Curriculum Vitae

Ben Knowles – Curriculum Vitae

Professional Preparation

2016 – 2020    Post-doctoral Research Fellow, Department of Marine and Coastal                                                            Sciences, Rutgers University

2011 – 2016    Doctorate in Cellular and Molecular Biology, University of California,

San Diego and San Diego State University (UCSD/SDSU Joint Program)

2001 – 2005    Bachelor of Science in Ecology and Marine Biology with Honours in Botany

University of Queensland, Australia


2020-current   Adjunct Assistant Professor, Department of Ecology and Evolutionary Biology, University of California, Los Angeles

2016 – 2020    Post-doctoral Research Fellow, Institute of Earth, Ocean, and Atmospheric Science, Department of Marine and Coastal Science, Rutgers University

2014 – 2016    Course Co-instructor, Advanced Cell and Molecular Biology, SDSU

2011 – 2014    Teaching Assistant, Introductory Cell and Molecular Biology, SDSU

2011                Research Assistant, Scripps Institution of Oceanography (Mitchell Lab)

2010 – 2011    Research Assistant, University of Queensland (Centre for Water Studies)

2010                Water Quality Monitor, South-East Queensland Water

2009 – 2010    Research Assistant, University of Southern California (Caron Lab)

2009                Research Specialist, Proteus Environmental Technologies

2008 – 2009    Research Assistant, University of Southern California (Manahan Lab)

2007                Ecological Consultant, FRC Environmental Consultancy

2006 – 2007    Technician, Commonwealth Scientific & Industrial Research Organisation

2004 – 2006    Research Assistant, University of Queensland (Marine Botany Group)

Teaching Positions

2020-2021       Course developer and instructor, Viral Ecology and Evolution, UCLA. Designed course to be implemented Spring 2021.

2014 – 2016    Course Co-developer and -instructor, Advanced Cell and Molecular Biology, SDSU

2011 – 2014    Teaching Assistant, Introductory Cell and Molecular Biology Lab, SDSU

Published Work (Google Scholar link)

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. doi: 0.1038/s41467-020-18078-4

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. 2020. Gut Microbes. doi: 0.1080/19490976.2019.1701353

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. 2019. Biochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology. Environmental Microbiology 21(6):2182-2197

Thamatrakoln K, Talmy D, Haramaty L, Maniscalco C, Latham J, Knowles B, Natale N, Coolen MJL, Follows MJ, and KD Bidle. 2018. Light regulation of coccolithophore host-virus interactions. New Phycologist, doi:10.1111/nph.15459.

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. 2017. Variability and host density independence in inductions-based estimates of environmental lysogeny. Nature Microbiology 2, 17064.

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

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

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. 2016. Lytic to temperate switching of viral communities. Nature 531; 466–470.

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. 2016. Global microbialization of coral reefs. Nature Microbiology 1: 16042.

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. 2015. Closing the gaps on the viral photosystem photosystem-I psaDCAB gene organization. Environmental Microbiology, doi:10.1111/1462-2920.13036.

Haas A, Knowles B, Lim YW, McDole-Somera T, Kelly LW, Hatay M, and F Rohwer. 2014. Unraveling the unseen players in the ocean – a field guide to water chemistry and marine microbiology. Journal of Visualized Experiments (JoVE); e52131, doi:10.3791/52131.

Knowles B. 2014. March from the sea: A brief history of environmental phage ecology from marine to human ecosystems. In Rohwer F, Youle M, Maughan H, and N Hisakawa (Eds.) Life in Our Phage World, Wholon Publishing, San Diego.

Publications in Revision, Review, or Preparation

Diaz B, Knowles B, Johns C, Laber C, Harvey E, Lowenstein D, Hunter J, Haramaty L, Natale F, Bondoc K, Graff J, Haentjens N, Baetge N, Boss E, Carlson C, Behrenfeld M, Van Mooy B, and KD Bidle. Contextualizing phytoplankton accumulation and loss in the North Atlantic with physiological state, virus infection, and mixing dynamics. In revision at Nature Communications.

Silveira CB, Luque A, Haas AF, Roach TNF, George EE, Knowles B, Little M, Sullivan CJ, Kelly LW, Brainard R, Rohwer F, and BA Bailey. Microbial predators governing state transitions in coral reefs. In review at Science.

Knowles B, Bonachela J, Cieslik N*, DellaPenna A, Baetge N, Behrenfeld M, Bondoc K, Boss E, Diaz B, Graff J, Halsey K, Haramaty L, Karp-Boss L, Natale F, and KD Bidle. Many mechanisms operate within dilution-based predator-prey assays. Reviewed at Communications Biology; in revision for resubmission.

Knowles B. An empiricist’s guide to theoretical viral ecology. In preparation for submission to mBio.

Knowles B, Edwards R, Green K*, Haas AF, Hester E, George E, Lim YW, Little M, Kelly LW, Sandin S, Smith J, Young C, Zgliczynski B, F Rohwer, et al. Metagenomic functional profiling of viral communities across the temperate to lytic spectrum. In Preparation for submission to Nature Microbiology.

* Indicates undergraduate authors I mentored.

Awards and Funding

2019                Co-PI. ‘Temperate viral infection as symbiosis in the Emiliania huxleyi-EhV system.’ Submitted to Moore Foundation Symbiosis Model Systems (invited for full submission after pre-submission, not funded).

2019                Co-PI. ‘The landscape of stress, death, and virus infection in the annual North Atlantic bloom across different physical mixing regimes and patterns of carbon accumulation and loss.’ Submitted to Joint Genome Institute Community Science Program (invited for full submission after pre-submission, not funded).

2016 – 2018    PI; ‘Mechanisms of Viral Inhibition of Grazing in the Environment.’ Post-doctoral Research Fellowship from the Institute of Earth, Ocean, and Atmospheric Science (funded).

Professional Service

Reviewer: Current Biology, Environmental Microbiology, FEMS Microbiology Ecology, Frontiers in Microbiology, The ISME Journal, mBio, PLoS One, Science Advances.

Ad-hoc Reviewer: NSF Dimensions of Biodiversity

Synergistic Activities

2015 – 2016    Bioinformatic Breakfast: founded an ongoing working group of biologists and computational scientists to improve inter-disciplinary communication.

2015                Bioinformatics for Ecologists: using my expertise in both ecology and computational science, I initiated and conducted a workshop teaching basic bioinformatics to traditional ecologists and oceanographers.

2013 – 2016    Coral Club: coordinated monthly informal outreach meetings and talks from coral reef researchers from across institutions in San Diego, covering and integrating across a broad range of disciplines and interests.

2011 – 2016    BioMath Group: contributed to weekly interdisciplinary fusion of biological and mathematic approaches and problem-solving for projects across viral ecology, metagenomics, proteomics, metabolomics, thermodynamics, evolution, theoretical modeling, and coral reef biology.


2020    ASLO Multicultural Program Mentor and Career and Research Advice Mentorship; Ocean Sciences Meeting Feb 2020

2019                Meeting Mentor at ASLO 2019 Aquatic Sciences

2017-2020       Nicole Cieslik*             Undergraduate Aresty Research Assistant (Rutgers)

Physiology- vs. density-dependence of viral predation; now lab tech at Gingko BioWorks. *see publications

2016                Kevin Green*              Undergraduate student ; now Master student (SDSU)

Microbial metagenomic sequencing; *see publications

2015 – 2016    Group leader, Holobiont Evolution Group, Rohwer Lab (SDSU): mentored a group with differing experience levels and backgrounds probing symbiotic biological interactions over evolutionary time.

2012                Undergraduate Research Program Judge; San Diego State University

Invited Talks

Nov 2020        Oregon State University (virtual)                    Host: Kimberly Halsey

Oct 2020         Weizmann Institute, Israel (virtual)                 Host: Assaf Vardi

Feb 2020         San Diego State University                            Host: Forest Rohwer

Oct 2019         University of Maine                                         Host: Lee Karp-Boss

Oct 2018         University of California, Santa Barbara          Host: Craig Carlson

July 2018        Oregon State University                                 Host: Mike Behrenfeld

June 2018       NIOZ, Netherlands                                         Host: Andreas Haas

May 2017        University of Bergen, Norway                         Host: Frede Thingstad

April 2016        University of Exeter, UK                                 Host: Tom Richards

Feb 2014         Scripps Institution of Oceanography              Host: Stuart Sandin

Conferences and Workshops

2020                Association for the Sciences of Limnology and Oceanography (San Deigo 2020, San Juan 2019, Portland 2018).

2019                American Society for Microbiology ASM Microbe conference, San Francisco, USA.

2018                Gordon Research Conference and Seminar on Marine Microbes, Lucca, Italy.

2017 – 2019    NASA North Atlantic Atmospheric and Marine Ecosystem Study Science Team Meetings (annual meetings in 2017, 2018, and 2019), Langley Research Center, Virginia and Corvallis, Oregon, USA.

2016                International Coral Reef Symposium, Honolulu, USA.

2015                Canadian Institute for Advanced Research Integrative Microbiology Workshop, Victoria, Canada.

2015                Single Cell Genomics Workshop, Bigelow Laboratory for Ocean Sciences, USA.

2015                Year of the Phage Conference, San Diego, USA.

2013                Environmental Virology Workshop, Tucson, USA.

2012                International Coral Reef Symposium, Cairns, Australia.

Relevant Research Cruises and Field Work

Over 1000 Scientific SCUBA dives logged, hundreds of hours in small boats.

2017 – 2018    Characterizing viral mortality terms as drivers in the annual bloom cycle of the North Atlantic Ocean, (R/V Atlantis, Aug-Sept, 2017, Mar-Apr, 2018); NASA NAAMES project.

2017                Emiliania huxleyi – virus mesocosm experiments, Bergen, Norway (shore-based, May-June, 2017).

2015                Microbial virus- and protist-predation dynamics along a disturbance gradient in the near-shore waters of Curaçao, South Caribbean Sea (shore-based, April 2015).

2012 – 2015    Characterizing coral reef viral and microbial communities in the Manu’a Islands group (2015), North-West Hawaiian Islands (2013), and from Hawai’i to American Samoa (2012) collaborating with NOAA Coral Reef Ecosystem Division (NOAA RV Hi’ialakai; 3 cruises, 4 months at sea).

2011                Characterizing biological and optical properties of the Bering and Chukchi Seas to develop remote sensing algorithms (USCG Cutter Healy, June-August 2011); NASA Icescape project.

2003- 2010     Extensive small boating and Scientific SCUBA diving work in the Great Barrier Reef (especially Heron Island) and Moreton Bay, Australia, and Catalina Island, California, USA.