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Open, textbook-style readings for undergraduate biology, microbiology and environmental science students. Read them in order as a course or use them as a reference while you plan fieldwork. Every claim is cited, and every chapter ends with knowledge checks and a link to local research.
Cyanobacteria: Biology, Ecology, and Harmful Freshwater Blooms
Unit overview →Ten chapters on the photosynthetic bacteria that oxygenated Earth, form most harmful freshwater blooms, and may — or may not — live in the biofilms of Allen Branch. Chapters 1, 2, 5 and 10 are complete; the others are reviewed outlines.
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Chapter 1
What Are Cyanobacteria?
Photosynthetic bacteria, not algae: cell structure, oxygenic photosynthesis, pigments, and their role in Earth's oxygenation and the origin of chloroplasts.
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Chapter 2
Cyanobacterial Diversity and Identification
Unicellular, colonial and filamentous forms; heterocytes, akinetes and gas vesicles; eight freshwater genera; why names change; and the limits of identification by microscope.
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Chapter 3
Freshwater Ecology of Cyanobacteria
Planktonic versus benthic life; light, temperature, mixing and residence time; succession, competition, grazing and microbial partners — from shaded streams to sunlit ponds.
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Chapter 4
Nutrient Cycling and Agricultural Watersheds
Nitrogen and phosphorus forms, limitation and co-limitation, eutrophication, and how fertilizer, manure, soil, wastewater and stormwater reach water — and when they don't.
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Chapter 5
Harmful Algal Blooms
What a bloom is, why some are harmful, the four major cyanotoxin groups, oxygen depletion, health effects, U.S. guidance values and how Kentucky issues advisories.
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Chapter 6
Cyanobacteria and Aquatic Food Webs
How green algae, diatoms, rotifers, copepods, Daphnia, snails, fish and decomposers interact with cyanobacteria — and why cyanobacteria are hard to eat.
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Chapter 7
Bloom Prevention and Biological Control
Nutrient management, restoration, buffers, mixing, algaecides, biomanipulation, grazer–cyanobacteria coevolution, microbiomes — and a careful look at engineered organisms.
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Chapter 8
Studying Cyanobacteria in the Laboratory
Wet mounts, brightfield microscopy, calibration and photomicrography, metadata, water chemistry, pigments, molecular concepts and toxin testing — with the limits and safety rules for each.
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Chapter 9
Cyanobacteria in Kentucky
What is documented about blooms in Kentucky's reservoirs, rivers and ponds since 2013, the agricultural and karst setting, and how much remains unknown near Somerset.
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Chapter 10
Open Research Questions
Undergraduate-scale research directions for Allen Branch and other south-central Kentucky waters, each linked to background, methods and references.
Topics in development
These topics will become their own units. Until then, each begins in the chapter linked below.