Keystone Taxa Driving Nutrient Cycling in Freshwater Lakes

Keystone taxa shape the architecture of nutrient cycling in freshwater lakes, steering the flow of elements through complex, interdependent food webs. In these aquatic systems, a handful of organisms exert outsized influence on how nutrients are transformed, stored, and released. By shaping microbial community structure, enabling or constraining metabolic pathways, and mediating chemical transformations at interfaces such as sediments and littoral zones, these taxa determine rates of primary production, decomposition, and nutrient retention. This article surveys the key keystone players across microbial, plant, and animal communities, and illuminates how their interactions govern the cycling of carbon, nitrogen, and phosphorus. It also considers how environmental change—warming, eutrophication, stratification, and altered hydrology—reshapes the influence of these taxa, with implications for lake health, clarity, and resilience.

Keystone taxa and the architecture of nutrient cycles

Nutrient cycles in freshwater lakes hinge on a web of exchanges among inorganic nutrients, organic substrates, and living organisms. Keystone taxa are species or functional groups whose presence, absence, or specific interactions disproportionately alter the trajectory of nutrient transformations. In lakes, these taxa span bacterial lineages that drive mineralization and nitrification, microalgal and macrophyte producers that fix carbon and release organic matter, meiofaunal and zooplankton consumers that regulate microbial grazers, and sediment-dwelling organisms that mediate porewater chemistry. The concerted activity of these groups shapes the balance between burial, release, uptake, and remineralization of nutrients, ultimately influencing productivity, water quality, and ecosystem stability.

The following sections identify prominent keystone taxa or taxonomic groups within four functional arenas of nutrient cycling: carbon processing, nitrogen transformation, phosphorus dynamics, and sediment and interface processes. Each section highlights mechanisms by which that group exerts control, the ecological contexts in which their influence is strongest, and the potential consequences of changes in their abundance or activity.

Carbon processing keystone taxa

Carbon processing in freshwater lakes is driven by producers that fix inorganic carbon, heterotrophs that mineralize organic carbon, and a suite of organisms that bridge these pools by transforming dissolved and particulate organic matter. Keystone taxa in this arena regulate the rate at which carbon is sequestered in sediments, emitted as CO2, or exported in organic matter to downstream ecosystems.

Microalgae and aquatic macrophytes act as primary producers that capture carbon through photosynthesis. Within lakes, cyanobacteria and eukaryotic algae can be keystone in the sense that their seasonal blooms dominate the pool of available organic carbon, influence light attenuation, and modulate subsequent microbial processing. The composition of the photosynthetic community determines the quality and quantity of dissolved organic carbon (DOC) released into the water column, which in turn shapes heterotrophic bacterial activity and the trajectory of carbon remineralization. In nutrient-poor or relatively pristine lakes, diverse phytoplankton communities support balanced carbon cycling, while in eutrophic systems, bloom-forming taxa can drive rapid DOC production and alter the stoichiometry of carbon and nutrients.

Heterotrophic bacteria act as crucial drivers of carbon remineralization. Among these, certain bacterial clades are repeatedly observed as keystone due to their high potential for organic matter degradation and their sensitivity to substrate quality. Members of the Proteobacteria, Bacteroidota, Actinobacteriota, and Verrucomicrobiota lineages often dominate heterotrophic communities in freshwater systems and specialize in breaking down complex polysaccharides, proteins, and lipids released by primary producers and microbial grazers. Their enzymatic repertoires—extracellular hydrolytic enzymes and transport systems—facilitate the conversion of particulate and dissolved organic matter into simpler compounds that fuel respiration and generate CO2. The relative abundance of fast-growing, copiotrophic heterotrophs versus slower-growing, oligotrophic specialists can shift under varying nutrient regimes, thereby altering remineralization rates and carbon storage in sediments.

Fermentative and anaerobic taxa become particularly important in anoxic microhabitats such as hypolimnetic zones or sediment interfaces. Bacteria capable of fermenting carbohydrates and producing short-chain fatty acids contribute to carbon turnover under stratified conditions when oxygen becomes limiting. Methanogenic archaea, while often a minority in oxygenated littoral zones, can become keystone in anoxic microenvironments, channeling complex organic carbon into methane and CO2. The balance between methanogens and methanotrophs (aerobic or anaerobic methane-oxidizing bacteria) helps regulate methane emissions from lakes, a critical component of the carbon balance with climate implications.

Diatoms and other siliceous phytoplankton also influence carbon dynamics by producing extracellular polysaccharides that can stabilize aggregated organic matter, promoting sedimentation and long-term carbon burial. In littoral zones, rooted macrophytes contribute to carbon sequestration through litter fall and root exudates that feed decomposer communities. The structural role of macrophyte beds in shaping hydrodynamics and sedimentation patterns further modulates the fate of carbon by enhancing burial efficiency in sediments.

Taken together, carbon processing keystone taxa shape whether a lake functions as a source or sink of atmospheric carbon, influence the residence time of organic carbon, and regulate the ratio of CO2 to methane released from the system. The interplay between primary producers, heterotrophs, and anaerobic specialists determines the overall carbon trajectory and the resilience of carbon cycling to environmental perturbations.

Nitrogen transformation keystone taxa

Nitrogen turnover in lakes is governed by a suite of microbial processes: mineralization, assimilatory and dissimilatory anaerobic and aerobic transformations, nitrification and denitrification, anammox, and nitrogen fixation. Keystone taxa in this domain are those that enable or constrain these transformations, thereby setting the pace and pathways of nitrogen cycling. The emergent pattern across freshwater lakes is that functional guilds, rather than single species, often serve as keystones because redundancy and metabolic coupling can buffer or amplify the system’s response to change.

Nitrifying bacteria and archaea are central to the aerobic oxidation of ammonium to nitrite and nitrate. Ammonia-oxidizing bacteria (AOB) such as Nitrosomonas and ammonia-oxidizing archaea (AOA) like Nitrosopumilus are commonly cited keystone players in oxic waters, driving the first step of nitrification. The second step, oxidation of nitrite to nitrate, is carried out by nitrite-oxidizing bacteria (NOB) such as Nitrobacter and Nitrospira. The activity of these organisms sets the availability of nitrate for uptake by phototrophs, denitrifiers, and for assimilation into biomass. Environmental factors such as oxygen concentration, temperature, pH, and ammonium availability modulate their relative abundance and activity, thereby controlling nitrification rates.

Denitrification and dissimilatory nitrate reduction to ammonium (anammox and DNRA pathways) convert nitrate into gaseous nitrogen or ammonium, returning nitrogen to the lake in reduced forms or removing it from the system as N2 gas. Denitrifying bacteria and archaea, often belonging to diverse groups within Proteobacteria and other phyla, are keystone for reducing nitrate under low-oxygen conditions. Anammox bacteria, a specialized group within the Planctomycetota, carry out anaerobic ammonium oxidation with nitrite to form N2 gas, representing a significant pathway for fixed nitrogen loss in many stratified lakes. The prevalence of denitrification and anammox depends on substrates, oxygen availability, and the balance between nitrate and nitrite, all of which are shaped by microbial interactions and hydrology.

Nitrogen fixation, the conversion of atmospheric N2 to bioavailable ammonia, introduces new nitrogen into the ecosystem. Keystone taxa here include diazotrophic cyanobacteria and certain heterotrophic bacteria with nitrogen-fixation capabilities. In nutrient-limited systems, diazotrophs can become pivotal for sustaining primary production by supplying a steady source of bioavailable nitrogen. However, nitrogen fixation is energetically costly and tightly regulated by nutrient status, especially the availability of fixed nitrogen and phosphorus, so the keystone status of diazotrophs is context-dependent and linked to the overall nutrient regime of the lake.

Ammonification and mineralization processes driven by heterotrophic bacteria and fungi release ammonium from organic matter, fueling primary production and nitrification. The efficiency and rate of mineralization influence the substrate pool available for nitrifiers and for assimilatory uptake, thereby shaping the entire nitrogen loop. In littoral and benthic zones, microbial communities associated with sediments and macrophyte rhizospheres can act as localized keystones by controlling ammonium release, diffusion gradients, and redox conditions that govern subsequent transformations.

In addition to microbial actors, zooplankton and benthic invertebrates influence nitrogen cycling by grazing on nitrifying organisms, competing microbial grazers, and excreting nitrogen-rich wastes that become substrates for microbial processing. The interactions among producers, consumers, and decomposers create feedbacks that can amplify or dampen nitrogen turnover, with consequences for algal blooms and hypoxia risk.

Phosphorus dynamics keystone taxa

Phosphorus is typically a limiting nutrient in freshwater ecosystems, and keystone taxa here regulate the mobilization, sequestration, and release of phosphorus across water column, sediment, and biotic interfaces. The fate of phosphorus is tightly linked to redox conditions, mineral sorption processes, and the complex chemistry of particulate and dissolved P species. Keystone taxa influence phosphorus cycling through uptake and storage, mineral weathering, and interactions with iron and calcium minerals that modulate phosphate binding and release.

Phytoplankton and aquatic macrophytes store phosphorus in their biomass and can act as buffers against rapid P fluctuations. When biomass turns over, phosphorus is released back into the water column, potentially fueling subsequent growth or becoming trapped in sediments. The capacity of plants to take up inorganic phosphate efficiently and to exude organic ligands that mobilize bound phosphorus can shape the timing and magnitude of P availability.

Bacteria involved in phosphate solubilization and mineralization are key players in unlocking organic phosphorus compounds and releasing inorganic phosphate. Certain Carbon- and phosphorus-cycling bacteria possess alkaline phosphatases and other enzymes that mobilize phosphate from organic matter, enabling continued productivity in P-limited contexts. The efficiency of these processes depends on the community composition and the presence of co-factors such as micronutrients.

Sediment-associated microbes and chemists influence phosphorus dynamics through redox-driven processes that control iron-phosphorus interactions. In anoxic sediments, iron-bound phosphate can be released when iron(III) oxides are reduced, increasing dissolved phosphate in the porewater and overlying water. Sediment-dwelling microbes that catalyze redox reactions thus act as keystones by governing the internal loading of phosphate into the lake column. Conversely, oxic conditions promote the sequestration of phosphorus as iron-phosphate minerals, reducing bioavailable P in the water.

Benthic invertebrates and microbial biofilms on sediments create microhabitats that alter phosphorus sorption and desorption dynamics. The structure and function of biofilms influence phosphate binding capacity, transport of phosphorus within the littoral zone, and the formation of particulate phosphorus that may settle and become buried. Macrophyte root systems also contribute to phosphorus dynamics by releasing exudates that influence microbial activity and by physically stabilizing sediments, which can enhance burial and limit internal loading.

Phosphorus management in lakes often hinges on understanding how keystone taxa regulate internal loading versus external supply. In systems with ample internal loading due to redox fluctuations or sediment release, keystone microbial communities determine whether phosphorus remains sequestered or returns to the water column, potentially driving eutrophication or recovery. Management strategies that influence community composition—such as nutrient reduction, hydrological alterations, or restoration of macrophyte beds—can shift keystone dynamics and improve water quality outcomes.

Sediment and interface process keystone taxa

The sediment-water interface acts as a crucible where nutrient pools are exchanged, transformed, and partitioned between the water column and sediments. Keystone taxa in these zones wield outsized influence on nutrient residence times, redox gradients, and the fate of carbon, nitrogen, and phosphorus. Microbial consortia, benthic invertebrates, and plant roots collectively shape the geochemical microenvironments that govern nutrient processing.

Sediment-dwelling microbes, including anaerobic bacteria and archaea, drive key transformations such as sulfate reduction, methanogenesis, and anaerobic oxidation of ammonium. These processes alter the chemical speciation of nutrients and the release of reduced or oxidized forms into porewater. The spatial structure of microbial communities within sediments—vertical stratification, micro-niche partitioning, and biofilm formation—determines reaction rates and product distributions. Keystone taxa here include methanogens and sulfate-reducing bacteria, whose metabolic activities influence not only internal nutrient cycling but also greenhouse gas emissions, such as methane and hydrogen sulfide, with broader implications for biogeochemical feedbacks.

Benthic invertebrates, including polychaetes, oligochaetes, mollusks, and insect larvae, play multiple roles at the sediment interface. They facilitate bioirrigation and bioturbation, redistributing sediment and porewater, which in turn enhances oxygen penetration and stimulates microbial activity. By altering sediment structure and redox conditions, these organisms influence the balance between mineralization and sequestration of nutrients. Some species also directly consume detritus and microbial biofilms, thereby shaping the composition and function of microbial communities that perform critical transformations.

Rooted aquatic plants and their rhizospheres contribute significantly to interface processes by exuding organic compounds, releasing oxygen into the rhizosphere, and physically stabilizing sediments. The oxygen released by roots creates micro-oxic pockets that support aerobic processes, including nitrification, while inhibiting anaerobic processes in the immediate vicinity. Roots also harbor unique microbial communities that colonize the rhizosphere, enabling nutrient cycling through symbiotic relationships and enhancing phosphorus uptake via root exudates and mycorrhizal-like associations. In addition, root structures provide physical channels for water movement and nutrient diffusion, influencing local gradients and reaction zones.

Biofilms formed by microbial communities on sediment grains and interfaces act as microhabitats where chemical gradients drive coupled reactions across spatial scales. These biofilms concentrate enzymes, create microenvironments with distinct redox states, and enable cooperative interactions among diverse taxa. In particular, iron- and manganese-oxidizing bacteria within biofilms can mediate phosphorus sequestration by forming iron-phosphate minerals, while nitrifying and denitrifying microbes within biofilms coordinate nitrogen transformations in zones with alternating oxygen levels. The stability and composition of these biofilms influence the rate and direction of nutrient flux between sediments and the water column.

Keystone taxa at sediments and interfaces also include organisms that influence the physical turnover of materials, such as burrowing gastropods and certain crustaceans. By creating channels and increasing sediment turnover, these organisms enhance the exchange of nutrients between porewater and overlying water and alter the burial efficiency of organic matter. Their activities can indirectly modulate redox boundaries and nutrient speciation, thereby shaping overall nutrient cycling dynamics in the lake.

Integrated effects and ecosystem-level implications

The keystone taxa described above do not act in isolation. Their effects cascade through trophic levels and across spatial scales, creating emergent properties that define lake nutrient cycling at the ecosystem level. For instance, a shift in the cyanobacterial community can alter the quality and quantity of dissolved organic matter, which then selects for particular heterotrophic bacterial assemblages. This, in turn, affects remineralization rates and the release of inorganic nutrients, potentially fueling algal blooms or dampening productivity depending on the balance of processes.

The interaction between phosphorus availability and nitrogen cycling often hinges on microbial community structure. Phosphorus limitation can constrain nitrogen fixation, while available nitrogen can regulate the competitive dynamics among diazotrophs, nitrifiers, denitrifiers, and non-diazotrophic primary producers. Keystone taxa mediate these interactions by shaping substrate supply (e.g., DOC and NH4+) and redox conditions, thereby steering nutrient limitation and release dynamics.

Environmental context modulates the influence of keystone taxa. Temperature, stratification, hydrology, sediment texture, and pollutant loads all reshape the relative importance of specific taxa. For example, warming can accelerate microbial metabolism, increasing remineralization and potentially enhancing internal loading of phosphorus via iron cycling. Eutrophication can shift community composition toward bloom-forming taxa with cascading effects on nutrient processing pathways. Conversely, restoration efforts that promote macrophyte growth or solid-phase sediment stabilization can reconfigure microbial networks and biogeochemical gradients to favor nutrient retention and reduced internal loading.

Resilience and stability in lake nutrient cycling emerge when keystone taxa fulfill complementary roles and maintain functional redundancy. A diverse microbial community with multiple taxa capable of performing similar transformations provides buffers against disturbances. In contrast, the loss or suppression of key taxa—due to pollution, invasive species, or climate stress—can reduce functional redundancy and render the system more susceptible to regime shifts, such as persistent eutrophication or chronic hypoxia.

Methods to identify and study keystone taxa in lakes

Understanding which taxa act as keystones in a given lake involves integrating observational data, experimental manipulations, and modeling approaches. Key methods include:

• High-throughput sequencing and metagenomics to characterize microbial community composition and potential metabolic capabilities.
• Stable isotope tracing to link specific taxa to nutrient transformations, such as nitrate production and consumption or carbon mineralization pathways.
• Fluorescence in situ hybridization (FISH) and nano-scale secondary ion mass spectrometry (nanoSIMS) to localize metabolic activity within complex communities and spatially resolve microenvironments at interfaces.
• Microcosm or mesocosm experiments that manipulate nutrient levels, oxygen availability, and temperature to observe responses of keystone taxa and downstream nutrient fluxes.
• Sediment core studies to quantify porewater chemistry, redox gradients, and mineral-specific phosphorus dynamics, linking taxa distribution to geochemical patterns.
• Ecological network analyses to infer key interactions among taxa and identify hub species or functional guilds consistent with keystone status.

An integrated, multi-method framework helps reveal not only which taxa are present but also which exert outsized influence on nutrient transformations under particular environmental conditions. Long-term monitoring and cross-system comparisons further illuminate how keystone roles shift across seasons, lake types, and disturbance regimes.

Implications for lake management and restoration

Recognizing keystone taxa in nutrient cycling informs management strategies aimed at reducing eutrophication, enhancing water quality, and promoting ecosystem resilience. Management actions that support keystone processes include:

• Nutrient management to prevent legacies of phosphorus, which can sustain internal loading. Reducing external inputs helps maintain redox conditions that favor phosphorus burial rather than release.
• Restoration of macrophyte beds to stabilize sediments, enhance oxygenation in the rhizosphere, and promote beneficial microbial associations that sequester nutrients.
• Aeration or oxygenation strategies in stratified or hypoxic lakes to preserve aerobic processes, reducing methane production and promoting nitrification-denitrification balance.
• Sediment dredging or capping to limit internal nutrient release, while considering potential disruptions to sediment-dwelling keystone taxa and habitat structure.
• Biomanipulation of food webs to influence the abundance of grazers and detritivores, indirectly shaping microbial community structure and nutrient processing rates.

Any management intervention should consider potential trade-offs, including unintended consequences on keystone taxa and interactions across nutrient cycles. Adaptive management, informed by ongoing monitoring of microbial communities, redox conditions, and nutrient fluxes, can help sustain lake health while preserving the ecological functions mediated by keystone taxa.

Case examples and synthetic patterns

Across freshwater lakes worldwide, recurring patterns emerge regarding keystone taxa and nutrient cycling. In many stratified temperate lakes, hypolimnetic anoxia fosters denitrification and anammox by sediment- and water-column-associated microbes, reducing nitrate but potentially enhancing ammonium release. In oligotrophic lakes, diazotrophic activity can contribute essential nitrogen inputs that support phytoplankton productivity, with keystone diazotrophs responding to phosphorus availability and trace nutrient status. Eutrophic systems often exhibit cyanobacterial blooms linked to shifts in carbon processing and nutrient availability, where bloom-forming taxa and associated heterotrophs act as keystones in governing carbon turnover and toxin production.

Seasonal dynamics reveal temporal keystone shifts. Spring phytoplankton blooms can set the stage for subsequent microbial food webs by supplying labile organic matter that fuels heterotrophic bacterial growth, while autumnal inputs of organic matter from senescent plant material and increased rainfall alter redox conditions and nutrient flux patterns. Wetland-influenced littoral zones may harbor robust biofilm communities at sediment interfaces, acting as keystones by regulating phosphorus sorption and iron cycling, thereby modulating internal loading during seasonal transitions.

Comparative analyses across lakes differing in watershed characteristics, climate, and land use demonstrate that keystone taxa are not universal constants but context-dependent agents. Systems with similar nutrient regimes may rely on different taxa to fulfill equivalent functional roles. This functional redundancy can provide resilience, but it may also mask underlying vulnerabilities if disturbances target multiple taxa that perform the same function.

Concluding perspective

Keystone taxa are the linchpins of nutrient cycling in freshwater lakes, orchestrating the transformation, storage, and movement of carbon, nitrogen, and phosphorus through intricate networks of producers, decomposers, and interface communities. Their influence emerges from metabolic capabilities, ecological interactions, and the physical structure of lake ecosystems. Understanding which taxa serve as keystones in a given system—and how environmental change reshapes their roles—offers a powerful lens for diagnosing ecosystem health, predicting responses to perturbations, and guiding management toward sustainable, resilient lakes. As research advances with integrative omics, microenvironment imaging, and long-term ecological datasets, the ability to map keystone dynamics will sharpen, enabling targeted interventions that preserve the functional integrity of nutrient cycling in freshwater lakes for generations to come.