Evolutionary genomics of uncultivated microbial groups

The majority of biodiversity on the planet resides in microbial lineages, most of which lack cultivated representatives. Many of these microbial groups are ancient and have had a profound influence in shaping the chemical environment of Earth, yet their ecology and evolutionary history often remains obscure. For this research we use evolutionary genomic approaches to analyze the phylogenetic relationships within and between uncultivated microbial groups in order to discern the environmental factors have shaped their genomic repertoires.

Related Publications

CA Martinez-Gutierrez & FO Aylward. Strong purifying selection is associated with genome streamlining in epipelagic Marinimicrobia. Genome Biology and Evolution, In press.

EW Getz, SS Tithi, L Zhang, FO Aylward. Parallel evolution of key genomic features and cellular bioenergetics across the marine radiation of a bacterial phylum. mBio, 2018.

Temporal dynamics of marine microbial communities

Understanding the dynamics of microbial community ecology and metabolism is often complicated by difficulties in pinpointing the appropriate scale to analyze the processes of interest. Marine microbial communities inhabiting the surface waters of the ocean are a useful system for understanding these dynamics since diel cycles are known to be important aspects of the physiology of many marine microbes. This research coupled high-throughput transcriptomic sequencing together with high-temporal resolution sampling of marine microbial communities to investigate ecological and metabolic dynamics over daily timescales. A prominent finding of this work is the apparent coordination between photoautotrophic and heterotrophic community members which underscores important ecological dynamics underpinning carbon and nutrient transformations in these systems. 

Related publications

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.

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]