Biological Oceanography (BO)

Oceanographic research in the Antarctic

Biological Oceanography is concerned with the interactions of populations of marine organisms with one another and with their physical and chemical environment. Because these interactions are frequently complex, and because the concepts and techniques draw from many fields, biological oceanography is, of necessity, an interdisciplinary science. Training in physical oceanography, marine chemistry, marine geology, and several biological areas are therefore pertinent.

Biological oceanography research is conducted on space/time scales ranging from short-term interactions between individual organisms (mm., sec.) to interdecadal variation in widely dispersed populations. The techniques used are diverse, and even within one space/time domain can include field observation, experimentation in the laboratory, and mathematical modeling.

Research topics include:

Primary and secondary productivity and nutrient regeneration
Community ecology of benthic and pelagic organisms
Food web structure and trophic ecology
Population dynamics, habitat changes and disruptions
Nonequilibrium ecosystems
Microbial ecology and biogeochemical cycling
Fishery biology and management
Marine mammal ecology and communication
Systematics and biogeography
Population genetics and evolution
Behavior as it affects distributions and food web interactions
Climate change impacts including warming, ocean acidification and deoxygenation

California current ecosystems, deep sea biology, kelp forest and coral reef ecology, and polar biology are among the realms addressed. Development and testing of new tools (molecular, optical, acoustic), design of sampling programs, and statistical/mathematical analyses of data and modeling also are significant activities.

Potential Advisors for Students Applying for 2020

Applicants are encouraged to reach out early to all curricular group members who are potential advisors. The following curricular group members have indicated a particular interest in talking to students about 2020 admissions.

Andrew E. Allen - The A.E. Allen Lab combines laboratory and field studies to investigate the ecology, evolution, and biogeochemistry of phytoplankton and other microbes. We are motivated by basic research questions related to identification of the genetic basis for physiological and biochemical mechanisms and ecological principles that govern key pelagic ocean microbiome processes. Key Words: DNA, RNA, molecular ecology, phytoplankton ecology, pelagic ocean microbiome, systems biology, model systems, functional genomics, evolution, experimental biology, computational biology, iron, nitrogen, carbon, micronutrients, macronutrients, diatoms, algal biotechnology (learn more at https://scripps.ucsd.edu/labs/aallen/)

Andrew D. Barton - Research in the Barton Lab seeks to map the distribution of phytoplankton species in the ocean, and illuminate the fundamental biological and ecological processes that underpin these patterns. We investigate how changes in Earth’s climate, including natural variability and long-term changes driven by human activities, have the potential to alter phytoplankton species distributions and community composition. To illustrate and study these complex natural processes, we develop cutting-edge computer models that simulate the marine environment and the many types of plankton living in the ocean. We integrate these models with real observations from the sea, using large compilations of environmental, ecological, and biological data to glean novel inferences about marine plankton life.

Simone Baumann-Pickering

Jeff S. Bowman - The Bowman Lab investigates the role of microbes in the Earth System. We use a variety of tools including DNA and RNA sequence analysis, flow cytometry, and modeling, and work in marine and terrestrial environments from the high latitudes to the tropics (learn more at www.polarmicrobes.org).

Anela Choy

Julia Diaz - Research in the Diaz lab explores aspects of ocean ecosystem functioning at the intersection of microbiology and geochemistry. Specific projects focus on the role of microbal stress and adaptation in the biogeochemical cycles of phosphorus and reactive oxygen species, with a growing interest in enzyme discovery (learn more at https://juliamdiaz.wordpress.com).

Peter Franks

Maria Vernet

Requirements for Admission

In addition to the general requirements for admission to the PhD program listed here, two years of chemistry, including general and organic chemistry, and a year of general biology are required. Physical chemistry with calculus may be substituted for physics with calculus where a more elementary physics course was taken. Zoology or botany may be substituted for general biology.

Preparation should also include a course in general geology and at least one course in each of the following categories: systematics (e.g., invertebrate zoology), population biology (e.g., ecology), functional biology (e.g., physiology).

In special cases, other advanced courses in mathematics or natural sciences may be substituted. Applicants are encouraged, but not required, to submit scores from the biology subject test of the GRE.

Program of Study for PhD

Required course work:

SIOC 210 Physical Oceanography (4 units)
SIOG 260 Marine Chemistry (4 units)
SIOB 280 Biological Oceanography (4 units)
Graduate-level course in statistics/quantitative analysis
One of the following:
- SIOB 270 Pelagic Ecology (4 units)
- SIOB 270A Fisheries Oceanography (4 units)
One of the following:
- SIOB 275A Benthic Ecology (4 units)
- SIOB 277 Deep-Sea Biology (4 units)
One of the following:
- SIO 183 Phycology: Marine Plant Biology (5 units)
- SIO 184 Marine Invertebrates (6 units)
- SIOB 271 Marine Zooplankton (5 units)
- SIOB 282 Phytoplankton Diversity (4 units)
- SIOB 294 Biology of Fishes (5 units)
- SIOB 296 Marine Tetrapods (4 units)
SIOB 273 Professional Ethics in Science
SIOB 278 Seminar in Biosciences (annual after Y1)
SIO 299 Research

Program of Study for MS

Required course work:

SIOC 210. Physical Oceanography (4 units)
SIOG 260. Marine Chemistry (4 units)
SIOG 280. Biological Oceanography (4 units)
One of the following:
- SIOB 270. Pelagic Ecology (4 units)
- SIOB 270A. Fisheries Oceanography (4 units)
- SIOB 275A. Benthic Ecology (4 units)
- SIOB 277. Deep-Sea Biology (4 units)
One of the following:
- SIOB 271. Marine Zooplankton (5 units)
- SIOB 282. Phytoplankton Diversity (4 units)
- SIOB 283. Phycology: Marine Plant Biology (5 units)
- SIOB 284. Marine Invertebrates (6 units)
- SIOB 294. Biology of Fishes (5 units)
- SIOB 296. Marine Tetrapods (4 units)

Elective course work:

Other course work will be recommended by the student’s guidance committee, usually including one quarter of SIO 278, Seminar in Ocean Biosciences (or equivalent participatory seminar); a course in introductory parametric statistics; and at least one advanced-level course in physical, chemical, or geological oceanography.

Research in Biological Oceanography

Biological Oceanography Faculty and Researchers:

Emeritus Biological Oceanography Faculty and Researchers: