Glossary

A working glossary of the terms you will encounter in AquaMind V2 reports and in the rest of these docs. Where two definitions exist in the field, the one used in this glossary is the one AquaMind uses internally.

Systems and biology

RAS (Recirculating Aquaculture System) — A closed-loop culture system in which most of the water is treated and recirculated rather than exchanged with the environment. Biological filtration, mechanical solids removal, and gas exchange are the three core unit operations.

Pond / earthen pond — Open culture system, typically static or low-exchange, where the pond itself acts as a slow biological reactor.

Hapa-in-pond — A net enclosure suspended in a pond, used for nursery or treatment isolation; behaves hydraulically like the surrounding pond but biologically like a higher-density mini-system.

Biofloc — A culture system that intentionally maintains a high suspended-solids microbial community to process nitrogenous waste in situ.

Stocking density — Biomass per unit volume (kg/m³ in RAS) or per unit area (kg/m² in ponds). One of the strongest covariates for nearly every disease-related signal.

Water quality

DO (Dissolved Oxygen) — Free O₂ in the water column, in mg/L. The single most operationally critical reading; below species-specific thresholds, mortality follows fast.

TAN (Total Ammonia Nitrogen) — Sum of ionized (NH₄⁺) and unionized (NH₃) ammonia. The unionized fraction is the toxic one and increases sharply with pH and temperature.

NO₂ / nitrite — Intermediate in the nitrification pathway; persistent elevation suggests biofilter immaturity, recent disinfection, or load shock.

NO₃ / nitrate — End product of nitrification under aerobic conditions. Accumulates in low-exchange RAS unless denitrification (or water exchange) closes the loop.

Microbiology

SND (Simultaneous Nitrification and Denitrification) — The microbial process WaterDoctor's functional engine is built around: nitrification (NH₃ → NO₂ → NO₃) and denitrification (NO₃ → N₂) running in adjacent micro-niches inside the same biofilm. Reduces nitrogen end-to-end without separate anoxic reactors.

Nitrifier / AOB / NOB — Autotrophic nitrifiers: ammonia-oxidizing bacteria (AOB, e.g. Nitrosomonas) and nitrite-oxidizing bacteria (NOB, e.g. Nitrobacter, Nitrospira). Slow growers; biofilter maturity is mostly about getting their populations stable.

Heterotroph bloom — Fast-growing heterotrophic bacteria that respond to organic-carbon spikes (overfeeding, mortality events) and out-compete the slow nitrifiers, often spiking NO₂.

AquaMind pipeline terms

T1 specialist — A first-tier domain-expert agent. Phase 1 runs five: Disease, Treatment, Microbiology, Water Quality, Nutrition. They analyze in parallel on every case. The Microbiology specialist is the seat that runs WaterDoctor's SND Functional Microbial Engine — where you see an "SND engine" node elsewhere, that is this specialist.

Virtual Round Table — The synthesis step where the five specialist outputs are reconciled into a single coherent report. Conflicts are surfaced, not hidden.

Verifier / DOI-strict — The citation gate that runs after synthesis. Every load-bearing citation is checked against Crossref or DataCite by DOI; citations that fail are downgraded or removed before delivery, never silently kept.

Expert sign-off — Async human review by a domain-matched reviewer from the professionals pool. Triggered automatically for high-stakes recommendations (drug dosing, mass water exchange, system shutdown, harvest, food-safety/compliance) and on verifier failure.

Insufficient evidence — A specialist verdict meaning the supplied case data, plus retrievable corpus, did not let the specialist commit to a confident assessment. Almost always a signal to add more intake detail, not a model failure.

Showcase — The public, anonymized archive of past cases that customers have explicitly opted into publishing. Operator-identifying details are stripped before publication.