Research Areas

Ecology, Marine Biology, Physiological Ecology, Theory

Research Interests

Viral infection of microbes is probably the most common ecological interaction on the planet. However, it is unknown what fraction of infections are rapidly lethal or establish long-term virus-host symbioses because viruses can act as lytic predators or temperate parasites. Viruses sculpt the evolution, composition, structure, and vital rates of host communities from molecular to global scales and affect ecosystem processes like biogeochemical cycling, productivity, and food webs. While most viral ecologists have focused on these phenomena as an outcome of density-dependent lethal lytic infection, my PhD and post-doctoral research shows that these ecosystem processes are more likely to the outcome of physiology-dependent long-term temperate infections. This changes – even upends – the narrative of virus-host interactions from being deterministic and easily measured as host and viral densities to a much more challenging and long-term one centered around host physiology. Importantly, this mechanistic shift also means that accepted outcomes of infection like how and why energy and matter flow through ecosystems must be revised from cellular to global scales.

Selected Publications

Knowles B, Bonachela JA, Behrenfeld MJ, Bondoc KG, Cael BB, Carlson CA, Cieslik N*, Diaz BP, Fuchs HL, Graff JR, Grasis J, Halsey H, Haramaty L, Johns CT, Natale F, Nissimov JI, Schieler B, Thamatrakoln K, Thingstad TF, Våge S, Watkins C, Westberry T, and KD Bidle., "Temperate infection in a virus-host system previously known for virulent dynamics", Nature Communications, 11 (4626): 1-13 (2022) .

Boling L, Cuevas DA, Kang HS, Knowles B, Maughan H, McNair K, Rojas MI, Sanchez SE, Smurthwaite C, and F Rohwer., "Dietary anti-microbials and prophage inducers – towards landscaping of the human gut microbiome", Gut Microbes, 11 (4626): - (2020) [link].

Nissimov JI, Talmy D, Haramaty L, Fredricks H, Zelzion E, Knowles B, Eren M, Vandzura R, Laber C, Schieler B, Johns C, More KD, Coolen MJL, Follows MJ, Bhattacharya D, Van Mooy BAS, and K.D. Bidle., "Biochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology", Environmental Microbiology, 21 (6): 2182-2197 (2019) .

Thamatrakoln K, Talmy D, Haramaty L, Maniscalco C, Latham J, Knowles B, Natale N, Coolen MJL, Follows MJ, and KD Bidle., "Light regulation of coccolithophore host-virus interactions", New Phycologist, 21 (6): - (2018) [link].

Roach T, Abieri M, George E, Knowles B, Smurthwaite C, Haas A, and F Rohwer., "Microbial bioenergetics of coral-algal interactions", PeerJ, 5 : e3423- (2017) .

Knowles B and F Rohwer., "Reply to Brief Communication Arising: Lysis, lysogeny, and virus-microbe ratios", Nature, 549 : E3-E4 (2017) .

Knowles B, Bailey B, Boling L, Breitbart M, Cobián-Güemes A, del Campo J, Edwards R, Felts B, Grasis J, Haas AF, Katira P, Wegley Kelly L, Luque A, Nulton J, Paul L, Peters G, Robinett N, Sandin S, Segall A, Silveira C, Youle M, and F Rohwer., "Variability and host density independence in inductions-based estimates of environmental lysogeny", Nature Microbiology, 2 : 17064- (2017) .

Haas A, Fairoz M, Kelly LW, Nelson C, Dinsdale E, Edwards R, Giles S, Hatay M, Hisakawa N, Knowles B, Lim YW, Maughan H, Pantos O, Roach T, Sanchez S, Silveira C, Sandin S, Smith J, and F Rohwer., "Global microbialization of coral reefs", Nature Microbiology, 1 : 16042- (2016) .

Knowles B, Silveira C, Bailey B, Barott K, Cantu V, Cobián-Güemes A, Coutinho F, Dinsdale E, Felts B, Furby K, George E, Green K*, Gregoracci G, Haas A, Haggerty J, Hester E, Hisakawa N, Kelly LW, Lim YW, Little M, Luque A, McDole-Somera T, McNair K, de Oliveira L, Quistad S, Robinett N, Sala E, Salamon P, Sanchez S, Sandin S, Silva G, Smith J, Sullivan C, Thompson C, Vermeij M, Youle M, Young C, Zgliczynski B, Brainard R, Edwards R, Nulton J, Thompson F, and F Rohwer., "Lytic to temperate switching of viral communities", Nature, 531 : 466-470 (2016) .

Roitman S, Flores-Uribe J, Philosof A, Knowles B, Rohwer F, Ignacio-Espinoza J, Sullivan M, Acinas S, Cornejo-Castillo F, Sánchez P, Dupont C, and O Beja., "Closing the gaps on the viral photosystem photosystem-I psaDCAB gene organization", Environmental Microbiology, 531 : - (2015) [link].