The Food Web: Who Eats Whom

An aquatic ecosystem is not a simple chain where "A eats B eats C." It is a web -- a tangle of interconnected feeding relationships where most organisms eat multiple food sources and most food sources are eaten by multiple consumers. Understanding this web is essential for understanding why ecosystems behave the way they do: why removing one species can cause unexpected changes elsewhere, or why a population might be stable even when one of its food sources disappears.

Trophic Levels

The food web is organized into levels based on how organisms get their energy:

Level 0 -- Dissolved nutrients and dead matter Ammonium (NH4), nitrate (NO3), phosphate (PO4), dissolved CO2, dissolved organic matter (DOM), and detritus. These are the raw materials that fuel everything above.

Level 1 -- Primary producers (algae and macrophytes) Algae use sunlight and dissolved nutrients to build biomass through photosynthesis. They are the foundation of the food web. The model includes planktonic algae (free-floating), surface-attached algae, and periphyton microalgae on surfaces. Floating macrophytes (Salvinia) also occupy this level: they live at the air-water interface, absorbing nutrients from the water column while casting a shading canopy over all submerged organisms. Rooted macrophytes (Cryptocoryne, Vallisneria) draw nutrients from both the water column and sediment pore water and photosynthesize via submerged leaves.

Level 1.5 -- Decomposers (heterotrophic bacteria and fungi) Bacteria and fungi feed on dead organic matter (DOM and detritus) rather than on living organisms or sunlight. They sit between the nutrient pool and the living food web, converting waste back into living biomass. Bacteria specialize in labile dissolved material; fungi specialize in refractory substrates (humic polymers, settled detritus, soil OM), converting them to labile DOM that bacteria then exploit.

Level 2 -- Primary consumers These eat the producers and bacteria:

• Heterotrophic nanoflagellates (HNF) -- small protist bacterivores (2-20 um) that are the dominant consumers of bacteria
• Daphnia (water fleas) -- filter feeders that sweep up planktonic algae, bacteria, ciliates, nanoflagellates, and fine particles; can strongly suppress the microbial loop
• Rotifers -- microscopic ciliary filter feeders (100-350 um) that sweep up planktonic algae, bacteria, nanoflagellates, and fine particles
• Ciliates -- single-celled bacterivores that eat bacteria and HNF
• Bladder snails (Physa acuta) -- benthic scrapers that eat periphyton biofilm from surfaces and settled detritus; non-predatory
• Cherry shrimp (Neocaridina davidi) -- larger benthic scrapers (1.5–3 cm); primary diet is periphyton biofilm + settled detritus; also consume bacteria, cyanobacteria, suspended detritus, and meiofauna (ciliates, rotifers)

Level 2.5 -- Omnivorous consumers

• Copepods (copepods) -- raptorial omnivores that eat periphyton, bacteria, ciliates, nanoflagellates, rotifers, detritus, and some planktonic algae. They span levels 2 and 3 because they eat both primary producers and other consumers.

Level 3 -- Secondary consumers Copepods eating ciliates and rotifers represents the highest trophic level interaction in the model. This completes the microbial loop: dead matter flows to bacteria, bacteria flow to HNF, HNF flow to ciliates, and ciliates flow to copepods.

The Food Web Diagram

                         SUNLIGHT
                            |
                            v
NH4, NO3, PO4, CO2 --> [ ALGAE ] <------ photosynthesis
                       /    |    \
                      /     |     \
                     v      v      v
               planktonic  surface  periphyton
               algae       algae    algae
                 |    \      |       /   |  \
                 |     \     |      /    |   \
                 v      v   v     v     v    v
             [DAPHNIA]  [ROTIFERS]  [COPEPOD] [BLADDER
              filter     ciliary     raptorial  SNAIL]
              feeder     filter      omnivore  benthic
                 |         |  ^        |  ^    scraper
                 |         v  |        |  |      |
                 |        [HNF]<-------+  |      |
                 |         |  ^        v  |      |
                 |         v  |   [CILIATES]     |
                 |      [BACTERIA] <--- DOM, detritus
                 |          ^    |              |
                 |          |    v              v
                 +--death-> DETRITUS/DOM <---death---+
                   (settl.) ^  ^  ^    |
                      |     |  |  |    v
                    [SNAIL]-+  |  +-- viral lysis
                    grazes     |      recycling
                    settled    |
                    det.    [FUNGI] ----> labile DOM
                            refractory      |
                            decomposer      v
                               |        [BACTERIA]
                               v
                           zoospores ---> [CILIATES/HNF]

    Arrows show direction of energy flow (eaten by).
    All organisms produce detritus/DOM when they die or excrete waste.
    Fungi convert refractory OM → labile DOM (conditioning) and
    produce zoospores grazed by ciliates and HNF (mycoloop).

Feeding Relationships by Consumer

Bladder Snails (Physa acuta)

Bladder snails are benthic scrapers, 3-10 mm in size. They crawl on all available surfaces and scrape algal biofilm using their radula. They are non-predatory: they eat only producers and detritus, never other consumers.

Snails are the most effective biofilm scrapers in the model — their radula gives them up to 92% access to periphyton on smooth glass. They are strictly benthic and non-predatory: no animal prey, very limited water-column access. Their role in the web is converting surface biofilm and settled detritus into consumer biomass and excreted nutrients. Shell building consumes Ca²⁺ and alkalinity (see consumers.md for details).

Cherry Shrimp (Neocaridina davidi)

Cherry shrimp are benthic scraper-detritivores, 1.5–3 cm in size — the largest-bodied consumer in the model. They are the most effective biofilm scrapers for rough substrates (gravel, porous ceramic) and the dominant consumer of settled detritus among the mesofauna.

Cherry shrimp are the largest consumer and the dominant benthic processor. Their web role is twofold: they are the top biofilm and detritus consumer on rough substrates (80% access to settled detritus, 85% to periphyton), and they are a moderate predator of meiofauna (ciliates, rotifers). Unlike other consumers, poor water quality suppresses their reproduction rather than increasing mortality — they stagnate instead of crashing (reproduction suppression). See consumers.md for full reproduction suppression and molting details.

Copepods

Copepods are raptorial omnivores, 0.5-2 mm in size. Unlike filter feeders, they actively hunt and capture individual prey items. They are the most versatile feeders in the model.

Copepods are the most versatile feeders and the critical link that completes the microbial loop. Their high preference for ciliates (0.9) channels energy from the bacterial decomposition pathway back into the main food web — dead matter to bacteria to HNF to ciliates to copepods. They also prey on rotifers (0.5), making them the apex predator in the model. Despite a moderate preference for bacteria (0.6), effective access is very low (~10%) because bacteria are too small for raptorial capture and are protected within biofilms. Periphyton access varies strongly by surface type (95% on glass, 25% in gravel interstices) — see the refugia documentation at consumers/refugia.md for details.

Daphnia (Water Fleas)

Daphnia are filter feeders, 0.2-5 mm in size. They sweep water through a fine mesh and capture whatever particles pass through. This makes them excellent at harvesting suspended particles but poor at scraping surfaces.

Daphnia are the dominant planktonic filter feeder — 95% access to free-floating algae makes them the primary controller of planktonic algae blooms. Their most important web-level effect is microbial loop suppression: because they non-selectively filter particles 0.5–40 µm, dense Daphnia populations directly remove ciliates, HNF, and bacteria from the water column (Porter et al. 1983; Jürgens 1994), short-circuiting the bacteria → HNF → ciliate → copepod chain. This makes Daphnia and copepods functionally complementary — Daphnia suppresses the microbial loop from above while Copepods feed on it from within.

Ciliates

Ciliates are single-celled bacterivores, 10-300 micrometers in size. They are swimming predators specialized for capturing bacterial-sized prey and small protists.

Ciliates are the "packaging service" of the microbial loop — they eat bacteria (~70% access) and HNF (preference 0.7), concentrating microbial biomass into a size range (10–300 µm) that copepods can capture. Without ciliates, bacterial production would be largely inaccessible to the macro food web. Their small size gives them far better bacterial access than copepods (~70% vs ~10%), because they can penetrate biofilm structures that larger organisms cannot.

Nanoflagellates (HNF)

Nanoflagellates are small protist bacterivores, 2-20 micrometers in size. They are specialized for capturing bacterial-sized prey and are the dominant consumers of bacteria in freshwater systems.

HNF are the first link in the microbial loop — the dominant consumers of bacteria in freshwater systems. Their small body size (2–20 µm) gives them even higher bacterial access than ciliates (~75% vs ~70%), because they can penetrate finer biofilm structures. HNF concentrate bacterial biomass into a package that ciliates can eat, creating the bacteria → HNF → ciliates → copepods chain that recycles dead matter back into the living food web.

Rotifers

Rotifers are microscopic ciliary filter feeders, 100-350 micrometers in size. Like Daphnia, they sweep water through a ciliary mesh, but they target smaller particles (1-20 micrometers) and have higher weight-specific feeding rates.

Rotifers occupy a niche between Daphnia and ciliates in the web. Like Daphnia, they filter planktonic algae (95% access), but their finer ciliary mesh also captures bacteria (~55% access) and HNF (~60% access), putting them in competition with ciliates for microbial prey. They are simultaneously prey for Copepods (preference 0.5) and victims of mechanical interference from large Daphnia populations — making their persistence sensitive to the balance of other consumer populations.

Ostracods

Ostracods are tiny benthic crustaceans (~0.75 mm) enclosed in a bivalved carapace. They are generalist benthic scrapers that crawl over substrate and surfaces consuming biofilm, settled organic matter, and small organisms they encounter.

Ostracods fill a unique niche as the most effective settled detritus consumer among the small-bodied grazers (75% access, compared to ~0% for filter feeders). This makes them a key link in the decomposition loop: they physically break down and assimilate dead organic matter sitting on the bottom, recycling nutrients that would otherwise depend entirely on bacterial decomposition. Their small body size lets them crawl into gravel interstices (50% periphyton access) that larger consumers cannot reach. They are strictly benthic — negligible access to water-column food.

Heterotrophic Bacteria

Bacteria do not "eat" in the same way animals do. They absorb dissolved molecules and colonize particles. Their feeding is handled differently from the grazers above.

Bacteria prefer DOM over detritus by a factor of 2 (dissolved molecules are easier to absorb). The 28% growth efficiency (BGE) is the fundamental bottleneck of the microbial loop — for every 100 units of dead organic carbon that bacteria consume, only 28 become living biomass available to the food web; the other 72 are respired as CO2. See microbes.md for full details on bacterial feeding and growth.

Aquatic Fungi

Like bacteria, fungi absorb substrates rather than hunting prey. But their substrate preferences are essentially inverted — fungi specialize in refractory material that bacteria handle poorly.

Fungi have 60 times stronger preference for refractory DOM than for labile DOM — the inverse of bacteria. Their growth efficiency on refractory substrates (15%) is lower than bacterial BGE on labile DOM (28%) because breaking down complex polymers requires investing in extracellular enzyme production. Their key web-level role is not the biomass they produce but the fungal conditioning effect: about 20% of respired refractory carbon is released as labile DOM rather than CO2, feeding bacteria and sustaining the microbial loop on substrates that bacteria alone could not access. The grazeable portion of fungal biomass — chytrid zoospores (2-10 um) — is consumed by ciliates (20% access) and HNF (12% access) via the mycoloop. See microbes.md for full details.

How Web Structure Creates Stability

The food web above is not just a list of who eats whom -- its structure creates emergent dynamics that no single feeding relationship would produce on its own.

Complementary grazers. Daphnia and copepods control different parts of the food web simultaneously. Daphnia suppresses the microbial loop from above by non-selectively filtering out bacteria, HNF, and ciliates along with planktonic algae. Copepods feed within the microbial loop, channeling energy from ciliates and HNF back into the macro food web. A system with both grazers tends to be more stable than one with either alone, because they regulate different trophic pathways.

Competitive exclusion among filter feeders. Rotifers and Daphnia both filter planktonic algae with high efficiency (95% access). But Daphnia are larger, with a higher absolute ingestion rate, and their feeding currents physically damage rotifers through mechanical interference. In systems with dense Daphnia populations, rotifers are often suppressed -- not by being eaten, but by being outcompeted and physically disrupted.

Trophic cascades. Removing a consumer can have effects two levels down the web. If Copepods are absent, ciliate populations grow unchecked, which suppresses bacteria, which slows decomposition, which allows detritus to accumulate. The initial perturbation (no copepods) cascades through the microbial loop to affect nutrient recycling -- a process with no direct connection to copepod feeding.

Surface composition and maturity reshape the web. The same set of species can produce very different dynamics depending on the physical environment. A jar with only smooth glass surfaces provides minimal refugia -- grazers can eat nearly everything, making boom-bust oscillations likely. Adding porous ceramic or gravel creates protected zones where prey survive intense grazing, dampening oscillations and promoting coexistence. Surfaces also have a temporal dimension: the biofilm maturity of each surface determines how much EPS-based protection it provides beyond its geometric texture. A young tank with bare surfaces (M near 0) has weaker refugia, more exposed nitrifiers, and poor habitat for benthic meiofauna compared to the same tank after several months of biofilm development. The physical structure and age of the container are as important as the species list for determining ecosystem stability.

Reading the Feeding Tables

Three numbers define each feeding relationship in the tables above: preference (how much a consumer wants a given food source relative to others), assimilation efficiency (what fraction of ingested food is absorbed, with the rest ejected as fecal detritus), and access (what fraction of the food is physically reachable, with the remainder protected in refugia). Intake from each food source is proportional to its available amount times preference times access, so a scarce high-preference food may contribute less than an abundant low-preference one. For the full explanation of how these parameters interact -- including the Holling Type II functional response (the saturating feeding curve), stoichiometric homeostasis, and density-dependent refugia -- see Consumers and the feeding mechanics deep dive.

The Detrital Pathway

Not all energy flows through living organisms. A parallel pathway runs through dead organic matter. When organisms die, their biomass becomes detritus (particulate dead matter) or DOM (dissolved dead matter). The split depends on body size — tiny organisms like bacteria mostly lyse to DOM (80%), while large-bodied organisms like snails and shrimp mostly settle as detritus (95%). DOM also enters the water from sloppy feeding (~10% of egestion dissolves immediately) and algal exudation.

Bacteria consume DOM and suspended detritus, converting 28% into biomass and respiring the rest. Ciliates and grazers eat the bacteria, channeling that energy back into the living food web. For the full per-species death product routing and decomposition mechanics, see Death and Decomposition.

Density-Dependent Controls

Every consumer population in the model faces at least one mechanism that prevents unlimited growth. These include volumetric crowding mortality (Daphnia, rotifers), area-based benthic crowding (ostracods, bladder snails, cherry shrimp), cannibalism (copepods), viral lysis (bacteria, ciliates, HNF, and planktonic phytoplankton — the primary bloom-termination mechanism for cyanobacteria and green water), reproduction suppression (cherry shrimp), and density-dependent refugia (all prey). These feedbacks are crucial for ecosystem stability — without them, populations oscillate wildly or crash to extinction. For the full list with parameter values, see Consumers, Microbes, and Mortality Mechanisms.

Further Reading

• Feeding mechanics (detailed) -- Holling Type II functional response, multi-food selection, assimilation, stoichiometric homeostasis
• Refugia (detailed) -- How surface type, prey density, and grazer species interact to create protected zones for prey
• Species Catalog -- Reference guide to all species, including per-species feeding tables and parameter values
• Stability and Failure -- How food web structure affects ecosystem stability and common failure modes