Phycology

9.

Methodology in Phycology

9.1.

Field Collection and Sampling

9.1.1.

9.1.1.1.

Mesh Sizes and Types

9.1.1.1.1.

Phytoplankton Nets

9.1.1.1.2.

Zooplankton Nets

9.1.1.2.

Sampling Techniques

9.1.1.2.1.

9.1.1.2.2.

Horizontal Tows

9.1.1.2.3.

Oblique Sampling

9.1.2.

9.1.2.1.

9.1.2.2.

Van Dorn Samplers

9.1.2.3.

Depth Profiling

9.1.2.3.1.

9.1.2.3.2.

Discrete Depth Sampling

9.1.3.

Benthic Sampling

9.1.3.1.

9.1.3.1.1.

9.1.3.1.2.

Random vs. Systematic Sampling

9.1.3.2.

Scraping and Coring

9.1.3.3.

Transect Methods

9.1.4.

Specialized Sampling

9.1.4.1.

Ice Core Sampling

9.1.4.2.

Sediment Core Analysis

9.1.4.3.

Aerial Photography

9.2.

Preservation and Herbaria

9.2.1.

Fixatives and Preservatives

9.2.1.1.

Formaldehyde Solutions

9.2.1.2.

9.2.1.3.

9.2.1.4.

Ethanol Preservation

9.2.2.

Mounting Techniques

9.2.2.1.

9.2.2.2.

Permanent Slides

9.2.2.3.

Herbarium Sheets

9.2.3.

Herbarium Curation

9.2.3.1.

Specimen Labeling

9.2.3.2.

Database Management

9.2.3.3.

Storage Conditions

9.2.4.

Digital Archiving

9.2.4.1.

Photography Standards

9.2.4.2.

Metadata Requirements

9.3.

Algal Culturing Techniques

9.3.1.

Isolation Methods

9.3.1.1.

Single-Cell Isolation

9.3.1.1.1.

Micropipette Isolation

9.3.1.1.2.

Micromanipulation

9.3.1.2.

Serial Dilution

9.3.1.2.1.

Dilution-to-Extinction

9.3.1.3.

9.3.2.

Culture Media Preparation

9.3.2.1.

Media Formulations

9.3.2.1.1.

9.3.2.1.2.

Enriched Seawater

9.3.2.1.3.

Freshwater Media

9.3.2.2.

Sterilization Procedures

9.3.2.2.1.

9.3.2.2.2.

Filter Sterilization

9.3.2.2.3.

UV Sterilization

9.3.3.

Maintaining Cultures

9.3.3.1.

Axenic Cultures

9.3.3.1.1.

Contamination Control

9.3.3.1.2.

Antibiotic Treatment

9.3.3.2.

Stock Culture Maintenance

9.3.3.2.1.

Transfer Schedules

9.3.3.2.2.

Storage Methods

9.3.3.3.

Monitoring Culture Health

9.3.3.3.1.

Growth Measurements

9.3.3.3.2.

Purity Assessment

9.3.4.

Large-Scale Cultivation

9.3.4.1.

Photobioreactors

9.3.4.2.

Open Pond Systems

9.3.4.3.

Continuous Culture Systems

9.4.

Microscopy and Imaging

9.4.1.

Light Microscopy

9.4.1.1.

Brightfield Microscopy

9.4.1.1.1.

Basic Principles

9.4.1.1.2.

Sample Preparation

9.4.1.2.

9.4.1.2.1.

Optical Principles

9.4.1.3.

Differential Interference Contrast

9.4.1.3.1.

Nomarski Optics

9.4.1.3.2.

Image Enhancement

9.4.1.4.

Polarized Light Microscopy

9.4.1.4.1.

Birefringent Structures

9.4.2.

Fluorescence Microscopy

9.4.2.1.

Fluorochrome Staining

9.4.2.1.1.

9.4.2.1.2.

Chlorophyll Autofluorescence

9.4.2.2.

Confocal Microscopy

9.4.2.2.1.

Optical Sectioning

9.4.2.2.2.

3D Reconstruction

9.4.2.3.

9.4.2.3.1.

9.4.2.3.2.

9.4.3.

Electron Microscopy

9.4.3.1.

Scanning Electron Microscopy (SEM)

9.4.3.1.1.

Sample Preparation

9.4.3.1.2.

Critical Point Drying

9.4.3.1.3.

Sputter Coating

9.4.3.2.

Transmission Electron Microscopy (TEM)

9.4.3.2.1.

Ultrathin Sectioning

9.4.3.2.2.

Negative Staining

9.4.3.2.3.

Freeze-Fracture

9.4.4.

Specialized Imaging

9.4.4.1.

Atomic Force Microscopy

9.4.4.2.

X-ray Microscopy

9.5.

Physiological and Biochemical Analysis

9.5.1.

Pigment Analysis

9.5.1.1.

Spectrophotometry

9.5.1.1.1.

Absorption Spectra

9.5.1.1.2.

Quantification Methods

9.5.1.1.3.

In Vivo vs. In Vitro

9.5.1.2.

High-Performance Liquid Chromatography (HPLC)

9.5.1.2.1.

Pigment Separation

9.5.1.2.2.

Identification Methods

9.5.1.2.3.

Quantitative Analysis

9.5.1.3.

9.5.1.3.1.

Chlorophyll Fluorescence

9.5.1.3.2.

Photosynthetic Efficiency

9.5.2.

Photosynthesis Measurements

9.5.2.1.

Oxygen Evolution

9.5.2.1.1.

Clark Electrode

9.5.2.1.2.

9.5.2.2.

Carbon Fixation

9.5.2.2.1.

14C Incorporation

9.5.2.2.2.

9.5.2.3.

Pulse Amplitude Modulation (PAM)

9.5.2.3.1.

Photosystem II Efficiency

9.5.3.

Growth Measurements

9.5.3.1.

9.5.3.1.1.

9.5.3.1.2.

Electronic Counters

9.5.3.2.

Biomass Determination

9.5.3.2.1.

9.5.3.2.2.

Chlorophyll Content

9.5.3.2.3.

Optical Density

9.5.4.

Metabolite Analysis

9.5.4.1.

9.5.4.1.1.

Fatty Acid Profiling

9.5.4.1.2.

9.5.4.2.

Carbohydrate Analysis

9.5.4.2.1.

Sugar Composition

9.5.4.3.

Protein Analysis

9.5.4.3.1.

Amino Acid Composition

9.6.

Molecular Techniques

9.6.1.

9.6.1.1.

Cell Lysis Methods

9.6.1.2.

Purification Protocols

9.6.1.3.

Quality Assessment

9.6.2.

9.6.2.1.

9.6.2.1.1.

9.6.2.1.2.

9.6.2.1.3.

9.6.2.2.

PCR Amplification

9.6.2.3.

Sequencing Protocols

9.6.3.

Phylogenetic Analysis

9.6.3.1.

Sequence Alignment

9.6.3.1.1.

Multiple Sequence Alignment

9.6.3.1.2.

Alignment Software

9.6.3.2.

Tree Construction Methods

9.6.3.2.1.

Maximum Likelihood

9.6.3.2.2.

Neighbor-Joining

9.6.3.2.3.

Bayesian Inference

9.6.3.3.

Tree Evaluation

9.6.3.3.1.

Bootstrap Analysis

9.6.3.3.2.

Posterior Probabilities

9.6.4.

Advanced Molecular Methods

9.6.4.1.

9.6.4.1.1.

Whole Genome Sequencing

9.6.4.1.2.

Comparative Genomics

9.6.4.2.

Transcriptomics

9.6.4.2.1.

9.6.4.2.2.

Gene Expression Analysis

9.6.4.3.

9.6.4.3.1.

Protein Identification

9.6.4.3.2.

Functional Analysis

9.6.4.4.

9.6.4.4.1.

Metabolite Profiling

9.6.4.4.2.

Pathway Analysis

9.6.5.

Environmental Molecular Techniques

9.6.5.1.

Environmental DNA (eDNA)

9.6.5.2.

9.6.5.3.

Community Analysis

9.6.5.3.1.

Diversity Indices

9.6.5.3.2.

Ordination Methods

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8. Applied Phycology and Biotechnology

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1. Introduction to Phycology