Coastal Ocean Studies in Biogeochemistry

Course Description

Oceanography: Coastal Ocean Studies in Biogeochemistry and Lab takes a systems approach to the study of the world's oceans, integrating elements of biological, chemical, geological, and physical oceanography, examining basic oceanographic principles and processes with a focus on the marine ecosystems of East Central Florida.

Within the SCNS taxonomy, OCE is the Oceanography prefix and the C suffix marks an integrated lecture-and-laboratory course. Daytona State publishes this at 4 credits, prerequisites CHM1045C, OCE1001, and MAT1033, offered spring, with a $42.35 lab fee. Contact hours are approximately 90, matching this college's own 4-credit integrated science pattern — the published EVR2001 (3 cr / 45 hrs) plus EVR2001L (1 cr / 45 hrs) pair at the same total credit value.

Two things make this course distinctive. First, biogeochemistry is explicitly integrative — it is the study of how elements cycle among living things, water, sediment, and atmosphere, and it refuses the usual division of oceanography into four separate sub-disciplines. Second, the focus on East Central Florida is a genuine advantage: the Indian River Lagoon, the Halifax River, Ponce Inlet, and the nearshore Atlantic are among the most intensively studied and most stressed coastal systems in the country, and they are within driving distance of the classroom.

Learning Outcomes

Required Outcomes

• Describe the ocean as an integrated system linking physical, chemical, geological, and biological processes.
• Describe seawater composition, major and minor constituents, and residence times.
• Describe the carbonate system, alkalinity, and pH buffering in seawater.
• Describe ocean acidification, its chemistry, and its biological consequences.
• Describe the marine carbon cycle, including the biological and solubility pumps.
• Describe the marine nitrogen cycle and its microbial transformations.
• Describe the phosphorus and silica cycles and the concept of limiting nutrients.
• Describe oxygen dynamics, hypoxia, and the formation of dead zones.
• Describe trace metals and their biological roles and toxicity.
• Describe primary production, its measurement, and its controls.
• Describe microbial processes and the microbial loop.
• Describe benthic-pelagic coupling and sediment biogeochemistry.
• Describe estuarine circulation, mixing, and residence time.
• Describe coastal ecosystems: seagrass, mangrove, salt marsh, oyster reef, and coral.
• Describe the ecosystem services these systems provide and their valuation.
• Describe eutrophication, harmful algal blooms, and their biogeochemical drivers.
• Design a sampling plan appropriate to a coastal biogeochemical question.
• Collect water and sediment samples using correct technique and chain of custody.
• Perform analytical procedures and apply quality assurance and quality control.
• Analyze, graph, and interpret biogeochemical data quantitatively.
• Compare results to applicable standards and to published values.
• Describe human impacts on coastal biogeochemistry and management responses.
• Read and critically evaluate primary scientific literature.
• Report investigations in scientific written form to professional standard.

Optional Outcomes

• Use stable isotopes as biogeochemical tracers.
• Describe biogeochemical modelling approaches.
• Describe blue carbon and coastal carbon sequestration.
• Describe restoration ecology and its biogeochemical goals.
• Describe emerging contaminants, including microplastics and PFAS.
• Present research at a conference or symposium.

Major Topics

Required Topics

• The ocean as an integrated system
• Seawater composition and residence times
• The carbonate system and alkalinity
• Ocean acidification
• The marine carbon cycle
• The nitrogen cycle
• Phosphorus, silica, and limiting nutrients
• Oxygen dynamics and hypoxia
• Trace metals
• Primary production and its controls
• Microbial processes and the microbial loop
• Sediment biogeochemistry and benthic-pelagic coupling
• Estuarine circulation and residence time
• Coastal ecosystems
• Ecosystem services
• Eutrophication and harmful algal blooms
• Sampling design
• Field sampling and chain of custody
• Analytical procedures and QA/QC
• Data analysis and interpretation
• Comparison to standards
• Human impacts and management
• Primary literature
• Scientific reporting

Optional Topics

• Stable isotope tracers
• Biogeochemical modelling
• Blue carbon
• Restoration ecology
• Microplastics and emerging contaminants
• Conference presentation

Resources & Tools

• Chemical Oceanography (Frank Millero) or Marine Biogeochemical Cycles — the disciplinary references.
• Biogeochemistry: An Analysis of Global Change (Schlesinger & Bernhardt) — the standard text and genuinely readable.
• Estuarine Ecology (Day et al.) — directly relevant given the East Central Florida focus.
• Standard Methods for the Examination of Water and Wastewater — the analytical authority behind the laboratory procedures.
• NOAA — free buoy data, sea surface temperature, and the Ocean Acidification Program resources.
• Florida DEP — free: Chapter 62-302 F.A.C. surface water quality standards, impaired waters and TMDL programmes, and Basin Management Action Plans — including for the Indian River Lagoon. See this repository's EVR2647 and EVS2026C guides.
• Florida DEP WIN/STORET and the St. Johns River Water Management District — free long-term monitoring data for exactly the systems this course studies. Real local data you can analyze.
• FWC Fish and Wildlife Research Institute — free red tide and HAB monitoring, seagrass mapping, and fisheries data.
• Indian River Lagoon National Estuary Program — free reports and data; the single best resource for the course's regional focus.
• R or Python — free, and the analytical standard in this field. Learn one; it is the skill that most distinguishes a graduate in ocean and environmental science.
• Google Scholar and your library's databases — this course expects primary literature, and library access ends when you leave the institution.

Career Pathways

• Environmental scientist and specialist — SOC 19-2041.
• Water quality scientist and technician — SOC 19-4042; see this repository's EVS2026C guide.
• Estuary and lagoon programme staff — the Indian River Lagoon National Estuary Program and comparable bodies.
• Water management district staff — the St. Johns River district covers this course's study area, and the five districts are major Florida employers.
• Florida DEP and FWC — regulatory, monitoring, and research roles.
• Environmental consulting — coastal permitting, monitoring, and assessment; see this repository's EVR2647 guide.
• Restoration practitioner — seagrass, oyster reef, mangrove, and living shoreline projects, which are substantial and growing in Florida.
• Marine laboratory research technician — Harbor Branch, Smithsonian Marine Station, Rosenstiel, and the university marine labs.
• Coastal management and resilience planning — a growing municipal and county function in Florida.
• Aquaculture — water chemistry is the operational core.
• Graduate study in oceanography, marine science, or environmental science — this course is genuine preparation for it, and undergraduate research experience is what gets students admitted.

Special Information

⚠ Biogeochemistry is integrative by design — resist studying it in silos

• The whole point is that the compartments are connected. A nitrogen atom moves from fertilizer to groundwater to the lagoon to an algal cell to a grazer to sediment to the atmosphere, and the interesting questions are about the transfers.
• Learn the cycles as budgets. Sources, sinks, reservoirs, fluxes, and residence times — that framework applies to every element and makes the material tractable rather than encyclopaedic.
• Residence time is the concept that explains most behaviour. An element with a short residence time responds quickly to inputs; one with a long residence time buffers change and then recovers slowly. This explains why some lagoon problems persist for decades after inputs are reduced.
• Redox chemistry drives sediment biogeochemistry. The sequence of terminal electron acceptors — oxygen, nitrate, manganese, iron, sulfate, carbon dioxide — organizes an enormous amount of otherwise disconnected material.
• Microbes do most of the transformations. Nitrification, denitrification, sulfate reduction, and methanogenesis are microbial, and the microbial loop is the reason so much production never reaches larger organisms.
• Your general chemistry prerequisite is genuinely used. Equilibrium, acid-base chemistry, and stoichiometry all appear directly, and students who arrive shaky on them struggle with the carbonate system in particular.
• Stoichiometry matters ecologically. The Redfield ratio and the idea that organisms have characteristic elemental composition explains limitation, and it is the bridge between chemistry and ecology.
• Draw the cycles from memory. Sketching a nitrogen cycle with its transformations and the organisms responsible is the single most effective study technique for this material.

⚠ East Central Florida is the case study — and it is a hard case

• The Indian River Lagoon is among the most biodiverse estuaries in North America and among the most stressed. It is a textbook illustration of coastal eutrophication and it is local.
• Seagrass loss has been catastrophic in parts of the lagoon, driven by reduced light penetration from algal blooms, which are driven by nutrient loading. The consequence reached the public as manatee mortality — a food web failure traced directly to biogeochemistry.
• Septic systems are a major and underappreciated nitrogen source in this region, and conversion to sewer is a recurring, expensive policy fight.
• Stormwater and fertilizer runoff are the other principal non-point sources, and several Florida municipalities have adopted seasonal fertilizer ordinances in response.
• Muck accumulation in the lagoon is a sediment biogeochemistry problem — organic-rich sediment that consumes oxygen and releases nutrients back to the water column, so legacy loading continues to drive the system long after inputs are cut.
• Brown tide and other HABs have recurred in the lagoon, distinct from Gulf coast red tide; see this repository's EVS2026C guide for the toxin and public health content.
• Inlets control exchange. Ponce Inlet and the lagoon's limited connections to the ocean determine flushing and residence time, which is why the same nutrient load has very different effects in different segments.
• Restoration is active here — oyster reef construction, living shorelines, muck dredging, and seagrass planting — which makes this a place where the science connects visibly to practice.
• Regulatory response runs through TMDLs and Basin Management Action Plans. Rule 11 applies — standards, criteria, and BMAP requirements change; verify with DEP.

⚠ The data is only as good as the sample — QA/QC is a real part of the grade

• Most errors happen before the sample reaches the instrument. Contaminated bottles, wrong preservative, exceeded holding time, and sampling in the wrong place all produce numbers that look fine and mean nothing.
• Some parameters must be measured in the field — temperature, pH, dissolved oxygen, and conductivity all change in transit.
• Trace metal and nutrient work is contamination-prone. Acid-washed bottles, powder-free gloves, and clean technique are requirements rather than fussiness — you are measuring quantities far below what your fingertips carry.
• Run blanks and duplicates. A field blank detects contamination from your own procedure; duplicates measure precision. Skipping them leaves you unable to defend an anomalous result.
• Calibrate before every use and document it. An uncalibrated meter produces confident, precise, wrong numbers.
• Detection limits are part of the result. A non-detect at a reporting limit above the threshold of interest answers nothing.
• Record field conditions — tide stage, recent rain, wind, visible algae, water clarity. Context makes numbers interpretable months later, and in an estuary tide stage can change a result more than the treatment you are studying.
• Sample design determines what you can conclude. Where, when, how deep, how often, and how many — a single grab sample characterizes one moment at one point, and treating it otherwise is a category error.
• Chain of custody matters wherever data may be used in a regulatory context, which in this field is often.

⚠ Florida field and vessel safety

• Wear a PFD on any vessel and around deep or moving water, and never wade a current you have not assessed.
• Heat is the most underrated Florida field hazard. Sun exposure on open water is intense and reflected; hydrate deliberately, wear a hat and long sleeves, and recognize heat illness in yourself and others.
• Wildlife is routine, not exotic — alligators, venomous snakes, stingrays, jellyfish, fire ants, and mosquitoes carrying disease. Shuffle your feet in shallow water for rays.
• Weather changes fast. Afternoon thunderstorms are a daily summer feature and lightning over open water is lethal; know the abort criteria before you leave the dock.
• Contaminated water carries pathogens. Cover cuts, avoid waters under a health advisory, and wash thoroughly afterwards.
• Never work alone without a check-in protocol, and file a plan before you go.
• Follow the vessel operator's instructions without argument. On a boat the captain's word is final, and that is a safety structure rather than a hierarchy.

How Florida course levels affect transfer

The first digit of an SCNS number denotes the year of offering, not transferability. Courses at the 1000 and 2000 levels transfer transparently between Florida public institutions, and 3000 to 4000 is unproblematic since both are upper division. The boundary that actually matters is 2000 to 3000, where lower-division credit generally cannot satisfy an upper-division requirement.

OCE3014C is 4 credits and approximately 90 contact hours, offered spring with a $42.35 lab fee and prerequisites CHM1045C, OCE1001, and MAT1033. Expect substantial laboratory and field work with formal scientific reports, and expect primary literature reading.

As a 3000-level course it belongs to a bachelor's programme, and lower-division oceanography credit — including OCE1001 and OCE1001L — will not substitute for it. If you intend graduate study, treat the field and analytical work here as research training: ask about faculty projects, volunteer for extra sampling, and turn a course project into something you can present. Undergraduate research experience is what gets students admitted to graduate programmes in this field.