, P Chain, A Chen, KW Davenport, C Detter, CS Han, J Han, Marcel Huntemann, NN Ivanova, NC Kyrpides, V Markowitz, K Mavrommatis, M Nolan, I Pagani, A Pati, S Pitluck, H Teshima, S Deshpande, LA Goodwin, T Woyke, CR Currie. Complete genome of Serratia sp. strain FGI 94, a strain associated with leaf-cutter ant fungus gardens. Genome Announcements, 2013; 1(2): e00239-12.


FO Aylward, KE Burnum, JJ Scott, G Suen, SG Tringe, SM Adams, GJ Starrett, KJ Berry, LA Goodwin, MS Lipton, CR Currie. Metagenomic and proteomic insights into the fungus gardens of leaf-cutter ants. The ISME Journal, 2012; 6(9): 1688-1702.

FO Aylward, CR Currie, G Suen. The evolutionary innovation of nutritio­nal symbioses in fungus-growing ants. Insects, 2012; 3(1): 41-61.


G Suen, PJ Weimer, DM Stevenson, FO Aylward, J Boyum, J Deneke, C Drinkwater, NN Ivanova, N Mikhailova, O Chertkov, LA Goodwin, CR Currie, D Mead, PJ Brumm. The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist. PLOS ONE, 2011;

G Suen, JJ Scott, FO Aylward, CR Currie. The microbiome of leaf-cutter ant fungus gardens. In: Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats. 2011. Editor: FJ de Bruin, pp. 367-380. John Wiley and Sons, Inc., Hoboken, NJ, USA.


G Suen, JJ Scott, FO Aylward, SM Adams, SG Tringe, A Pinto-Tomás, CE Foster, M Pauly, PJ Weimer, K Barry, LA Goodwin, P Bouffard, L Li, J Osterberger, TT Harkins, SC Slater, TJ Donohue, CR Currie. An insect herbivore microbiome with high plant biomass-degrading capacity. PLOS Genetics, 2010; 6(9): e1001129.

G Suen, FO Aylward, SC Slater, BS Goldman. From Genetics to Genomics. In: The Lure of Bacterial Genetics, 2010. Editors: S Maloy, KT Hughes, J Casadesus, pp. 257-266. American Society for Microbiology Press, Washington, D.C., USA.


MD Herron, JD Hackett, FO Aylward, RE Michod. Triassic origin and early radiation of multicellular Volvocine algae. Proceedings of the National Academy of Sciences, USA, 2009; 106(9): 3254-8.

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