Aylward FO, Santoro AE. 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.
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, 2018. 9: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.
[Highlighted by the editors as an article of significant interest in Issue 11, Vol. 79]
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.
[Included as a chapter in The Social Biology of Microbial Communities, Workshop Summary, 2012, presented by the Institute of Medicine of the National Academies. A press release describing this article was also featured in Science Daily.]
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.