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PubMed2026

Mikania micrantha invasion restructures rhizosphere nitrogen cycling through enzyme activation, microbial recruitment, and allelopathic regulation.

BACKGROUND: Plant invasions profoundly influence terrestrial ecosystems by reshaping nutrient cycling processes. However, the mechanisms through which invasive plants such as Mikania micrantha modulate soil nitrogen (N) cycling and microbial communities remain insufficiently explored. Moreover, comparative studies with indigenous congener are scarce, limiting insights into whether such effects reflect species-specific strategies or genus-wide traits. This study investigates how M. micrantha modulates nitrogen metabolic pathways and rhizosphere microecology using combined metagenomic and metabolomic analyses. RESULTS: Integrated analyses revealed that M. micrantha established a distinctive "high total nitrogen-low mineral nitrogen" profile in the rhizosphere soil. Metagenomic profiling showed consistent enrichment of key ammonium assimilation enzymes, including glutamine synthetase and glutamate dehydrogenase, promoting enhanced incorporation of NH₄⁺ into organic nitrogen pools. In contrast, genes encoding nitrate reductase and nitrate transporters were significantly lower in relative abundance, limiting nitrate assimilation. Mikania micrantha also selectively enriched nitrogen-fixing microbes (notably rhizobia genera) and plant growth-promoting rhizobacteria (PGPR), thereby enhancing biological nitrogen fixation capacity. Metabolomic analysis further identified several allelopathic compounds in invaded soils at higher relative abundance, particularly epicatechin, which exhibited inhibitory effects on nitrifying bacteria. Compared with the congener Mikania cordata, which exerted weaker impacts on soil nitrogen cycling and microbial assembly, M. micrantha deployed a more comprehensive strategy integrating biochemical, microbial, and metabolic regulation. CONCLUSIONS: These findings demonstrate that under greenhouse-controlled conditions, M. micrantha reconfigures rhizosphere nitrogen cycling through a multi-dimensional strategy that couples biochemical regulation, microbial recruitment, and metabolite-mediated interference, thereby suggesting a potential mechanism that may contribute to its ecological advantage in natural settings. Video Abstract.

Rhizosphere↗
PubMed2004

[Nitrogen cycling and its dynamic feature in fine roots of poplar trees and herbs].

The nitrogen cycling and its dynamic feature in fine roots of poplar trees and herbs were studied in Shenyang of Liaoning Province. The results showed that the nitrogen content in the standing biomass of fine roots of poplar trees and herbs was 20.3 kg.hm-2, and its net accumulation was 10.0 kg.hm-2. With regard to the biological cycling of nitrogen, the annual uptake was 14.6 kg.hm-2 of which, the retention and the return was 9.6 and 5.1 kg.hm-2.yr-1 respectively, and the turnover period was 4 year. The relationship between total nitrogen in roots of poplar trees, and herbs and the available nitrogen in soil was also studied, which indicated that there were similar dynamic trends between total nitrogen in herb roots and the NH3-N in soil in growth season. The total nitrogen in fine roots of poplar trees was positively related to the biomass.

Ammonia↗
PubMed1999

Nitrogen cycling in coastal marine ecosystems.

It is generally considered that nitrogen availability is one of the major factors regulating primary production in temperate coastal marine environments. Coastal regions often receive large anthropogenic inputs of nitrogen that cause eutrophication. The impact of these nitrogen additions has a profound effect in estuaries and coastal lagoons where water exchange is limited. Such increased nutrient loading promotes the growth of phytoplankton and fast growing pelagic macroalgae while rooted plants (sea-grasses) and benthic are suppressed due to reduced light availability. This shift from benthic to pelagic primary production introduces large diurnal variations in oxygen concentrations in the water column. In addition oxygen consumption in the surface sediments increases due to the deposition of readily degradable biomass. In this review the physico-chemical and biological factors regulating nitrogen cycling in coastal marine ecosystems are considered in relation to developing effective management programmes to rehabilitate seagrass communities in lagoons currently dominated by pelagic macroalgae and/or cyanobacteria.

Bacteria↗
PubMed2001

Microbial nitrogen cycles: physiology, genomics and applications.

Genes and pathways involved in inorganic nitrogen cycles have been found in traditional as well as unusual microorganisms. These pathways or enzymes play a very important role in the adaptation or survival of these microorganisms under a variety of environmental conditions. Microbial nitrogen metabolism has industrial applications ranging from wastewater treatment to bioremediation and potential future use in biocatalysis for chemical production.

Ammonia↗
PubMed1988

The evolution of nitrogen cycling.

Based upon arguments concerning properties of the environment and the energetics of nitrogen transformation reactions, new hypotheses regarding their evolution are presented. These hypotheses are supported by new calculations and observations germane to understanding the evolution of the nitrogen cycle. From calculations of shock production by meteor impact, we suggest that impact produced fixed nitrogen could have resulted in the entire reservoir of Earth's N2 being converted into fixed nitrogen at the end of accretion. We have significantly improved upon previous calculations of the abiotic fixation rate on the early earth and find a rate of fixation by lightning of approximately 1-3 x 10(16) molecules NO/J, which is 2 to 3 times greater than previous estimates. This strengthens the suggestion, corroborated by the predominance of a single nitrogenase enzyme, that biological nitrogen fixation may have been a late evolutionary development, after the development of an aerobic atmosphere. In addition, we show for the first time that HNO, predicted to be the main product of atmospheric photochemical reactions involving NO on the primitive Earth by photochemical models, would eventually become NO2- and NO3- after reaching the Earth's surface. Based upon microbe-environment interactions on an ecological as well as a biochemical scale we suggest that denitrification arose prior to aerobic respiration and that nitrification arose after the advent of an aerobic atmosphere. We hypothesize the following evolutionary sequence for the biological transformation of nitrogen compounds: Ammonification --> Denitrification --> Nitrification --> Nitrogen fixation.

Ammonia↗
PubMed2004

Human acceleration of the nitrogen cycle: drivers, consequences, and steps toward solutions.

Human activity has greatly altered the nitrogen cycle on Earth over the past few decades, with major effects on both human health and the ecological functioning of natural ecosystems, particularly coastal marine systems where nitrogen is now the largest pollution problem. Agriculture is the largest driver of this change, with pollution from fossil-fuel combustion being a smaller but still significant driver globally. Much of the nitrogen pollution from agriculture derives from animal-production systems, both as a direct result of nitrogen leakage to the atmosphere and waters from these systems, and from the demand for increased crop production that these animal-production systems demand. Wastewater from urban centers is also a significant component of the nitrogen problem, contributing 12% of the nitrogen pollution in rivers in the US, 25% in Europe, and 33% in China. Wastewater sources dominate the inputs of nitrogen to some coastal ecosystems, but globally and in most regions the non-point sources are larger. Many technical solutions to reducing nitrogen pollution exist, so to some extent the current problem reflects policy and political failures. Nonetheless, further technical solutions can and should be developed. These should recognize the significantly greater mobility of nitrogen than phosphorus in the environment.

Agriculture↗
PubMed2005

The nitrogen cycle, scientific uncertainty and policy relevant science.

Much of the research on the nitrogen cycle aims to improving scientific understanding but is not focused specifically on removing or reducing the scientific uncertainties that constrain policy makers in the formulation of appropriate responses to old or emerging environmental problems. Policy makers, for example, commonly find it difficult to assess the spatial or temporal importance of the various risks to human and ecosystem health that stem from man's interference with the natural N cycle. This paper will justify this conclusion by reference to the findings of a recent study on non-point pollution from crop production in China. The findings concern the perceived risks of groundwater nitrate to human health; uncertainties about critical NOx levels and their interactions with other pollutants; various other dimensions of man's impact on the N cycle. The paper will go on to suggest a more systematic process or pathway by which scientists can select and design their research in a manner that could give more effective support to policy makers.

China↗
PubMed1983

Initial effects of the mount st. Helens eruption on nitrogen cycle and related chemical processes in ryan lake.

Ryan Lake, a 1.6-hectare basin lake near the periphery of the tree blowdown area in the blast zone 19 km north of Mount St. Helens, was studied from August to October 1980 to determine the microbial and chemical response of the lake to the eruption. Nutrient enrichment through the addition of fresh volcanic material and the organic debris from the surrounding conifer forest stimulated intense microbial activity. Concentrations of such nutrients as phosphorus, sulfur, manganese, iron, and dissolved organic carbon were markedly elevated. Nitrogen cycle activity was especially important to the lake ecosystem in regulating biogeochemical cycling owing to the limiting abundance of nitrogen compounds. Nitrogen fixation, both aerobic and anaerobic, was active from aerobic benthic and planktonic cyanobacteria with rates up to 210 nmol of N(2) cm h and 667 nmol of N(2) liter h, respectively, and from anaerobic bacteria with rates reaching 220 nmol of N(2) liter h. Nitrification was limited to the aerobic epilimnion and littoral zones where rates were 43 and 261 nmol of NO(2) liter day, respectively. Potential denitrification rates were as high as 30 mumol of N(2)O liter day in the anaerobic hypolimnion. Total bacterial numbers ranged from 1 x 10 to 3 x 10 ml with the number of viable sulfur-metal-oxidizing bacteria reaching 2 x 10 ml in the hypolimnion. A general scenario for the microbial cycling of nitrogen, carbon, sulfur, and metals is presented for volcanically impacted lakes. The important role of nitrogen as these lakes recover from the cataclysmic eruption and proceed back towards their prior status as oligotrophic alpine lakes is emphasized.

Journal Article↗
PubMed1996

Nitrification and Denitrification: Probing the Nitrogen Cycle in Aquatic Environments

Methods designed to detect microorganisms involved in the biogeochemistry of nitrogen in the marine environment are rapidly being developed and deployed in ecological investigations. Probes based on phylogenetic sequences (usually rRNA) and those based on the sequences of functional genes or proteins have both been demonstrated in the nitrogen cycle. The most progress has been made for ammonia oxidizers; several sets of PCR primers have been described and their specificity may be optimized to allow detection of genetically and ecologically meaningful groups. For denitrifying bacteria, functional probes based on nitrite reductase show most promise. These approaches should complement the more familiar, but no less sophisticated, methods that focus on quantification of in situ transformation rates. Both approaches in combination will be useful in understanding regulation and environmental control of biogeochemical processes.

Journal Article↗
PubMed2005

[Relationships between net primary production and nitrogen cycling in Chinese forest ecosystems].

In order to better understand the relationships between net primary production (NPP) of forest ecosystem and nitrogen cycling, we studied and analyzed the relationships between NPP, litter nitrogen, plant nitrogen retention, and soil net nitrogen mineralization rate in Chinese forest ecosystems. The results indicated that NPP was linearly and positively related to litter nitrogen, plant nitrogen retention and soil net nitrogen mineralization rate, with the most correlation with soil net nitrogen mineralization rate (R2 = 0.74, n = 37), and the next with plant nitrogen retention (R2 = 0.60, n = 37).

Biomass↗
PubMed1997

Haem-ligand switching during catalysis in crystals of a nitrogen-cycle enzyme.

Cytochrome cd1 nitrite reductase catalyses the conversion of nitrite to nitric oxide in the nitrogen cycle. The crystal structure of the oxidized enzyme shows that the d1 haem iron of the active site is ligated by His/Tyr side chains, and the c haem iron is ligated by a His/His ligand pair. Here we show that both haems undergo re-ligation during catalysis. Upon reduction, the tyrosine ligand of the d1 haem is released to allow substrate binding. Concomitantly, a refolding of the cytochrome c domain takes place, resulting in an unexpected change of the c haem iron coordination from His 17/His 69 to Met106/His69. This step is similar to the last steps in the folding of cytochrome c. The changes must affect the redox potential of the haems, and suggest a mechanism by which internal electron transfer is regulated. Structures of reaction intermediates show how nitric oxide is formed and expelled from the active-site iron, as well as how both haems return to their starting coordination. These results show how redox energy can be switched into conformational energy within a haem protein.

Catalysis↗
PubMed2005

Comparison of marine copepod outfluxes: nature, rate, fate and role in the carbon and nitrogen cycles.

We compare the nature of copepod outfluxes of nonliving matter, the factors controlling their rate and their fate, and finally their role, particularly their relative importance in the carbon and nitrogen cycle. Copepods release dissolved matter through excretion and respiration and particulate matter through production of faecal pellets, carcasses, moults, and dead eggs. Excretion liberates several organic C, N, and P compounds and inorganic N and P compounds, with inorganic compounds constituting the larger part. The faecal pellets of copepods are covered by a peritrophic membrane and have a highly variable size and content. There is less information on the nature of other copepod particulate products. The weight-specific rates of posthatch mortality, respiration, excretion, and faecal pellet production have similar C or N levels and are higher than those of moulting and egg mortality. In general, most important factors controlling these rates are temperature, body mass, food concentration, food quality, and faunistic composition. Physical and biological factors govern the vertical fate of copepod products by affecting their sedimentation speed and concentration gradient. The physical factors are sinking speed, advection, stratification, turbulent diffusion, and molecular diffusion. They influence the sedimentation speed and degradation of the copepod products. The biological factors are production, biodegradation (by zooplankton, nekton, and microorganisms) and vertical migration of copepods (diel or seasonal). Physical degradation and biodegradation by zooplankton and nekton are faster than biodegradation by microorganisms. The most important copepod outfluxes are excretion and faecal pellet production. Excretion offers inorganic nutrients that can be directly used by primary producers. Faecal pellets have a more important role in the vertical transport of elements than the other particulate products. Most investigation has focused on carbon burial in the form of copepod faecal pellets, measured by sediment traps, and on the role of ammonia excretion in nutrient recycling. Full evaluation of the role of copepod products in the transport and recycling of elements and compounds requires a quantification of all copepod products and their different fates, particularly detritiphagy, remineralization, and integration as marine snow.

Animals↗
PubMed2002

The Asian nitrogen cycle case study.

We analyzed nitrogen budgets at national and regional levels on a timeline from 1961-2030 using a model, IAP-N 1.0. The model was designed based upon the Inter-governmental Panel on Climate Change (IPCC) methods using Asia-specific parameters and a Food and Agriculture Organization of the United Nations (FAO) database. In this paper we discuss new reactive-nitrogen and its various fates, and environmental nitrogen enrichment and its driving forces. The anthropogenic reactive nitrogen of Asia dramatically increased from approximately 14.4 Tg N yr-1 in 1961 to approximately 67.7 Tg N yr-1 in 2000 and is likely to be 105.3 Tg N yr-1 by 2030. Most of the anthropogenic reactive-nitrogen has accumulated in the environment. We found that an increasing demand for food and energy supplies and the lack of effective measures to improve the efficiency of fertilizer nitrogen use, as well as effective measures for the prevention of NOx emissions from fossil-fuel combustion, are the principal drivers behind the environmental nitrogen-enrichment problem. This problem may be finally solved by substituting synthetic nitrogen fertilizers with new high-efficiency nitrogen sources, but solutions are dependent on advances in biological technology.

Asia↗
PubMed1972

Newly recognized vital nitrogen cycle.

Soil and sea bacteria produce a small amount of nitrous oxide (N(2)O); a small part of this N(2)O is photochemically converted to nitric oxide (NO) in the stratosphere. This process has recently been shown to be the principal source of the active oxides of nitrogen (NO and NO(2)) in the stratosphere. The active oxides of nitrogen catalytically destroy ozone, and NO and NO(2) appear to be a principal factor in the natural ozone balance. Stratospheric ozone is the only effective shield for the surface of the Earth against the harsh ultraviolet radiation between 300 and 250 nm. Thus, soil bacteria indirectly control the intensity of ultraviolet radiation reaching the Earth's surface. This subcycle of the major nitrogen cycle involves a relatively small amount of nitric oxide, estimated to be between 0.26 and 1.2 x 10(9) kg of NO per year on a worldwide basis. A recent estimate of the future nitric oxide emission in the stratosphere by the Concord supersonic transport is 0.37 x 10(9) kg/year on a world-wide basis, which is similar to the amount estimated from the natural source.

Air↗
PubMed2006

Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle?

Cultivation-independent molecular surveys show that members of the kingdom Crenarchaeota within the domain Archaea represent a substantial component of microbial communities in aquatic and terrestrial environments. Recently, metagenomic studies have revealed that such Crenarchaeota contain and express genes related to those of bacterial ammonia monooxygenases. Furthermore, a marine chemolithoautotrophic strain was isolated that uses ammonia as a sole energy source. Considering the ubiquity and abundance of Crenarchaeota, these findings considerably challenge the accepted view of the microbial communities involved in global nitrogen cycling. However, the quantitative contribution of Archaea to nitrification in marine and terrestrial environments still remains to be elucidated.

Ammonia↗
PubMed2006

Leachates from municipal solid waste disposal sites harbor similar, novel nitrogen-cycling bacterial communities.

High emissions of nitrous oxide (N(2)O) have recently been documented at municipal solid waste (MSW) landfills. However, the biodiversity of the bacterial populations involved remains unexplored. In this study, we investigated communities of ammonia-oxidizing bacteria (AOB) and denitrifying bacteria associated with the leachates from three MSW disposal sites by examining the diversity of the ammonia monooxygenase structural gene amoA and the nitrous oxide reductase gene nosZ, respectively. Cloning and phylogenetic analysis of the functional genes revealed novel and similar groups of prokaryotes involved in nitrogen cycling in the leachates with different chemical compositions. All amoA sequences recovered grouped within the Nitrosomonas europaea cluster in the Betaproteobacteria, with the vast majority showed only relatively moderate sequence similarities to known AOB but were exclusively most similar to environmental clones previously retrieved from wastewater treatment plants. All nosZ sequences retrieved did not cluster with any hitherto reported nosZ genes and were only remotely related to recognized denitrifiers from the Gammaproteobacteria and thus could not be affiliated. Significant overlap was found for the three denitrifying nosZ leachate communities. Our study suggests a significant selection of the novel N-cycling groups by the unique environment at these MSW disposal sites.

Bacteria↗
PubMed2003

Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment.

The analysis of functional diversity and its dynamics in the environment is essential for understanding the microbial ecology and biogeochemistry of aquatic systems. Here we describe the development and optimization of a DNA microarray method for the detection and quantification of functional genes in the environment and report on their preliminary application to the study of the denitrification gene nirS in the Choptank River-Chesapeake Bay system. Intergenic and intragenic resolution constraints were determined by an oligonucleotide (70-mer) microarray approach. Complete signal separation was achieved when comparing unrelated genes within the nitrogen cycle (amoA, nifH, nirK, and nirS) and detecting different variants of the same gene, nirK, corresponding to organisms with two different physiological modes, ammonia oxidizers and denitrifying halobenzoate degraders. The limits of intragenic resolution were investigated with a microarray containing 64 nirS sequences comprising 14 cultured organisms and 50 clones obtained from the Choptank River in Maryland. The nirS oligonucleotides covered a range of sequence identities from approximately 40 to 100%. The threshold values for specificity were determined to be 87% sequence identity and a target-to-probe perfect match-to-mismatch binding free-energy ratio of 0.56. The lower detection limit was 10 pg of DNA (equivalent to approximately 10(7) copies) per target per microarray. Hybridization patterns on the microarray differed between sediment samples from two stations in the Choptank River, implying important differences in the composition of the denitirifer community along an environmental gradient of salinity, inorganic nitrogen, and dissolved organic carbon. This work establishes a useful set of design constraints (independent of the target gene) for the implementation of functional gene microarrays for environmental applications.

Bacteria↗