Introduction

The health and sustainability of aquatic ecosystems are under significant threat due to a multitude of challenges. These challenges, primarily stemming from increasing pollutants discharged from both natural and anthropic activities and inefficient solutions for pollution management, necessitate urgent and effective responses to ensure the resilience and well-being of these critical water ecosystems. Microorganisms, as the most abundant and pivotal living entities, play a central role in biogeochemical cycles in diverse water ecosystems1. Their reliance on carbon and nutrients as energy sources and building blocks is crucial for sustaining metabolic processes, microbial growth, and, consequently, the functioning and sustainability of entire water ecosystems2,3,4,5.

Aquatic ecosystems are broadly categorized into eutrophic and oligotrophic environments, based on the abundance of carbon and nutrients (Fig. 1). Eutrophic environments are characterized by ample resources, high carbon or nutrient concentrations, and densely populated microbial communities6. Under such conditions, microorganisms encounter an abundance of labile compounds, readily available for energy and substrate acquisition7. How microbes utilize substrates in eutrophic ecosystems has received considerable scientific attention, with extensive research focusing on the dynamics of carbon and nutrient inputs, microbial decomposition, and biogeochemical cycle8,9,10. Attention to the metabolic properties of microorganisms under eutrophic conditions has effectively contributed to many sustainable development goals (SDGs). For example, anaerobic digestion can purify wastewater while converting high concentrations of organic pollutants in the wastewater into renewable energy methane11,12, benefiting SDG-6 (clean water and sanitation) and SDG-7 (affordable and clean energy).

Fig. 1: The overall concept of microbial utilization of low concentration substances and their roles in achieving sustainable development goals.
figure 1

a In oligotrophic environments, substrate (left green circle) and microbial concentrations (left yellow circle) are low. In eutrophic environments, substrate (right green circle) and microbial concentrations (right yellow circle) are high. The red line represents common (conventional) organic carbon and nutrient concentrations, and the blue line represents emerging organic compound concentrations. The solid red circle in the center refers to the microbial intracellular and extracellular concentration threshold. Dashed lines indicate that the concentration profiles near the intracellular and extracellular boundary are not necessarily continuous. The substrate concentration in the environment mainly includes three common cases: ① low concentration of common organic carbon and nutrients in oligotrophic environments; ② high concentration of common organic carbon and nutrients in eutrophic environments; and ③ low concentration of emerging organic compounds in both oligotrophic and eutrophic environments. This review focuses on scenarios ① and ③. b Microorganisms play crucial roles in achieving multiple sustainable development goals such as by transforming wastewater to clean water, conversing pollutants to renewable resources and energy, and recycling carbon, sulfur, nitrogen, and phosphate. AOC: assimilable organic carbon.

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Oligotrophic environments, on the other hand, are resource-limited and challenge microorganisms to adapt to low concentrations (e.g., ng L–1 – µg L–1) of poorly degradable nutrients and organic carbon. Under oligotrophic conditions, microorganisms must employ specialized metabolic strategies to effectively compete for limited resources. This includes producing extracellular enzymes capable of degrading complex organic compounds and scavenging to efficiently utilize scarce organic substrates13,14,15. The understanding of microbial adaptation in oligotrophic environments is critical for managing emerging environmental concerns16. For example, carbon dioxide (CO2) concentrating mechanisms (CCMs) which benefit the mitigation of greenhouse gas emission, are evolved by microorganisms under low-CO2 conditions. Despite the ecological significance of oligotrophic environments, our knowledge of carbon and nutrient cycling under these conditions is relatively limited compared to eutrophic systems.

Understanding how microorganisms survive under oligotrophic conditions also helps to comprehend the biodegradation mechanisms of ‘emerging organic carbon’, which have received much attention in recent years. ‘Emerging organic carbon’ refers to anthropogenic compounds that enter the environment at low concentrations but exerts profound ecological effects toward, or are toxic to, both aquatic life and human health17,18. Micropollutants, a subset of emerging organic carbon, encompass a broad range of chemical compounds released from industrial, agricultural, and urban activities19,20. These compounds include pharmaceuticals, personal care products, pesticides, and industrial chemicals, along with their metabolites21,22,23. Despite their low individual concentrations, the presence of micropollutants in both eutrophic and oligotrophic environment has raised concerns about their ecological impact and potential risks to human health24,25.

The recent proposals by the European Commission to introduce stricter standards for controlling emerging pollutants in surface and groundwater, set to be implemented by 2040, underscore the urgency and importance of understanding microbial interactions with low-concentration contaminants. These standards aim to tackle a broad spectrum of micropollutants and improve urban wastewater treatment to better protect public health and the environment. This regulatory shift highlights the need for robust theoretical frameworks and practical strategies to manage these pollutants effectively. Therefore, revealing the delicate mechanisms through which microorganisms interact with, and respond to, low-concentration pollutants is critical in assessing ecological risk and developing effective removal strategies.

Exploring the metabolic processes of microorganisms in both eutrophic and oligotrophic aquatic environments is vital to addressing environmental challenges, including the remediation of deteriorated water bodies, effective management of water ecosystem services, and adaptation strategies in the face of climate change. For hundreds of years, efforts to sustain water ecosystems have evolved through recognizing, understanding, imitating, and utilizing microorganisms26. Nowadays, the microbiome-based water treatment process stands as a cornerstone in maintaining a healthy water cycle27,28,29. However, identifying the intricate connections between biogeochemical cycle and microbial metabolism (especially under low-concentration substrate settings) is still imperative in addressing environmental challenges11 and achieving multiple SDGs such as SDG-6 (clean water and sanitation), SDG-11 (sustainable cities and communities), SDG-13 (climate action), and SDG-14 (life below water) (Fig. 1).

This review aims to bridge the gap of limited understanding of nutrient and carbon cycling in oligotrophic environments by focusing on how microorganisms manage low-concentration resources. The novelty of this manuscript lies in the comprehensive analysis of microbial strategies in low-resource environments and their implications for environmental management and sustainability. We highlight the potential of microbiome-based water treatment processes and discuss future research directions in the control of low-concentration contaminants. By illuminating the intricate connections between biogeochemical cycles and microbial metabolism under these conditions, this review contributes to the understanding of sustainable remediation strategies, particularly for micropollutants with significant ecological impacts. This understanding is crucial not only for preserving and restoring ecosystems but also for protecting human health against escalating environmental threats.

Microbial growth at low-substrate concentrations

Substrates at low concentrations cannot adequately support the survival or growth of microorganisms but impose important environmental effects. The availability and concentration of organic carbon play important roles in determining microbial growth. There are notable differences in concentrations of organic carbon across various aquatic ecosystems. For example, soluble organic carbon concentrations tend to be high in wastewater, but low in groundwater, drinking water, and surface water. In ground, drinking, and surface waters, dissolved organic carbon concentrations typically range from 0.5 to 5 mg L−1 14. Most of this carbon exists in polymeric forms inaccessible to microorganisms30. Microbially-available organic carbon compound, referred to as the assimilable organic carbon (AOC), is widely used to describe bioavailable organic carbon in drinking water and reclaimed wastewater31,32,33. Assimilable organic carbon is generally present at concentrations of 10–100 μg L–1, while individual sugars or amino acids are found at levels not exceeding a few μg L–1 14.

Irrespective of low extracellular concentrations of organic carbon, intracellular substrate concentrations are usually higher. For example, the concentration of glutamate in the extracellular environment is typically in the micromolar (µM) range34, whereas intracellular concentrations are millimolar (mM)35. Consequently, different substrate uptake mechanisms need to be induced, due to the distinct substrate gradients between extracellular and intracellular environments (Fig. 1).

Previously, researchers assumed that nutrient-poor environments were inhospitable to life, and most bacterial cells observed microscopically were dead, dormant, or severely starved14. However, despite the low concentrations of available carbon compounds, prokaryotic cell concentrations in oligotrophic environments typically range from 105 to 106 cells mL−1 14. We have now come to understand that most such microorganisms are, indeed, alive, metabolizing, and ready to grow when provided with the opportunity. For example, studies have shown that concentrations as low as 0.5 mg L–1 of tryptone or peptone are sufficient to support oligotrophic growth36. However, typical investigations of Bacillus subtilis usually employ rich growth media, such as the Luria-Bertani broth, which contains tryptone and yeast extract at concentrations approximately 10,000 times higher than those required for oligotrophic growth36. This has resulted in widespread overlooking of microbial survival mechanisms in natural environments.

Microorganisms exhibit a range of survival strategies depending on substrate availability. These strategies, essential for sustaining life in challenging environments, also play a significant role in the broader context of environmental sustainability. By adapting to low-concentration substrates, microbes not only ensure their survival but also contribute to the functioning and resilience of aquatic ecosystems. This ability to thrive in nutrient-limited conditions is closely aligned with efforts to achieve SDGs, particularly those focused on preserving water quality and ecosystem health (Fig. 1). The fascinating metabolic adaptations of these microorganisms in response to substrate availability are further explored in the following sections, offering insights into their potential applications in sustainable environmental management.

Microbial substrate concentrating strategies

Microorganisms degrading low concentrations of substrates first need to concentrate as many of these compounds as possible in the environment. Therefore, concentrating strategies of different substrates represent critical survival mechanisms in the microbial world, allowing microorganisms to survive even in resource-limited environments. Microorganisms employ a diverse array of concentration mechanisms and competition strategies to cope with resource scarcity in various ecological settings. This section delves into the intricacies of microbial concentrating strategies, including how microorganisms concentrate substrates (e.g., carbon, nitrogen, and sulfate) at the level of individual cells and how structured biofilms are formed to optimize microbial survival. Recognizing the intricate ways that microorganisms adapt for concentrating substrates contributes to the broader understanding of ecosystem resilience and supports endeavors towards the achievement of clean and healthy aquatic environments.

Microbial concentrating mechanisms at the level of individual cells

Carbon concentrating mechanisms

In the context of global efforts to achieve carbon neutrality, understanding and leveraging microbial carbon concentrating mechanisms have become increasingly important37,38. Aquatic systems, encompassing oceans, lakes, and rivers, serve as both sources and sinks of CO2 through processes like photosynthesis, respiration, and the dissolution of CO2 in water. The ocean is a sink for about 25% of the atmospheric CO2 emitted by human activities39. Ocean acidification, resulting from CO2 absorption by oceans, poses challenges to marine ecosystems. These processes create feedback loops with climate change implications, emphasizing the interconnectedness of aquatic environments with global climate systems.

In marine ecosystems, however, the capture and utilization of CO2 face a severe challenge: despite the large surface ocean-atmosphere CO2 flux, CO2 in the ocean depths is too low to be efficiently utilized. To adapt to this, marine phytoplankton evolves CCMs (Fig. 2a). CCMs comprise a group of biological strategies to concentrate cellular CO2, enabling metabolic processes, such as CO2 fixation, that require high concentrations of CO240. CCMs are used by certain photosynthetic organisms, such as some types of algae, to increase photosynthesis rates in CO2-limited environments. For example, to adapt to CO2 limitation, nearly all marine phytoplankton have evolved CCMs, which support photosynthetic carbon fixation at the concentrations of CO2 present in ocean surface waters (<10–30 μM)41.

Fig. 2: Examples of microbial concentrating mechanisms in oligotrophic environments.
figure 2

a Marine phytoplankton utilise a RuBisCO-based CO2 concentrating mechanism to increase CO2 concentrations for photosynthetic carbon fixation under low-CO2 conditions. b Ammonia-oxidizing microorganisms change the proteinaceous S-layer and ammonia monooxygenase enzyme complex to regulate substrate and nutrient transport. This panel is recreated from the reference44. c Cable bacteria use hydrogen sulfide oxidation, iron sulfide oxidation, and electric field to increase the surrounding sulfate concentration. d Microorganisms (orange) form aggregates (biofilm) to accumulate nutrients, signals and organic carbon in adapting to poor substrate conditions. e Synergistic or antagonistic effects among carbon, nitrogen, and sulfur elements.

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CCMs involve the use of active bicarbonate (HCO3−) uptake transporters, strategically positioned carbonic anhydrases inside the cells, and the creation of a sub-cellular micro-compartment called the carboxysome40, where most of the RuBisCO—a key enzyme in carbon fixation—is located. Certain marine phytoplankton species have developed various adaptations with respect to RuBisCO to support photosynthesis in low-CO2 environments42. For instance, Tortell et al. 43 observed increased RubisCO production, in response to low CO2 levels. Subsequently, Tchernov et al. 44 suggested that the evolution of high-CO2-affinity RubisCO may also enhance photosynthesis under low-CO2 conditions. In fact, under low-CO2 conditions, phytoplankton species equipped with efficient CCMs were observed to outcompete their counterparts with less efficient CCMs, provided that the availability of nutrients and light was sufficient to support the additional biochemical and energetic demands of active transport of inorganic carbon into the cell45,46.

The discovery and understanding of CCMs provide a template for developing microbial-based strategies for carbon capture and carbon neutralization. For example, numerous studies have explored the potential of engineering, transplantation, and heterologous functional expression of CCMs to enhance CO2 fixation47. In this regard, CO2-fixing micro-compartments were successfully transplanted into Escherichia coli, and their functionality was validated both in vivo and in vitro. Additionally, a Bacillus sp. strain SS105 was identified as an efficient candidate for CO2 fixation by CCM, exhibiting a high CO2 concentrating rate of 287.21 mg L–1 day−1 48. These findings have important implications for promoting carbon fixation and reducing greenhouse gas emissions.

Nitrogen concentrating mechanisms

Nitrogen is integral to the sustainability of aquatic ecosystems, contributing to nutrient cycling, primary productivity, and biodiversity. Its significance lies in supporting key ecological processes such as the nitrogen cycle, essential for the growth of aquatic organisms and the maintenance of water quality49. Microbial degradation of nitrogen, facilitated by diverse microbial communities, plays a crucial role in regulating nitrogen levels50. Processes like denitrification, ammonification, and nitrogen fixation carried out by these microbes help prevent water pollution, eutrophication, and harmful algal blooms51. By efficiently recycling nitrogen, microbial activity ensures a balanced aquatic ecosystem, influencing food web dynamics and promoting the overall health and resilience of aquatic environments.

In nitrogen-limited conditions, to concentrate nitrogen, microorganisms may modify the proteinaceous surface layer (S-layer), or lipid cell membrane, to regulate substrate transport and enzyme complex stability52 (Fig. 2b). This physiology is typically observed in ammonia-oxidizing microorganisms. All ammonia-oxidizing microorganisms share ammonia monooxygenase – the primary enzyme involved in ammonia oxidation53 – which is located in the cytoplasmic membrane with its substrate-binding site most likely facing outside of the cell53. Thus, increasing the surface-area-to-volume (SA/V) ratio of a cell is understood to provide more space for ammonia monooxygenase, and further enhance the chance of binding NH3 even at very low concentrations. Some ammonia-oxidizing bacteria (AOB) can accumulate very high intracellular NH4+ concentrations of up to 1 M54, which can act as a concentrated substrate reservoir, indirectly increasing the concentration of NH3 around the ammonia monooxygenase enzyme complex. Similarly, the negatively charged surface layer (S-layer) of ammonia-oxidizing archaea (AOA), e.g., Nitrosopumilus maritimus, has been shown to act as a substrate reservoir for positively charged ammonium52. The enriched ammonium in the pseudo-periplasmic space of AOA may also indirectly increase NH3 concentrations around the ammonia monooxygenase enzyme complex53. These discoveries were found using many advanced methodologies including but not limited to phylogenetic reconstruction with the IQ-TREE algorithm, model determination with ModelFinder, substrate-dependent oxygen uptake measurements using micro-respirometry systems equipped with high-precision microsensors, 2D Poisson–Nernst–Planck electro-diffusion reaction transport model, and electron cryotomographic imaging52,53.

Sulfate concentrating mechanisms

The sulfur cycle is another critical component of ecosystem functioning, ecological sustainability, water management, and climate regulation. Sustainable management of sulfur cycling is essential for maintaining ecological balance, supporting human livelihoods, and achieving broader goals related to environmental and social sustainability55. One example for microbial concentrating mechanisms at the level of individual cells is the enrichment of sulfate concentrations in freshwater sediments by cable bacteria56 (Fig. 2c). Generally, the concentration of sulfate in freshwater is 2–3 orders of magnitude lower than that in marine systems57, but cable bacteria could enrich the sulfate concentration in freshwater sediments by three- to ten-fold56 (Table 1). A custom-built electric potential microelectrode, three-dimensional micro-profiling system, as well as custom made H2S, O2, and pH microsensors were applied to enable the precise control and measurement of environmental conditions56. Micro-environmental sulfate enrichment enhanced rates of sulfate reduction. The possible mechanisms of sulfate enrichment included the cable bacteria-driven oxidation of sulfide and the cable bacteria-mediated dissolution and oxidation of iron sulfides. The cable bacteria were able to generate an electric field that enhanced sulfate retention by initiating ionic drift and further elevating the sulfate concentration58,59.

Table 1 Characteristics of representative microbial species in oligotrophic environments
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The sulfate concentrating mechanisms benefit SDG-14 (life below water) because cable bacteria contribute to the sulfur cycle in marine and freshwater ecosystems58, influencing the health and biodiversity of ocean environments, aligning with the focus of SDG-14 on conserving and sustainably using marine resources. In addition, microbial processes involving sulfur play a role in wastewater treatment60, contributing to the purification of water and aligning with the objective of SDG-6 (clean water and sanitation).

Synergistic or antagonistic effects of C, N, and S

Interactions among carbon, nitrogen, and sulfur in microbial ecosystems, especially under low-concentration conditions, is critical for assessing their synergistic and antagonistic effects on microbial metabolism61. These interactions can significantly influence the efficiency of microbial concentrating mechanisms and the overall biogeochemical cycles in nutrient-limited environments62. Sometimes, synergistic effects are found among different element cycles. In carbon-rich but nitrogen-limited environments, the presence of even minimal nitrogen can greatly enhance microbial growth and metabolic activities. For instance, low nitrogen levels can be efficiently utilized by phytoplankton using CCMs to enhance photosynthesis, leading to more robust growth and ecological dominance in oligotrophic waters63. The sulfur cycle is also influenced by the availability of organic carbon especially in anaerobic environments where organic carbon is often limited. Studies have shown that the activity of sulfate reduction by sulfate reducing bacteria depend on the activity of the phototroph with respect to availability of degradable carbon sources, when inorganic sulfur pool is large such as in marine ecosystems64.

On the other hand, antagonistic effects also exist. For example, at low concentrations, the competition between sulfur and nitrogen for metabolic processing becomes more pronounced. Even minimal hydrogen sulfide (60 and 100 μM) can inhibit nitrification as microbes prioritize sulfate reduction to meet basic metabolic needs over nitrogen processing, which could lead to reduced rates of nitrification and nitrogen fixation in sulfur-poor environments65,66. Similarly, low concentrations of sulfide can interact antagonistically with microbial processes dependent on organic carbon. Even low levels of sulfide can inhibit key aerobic and anaerobic processes, such as methanogenesis, or the aerobic degradation of organic compounds, by imposing toxic stress on microbial communities66. Therefore, such interactions are particularly significant in environments where one or more nutrients are in limited supply, influencing microbial adaptations and the ecological balance of aquatic systems. For instance, in oligotrophic lakes, where nutrient levels are low but their demand by microbial communities and aquatic plants is high, understanding how microbes adapt their metabolic strategies to optimize resource utilization is crucial for managing ecosystem health and preventing phenomena like harmful algal blooms.

Substrate concentrating mechanisms at the level of biofilms

In real-world settings, microorganisms exist in populations, with complex interactions between individual microorganisms. One of these is that microorganisms form aggregates under suitable conditions to better obtain food, communicate, or defend themselves against unfavorable environments. Microbial aggregates (e.g., biofilms and granules) can be formed not only in nutrient-rich environments (e.g., anaerobic digesters) but also in environments where nutrients are scarce and competition for resources is high67,68. Under such conditions, individual microorganisms may struggle to survive. By forming a biofilm, microorganisms can build a highly organized structure that facilitates concentrating and sharing of resources, including nutrient trapping, signal accumulation, and antibiotic tolerance69. In specific biofilm structures, nutrient-rich microenvironments may be formed by accumulating substrates, such as ammonium, nitrate, and sulfate, from the surrounding water phase11 (Fig. 2d). Electrostatic attractive interactions between charged sites on biofilm polymers and oppositely charged ions outside the biofilm appear to be significant factors in accumulating nutrient ions from the surrounding water into the biofilm70. This phenomenon has been confirmed by lake microbial biofilm systems where the concentrations of NH4+ and NO3− inside the biofilm were much higher than those in the surrounding water70.

The concentrating capacity of biofilms can be partially attributed to extracellular polymeric substances (EPS), which typically comprise of polysaccharides, proteins, extracellular DNA, and humic substances71,72. These self-organizing microbial assemblages may adsorb nutrients and micropollutants from water environments, based on electrostatic attractive interactions and ion-exchange73,74. For example, carboxyl- and hydroxyl-groups in EPS infer a high capacity for sorption of heavy metals75, and biofilms can enrich polycyclic aromatic hydrocarbons with high molecular weight and high partition coefficients (e.g., Benzo(ghi)perylen)76. The EPS not only accumulates hydrophobic organic pollutants by binding them through hydrophobic-hydrophobic interactions, but also accumulates moderately hydrophilic compounds, such as toluene, xylene, and benzene77. Therefore, the EPS matrix serves as a medium in which organic pollutants can either undergo degradation or persist until they are degraded.

Accumulation or adsorption of nutrients may affect biofilm activity and density or select for specific functional microbial populations78. For example, biofilm biomass was found to be far higher (109 cells wet-g−1) than lake water biomass (106 cells wet-g−1)70, and the increased microbial activity or biomass will further enhance adsorption capacities. Some studies also found that quorum-sensing signal substances are accumulated in the EPS phase, compared with the water phase, which may enhance microbial communication within microbial aggregates79,80 and, in turn, further promote EPS formation and micropollutant degradation.

In essence, the development of biofilms exemplifies the collective ingenuity of microorganisms in adapting to challenging substrate conditions. By forming biofilm communities and collaborating to share resources, microorganisms demonstrate a sustainable strategy for survival that transcends the limitations faced by individual cells or species81,82. This cooperative behavior underscores the role of biofilms as a resilient and resourceful mechanism in promoting the stability of microbial ecosystems83. The capacity of biofilms to degrade or persist pollutants, particularly micropollutants, also underscores their importance in ecological risk assessment and sustainable environmental management84. The innovative use of biofilm systems in water environment management can lead to more sustainable and resilient water ecosystems.

Microbial strategies for low-concentration substrate utilization

Following the successful concentration of substrates, microorganisms face the subsequent challenge of efficiently utilizing these substrates, particularly in environments where they are available only at low concentrations. This ability to not only concentrate but also effectively utilize minimal resources is a testament to the remarkable adaptability of microbial life. These strategies, which bridge the gap between substrate availability and metabolic demand, are crucial for the maintenance and resilience of aquatic ecosystems. They represent a sophisticated response to the dual challenges of scarcity and competition, underscoring the role of microorganisms in sustaining ecological balance and contributing to the overall health of aquatic habitats.

Substrate uptake and transportation into and within the cell

Microbial transport mechanisms are essential for regulating nutrient uptake and facilitating substrate utilization. Under low substrate concentrations, transport through cell layers becomes a primary challenge85. Mass-transfer limitations may become particularly relevant at extracellular substrate concentrations below the Monod or Michaelis–Menten constants of growth and enzymatic turnover, causing a shift in enzyme kinetics from zero-order to first-order86,87. Indeed, this scenario is especially relevant in the context of the persistence of organic micropollutants, which are commonly found at low concentrations in aquatic environments and pose significant challenges to ecosystem health and sustainability88.

In the case of Gram-negative bacteria, transport through porins in the outer membrane can be an initial challenge. However, physiological adjustments in outer membrane permeability are possible. For example, in E. coli, the expression of OmpF proteins that form large porins is enhanced 20-fold at a moderate degree of glucose limitation89 (Fig. 3a). Regulating nutrient transport in this way is critical in balancing the flux of limiting substrates into the cytoplasm and the intracellular capacity to transform substrates into autocatalytic macromolecules, such as RNA and proteins90,91.

Fig. 3: Substrate uptake and transportation in oligotrophic environments.
figure 3

a Escherichia coli upregulate the expression of OmpF proteins to form large porins at a moderate degree of substrate limitation. b Selective uptake strategies of microorganisms in oligotrophic environments. Cells manage their substrate priorities to ensure the uptake of preferential compounds (yellow triangles) when substrate concentrations are low.

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When nutrient concentrations are low, microbial cells must discriminate between which nutrients to take up and utilize, prioritizing based on costs and benefits92. Microbial cells must manage priorities between different nutrients and transporters93 (Fig. 3b). This decision-making process is complex and depends on several factors, including the extracellular concentration of nutrients and the need to limit intracellular density to ensure suitable diffusion of all cell components inside the cell94. One well-known microbial transport strategy is catabolite repression, whereby high-affinity transporters are repressed in the presence of a more readily available substrate95. This strategy can be interpreted in cost-benefit terms, depending on the extracellular concentration of nutrients96. Indeed, under oligotrophic conditions, higher energy expenditure may be required for substrate uptake.

The decision-making process of microbial cells in discriminating between substrates may be applied to bioremediation and water treatment processes in several innovative ways. For example, in bioremediation, certain microorganisms may be utilized based on their ability to selectively uptake specific pollutants. Microorganisms that exhibit catabolite repression may be used in staged bioreactors where the sequence of available substrates is controlled. This approach can ensure that microbes first degrade the most harmful pollutants before moving on to less harmful ones, thereby optimizing the bioremediation process.

Intracellular concentration also matters. For example, the phosphotransferase system (PTS) is the main substrate uptake system in E. coli under excess-glucose conditions, and its activity can also impact glucose transport under low-nutrient conditions97. Glucose transport is not solely dependent on extracellular concentrations, but also on intracellular concentrations of other metabolites, such as glucose-6-phosphate, phosphoenolpyruvate, and pyruvate – the key components of PTS98.

These microbial transport mechanisms enable microbes to thrive in nutrient-scarce environments, influencing nutrient cycling and ecosystem productivity. Understanding these processes also offers potential for enhancing bioremediation techniques, where engineered microbes with optimized nutrient uptake systems could more effectively remove pollutants. Further research into these transport systems could lead to advancements in microbial biotechnology, improving environmental sustainability and ecosystem resilience.

Substrate affinity

To survive in environments with extremely low substrate concentrations, microorganisms also employ strategies involving specialized mechanisms based on high substrate affinity. Oligotrophic bacteria possess higher affinity transport systems for substrates than eutrophic bacteria99, indicating the basis for their preferential adaptation to oligotrophic environments. This adaptation allows them to thrive in nutrient-scarce environments, contributing to the sustainability of aquatic ecosystems by maintaining nutrient cycling and reducing the accumulation of pollutants.

Understanding substrate affinity is essential for comprehending microbial nutrient acquisition strategies. One approach to evaluate the competitive advantage of microbes for nutrients at low concentrations is the maximum specific growth rate/substrate saturation constant (μmax/Ks) ratio, also known as the specific substrate affinity from Monod modeled kinetic properties100,101. This parameter bridges the gap between enzymatic substrate uptake kinetics and microbial growth, providing insights into the efficiency of nutrient utilization100. In the context of water treatment processes, microorganisms with high substrate affinity can be strategically employed to remove trace contaminants from wastewater. Microorganisms that exhibit high μmax/Ks ratios are particularly effective in degrading or transforming these contaminants, even when present at very low concentrations, thus enhancing the efficacy of bioremediation strategies. When the substrate affinity of a microorganism is expressed with Michaelis–Menten kinetic equations (Eq. 1), a similar Vmax/Km(app) (maximal reaction rate divided by substrate affinity constant) ratio can be used without taking other cellular process (e.g., growth, division, stress, and repair) into account52,101.

$$V=\left({V}_{\max }\times \left[S\right]\right)\times {({K}_{m\left({app}\right)}+\left[S\right])}^{-1}$$
(1)

where V is the reaction rate, Vmax is the maximum reaction rate, S is the substrate concentration, and Km(app) is the substrate saturation constant.

The significance of (specific) substrate affinity becomes evident when examining specific examples from microbial communities. For instance, AOA, including marine, agricultural soil, and thermal spring isolates, exhibit a wide range of affinities (e.g., Km(app) = ~2.2 to 24.8 nM for Nitrosopumilales and ~0.14 to 31.5 µM for Nitrososphaerales), and specific affinities, for NH352. Among AOA, those that have adapted to oligotrophic conditions were believed to possess both high substrate affinities (low Km(app)) and high specific affinities. Oligotrophic environments have already been postulated to select for organisms with a high SA/V ratio, enhancing their nutrient uptake capabilities102,103. In contrast, AOA, such as ‘Candidatus Nitrosocosmicus oleophilus’ MY3 and ‘Candidatus Nitrosocosmicus franklandus’ C13, with very low SA/V ratios possess low (specific) affinities for NH352.

In environments with extremely low oxygen concentrations, such as oceanic oxygen minimum zones, microbes (mainly AOA and nitrite-oxidizing bacteria) have been found to have high substrate affinities for oxidizing ammonium (333 ± 130 nmol L–1 O2) and nitrite (778 ± 168 nmol L–1 O2), repestively104. Despite the limited availability of oxygen (5-33 nmol L−1 O2), microorganisms have adapted, and developed, mechanisms, such as high-affinity terminal oxidases105,106,107, to perform aerobic nitrite oxidation even below the lowest in situ detection limit for oxygen achieved so far107.

These examples highlight the importance of understanding and leveraging microbial substrate affinity in various environmental applications. By selecting and employing microorganisms with appropriate substrate affinities, we can enhance the sustainability and efficiency of bioremediation processes, contributing to cleaner water bodies and healthier aquatic ecosystems.

Microbial metabolic pathways

Microbial metabolic pathways constitute the intricate web of chemical reactions that drive the survival, growth, and interactions of microorganisms in diverse environments. These pathways serve as the basis for life’s fundamental processes, allowing microorganisms to efficiently utilize resources, adapt to changing conditions, and thrive in challenging environments. In this section, we explore the world of microbial metabolic pathways, considering mixed-substrate utilization, syntrophic metabolisms, dynamic responses of microorganisms to changing substrate conditions, and density-based mechanisms under oligotrophic conditions. We highlight their pivotal roles in sustaining ecological processes, particularly in aquatic systems, and explore their potential biotechnological applications108. These applications range from enhancing the efficiency of water treatment processes to contributing to sustainable ecosystem management109,110, thereby aligning with global efforts to achieve environmental sustainability and meet key SDGs.

Mixed-substrate utilization

In resource-limited conditions, microbial cells pursue remarkable strategies to utilize mixed substrates, even at very low concentrations. Specialized cells that solely rely on a single carbon compound would not be expected to experience significant growth111,112, aligning with the principle of diauxic growth observed in pure and mixed cultures100. However, extensive experimental evidence indicates that carbon-starved or slow-growing cells in carbon-limited environments actively express various carbon-cycling catabolic enzymatic systems (Fig. 4a), even in the absence of the corresponding carbon sources113,114,115. This enables cells to promptly utilize carbon substrates once available in the environment. The measured threshold concentration necessary for a nutrient flux to support growth and maintenance may also be reduced by the presence of other substrates. For example, when 3-chlorobenzoate and acetate were each fed as the single substrate for growth of Pseudomonas sp. strain B13, the minimum substrate concentrations (Smin) of each required for growth were higher than the individual Smin when fed as a mixture116.

Fig. 4: Microbial metabolic pathways responded to resource-limited conditions.
figure 4

a Mixed-substrate utilization strategies enable cells to express various carbon catabolic enzyme systems. Carbon substrates are efficiently utilised once they become available in environments. b Schematic of microbial metabolic division of labor. Different metabolic pathways for the degradation of complex substrates are distributed among various microbial members (orange dotted line). Microbes exchange metabolites and nutrients with other members to release burden of their functioning on cellular processes (green dotted line). Microbes exchange electrons via direct interspecies electron transfer (DIET) to enhance overall metabolic efficiency (yellow dotted line).

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Heterotrophic microorganisms demonstrate an astonishing capacity to simultaneously assimilate multiple carbonaceous compounds under low substrate concentrations. This includes the utilization of mixtures of carbon sources that traditionally lead to diauxic growth at high concentrations117,118, a growth behavior commonly referred to as mixed-substrate growth119. This metabolic adaptation enables microorganisms to efficiently exploit low concentrations of individual substrates. For instance, Pseudomonas aeruginosa could grow on a mixture of 45 carbonaceous compounds, each added to tap water at a concentration of 1 mg C L–1, even though none of these compounds individually supported growth at this concentration112.

In laboratory studies with pure cultures, bacterial cells have demonstrated two strategies for survival under low concentrations. The first involves a ‘multivorous’ lifestyle, whereby cells take up, and metabolize, dozens of different carbon substrates simultaneously, without specializing in a particular substrate14. This mixed-substrate growth provides cells with kinetic advantages and metabolic flexibility25. Simultaneous utilization of multiple carbon substrates allows for rapid growth even at extremely low concentrations of individual substrates120. Instead of a single specialist bacterium for each substrate, microbes compete for multiple substrates simultaneously, and utilization thresholds for certain compounds can be lowered through the simultaneous utilization of alternative carbon substrates121. Experimental evidence has demonstrated that the induction threshold for specific compounds, such as 3-phenyl-propionate, can be reduced by the presence of alternative carbon substrates14. For example, E. coli was found to exhibit induction of ppa-degrading enzymes and subsequent degradation of this aromatic compound in the presence of glucose, even at concentrations far below the threshold needed for induction122. The second strategy involves minimizing maintenance requirements, although the mechanisms for achieving this are not yet fully understood14.

The concept of mixed-substrate utilization is particularly relevant in the context of emerging pollutants, which are often difficult to degrade directly due to their complex structures and low concentrations. Microorganisms capable of ‘co-metabolizing’ these pollutants in the presence of more readily degradable organic carbons represent an asset in modern wastewater treatment. Emerging pollutants are often difficult to degrade directly, due to their complex chemical structures, toxicity, and low concentrations (ng L−1 - μg L−1)123. However, many studies observed the remarkable ability of microorganisms to co-metabolize these emerging pollutants in the presence of easily biodegradable organic carbons. Co-metabolism is often observed when certain compounds exhibit structural similarity to others that microorganisms are capable of degrading124,125,126.

The presence of easily biodegradable substrates provides a vital substrate for microorganisms to initiate the biodegradation process and activate the necessary enzymatic pathways to efficiently degrade and transform emerging pollutants that might otherwise remain persistent in the environment127. For instance, AOB were able to co-metabolize sulfamethoxazole (SFX) (10–100 μg L–1) whilst oxidizing ammonia and using ammonia monooxygenase128, and enhanced sulfamethoxazole removal percentages reached up to 98%128. Sulfamethoxazole was mainly degraded into 4-Nitro-SFX, Desamino-SFX, and N4-Acetyl-SFX.

Equally, impaired degradation of normally-readily-degradable substances may result in less effective micropollutant removal. For example, when ammonia oxidation was hindered by octyne or allylthiourea, a mechanistic inhibitor of ammonia oxidation that covalently binds to ammonia monooxygenases, micropollutants removal was inhibited by approximately 69%129. Interestingly, the degradation pathways of different sulfonamide antibiotics seemed different129. The thioether functional group and the thioether-like structure in the thiazole group might be active sites of the sulfathiazole biotransformation. Therefore, in contrast to other sulfonamides, sulfathiazole was not degraded into the common metabolic product, N4-acetyl sulfonamides129. Low concentrations (μg L–1) of atrazine and amoxicillin were also reported to be co-metabolized in anaerobic bioreactors along with COD degradation or nitrogen removal130. These examples illustrate the versatility of bioreactors in handling not only typical pollutants but also complex pharmaceuticals and pesticides at trace levels. This capability to concurrently degrade both organic matter and specific contaminants highlights the potential for integrated wastewater treatment solutions. Such systems are particularly valuable in settings where environmental preservation and resource recovery are priorities.

Syntrophic metabolism

Microbes also cooperate with each other to survive in oligotrophic environments (Fig. 4b). Among the modes of microbial interaction, one of the most widespread phenomena involves metabolic division of labor (MDOL), whereby distinct populations perform different, but complementary, steps of the same metabolic pathway131,132. This phenomenon controls many ecologically and environmentally important biochemical processes, and is particularly relevant in the degradation of complex organic compounds133. Under such scenarios, microbial degradation of organic substrates comprises complex metabolic pathways with multiple intermediates. Multi-omics studies have revealed that such pathways are distributed among various members of natural, multi-species communities—in an MDOL manner133—such as cooperative lignocellulose breakdown in goat gut microbiomes134, plant polysaccharide digestion in honey bee gut microbiota135, and degradation of polycyclic aromatic hydrocarbons by marine microbial communities136.

Overcoming nutritional limitations is one of the benefits microbes can accrue from MDOL137. A compelling example supporting this is the mutual relationship observed among bacteria in a microbial consortium growing in a nutrient-poor medium138. Specifically, in this microbial consortium, Carbonactinospora thermoautotrophica StC demonstrated carboxydotrophy and the ability to store carbon dioxide, whilst C. thermoautotrophica StC, Chelatococcus spp., and Sphaerobacter thermophilus carried genes encoding CO dehydrogenase and formate oxidase138. Notably, pure cultures were not obtained under the original growth conditions, suggesting that a tightly regulated interactive metabolism was likely necessary for the survival and growth of the group in this extreme oligotrophic system138.

Consortia of different bacteria also engage in cross-feeding to complement each other’s nutritional capabilities (Fig. 4b). Cross-feeding interactions involve exchanging primary trace metabolites (ng L−1 to μg L−1 139), such as vitamins, amino acids, nucleotides, or growth factors140,141,142. From an evolutionary perspective, keeping genes that do not contribute to an organism’s fitness is costly, due to the burden on cellular processes and energetics143. The expression of unnecessary proteins also depletes resources for other cellular functions. Hence, microbes benefit greatly from exchanging metabolites with other members. In fact, some free-living bacteria living in nutrient-deficient, though stable, aquatic ecosystems, have reduced—sometimes ‘minimal’ – genomes144,145. This reductive genomic evolution is explained by the Black Queen Hypothesis, which posits that gene loss, particularly of dispensable functions, can provide a selective advantage by conserving limited resources146. This suggests organisms can become ‘beneficiaries’ of reduced genomic content, depending instead on leaky ‘helpers’ in their communities, and thus contributing to the stability and resilience of the ecosystem147.

From the perspective of electron exchange, direct interspecies electron transfer (DIET) seems to be an effective microbial strategy under oligotrophic conditions (Fig. 4b). DIET allows members of a microbial community to exchange electrons directly using nanotubes, conductive pili, or c-type cytochromes148,149,150, thereby enhancing overall (community) metabolic efficiency and enabling utilization of low-concentration substrates that may not be otherwise efficiently utilized via other mechanisms148,151,152. Geobacter species are well-studied, electroactive bacteria with demonstrated DIET capabilities153,154,155, most of which were originally isolated from oligotrophic environments, such as subsurface and freshwater sediments156. Sulfur-driven autotrophic denitrifiers, dominant in an oligotrophic, deep-subsurface community, were also found to engage in complex interactions involving the production of S0 as an intermediate and nanowires for DIET157.

The implications of syntrophic metabolism extend to biotechnological applications, particularly in the field of wastewater treatment and bioremediation158,159. By harnessing these cooperative metabolic strategies, it is possible to enhance the degradation of pollutants and the efficiency of nutrient and energy recycling in wastewater treatment facilities78,160. For example, using consortia that engage in cross-feeding can lead to more efficient removal of complex pollutants from wastewater161,162. Similarly, leveraging DIET in bio-electrochemical systems can enhance the breakdown of organic matter and recovery of resources, contributing to sustainable water management practices152.

Response to dynamic nutrient conditions

Microorganisms in some natural environments, such as estuaries and wetlands, are subjected to temporal and spatial nutrient variations, characterized by fluctuations rather than constant low- or high-concentration substrate availabilities. Under such variable conditions, microorganisms exhibit distinct physiological responses at different levels, including rapid transcriptional changes within seconds, biomass production within minutes, and cell division within an hour163. Consequently, microorganisms can adapt their metabolic pathways in accordance with shifting nutrient availabilities.

Under glucose-limited conditions, various yeast species, including Saccharomyces cerevisiae, demonstrate diverse metabolic responses to glucose pulses. Certain yeast strains initiate alcoholic fermentation when subjected to variations in glucose concentrations, whereas others impede ethanol production by augmenting acetaldehyde oxidation164. Yeasts that undergo pulsed glucose fermentation into ethanol typically maintain an unaltered growth rate, whereas yeasts that abstain from fermentation triggered by glucose pulses exhibit enhanced biomass generation upon the introduction of glucose164. Similar metabolic flux allocation-dependent growth rates have been proposed for E. coli, which uses glycogen as a carbon storage molecule to maintain higher growth rates under pulsing nutrient conditions165. Interestingly, studies have challenged the traditional view that in E. coli under low-glucose concentrations glucose is solely transported via the glucose phosphotransferase system166,167. Instead, it has been suggested that glucose may be primarily transported through the high-affinity galactose binding protein/maltose system, providing an alternative glucose-transporting mechanism166,167. This underscores the complexity of substrate utilization pathways and microbial versatility in adapting to low substrate concentrations.

Experimental observations indicate elevated specific substrate and oxygen consumption rates of E. coli during feast-famine regimes compared to steady-state (chemostat) conditions98. Despite increased growth rates, biomass yield is reduced, indicating a trade-off between resource utilization efficiency and growth. Although metabolite concentrations change rapidly, cellular energy charge remains unaffected, suggesting a well-controlled balance between ATP production and consumption reactions98. Adaptations in substrate uptake systems, storage potential, and energy-spilling processes are crucial factors influencing energy utilization and growth dynamics in low-substrate-concentration environments168.

These microbial responses to dynamic nutrient conditions are particularly relevant in the context of bioremediation and ecosystem management. Understanding and harnessing these adaptive strategies can lead to more efficient bioremediation processes and sustainable water management practices. For instance, leveraging the metabolic flexibility of polyphosphate-accumulating organisms (PAOs) in wastewater treatment plants can enhance phosphorus removal. For instance, in enhanced biological phosphorus removal processes, PAOs show a preference for storing organic carbon under anaerobic, high-organic-carbon-concentration conditions169,170. PAOs subsequently utilize the stored carbon under aerobic conditions and when substrate availability is low171. Such metabolic flexibility enables PAOs to efficiently manage nutrient availability whilst maximizing growth potential under dynamic environmental conditions. Similarly, the ability of microorganisms to adapt to feast-famine regimes can be utilized to optimize bioprocesses in treatment facilities that experience variable nutrient loads.

Population density-based mechanisms

Under starvation conditions, microbial growth is not only restricted by the availability of resources, but also influenced by population density172. Simulations have indicated that population density-dependent recycling could be an advantageous behavior during starvation, facilitating effective utilization of limited resources for long-term survival172. Therefore, maintaining a high cell density (e.g., by forming, or maintaining, biofilms) is important in optimizing capacity to survive starvation. In such cases, nutrients (e.g., amino acids) from dead cells would diffuse slowly to the surrounding biofilm environment, where most of the resources would remain and benefit neighboring microorganisms172,173.

Interestingly, both cell growth and decay are dependent on population density. For example, at a high cell density, starving E. coli cells followed exponential decay, while at a low density, starving cells persisted for longer before experiencing rapid, exponential death174. Density-dependent survival kinetics are controlled by the master regulator rpoS, which orchestrates a thrifty strategy in bacteria. When anticipating starvation, cells restrain nutrient consumption to save resources for delayed cell death, utilizing the remaining environmental nutrients174. Understanding these population density-based mechanisms is pivotal for advancing our knowledge of microbial survival strategies in nutrient-poor environments and has significant implications for environmental management and biotechnological applications. For instance, leveraging knowledge of density-dependent survival can enhance the efficacy of bioremediation processes where maintaining a high density of effective microbial degraders is crucial. Additionally, insights into how microbial communities manage resources at different densities can inform the development of more efficient bioremediation, particularly in the management of biofilms in these treatment systems. Moreover, these insights can contribute to the revision of population dynamics models, leading to better predictions and management strategies for microbial communities in various environmental contexts.

Future outlook

Addressing the challenge posed by emerging micropollutants, particularly at low concentrations water environments, remains a crucial area for future research. Current studies often focus on high concentrations, not reflecting real-world levels, potentially biasing our development of bioremediation strategies. Future research should focus on metabolic pathways and enzymatic systems that microorganisms use to access and utilize low-concentration recalcitrant substrates, essential for comprehensive oligotrophic carbon cycling and efficient pollutant removal.

The integration of multiple disciplines is required to address the challenges associated with microbial utilization of low-concentration resources. Collaboration among microbiologists, ecologists, biotechnologists, environmental scientists, and others can lead to innovative solutions for environmental management and biotechnological applications. Advanced techniques like metagenomics, metatranscriptomics, stable isotope probing, and molecular imaging can provide a holistic understanding of microbial processes in resource-limited environments.

In the broader context of sustainability, understanding the microbial breakdown of low-concentration pollutants is crucial for water ecosystem management, extending beyond individual ecosystems to encompass water quality, health, ecology, and the environment (Fig. 5). Recognizing the impact of microbial degradation of low-concentration pollutants is integral to the holistic management of water resources. As we continue to face mounting challenges in water resource management, integrating our knowledge of microbial pollutant degradation is a critical step. It empowers targeted bioremediation and preserves ecosystem health. Beyond that, it underscores sustainability in water resource management. The synergy between microbial pollutant degradation, ecosystem health, and sustainable water management forms the cornerstone of a future where clean water is not just a necessity but a promise of a thriving planet.

Fig. 5: The overall mechanisms and metabolic pathways of microbial enrichment and utilization of low-concentration substrates.
figure 5

Understanding how microbial utilising low-concentration substrates benefits the water cycle, human health, ecology, and overall environmental management. Their integration is the key to achieving sustainable development.

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