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Review

Ecosystem and Climate Change Impacts on the Nitrogen Cycle and Biodiversity

by
Rohini Mattoo
*,
Suman B. Mallikarjuna
and
Naveenachar Hemachar
Divecha Centre for Climate Change, Indian Institute of Science, Bangalore 560012, India
*
Author to whom correspondence should be addressed.
Nitrogen 2025, 6(3), 78; https://doi.org/10.3390/nitrogen6030078
Submission received: 30 July 2025 / Revised: 26 August 2025 / Accepted: 3 September 2025 / Published: 5 September 2025
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Abstract

Nitrogen in all of its forms sustains Earth. In every known terrestrial and aquatic habitat, nitrogen controls microbial activity, plant productivity, trophic dynamics, and animal and human growth. This review has tried to show how nitrogen cycling is influenced by both terrestrial and marine ecosystems in addition to by changes spurred on by the climate. The availability, transformation, and final fate of nitrogen throughout the various ecosystems are influenced by these interconnected biochemical and biophysical processes, which are fueled by microbial communities. Predicting and reducing human impacts on the changing ecosystem requires an understanding of these complex interconnections. Anthropogenic and climatic changes alter the structure and function of soil microbial communities, as well as the main metabolic processes of the nitrogen cycle, such as nitrification, denitrification, nitrogen fixation, and ammonification. The mechanisms by which anthropogenic stress alters nitrogen cycling processes, the effects on ecosystem function, and possible mitigation techniques for a balanced nitrogen cycle are all discussed in this review.

1. Introduction

Nitrogen (N), one of the most essential for biological systems, is necessary for all life to persist [1]. All metabolic processes that result in the synthesis of proteins and the development of organs in humans, animals, and plants depend on nitrogen. In 3 oxidation states, nitrogen generates N-N bonds including N2 in conjunction with N0, hydrazine with N−II, and nitrous oxide (N2O) bonded to NI [2]. However, nitrogenases present in microbes have a fundamental ability to cleave the strong N-N bond. A carbon or oxygen seed is necessary for the stellar nucleosynthesis in the CNO cycle to create nitrogen [3], and the amount of N and its abundance will be determined based on the presence of CNO during planetary synthesis. Since NH3 is the main base in the troposphere of the Earth’s atmosphere and reduces the acidic gases produced by the oxidation of SO2 and NOx, 78% of molecular nitrogen is found [4]. Aerosols’ size, chemical makeup, and degree of neutralization are all influenced by NH3. In order to quantify reactive nitrogen species and trace gas fluxes at different spatial scales, atmospheric nitrogen is measured using satellite-based observations, box modelling, and leaf-level flux measurements [5]. Remarkably, trace levels of nitrates were found in Martian regolith by the Curiosity rover [6]. Titan shares a nitrogen-dominated atmosphere with Venus, and its atmosphere is rich in nitrogen (N2) [7]. As ammonia (NH3), it is also commonly found in comets and the gas giant planets of the solar system. The principal sources of naturally produced N are biological nitrogen fixation [8], wildfires [9], and lightning [10]. It is interesting to note that nitrogen is present in our surroundings as the gas dinitrogen. There are many recent changes in the nitrogen cycle [11,12], alterations in microbial diversity have resulted due to excess nitrogen fertilizer use, but this also opens the door to the discovery of sustainable methods, practices [13,14] and bacterial genes involved in the nitrogen cycle [15]. A study found a strong negative correlation between atmospheric nitrogen deposition and plant α-diversity, with a drop of 0.367 species for every kilogram increase in long-term N deposition per hectare, annually. High levels of atmospheric nitrogen deposition have been linked to a decline in plant species diversity [16]. In terms of total continuous radiative forcing, nitrogen cycling affects atmospheric concentrations of nitrous oxide (N2O), carbon dioxide (CO2), and methane (CH4) [17]. Microorganisms that fix nitrogen transform atmospheric nitrogen (N2) into forms that can be deployed, including ammonia (NH3). Ammonium (NH4+), which is widespread in soils, is absorbed by plant roots [18]. In situ spectroscopic detection techniques, flow injection analysis, ion-sensitive electrodes, etc., are used to quantify soil nitrogen [19].
Easily interconvertible form of nitrogen is nitrate (NO3−) especially in agricultural fields and water bodies. Urea, amino acids, and other compounds are examples of dissolved organic nitrogen (DON) in aquatic and forest systems. Although the process of biological N2H4 production is perhaps the least understood, it has been lately discovered that this molecule is relevant to primary metabolism [20]. The nitrogen cycle includes trace gases produced during nitrification and denitrification, such as nitrous oxide (N2O) and nitric oxide (NO). This review examines, briefly, the growing knowledge of how climate and ecosystems control nitrogen and their brief consequences biodiversity.

2. Ecosystems and Their Impacts on Nitrogen Dynamics

2.1. Forest Ecosystems

Different plant communities have a significant impact on nitrogen cycling in undisturbed soil ecosystems through microbial associations, soil organic matter, litter quantity and quality, and nitrogen mineralization rates. The ecological effects of human pressures like excessive fertilizer use and industrial pollutants are highlighted in Figure 1, which shows how nitrogen dynamics vary across healthy and disturbed ecosystems [21]. For example, grasslands with high root biomass promote steady nitrogen retention [22], while woods with high C:N litter promote delayed mineralization [23]. Additionally, tree growth is regulated and enhanced by nitrogen uptake by plant roots [24]. The annual net nitrogen mineralization (NNM) under pine has been demonstrated to be lower than that under birch and spruce, at roughly 12 kg N ha−1 yr−1 [25].

2.2. Terrestrial Agroecosystems

Rhizosphere activity, especially microbial activity that maintains the nitrogen cycle’s equilibrium, is influenced by a variety of exudates that are discharged by plant roots [26]. Legumes and the group of diazotrophic bacteria known as rhizobia (such as Rhizobium, Bradyrhizobium, and Azorhizobium spp.) have an endosymbiotic relationship that is orchestrated by a signaling network involving root exudates. Exudates including flavonoids catalyze the rhizobial nod genes expression in rhizobia involved in the soil nitrogen cycle [27]. Because organic acid exudates improve nitrogen mineralization and carbohydrate-rich exudates stimulate microbial nitrogen fixation, plants can access higher amounts of inorganic nitrogen [28]. Under natural agricultural practices like plant rotation and intercropping, leguminous plants facilitate biological nitrogen fixation, reducing the need for excessive amounts of synthetic fertilizer [29]. Modified litter inputs and climate stress also affect microbial activity and richness [30].
Reduced below-ground biodiversity [31], decreased nitrogen fixation [32], altered nitrogen and nitrogenous compounds, increased nitrification, and NO3− leaching all represent the outcomes of land use disturbances like agricultural conversion, deforestation, and urbanization that alter soil structure, organic matter, and microbial assemblages in terrestrial ecosystems [33]. The molecular alterations in ecosystems and climate physics responses that modify nitrogen cycle mechanisms, which in turn influence broader biological diversity, are less well understood. The overuse of synthetic N fertilizers to boost agricultural output worldwide has altered biodiversity (Table 1). Fast-growing species are promoted by N enrichment in aboveground biodiversity, which leads rare or N-efficient plants to be competitively removed. Climate change-induced N shifts influence the makeup of microbial communities, often favoring nitrophilous species. Nitrogen deposition encouraged the establishment of both common native species and invasive species in monoculture settings [34]. When N dynamics are disturbed, it affects ecosystem services like pollination [35], pest control [36], and carbon storage [37]. Changes in plant N have an effect on populations of herbivores and decomposers [38].
Negative anthropogenic factors include monoculture in agriculture along with excess application of synthetic N chemicals, use of machinery made of harmful synthetic material, deforestation, non-natural farming, etc., which impact BNF [14]. Inorganic nitrogen reduces symbiotic nitrogen fixation by blocking NRAMP2-mediated iron transport within soybean nodules, which is essential for appropriate nodule activity [49]. By artificially inflating the NH4+ and NO3− pools, this alters the rates of nitrification and denitrification and increases N2O emissions.
Ammonification is impacted by disruptions to microbial habitat and substrate availability [50]. Low pH from acid rain or ammonium-containing fertilizers, particularly in nitrifiers, impairs microbial enzymatic activity [51]. Salinity stress can inhibit BNF and denitrification by altering the osmotic balance and community composition of soil microorganisms [52,53]. By disrupting microbial metabolism and diversity, toxic substances reduce all nitrogen processes, especially nitrification and fixation [54]. Overuse of sewage sludge can accelerate ammonification and alter nitrogen pathways in anaerobic pockets towards DNRA. Similarly, increase in carbon may alter the abundance of denitrifying and nitrifying microorganisms.

2.3. Marine and Ocean Ecosystems

The nitrogen cycle processes, which in turn influence primary output and carbon dioxide uptake, are greatly influenced by marine ecosystems, which also play a crucial role in regulating the global N cycle [55]. The sequestration and storage of massive amounts of fixed nitrogen in the form of dissolved organic nitrogen (DON), one of the planet’s greatest fixed nitrogen reserves with roughly 70 Pg, is one of the most significant roles of marine ecosystems [56]. Importantly, recent research indicates that refractory DON is dominated by 15N-depleted heterocyclic-N structures, as opposed to the previously recognized amide-dominated high molecular weight (HMW) material [57].
The continuous transformation of nitrogen between its various forms has been rendered possible by an array of microbiological processes in marine ecosystems, some of which are analogous to the nitrogen cycle on land. By transforming atmospheric N2 into accessible ammonia (NH3), diazotrophs, for instance, conduct biological nitrogen fixation (BNF) in oceans, which supplies an additional nitrogen to marine systems [58]. In addition to warm, oligotrophic surface waters, its range is far more extensive than previously thought, encompassing hypoxic basins, oxygen minimum zones (OMZs), the deep sea, estuaries, and coral reefs. Intricate nitrogen cycle interactions are coordinated by the diverse and metabolically adaptive microbial community in conjunction with the dominant physical and chemical ocean conditions. Although the exact roles of some of these elements are still unknown, factors including light, oxygen, phosphorus, temperature, and iron have a significant impact on BNF rates and the distribution of diazotrophs [59,60]. Ocean nitrification requires the right balance of ammonia-oxidizing bacteria and archaea to catalyze the transformation of NH3 to nitrite (NO2−), and subsequently nitrite-oxidizing bacteria to utilize NO2− to form nitrate (NO3−) [61]. Denitrifying bacteria, the ocean’s main sink for fixed nitrogen, transform NO3− back into N2. Their primary habitats are sub-oxic water columns, such as OMZs, and marine sediments which are dependent on organic matter [62]. Anaerobic ammonium oxidation (Anammox) transforms ammonium (NH4+) and NO2− to N2 in the absence of oxygen and is a N depreciating process, notably in OMZs and sediments [61]. Dissimilatory nitrate reduction to ammonia (DNRA) is an anaerobic process that primarily occurs in anoxic environments such as sediments and OMZs and converts NO3− to NH4+. Nitrate/nitrite-dependent anaerobic methane oxidation, or N-damo, has been discovered as a process of N-loss that links the carbon and nitrogen cycles, but currently less understood [63]. The amount, form, and fate of nitrogen in marine habitats is determined by interdependent processes that are powered by marine microbial communities. They significantly affect the overall health of marine ecosystems as well as the cycling of nutrients.
Anthropogenic activities significantly disturb the typical marine N cycle [64]. Fossil fuel burning, human sewage, and agricultural runoff all contribute to nutrient pollution, which causes toxic algal blooms and oxygen deprivation, ultimately contributing to the loss of biodiversity [65,66]. Climate change can accelerate ocean acidification, increase river runoff, deoxygenate the atmosphere, and influence nitrification, all of which can worsen these effects [62]. Nitrogen loss, particularly in low-oxygen regions such as the Bay of Bengal, the Gulf of Guinea, and the region near the Amazon River mouth, where more denitrification paradoxically lowers primary production when high N supply is used [62,67]. Spectrophotometry, colorimetry, fluorometry, and other techniques are used to measure nitrogen species in aquatic systems, including total dissolved nitrogen (TDN), NO3−, and NH3. High-resolution monitoring is increasingly being performed using emerging technologies as remote sensing and microfluidic sensors [68].
Understanding these intricate relationships is necessary to forecast and lessen human impacts on the changing ocean. The atmosphere and its aerosol composition play a significant role in the marine nitrogen cycle as a source of fixed nitrogen to the oceans and as a medium for complex changes that affect marine biogeochemistry, productivity, and climate.
Anthropogenic influences include activities notably traffic and industry emissions, agricultural practices including the use of nitrogen-rich fertilizers, human waste, and farm animal feces. Agriculture, if conducted unsustainably, emits 93% ammonia. Reactive nitrogen molecules are released into the atmosphere, where they undergo a variety of complex chemical and photochemical reactions before being reintroduced into ecosystems (either wet or dry) through nitrogen deposition [69,70]. Reactive nitrogen plays a major role in atmospheric aerosol formation [71]. Aerosol catalysis requires gaseous ammonia to be absorbed and neutralized with nitric or sulfuric acids. The atmospheric concentration of NOx, mostly from industry and traffic, has a substantial impact on the generation of nitric oxide, which is dependent on the presence of ozone (O3) and specific radicals. Furthermore, these radicals are essential for the oxidation of SO2 and NO2 as well as the synthesis of peroxyacetylnitrate (PAN), a secondary pollutant in photochemical smog. Nitrogen wet deposition, which can damage already vulnerable ecosystems, relies upon cloud interactions. Chemical processes occurring inside cloud droplets and generate nitrogen-containing inorganic (such as ammonium nitrate) and organic aerosol particles influence air quality. Furthermore, nitrogen pollution can alter the properties of clouds, perhaps producing more numerous, smaller, more reflecting droplets that might lower the climate. Atmospheric organic nitrogen warrants future investigations as this may harbor important roles in atmospheric N cycle. Nitrogen increase in ocean surface may slow down BNF rates according to some models [66]. This is because non-nitrogen-fixing phytoplankton may become more competitive when nitrogen is more abundant. For instance, temperature-driven glacier meltwater may provide iron and nutrients, creating a favorable habitat for diazotrophs and helping to fix nitrogen in Arctic coastal waters [72].

3. Climate Effects on Nitrogen Cycling

Climate factors such as temperature, precipitation, pH, and CO2 levels impact nitrogen transformation processes, which in turn impact the related enzymatic pathways and biochemical reactions (Table 2).

3.1. Increased Temperatures

Warmer temperatures can alter the amount of nitrogen available in soils and water bodies by accelerating microbial processes such as nitrification (converting ammonium to nitrate), denitrification (reducing nitrate to gases), and mineralization. Temperature variations can either promote or inhibit biological nitrogen fixing by particular bacteria and cyanobacteria, which in turn affects the conversion of atmospheric nitrogen (N2) to ammonium (NH4+). For instance, strains of Azospirillum brasilense may fix nitrogen at temperatures as high as 42 °C [84], but the marine diazotroph Trichodesmium exhibits optimal development and nitrogen fixation between 24 °C and 30 °C, with considerable inhibition occurring at temperatures over 34 °C [85]. As temperatures rise, the microbial breakdown of organic nitrogen into ammonium (more specifically, mineralization or ammonification) accelerates the rate at which nitrogen becomes available in the soil [86]. The aerobic oxidation of ammonium (NH4+) to nitrate (NO3−) often enhances nitrification rates up to an optimum temperature; after that, activity may decline. Ammonia-oxidizing archaea exhibit optimal activity and growth between 30 °C and 37 °C, whereas ammonia-oxidizing bacteria thrive in the narrower temperature range of 16 °C to 23 °C [87]. Higher temperatures have been demonstrated to enhance earthworm activity, which significantly affects the microorganisms that cycle nitrogen in the soil. This involves promoting nitrogen cycle processes such as mineralization, denitrification, and plant absorption and increasing the amount of the amoA gene associated with ammonia-oxidizing bacteria (AOB) [88]. Furthermore, heat exacerbates nitrogen losses in earthworm-inhabited arable soils, particularly in systems with significant organic inputs, by increasing the likelihood of nitrate leaching and nitrous oxide (N2O) emissions [89]. High temperatures may accelerate denitrification rates, which may contribute to higher emissions of nitrogen gases like nitrous oxide (N2O), a potent greenhouse gas, especially in wet or anaerobic soil conditions [90]. Nitrogen loss to the atmosphere can originate from increased ammonia (NH3) volatilization from soils brought on by warmer temperatures [91]. Cyanobacterial and phytoplankton blooms spurred by rising temperatures significantly alter nitrogen cycle and worsen eutrophication in aquatic ecosystems. In habitats where abundant phytoplankton exist may influence phosphorus which affects nitrogen fixation. However, systems dominated by slow-growing phytoplankton with high ratios of nitrogen to phosphate consumption worsen nitrogen deficits and promote nitrogen fixation [92]. Rising water temperatures and marine heatwaves have been shown to reduce the number of Rotifers, while increasing the number of larger omnivorous Copepods [93]. By altering nitrifier activity and suppressing nitrification processes, this alteration weakens top-down regulation, allowing unrestrained phytoplankton growth, and increasing biomass, it impacts nitrate dynamics in ecosystems [94]. The dynamics of nitrogen input in marine ecosystems are significantly altered by warmer temperatures, which raise the biomass levels of cyanobacterial species in the pelagic environment [95]. Anammox bacteria have been demonstrated to be inhibited by warming, which may cause increased nitrogen flow towards denitrification and the subsequent production of N2O [82]. In conclusion, because rising temperatures accelerate nitrogen cycle activities, alter nitrogen availability, and increase emissions of nitrogenous gases, they have an impact on ecosystem function and climate feedback globally. The changes in nitrogen cycling brought about by climate change and their ripple effects on ecosystems and human health are summarized in Figure 2 (see the health section).

3.2. Unpredictable Rainfall

Increased precipitation raises the complexity and connectedness of arbuscular mycorrhizal fungal (AMF) networks through modifications to soil pH, which increases their ability to nitrify and denitrify [96]. Warmer soil conditions caused by increased precipitation can enhance the releases of nitrogen gases, including nitrous oxide (N2O), and create anaerobic conditions that promote denitrification [97]. Changes in soil moisture have an effect on microbial activity as optimal moisture levels encourage nitrogen mineralization; nevertheless excessive or insufficient water may limit microbial activity and impact nitrogen availability [98]. Strong winds and heavy rains can erode topsoil, removing nitrogen-rich organic matter and reducing soil fertility. Between the 1990s and 2010, the overall soil fertility in Northeast China decreased by 4.5%, leading to a general decline in soil health, according to [99]. Reduced precipitation or drought, on the other hand, can slow the nitrogen cycle by decreasing microbial activity and plant nitrogen uptake, which leads to nitrogen accumulation in soils. This is evident in grasslands and shrublands, where nitrification and mineralization either decrease or stay constant during dry conditions [100]. By reducing nitrogen mineralization and the transformation of nitrogen into compounds that plants can utilize, climate conditions can significantly restrict plant development. By lowering nitrogen losses from leaching and denitrification, dry conditions can momentarily preserve nitrogen in the soil. However, when the moisture returns, the nitrogen cycle resumes. During a longer dry season caused by decreased precipitation, soil NO3− concentrations increased by 25–64%, and mineralization and nitrification rates increased by 25–40%. Nitrogen declines due to excessive NO3− leaching when prolonged precipitation occurs [101]. Water pollution and increased soil nitrogen loss could result from changes in rainfall patterns’ effects on runoff and nitrogen leaching. Increased rainfall intensity can expedite the leaching of nitrogen, especially nitrate, from soils into groundwater [102]. This results in eutrophication in aquatic settings and a reduction in the quantity of nitrogen available in the soil [103]. Erratic and unpredictable cause alterations in concentrations N during atmospheric deposition. Dust discharge can alter marine bacterial populations and enhance N2 fixation by supplying active bacteria to the ocean surface and fostering viable microorganisms such diazotrophs [104,105]. Sporulating microorganisms during aerial transport germinate quickly when deposited in water bodies with higher nutrient concentrations [106] and this may be of concern if the populations of pathogenic microorganisms are higher [107]. Furthermore, dust inputs encourage phytoplankton development [108], which indirectly increases nitrogen demand and accelerates the nitrogen cycle. Moreover, increased ammonium (NHx) and nitrate (NOᵧ) reduce methanotrophy (methane oxidation) and long-term atmospheric N deposition caused by human activities reduces biological nitrogen fixation (BNF) in peatlands [109]. Because methanotrophic bacteria help these systems provide nitrogen-fixing microorganisms, this has an impact on BNF [110].

3.3. Elevated CO2

Growing plants are often stimulated by elevated CO2, which can increase their intake and need for nitrogen [111]. This could lead to changes in the availability of nitrogen in the soil. Plants have a higher requirement of N when high CO2 ensue [112]. Increased CO2 can have an impact on soil microbial populations and related processes, such as nitrification and nitrogen mineralization, albeit the impacts can differ depending on the ecosystem and soil conditions. In other cases, the increased plant biomass caused by higher CO2 may be constrained by the availability of nitrogen [113]. Because increased CO2 suppresses the growth and activity of autotrophic bacteria and archaea involved in nitrification, inorganic nitrogen stores (NH4) in lowland soil systems have decreased [114]. An increase in CO2 supports certain plant development, but the dilution of tissue N concentration alters metabolic pathways [115]. as seen in a study where legume N content decreased to ~2 mg g−1 when CO2 (400 ppm initially) concentration rose to 1200 ppm [116]. Furthermore, by changing C:N inputs to the soil, an increase in CO2 indirectly alters microbial activity, which may reduce the availability of soil nitrate and change the structure of plant communities.
Because nitrogenase efficacy decreases at elevated pCO2 levels above 400 μatm, Trichodesmium erythraeum development and N2 fixation rates are reduced in aquatic conditions [117]. Elevated CO2 causes ocean acidification, which changes the grazing pattern of microzooplanktons, increasing the growth of phytoplankton species and influencing nitrogen fixation and N loss rates [118]. Ocean acidification additionally results in increased rates of denitrification and N2O emissions from eutrophic waters.

4. Nutrient Imbalances and Its Impact on Nitrogen Cycle

Nutrient surpluses, primarily from the improper use of synthetic fertilizers, have caused significant nitrogen losses in terrestrial systems (Figure 1). Overfertilization raises the availability of ammonium, which encourages nitrification and denitrification and results in large gaseous nitrogen losses as N2O and N2. A long-term examination from 1970 to 2020 found that up to 45% of surplus nitrogen is lost by volatilization, 50% through denitrification, and 46% through nitrate leaching [119]. Irrigation trials showed that nitrification was enhanced by irrigation with higher salt levels (8 g L−1), while it was reduced by irrigation with moderately saline water (4 g L−1) as opposed to irrigation with groundwater (1 g L−1). Additionally, as salinity levels increased, denitrification gene expression increased likewise, showing how salt-induced nutrient imbalances can alter the balance and efficiency of nitrogen cycling processes [120]. The nitrogen cycle routes in aquatic environments can be significantly altered by nutrient imbalance. The Mississippi River’s nutrient runoff produces hypoxic zones in the Gulf of Mexico, where nitrification-denitrification dominates nitrogen loss and anammox has a negligible impact [121]. Ref. [122] found that hypoxia altered the benthic nitrogen cycle by increasing DNRA recycling and reducing nitrogen loss through anammox and denitrification, which is different from trends observed in the Gulf of Mexico. Nutrient imbalances caused by eutrophication, especially fluctuating nitrate (NO3−) levels, have a major effect on nitrogen cycling in aquatic sediments. The presence of macroalgae significantly boosts the production of nitrous oxide (N2O), dissimilatory nitrate reduction to ammonium (DNRA), and nitrate-ammonifying bacteria including Shewanella and Arcobacter when nitrate levels are low [123]. However, at high nitrate concentrations, denitrification represents the main mechanism for removing nitrogen, and DNRA and N2O emissions sharply decrease.

4.1. Effect on Human Health

Overfertilization accelerates nitrification [124], leading to elevated NO3− levels in crops, particularly in green vegetables like spinach and chard [125]. These NO3− can transform into NO2− when consumed, which can subsequently produce NOCs, which are carcinogenic compounds linked to an increased risk to humans [126]. Literature on how soil health affects human health has been summarized [11,127]. Nitrogen oxides have been implicated in mortality from respiratory diseases, according to [128].

4.2. Effect on Plants and Soil Habitats

A study [129], states that high nitrogen levels, particularly those of ammonium, can result in osmotic stress, rice photosynthetic inhibition, and oxidative damage to plant tissues.
Furthermore, elevated nitrogen levels hinder the synthesis of secondary metabolites necessary for plant defense, making crops more vulnerable to pests and illnesses [130]. Acidification of the soil due to ammonia re-deposition could eventually affect crop yields [131]. Because soil acidification inhibits key nitrogen-cycling microorganisms including ammonia-oxidizing bacteria (AOB) and complete ammonia oxidizers (Comammox), there is a decrease in nitrification activity. Acidified soils not only lower emissions of nitrous oxide (N2O), but they also limit the amount of substrate available and suppress the expression of denitrification genes (nirS, nirK), which limits the natural denitrification pathway that is necessary for nitrogen removal [132]. Vegetation declines significantly reduced soil total nitrogen (TN), ammonium (NH4+-N), and microbiological nitrogen while increasing nitrate (NO3−-N) content. The soil becomes more aerobic as vegetation undergoes decomposition, which promotes nitrifying bacteria to convert more NH4+ to NO3− [133]. Naturally occurring diazotrophs [134] and soil degradation that reduces carbon availability limit BNF [135].
PVC microplastics significantly raised the soil’s NH4+-N content and decreased the NO3−-N content by up to 91% (reduced nitrification), causing the soil microbiota to change into a microbial system with more nitrogen-fixing microorganisms which was estimated through gene abundance data [136].
The negative correlations between NO3−-N concentration and nitrification activity, in addition to the decrease in the archael taxon (Candidatus Nitrosocosmicus) and the rise in bacterial populations (e.g., Amycolatopsis, Sinomonas, Nocardia, Bradyrhizobium, and Burkholderia), provided evidence for the microbial shift away from nitrification pathways. Increases in fungi like Exophiala and Cladophialophora may be dangerous to both humans and vertebrates.
In a microcosm experiment using salt marsh sediment treated with microplastics consisting of polyethylene (PE), polyvinyl chloride (PVC), polyurethane foam (PUF), or polylactic acid (PLA), it was discovered that the makeup of the soil microbial population and nitrogen cycling mechanisms had changed [137]. In contrast to the control sediments free of microplastic, PUF and PLA-amended sediments promote nitrification and denitrification, whereas PVC amendment inhibits both processes. According to these results, different types of microplastics may significantly affect the nitrogen cycle processes in sediments by serving as organic carbon substrates for microbial populations NO2– and NO3– were highest in the 16-day PUF and PLA treatments, whereas NH4+ was lowest (high bacterial amoA gene and nirS implying high rates of nitrification and denitrification). High NH4+ was the outcome of PVC treatment; decreased denitrification activity and nitrification inhibition were indicated by the lowest abundance of the amoA and nirS genes.

5. Conclusions

The nitrogen cycle may be impacted by biodiversity, which is impacted by climate change and other human-caused changes to ecosystems. In ecosystems, particularly in agricultural and natural biological systems, nitrogen cycling is a complicated but essential process. Between soil, plants, microbes, and the atmosphere, nitrogen is absorbed, changed, and moved. As was previously mentioned, several nitrogen cycle reactions, including accumulation in some habitats and depletion in others, may be influenced by human activities and climate change triggers. The transport and balance of nitrogen in ecosystems are generally altered by climate change, which has an impact on water quality, plant development, and soil fertility. Future research must fill in the knowledge inadequacies in our existing understanding of nitrogen and its different forms.

5.1. Policy and Mitigation

Since increasing nitrogen pollution could have detrimental effects on biodiversity and climate change, policy and scientific management solutions are being pursued. Numerous principles, implementation frameworks, and concrete objectives for sustainable development and nitrogen have been compiled and published [138]. Reducing soil air and water contaminants that contribute to the disturbance of nitrogen compounds and cycles may be the goal of national and international initiatives. The nitrogen cycle is directly impacted by the growing integration of nutrient recovery and circular economy concepts into India’s waste management framework. Anaerobic digestion of organic residues and livestock waste is encouraged by the Swachh Bharat Mission (Urban and Gramin) and the Solid Waste Management Rules (2016). Complementary programs like GOBARdhan and the Waste-to-Energy/National Bioenergy Programme produce nitrogen-rich digestate and slurry that replace synthetic fertilizers and generate renewable energy. Additionally, by decreasing the waste of organic matter and excessive usage of fertilizer, NITI Aayog directly addresses nitrogen inefficiencies by promoting the closure of nutrient loops and the valorization of agricultural and urban leftovers. The UN Sustainable Development Goals, which focus on reducing nutrient pollution, creating sustainable urban systems, and reducing greenhouse gas emissions linked to nitrogen, are closely aligned with these actions. By promoting compost, green manures, and biofertilizers that substitute biologically fixed and recycled organic sources for mineral nitrogen, India’s Paramparagat Krishi Vikas Yojana (PKVY) encourages cluster-based organic farming. Similarly to this, Zero-Budget Natural Farming (ZBNF) encourages the use of microbial formulations and soil-restorative techniques like mulching and intercropping, which improve soil microbial activity, increase nitrogen fixation, and reduce runoff and volatilization. Although yield results differ by crop and location, there is evidence that these systems can significantly lower the costs of nitrogen inputs and environmental leakage. When taken as a whole, these programs represent a shift from a linear nitrogen-use model, which is characterized by significant losses and reliance on fertilizers, to a circular model, which values waste, conserves nitrogen, and lessens environmental effects.
Policy initiatives across many countries are being carried out and await positive outcomes. There is a special aim of the UN to reduce nitrogen waste by 2030 awaiting its outcome. Sewage regulation, the employing of agricultural fertilizers, wastewater management, agroforestry, conserving water bodies free of algae blooms, and the adoption of natural farming for healthy soil management are some of the measures depicted in Figure 3.

5.2. Future Directions

Further scientific investigation of the biochemistry of the nitrogen cycle in relation to natural ecosystems is necessary. Measurements of different forms of nitrogen are not available spatially and temporally across continents and these may be monitored in future. To minimize the trade-offs between carbon dioxide, methane, and nitrous oxide, a deeper comprehension of the effects of various decarbonization policies and measures, such as the use of alternate fuel for marine shipping, incentives to produce bioenergy, and soil carbon sequestration initiatives is required. It is essential to control the nitrogen and carbon cycles in concert. Encourage nature-based farming solutions, clean water, and efficient bioremediation of natural water bodies. Support international targets, such as the UN’s “halve nitrogen waste” to generate benefits for the entire world. The relationship between the marine DON, its components, and cycling is unclear, and it is unclear how microbial roles may contribute to its cycling. The effects of climate change on specific nitrogen cycle responses are still poorly known and must be considered considering biodiversity impacts. Despite the complexity of the nitrogen cycle, scientists and policymakers may collaborate to create more efficient methods for regulating nitrogen levels to support sustainability and environmental health by filling in these knowledge gaps and investigating potential avenues for future research.

Author Contributions

Conceptualization, R.M.; methodology, R.M.; software, R.M. and S.B.M.; validation, R.M. and S.B.M.; formal analysis, R.M.; investigation, R.M.; resources, R.M.; data curation, R.M., S.B.M. and N.H.; writing—original draft preparation, R.M. and S.B.M.; writing—review and editing, R.M., S.B.M. and N.H.; visualization, R.M. All authors have read and agreed to the published version of the manuscript.

Funding

This research received no external funding.

Acknowledgments

We thank our team members for useful discussions and inputs.

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. Impact of ecosystems on nitrogen. This figure illustrates a comparative overview of a healthy versus a disrupted ecosystem, highlighting key environmental processes, anthropogenic activities, and their impacts on nitrogen. The left side represents a healthy ecosystem where sustainable agricultural practices and low industrial emissions maintain balanced nitrogen inputs, resulting in low greenhouse gases (GHG) levels such as nitrous oxide (N2O). These conditions promote dynamic atmosphere-ocean interactions, biodiversity conservation, and favorable conditions that symbiotic nitrogen fixation, efficient nitrification and denitrification processes, and overall ecological balance, underpinning ecological stability and human well-being. In contrast, the right side depicts a disrupted ecosystem, where excessive fertilizer application, land use changes, and industrial pollution elevate nitrogen inputs. This leads to nutrient leaching, eutrophication, hypoxia in aquatic systems, and increased emissions of reactive nitrogen species (e.g., N2O, NH3), contributing to smog and elevated greenhouse gases. These disturbances suppress atmosphere-ocean interactions, reduce microbial diversity, including nitrogen-transforming microbes and contribute to biodiversity loss and negative health outcomes in humans.
Figure 1. Impact of ecosystems on nitrogen. This figure illustrates a comparative overview of a healthy versus a disrupted ecosystem, highlighting key environmental processes, anthropogenic activities, and their impacts on nitrogen. The left side represents a healthy ecosystem where sustainable agricultural practices and low industrial emissions maintain balanced nitrogen inputs, resulting in low greenhouse gases (GHG) levels such as nitrous oxide (N2O). These conditions promote dynamic atmosphere-ocean interactions, biodiversity conservation, and favorable conditions that symbiotic nitrogen fixation, efficient nitrification and denitrification processes, and overall ecological balance, underpinning ecological stability and human well-being. In contrast, the right side depicts a disrupted ecosystem, where excessive fertilizer application, land use changes, and industrial pollution elevate nitrogen inputs. This leads to nutrient leaching, eutrophication, hypoxia in aquatic systems, and increased emissions of reactive nitrogen species (e.g., N2O, NH3), contributing to smog and elevated greenhouse gases. These disturbances suppress atmosphere-ocean interactions, reduce microbial diversity, including nitrogen-transforming microbes and contribute to biodiversity loss and negative health outcomes in humans.
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Figure 2. Impact of climate change on nitrogen and its consequences on biological systems. Climate change may negatively hamper nitrogen cycling leading to environmental concerns and sustainable planetary development. Rising temperatures accelerate nitrogen transformations, resulting in increased emissions of nitrous oxide (N2O), a potent greenhouse gas that contributes to smog and air pollution, exacerbating respiratory health issues, ozone reduction in stratosphere, and human skin problem. Prolonged rainfall causes nitrate to leak into water bodies from excess synthetic N during farming leading to poor health. Drought conditions hinder biological nitrogen fixation (BNF), reducing plant growth and resulting in lower crop yields. Elevated CO2 levels contribute to soil acidification, enhancing nitrification and leading to an excess of nitrates in the soil. This negatively affects plant health by impairing root development and causing variability in crop yields. Nutrient leaching into water bodies triggers eutrophication and promotes the excessive growth of phytoplankton and cyanobacteria. When coupled with ocean acidification caused by elevated CO2 levels, these processes drive hypoxia and the loss of aquatic biodiversity. Several critical uncertainties and knowledge gaps continue to limit our understanding of nitrogen dynamics under changing climatic conditions (as highlighted in red, italics).
Figure 2. Impact of climate change on nitrogen and its consequences on biological systems. Climate change may negatively hamper nitrogen cycling leading to environmental concerns and sustainable planetary development. Rising temperatures accelerate nitrogen transformations, resulting in increased emissions of nitrous oxide (N2O), a potent greenhouse gas that contributes to smog and air pollution, exacerbating respiratory health issues, ozone reduction in stratosphere, and human skin problem. Prolonged rainfall causes nitrate to leak into water bodies from excess synthetic N during farming leading to poor health. Drought conditions hinder biological nitrogen fixation (BNF), reducing plant growth and resulting in lower crop yields. Elevated CO2 levels contribute to soil acidification, enhancing nitrification and leading to an excess of nitrates in the soil. This negatively affects plant health by impairing root development and causing variability in crop yields. Nutrient leaching into water bodies triggers eutrophication and promotes the excessive growth of phytoplankton and cyanobacteria. When coupled with ocean acidification caused by elevated CO2 levels, these processes drive hypoxia and the loss of aquatic biodiversity. Several critical uncertainties and knowledge gaps continue to limit our understanding of nitrogen dynamics under changing climatic conditions (as highlighted in red, italics).
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Figure 3. Strategies for terrestrial and aquatic nitrogen management. This diagram outlines holistic strategies for nitrogen management across terrestrial and aquatic ecosystems.
Figure 3. Strategies for terrestrial and aquatic nitrogen management. This diagram outlines holistic strategies for nitrogen management across terrestrial and aquatic ecosystems.
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Table 1. Effects of enhanced nitrogen on biodiversity (Based on studies from 1873 to 2022).
Table 1. Effects of enhanced nitrogen on biodiversity (Based on studies from 1873 to 2022).
Soil BiodiversityTemporal Scale of Experiments
GroupResponse to Nitrogen EnrichmentReference
DiazotrophsWhile some populations manage to sustain activity despite high N deposition, others decline.[39]The experiments were carried out with low N treatment: 3 years (2013–2016) and high N: 9 years (2007–2016).
In forest soils, diazotrophs maintain N fixation under heavy N deposition by modifying the composition of their communities.
Ammonia oxidizing bacteriaWhen N application is high, abundance rises.[40]Experiments from May 2011 to August 2011.
In particular, AOB populations rose under high N soil environment.
Ammonia oxidizing archaeaUnder high N, abundance and activity rise.[41]Experiments in 2015 and 2016.
DenitrifiersUnder high N deposition, abundance and activity rise.[42]In this long-term (12 years)
most genera got enriched with increasing N rates, except for Sphingobium and few others that reduced in numbers.
EarthwormsSome thrive with organic matter, others decline in acidified N-rich soils[43]Park Grass pasture studies (started in 1843) which demonstrated that earthworms decline during nitrogen addition versus organic farming
NematodesN addition decreases abundance of fungivores, plant-parasites, and omnivores + predators. No significant effect on except for bacterivores[44]Experiments during 1970–2021 demonstrated deleterious effect on soil fauna
Aquatic biodiversity
Cyanobacteria/
Phytoplanktons		Increase significantly under high N availability (blooms)[45,46]Experiments carried out from 2012 to 2022 and in 2020
Nitrifiers and denitrifiers in sedimentsActive in nutrient-rich, hypoxic zones[47]Integrated Ocean Drilling Program (IODP) Expedition 336 demonstrated quantitative information on ocean nitrogen cycle.
FishLoss of species due to N enrichment (hypoxia)[48]Estimates from 1970 to 2010
Table 2. Impact of climate on major nitrogen reactions.
Table 2. Impact of climate on major nitrogen reactions.
Nitrogen Transformation ProcessChemical Reaction with Enzymes InvolvedClimate ImpactsReference
Nitrogen fixationN2 → NH3
Nitrogenase
  • Increasing precipitation enhances nitrogen fixation
  • Elevated CO2 tends to increase nitrogen fixation
[73,74]
AmmonificationOrganic N → NH3
Urease and protease
  • Warmer temperatures and low pH increase ammonification rates
  • Reduced rainfall decreases rates
[75,76]
NitrificationNH3 → NH2OH
Ammonia monooxygenase (AMO)
NH2OH →NO → NO2−
Hydroxylamine oxidoreductase (HOR)
NO2− → NO3−
Nitrite oxidoreductase (NXR)
  • Increased temperature and precipitation enhance nitrification rates
  • Acidic conditions inhibit ammonia oxidation
  • Alkaline conditions inhibit nitrite oxidation
[77,78]
DenitrificationNO3− → NO2−
Nitrate reductase (NAR/NAP)
NO2− → NO (g)
Nitrite reductase (NIR)
NO → N2O
Nitric oxide reductase (NOR)
N2O → N2
Nitrous oxide reductase (NOS)
  • Higher temperature activates denitrification genes, low pH inhibits denitrification
  • Elevated CO2 inhibits denitrification enzymes
  • Soil acidification disrupts NosZ, inhibiting denitrification
[79,80,81]
AnammoxNH4+ + NO2− → N2H4 + H2O
Hydrazine synthase (HZS)
N2H4 → N2 + 4H+ + 4e−
Hydrazine dehydrogenase (HDH)
  • High temperatures suppress anammox activity
  • High salinity inhibits anammox
[82,83]
Table explanatory Note-High temperatures impede certain microbial processes, like anammox, while accelerating others, including ammonification, nitrification, and denitrification. Although it can inhibit denitrification activity, elevated CO2 frequently encourages nitrogen fixation. While less rainfall can restrict ammonification, more precipitation tends to encourage nitrogen fixation and nitrification. The pH of the soil is also important; alkaline circumstances can obstruct nitrite oxidation, while acidic conditions limit the enzymes involved in nitrification and denitrification. The anammox process is likewise suppressed by high salinity.
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Mattoo, R.; Mallikarjuna, S.B.; Hemachar, N. Ecosystem and Climate Change Impacts on the Nitrogen Cycle and Biodiversity. Nitrogen 2025, 6, 78. https://doi.org/10.3390/nitrogen6030078

AMA Style

Mattoo R, Mallikarjuna SB, Hemachar N. Ecosystem and Climate Change Impacts on the Nitrogen Cycle and Biodiversity. Nitrogen. 2025; 6(3):78. https://doi.org/10.3390/nitrogen6030078

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Mattoo, Rohini, Suman B. Mallikarjuna, and Naveenachar Hemachar. 2025. "Ecosystem and Climate Change Impacts on the Nitrogen Cycle and Biodiversity" Nitrogen 6, no. 3: 78. https://doi.org/10.3390/nitrogen6030078

APA Style

Mattoo, R., Mallikarjuna, S. B., & Hemachar, N. (2025). Ecosystem and Climate Change Impacts on the Nitrogen Cycle and Biodiversity. Nitrogen, 6(3), 78. https://doi.org/10.3390/nitrogen6030078

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