Consequence of altered nitrogen cycles in the coupled human and ecological system under changing climate: The need for long-term and site-based research

Planetary boundaries transgressions: A review on the implications to public health

This literature review systematically examines the impacts of violating planetary boundaries from 2009 to 2023, emphasizing the implications for human health. Planetary boundaries define safe operational limits for Earth's systems, and their transgression poses significant threats to environmental stability and public health. This paper reviews extensive research on the health effects of breaches in these boundaries, including climate change, biodiversity loss, freshwater use, and aerosol loading. The review integrates findings from numerous studies, providing a critical overview of health impacts across various global regions. The analysis underscores the intricate links between planetary boundaries breaching impacts, highlighting urgent policy and governance challenges. The study's outcomes aim to inform policymakers, businesses, and communities, promoting sustainable development and resilience in the face of escalating global challenges.

Atmospheric deposition patterns in bulk open field precipitation and throughfall in Aleppo pine forest and black pine forest on the eastern Adriatic coast

The Mediterranean region, with its unique ecological characteristics, is particularly sensitive to global environmental changes, including climate change and impact of air pollution. Although Aleppo pine and black pine forests are the most abundant on the eastern Adriatic coast, atmospheric deposition in these forests is poorly studied. Changes in the chemical composition of precipitation as it passes through the tree canopy can lead to soil and groundwater eutrophication, and soil acidification, which affects plant vitality. In this study, the dynamics of ion deposition in Aleppo pine forest (Pinus halepensis Mill.) and black pine forest (Pinus nigra Arnold) on the eastern Adriatic coast are investigated, focusing on throughfall and bulk open field depositions. The aim of our research was to fill the gaps in understanding the influence of tree canopies on deposition fluxes in two different Mediterranean pine stands and to compare total inorganic nitrogen loads with critical loads. Over a period of two years, bulk open field precipitation and throughfall were sampled, measured and analysed using the ICP Forest methodology. The results indicate significant differences in ion deposition between bulk open field and throughfall, with throughfall showing higher values for almost all ions. The highest enrichment ratio was determined for K+. The comparison of the actual inorganic nitrogen load with the critical nitrogen load for Mediterranean pine forests revealed that the inorganic nitrogen load exceeded the critical load in the Aleppo pine forest. Ion deposition increased in the throughfall compared to bulk precipitation, which can be attributed to the seasonality of precipitation, including leaching and long dry periods. These findings enhance our understanding of ion deposition fluxes in vulnerable Mediterranean pine ecosystems and emphasize the need for long-term research on this topic in the actual changing environmental conditions.

Unraveling the impact of human perturbation on nitrogen cycling in terrestrial ecosystems of lower Himalaya, Pakistan

Terrestrial ecosystems are under the enormous pressure of land use management regimes through human disturbances, resulting in the disruption of biogeochemical cycles and associated ecosystem services. Nitrogen (N) in soil ecosystems is of vital importance for primary productivity, hence estimating the extent of these human interventions on N-cycling processes becomes imperative from economic and environmental perspectives. This work investigated the impacts of variable anthropogenic activities on N cycling in three different terrestrial ecosystems (arable, grassland, and forest) in three regions of lower Himalaya, Pakistan. Potential nitrification (PNA) and denitrification (DEA) enzyme activities, relative distribution of inorganic N species (NH4, NO3), and the role of inherent edaphic factors were assessed. Results revealed high nitrification potentials and increased nitrous oxide (N2O) emissions in the incubated soil microcosms, in the order as arable > grassland > forest ecosystems. Notably, higher rates of both studied processes (~ 30-50%) and elevated soil mineral nitrogen pool were observed in arable ecosystems. Forest soils, assumed as pristine ecosystems relying mainly on natural N fixation, produced (de)nitrification rates relatively lower than grasslands, followed by arable soils which were moderately disturbed through long-term fertilization and intensive land-use regimes. Linear regression modeling revealed that the inorganic N species (particularly NO3), and inherent edaphic factors were the key determinants of high (de)nitrification rates, hence warn of accelerated N losses in these ecosystems. The study highlights that elevated PNA and DEA being proxies for the altered N cycling in the studied terrestrial ecosystems are of great ecological relevance in view of predicted N2O budget in the lower Himalaya.

Perspective: sustainability challenges, opportunities and solutions for long-term ecosystem observations

As interest in natural capital grows and society increasingly recognizes the value of biodiversity, we must discuss how ecosystem observations to detect changes in biodiversity can be sustained through collaboration across regions and sectors. However, there are many barriers to establishing and sustaining large-scale, fine-resolution ecosystem observations. First, comprehensive monitoring data on both biodiversity and possible anthropogenic factors are lacking. Second, some in situ ecosystem observations cannot be systematically established and maintained across locations. Third, equitable solutions across sectors and countries are needed to build a global network. Here, by examining individual cases and emerging frameworks, mainly from (but not limited to) Japan, we illustrate how ecological science relies on long-term data and how neglecting basic monitoring of our home planet further reduces our chances of overcoming the environmental crisis. We also discuss emerging techniques and opportunities, such as environmental DNA and citizen science as well as using the existing and forgotten sites of monitoring, that can help overcome some of the difficulties in establishing and sustaining ecosystem observations at a large scale with fine resolution. Overall, this paper presents a call to action for joint monitoring of biodiversity and anthropogenic factors, the systematic establishment and maintenance of in situ observations, and equitable solutions across sectors and countries to build a global network, beyond cultures, languages, and economic status. We hope that our proposed framework and the examples from Japan can serve as a starting point for further discussions and collaborations among stakeholders across multiple sectors of society. It is time to take the next step in detecting changes in socio-ecological systems, and if monitoring and observation can be made more equitable and feasible, they will play an even more important role in ensuring global sustainability for future generations. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.

Bacterial enzymatic degradation of recalcitrant organic pollutants: catabolic pathways and genetic regulations

Contamination of soil and natural water bodies driven by increased organic pollutants remains a universal concern. Naturally, organic pollutants contain carcinogenic and toxic properties threatening all known life forms. The conventional physical and chemical methods employed to remove these organic pollutants ironically produce toxic and non-ecofriendly end-products. Whereas microbial-based degradation of organic pollutants provides an edge, they are usually cost-effective and take an eco-friendly approach towards remediation. Bacterial species, including Pseudomonas, Comamonas, Burkholderia, and Xanthomonas, have the unique genetic makeup to metabolically degrade toxic pollutants, conferring their survival in toxic environments. Several catabolic genes, such as alkB, xylE, catA, and nahAc, that encode enzymes and allow bacteria to degrade organic pollutants have been identified, characterized, and even engineered for better efficacy. Aerobic and anaerobic processes are followed by bacteria to metabolize aliphatic saturated and unsaturated hydrocarbons such as alkanes, cycloalkanes, aldehydes, and ethers. Bacteria use a variety of degrading pathways, including catechol, protocatechuate, gentisate, benzoate, and biphenyl, to remove aromatic organic contaminants such as polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and pesticides from the environment. A better understanding of the principle, mechanisms, and genetics would be beneficial for improving the metabolic efficacy of bacteria to such ends. With a focus on comprehending the mechanisms involved in various catabolic pathways and the genetics of the biotransformation of these xenobiotic compounds, the present review offers insight into the various sources and types of known organic pollutants and their toxic effects on health and the environment.

Mitigation of greenhouse gas emission by nitrogen-fixing bacteria

Chemical nitrogen fixation by the Haber-Bosch method permitted industrial-scale fertilizer production that supported global population growth, but simultaneously released reactive nitrogen into the environment. This minireview highlights the potential for bacterial nitrogen fixation and mitigation of greenhouse gas (GHG) emissions from soybean and rice fields. Nitrous oxide (N2O), a GHG, is mainly emitted from agricultural use of nitrogen fertilizer and symbiotic nitrogen fixation. Some rhizobia have a denitrifying enzyme system that includes an N2O reductase and are able to mitigate N2O emission from the rhizosphere of leguminous plants. Type II methane (CH4)-oxidizing bacteria (methanotrophs) are endophytes in paddy rice roots and fix N2 using CH4 (a GHG) as an energy source, mitigating the emission of CH4 and reducing nitrogen fertilizer usage. Thus, symbiotic nitrogen fixation shows potential for GHG mitigation in soybean and rice fields while simultaneously supporting sustainable agriculture.

Nitrous oxide emission in altered nitrogen cycle and implications for climate change

Natural processes and human activities play a crucial role in changing the nitrogen cycle and increasing nitrous oxide (N₂O) emissions, which are accelerating at an unprecedented rate. N₂O has serious global warming potential (GWP), about 310 times higher than that of carbon dioxide. The food production, transportation, and energy required to sustain a world population of seven billion have required dramatic increases in the consumption of synthetic nitrogen (N) fertilizers and fossil fuels, leading to increased N₂O in air and water. These changes have radically disturbed the nitrogen cycle and reactive nitrogen species, such as nitrous oxide (N₂O), and have impacted the climatic system. Yet, systematic and comprehensive studies on various underlying processes and parameters in the altered nitrogen cycle, and their implications for the climatic system are still lacking. This paper reviews how the nitrogen cycle has been disturbed and altered by anthropogenic activities, with a central focus on potential pathways of N₂O generation. The authors also estimate the N₂O-N emission mainly due to anthropogenic activities will be around 8.316 Tg N₂O-N yr^-1 in 2050. In order to minimize and tackle the N₂O emissions and its consequences on the global ecosystem and climate change, holistic mitigation strategies and diverse adaptations, policy reforms, and public awareness are suggested as vital considerations. This study concludes that rapidly increasing anthropogenic perturbations, the identification of new microbial communities, and their role in mediating biogeochemical processes now shape the modern nitrogen cycle.

Predicting global numbers of teleomorphic ascomycetes

Sexual reproduction is the basic way to form high genetic diversity and it is beneficial in evolution and speciation of fungi. The global diversity of teleomorphic species in Ascomycota has not been estimated. This paper estimates the species number for sexual ascomycetes based on five different estimation approaches, viz. by numbers of described fungi, by fungus:substrate ratio, by ecological distribution, by meta-DNA barcoding or culture-independent studies and by previous estimates of species in Ascomycota. The assumptions were made with the currently most accepted, “2.2–3.8 million” species estimate and results of previous studies concluding that 90% of the described ascomycetes reproduce sexually. The Catalogue of Life, Species Fungorum and published research were used for data procurement. The average value of teleomorphic species in Ascomycota from all methods is 1.86 million, ranging from 1.37 to 2.56 million. However, only around 83,000 teleomorphic species have been described in Ascomycota and deposited in data repositories. The ratio between described teleomorphic ascomycetes to predicted teleomorphic ascomycetes is 1:22. Therefore, where are the undiscovered teleomorphic ascomycetes? The undescribed species are no doubt to be found in biodiversity hot spots, poorly-studied areas and species complexes. Other poorly studied niches include extremophiles, lichenicolous fungi, human pathogens, marine fungi, and fungicolous fungi. Undescribed species are present in unexamined collections in specimen repositories or incompletely described earlier species. Nomenclatural issues, such as the use of separate names for teleomorph and anamorphs, synonyms, conspecific names, illegitimate and invalid names also affect the number of described species. Interspecies introgression results in new species, while species numbers are reduced by extinctions.

Nutrient expert system optimizes fertilizer management to improve potato productivity and tuber quality

BACKGROUND

Improving potato productivity and quality plays an important role in enhancing global food security and human health. However, inappropriate fertilizer management negatively affects potato growth and tuber development, especially in developing countries where there are large numbers of smallholders without modern soil testing equipment. Nutrient Expert (NE), a new and convenient fertilization decision system, was evaluated in the present study by conducting four site-years field experiments in Northeast China, aiming to determine its effectiveness and applicability for potato production relative to local farmers' practice (FP) and fertilizer recommendation based on soil testing (ST).

RESULTS

The excessive fertilization at planting promoted seedling growth for potato plants in FP. Nevertheless, superior plant growth and tuber development were observed in NE at the middle and later growing stages, by optimizing fertilizer input and implementing split fertilization. Overall, compared to FP, the NE system increased total and marketable tuber yields by 12-15% and 16-26%, respectively, at the same time as obtaining 19-31% higher net returns and enhanced fertilizer use efficiencies. Moreover, NE improved tuber quality by increasing the contents of starch, soluble protein and vitamin C and decreasing reducing sugar content relative to FP, as well as increasing starch yields by 23-52%. The ST method also showed comprehensive improvements in potato performances compared to FP, although it did not show any advantages compared to NE system.

CONCLUSION

The NE system improved potato productivity and tuber quality by optimizing fertilization management, which is an effective and promising alternative to the ST method for potato production in China and other developing countries. © 2021 Society of Chemical Industry.

Current and future threats to human health in the Anthropocene

It has been widely recognised that the threats to human health from global environmental changes (GECs) are increasing in the Anthropocene epoch, and urgent actions are required to tackle these pressing challenges. A scoping review was conducted to provide an overview of the nine planetary boundaries and the threats to population health posed by human activities that are exceeding these boundaries in the Anthropocene. The research progress and key knowledge gaps were identified in this emerging field. Over the past three decades, there has been a great deal of research progress on health risks from climate change, land-use change and urbanisation, biodiversity loss and other GECs. However, several significant challenges remain, including the misperception of the relationship between human and nature; assessment of the compounding risks of GECs; strategies to reduce and prevent the potential health impacts of GECs; and uncertainties in fulfilling the commitments to the Paris Agreement. Confronting these challenges will require rigorous scientific research that is well-coordinated across different disciplines and various sectors. It is imperative for the international community to work together to develop informed policies to avert crises and ensure a safe and sustainable planet for the present and future generations.

Comparison of spatial and temporal changes in riverine nitrate concentration from terrestrial basins to the sea between the 1980s and the 2000s in Japan: Impact of recent demographic shifts

Nitrogen (N) is an essential nutrient but may become a pollution source in the environment when the N concentration exceeds a certain threshold for humans and nature. Nitrate is a major N species in river water with notable spatial and temporal variations under the influences of natural factors and anthropogenic N inputs. We analyzed the relationship between riverine N (focusing on nitrate) concentration and various factors (land use, climate, basin topography, atmospheric N deposition, agricultural N sources and human-derived N) in 104 rivers located throughout the Japanese Archipelago except small remote islands. We aimed to better understand processes and mechanisms to explain the spatial and temporal changes in riverine nitrate concentration. A publicly available river water quality database observed in the 1980s (1980-1989) and 2000s (2000-2009) was used. This study is the first to evaluate the long-term scale of 20 years in the latter half of Japan's economic growth period at the national level. A geographic information system (GIS) was employed to determine average values of each variable collected from multiple sources of statistical data. We then performed regression analysis and structural equation modeling (SEM) for each period. The forestland area influenced by the basin topography, climate (i.e., air temperature) and other land uses (i.e., farmland and urban area) played a major role in decreasing nitrate concentrations in both the 1980s and 2000s. Atmospheric N deposition (especially N oxides) and agricultural N sources (fertilizer and manure) were also significant variables regarding the spatial variations in riverine nitrate concentrations. The SEM results suggested that human-derived N (via food consumption) intensified by demographic shifts during the 2000s increased riverine nitrate concentrations over other variables within the context of spatial variation. These findings facilitate better decision making regarding land use, agricultural practices, pollution control and individual behaviors toward a sustainable society.

Dissection of FixK2 protein-DNA interaction unveils new insights into Bradyrhizobium diazoefficiens lifestyles control

The FixK₂ protein plays a pivotal role in a complex regulatory network, which controls genes for microoxic, denitrifying, and symbiotic nitrogen-fixing lifestyles in Bradyrhizobium diazoefficiens. Among the microoxic-responsive FixK₂ -activated genes are the fixNOQP operon, indispensable for respiration in symbiosis, and the nnrR regulatory gene needed for the nitric-oxide dependent induction of the norCBQD genes encoding the denitrifying nitric oxide reductase. FixK₂ is a CRP/FNR-type transcription factor, which recognizes a 14 bp-palindrome (FixK₂ box) at the regulated promoters through three residues (L195, E196, and R200) within a C-terminal helix-turn-helix motif. Here, we mapped the determinants for discriminatory FixK₂ -mediated regulation. While R200 was essential for DNA binding and activity of FixK₂ , L195 was involved in protein-DNA complex stability. Mutation at positions 1, 3, or 11 in the genuine FixK₂ box at the fixNOQP promoter impaired transcription activation by FixK₂ , which was residual when a second mutation affecting the box palindromy was introduced. The substitution of nucleotide 11 within the NnrR box at the norCBQD promoter allowed FixK₂ -mediated activation in response to microoxia. Thus, position 11 within the FixK₂ /NnrR boxes constitutes a key element that changes FixK₂ targets specificity, and consequently, it might modulate B. diazoefficiens lifestyle as nitrogen fixer or as denitrifier.

Plant Endophytic Fungus Extract ZNC Improved Potato Immunity, Yield, and Quality

Endophytic fungi play an important role in plant survival and reproduction, but the role of their metabolites in plant growth and immunity, as well as in crop quality formation, is poorly understood. Zhinengcong (ZNC) is a crude ethanol extract from the endophytic fungus Paecilomyces variotii, and previous studies have shown that it can improve the growth and immunity in Arabidopsis thaliana. The aim of the study was to reveal the trade-off balance between plant growth and immunity by evaluating the mechanisms of ZNC on potato growth, yield, and priming immunity against the oomycete Phytophthora infestans indoors and in the field. ZNC maintained a good balance between plant growth and resistance against P. infestans with high activity. It induced the reactive oxygen species (ROS) production, promoted plant growth, yield and quality parameters, enhanced the expression of indoleacetic acid (IAA) related genes, and increased the absorption of nitrogen from the soil. Moreover, the plant endophytic fungus extract ZNC stimulated the pathogen-associated molecular pattern (PAMP) triggered immunity (PTI) pathway and contributed to the ZNC-mediated defense response. Two years of field trials have shown that irrigation with ZNC at one of two optimal concentrations of 1 or 10ng/ml could significantly increase the output by 18.83% or more. The quality of potato tubers was also greatly improved, in which the contents of vitamin C, protein, and starch were significantly increased, especially the sugar content was increased by 125%. Spray application of ZNC onto potato plants significantly reduced the occurrence of potato blight disease with 66.49% of control efficacy at 200ng/ml and increased the potato yield by 66.68% or more in the field. In summary, plant endophytic fungus extract ZNC promoted potato immunity, yield, and quality and presented excellent potential in agricultural applications.

Biological denitrification in a macrophytic lake: implications for macrophytes-dominated lake management in the north of China

Denitrification plays an important role in nitrogen (N) removal in freshwater ecosystems. Aquatic plants might have an impact on the sediment denitrification of water body, especially in macrophytes-dominated lake; however, there were different opinions about it. Our hypothesis was that the sediment denitrification rates differ significantly in different vegetation zones and seasons because of direct and indirect effect of the aquatic plants. Therefore, we studied sediment denitrification in Dongping Lake, a typical macrophytes-dominated lake located in the north of China. The acetylene inhibition technique was used to quantify the sediment denitrification rates (DRs) in the Phragmites communis (P. communis) zone, aquaculture zone, Potamogeton crispus (P. crispus) zone and mixed vegetation zone in July (summer), October (autumn), December (winter) of 2015 and March (spring) of 2016. The results showed that the average DRs were significantly higher in the P. communis zone (69.0 ± 91.6 μmol N m^-2 h^-1) than the mixed vegetation zone (8.70 ± 5.44 μmol N m^-2 h^-1), and the average DRs represented significant seasonal difference as in the order of winter (74.5 ± 88.3 μmol N m^-2 h^-1) > autumn (15.7 ± 18.6 μmol N m^-2 h^-1) ≈ summer (10.7 ± 5.90 μmol N m^-2 h^-1) > spring (3.85 ± 1.29 μmol N m^-2 h^-1). The DRs generally decreased with the increasing of depth; however, significant increase of DRs with depth were found in certain seasons at the vegetated zones except the non-vegetated zone (the aquaculture zone) indicating the possible rhizosphere effect of aquatic plants on denitrification. The higher DRs and cycling rates of nitrate in the P. communis zone might be related to the larger biomass and oxygen transporting capacity of P. communis than those of the other aquatic plants. Winter peaks of DRs might be attributed to the higher NO₃^- load and the absence of the plant uptake. The high cycling rates of nitrate in Dongping Lake indicated an enhanced internal N cycling by aquatic plants. Sediment denitrification could remove about 537.7 t N every year, which was about 26.5% of annual TN loading in Dongping Lake.

Urease and Nitrification Inhibitors—As Mitigation Tools for Greenhouse Gas Emissions in Sustainable Dairy Systems: A Review

Currently, nitrogen fertilizers are utilized to meet 48% of the total global food demand. The demand for nitrogen fertilizers is expected to grow as global populations continue to rise. The use of nitrogen fertilizers is associated with many negative environmental impacts and is a key source of greenhouse and harmful gas emissions. In recent years, urease and nitrification inhibitors have emerged as mitigation tools that are presently utilized in agriculture to prevent nitrogen losses and reduce greenhouse and harmful gas emissions that are associated with the use of nitrogen-based fertilizers. Both classes of inhibitor work by different mechanisms and have different physiochemical properties. Consequently, each class must be evaluated on its own merits. Although there are many benefits associated with the use of these inhibitors, little is known about their potential to enter the food chain, an event that may pose challenges to food safety. This phenomenon was highlighted when the nitrification inhibitor dicyandiamide was found as a residual contaminant in milk products in 2013. This comprehensive review aims to discuss the uses of inhibitor technologies in agriculture and their possible impacts on dairy product safety and quality, highlighting areas of concern with regards to the introduction of these inhibitor technologies into the dairy supply chain. Furthermore, this review discusses the benefits and challenges of inhibitor usage with a focus on EU regulations, as well as associated health concerns, chemical behavior, and analytical detection methods for these compounds within milk and environmental matrices.

Microorganisms and Their Metabolic Capabilities in the Context of the Biogeochemical Nitrogen Cycle at Extreme Environments

Extreme microorganisms (extremophile) are organisms that inhabit environments characterized by inhospitable parameters for most live beings (extreme temperatures and pH values, high or low ionic strength, pressure, or scarcity of nutrients). To grow optimally under these conditions, extremophiles have evolved molecular adaptations affecting their physiology, metabolism, cell signaling, etc. Due to their peculiarities in terms of physiology and metabolism, they have become good models for (i) understanding the limits of life on Earth, (ii) exploring the possible existence of extraterrestrial life (Astrobiology), or (iii) to look for potential applications in biotechnology. Recent research has revealed that extremophilic microbes play key roles in all biogeochemical cycles on Earth. Nitrogen cycle (N-cycle) is one of the most important biogeochemical cycles in nature; thanks to it, nitrogen is converted into multiple chemical forms, which circulate among atmospheric, terrestrial and aquatic ecosystems. This review summarizes recent knowledge on the role of extreme microorganisms in the N-cycle in extremophilic ecosystems, with special emphasis on members of the Archaea domain. Potential implications of these microbes in global warming and nitrogen balance, as well as their biotechnological applications are also discussed.

Research questions to facilitate the future development of European long-term ecosystem research infrastructures: A horizon scanning exercise

Distributed environmental research infrastructures are important to support assessments of the effects of global change on landscapes, ecosystems and society. These infrastructures need to provide continuity to address long-term change, yet be flexible enough to respond to rapid societal and technological developments that modify research priorities. We used a horizon scanning exercise to identify and prioritize emerging research questions for the future development of ecosystem and socio-ecological research infrastructures in Europe. Twenty research questions covered topics related to (i) ecosystem structures and processes, (ii) the impacts of anthropogenic drivers on ecosystems, (iii) ecosystem services and socio-ecological systems and (iv), methods and research infrastructures. Several key priorities for the development of research infrastructures emerged. Addressing complex environmental issues requires the adoption of a whole-system approach, achieved through integration of biotic, abiotic and socio-economic measurements. Interoperability among different research infrastructures needs to be improved by developing standard measurements, harmonizing methods, and establishing capacities and tools for data integration, processing, storage and analysis. Future research infrastructures should support a range of methodological approaches including observation, experiments and modelling. They should also have flexibility to respond to new requirements, for example by adjusting the spatio-temporal design of measurements. When new methods are introduced, compatibility with important long-term data series must be ensured. Finally, indicators, tools, and transdisciplinary approaches to identify, quantify and value ecosystem services across spatial scales and domains need to be advanced.

Nitrate acts at the Arabidopsis thaliana shoot apical meristem to regulate flowering time

Optimal timing of flowering, a major determinant for crop productivity, is controlled by environmental and endogenous cues. Nutrients are known to modify flowering time; however, our understanding of how nutrients interact with the known pathways, especially at the shoot apical meristem (SAM), is still incomplete. Given the negative side-effects of nitrogen fertilization, it is essential to understand its mode of action for sustainable crop production. We investigated how a moderate restriction by nitrate is integrated into the flowering network at the SAM, to which plants can adapt without stress symptoms. This condition delays flowering by decreasing expression of SUPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) at the SAM. Measurements of nitrate and the responses of nitrate-responsive genes suggest that nitrate functions as a signal at the SAM. The transcription factors NIN-LIKE PROTEIN 7 (NLP7) and NLP6, which act as master regulators of nitrate signaling by binding to nitrate-responsive elements (NREs), are expressed at the SAM and flowering is delayed in single and double mutants. Two upstream regulators of SOC1 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 (SPL3) and SPL5) contain functional NREs in their promoters. Our results point at a tissue-specific, nitrate-mediated flowering time control in Arabidopsis thaliana.

Measuring and mapping the effectiveness of the European Air Quality Directive in reducing N and S deposition at the ecosystem level

To protect human health and the environment (namely ecosystems), international air quality protocols and guidelines, like the Gothenburg protocol (1999) and the 2001 EU Air Quality Directive (NECD), conveyed national emission ceilings for atmospheric pollutants (Directive 2001/81/EC), including the reduction of sulfur (S) and nitrogen (N) emissions by 2010. However, to what degree this expected reduction in emissions had reflections at the ecosystem level (i.e. pollutant levels reaching and impacting ecosystems and their organisms) remains unknown. Here, we used lichens as ecological indicators, together with reported air and precipitation pollutant concentrations, to determine and map the consequences of the S and N atmospheric emission's reduction, during the implementation of the 2001 Directive (in 2002 and 2011), due primarily to the industrial-sector. The study area is a mixed-land-use industrialized Mediterranean agroforest ecosystem, in southwest Europe. The reduction of S emissions (2002-2011) was reflected at the ecosystem level, as the same S-declining trend was observed in atmospheric measurement stations and lichens alike (-70%), indicating that most S deposited to the ecosystem had an industrial origin. However, this was not the case for N with a slight N-reduction near industrial facilities, but mostly N-deposition in lichens increased in areas dominated by agricultural land-uses. Taken together, these results highlight the importance of going beyond emissions estimation and modeling, to assess the success of the implementation of the NECD in lowering pollutant accumulation in living organisms and their environment. This can only be achieved by measuring pollutant deposition at the ecosystem level (e.g. living organisms). By doing so, we were able to show that the 2001 NECD was successful in reducing S concentrations from Industry, whereas N remains a challenge. Despite the small reduction in N-emissions, deposition into ecosystems did not reflect these changes as agriculture and transport sectors must reduce NH₃ and NO_x emissions.

Adaptive Introgression: An Untapped Evolutionary Mechanism for Crop Adaptation

Global environmental changes strongly impact wild and domesticated species biology and their associated ecosystem services. For crops, global warming has led to significant changes in terms of phenology and/or yield. To respond to the agricultural challenges of this century, there is a strong need for harnessing the genetic variability of crops and adapting them to new conditions. Gene flow, from either the same species or a different species, may be an immediate primary source to widen genetic diversity and adaptions to various environments. When the incorporation of a foreign variant leads to an increase of the fitness of the recipient pool, it is referred to as "adaptive introgression". Crop species are excellent case studies of this phenomenon since their genetic variability has been considerably reduced over space and time but most of them continue exchanging genetic material with their wild relatives. In this paper, we review studies of adaptive introgression, presenting methodological approaches and challenges to detecting it. We pay particular attention to the potential of this evolutionary mechanism for the adaptation of crops. Furthermore, we discuss the importance of farmers' knowledge and practices in shaping wild-to-crop gene flow. Finally, we argue that screening the wild introgression already existing in the cultivated gene pool may be an effective strategy for uncovering wild diversity relevant for crop adaptation to current environmental changes and for informing new breeding directions.

The Impact of Carbon Source as Electron Donor on Composition and Concentration of Dissolved Organic Nitrogen in Biosorption-Activated Media for Stormwater and Groundwater Co-Treatment

Eutrophication has been a long-term issue in aquatic environments, where dissolved organic nitrogen (DON) recalcitrance is important. Bioavailable nitrogen qualification and quantification for effluents from stormwater and wastewater are always a challenge. The information in this study deepens the understanding of the interactions between carbon addition and DON decomposition through linear-ditch best management practices for stormwater and groundwater cotreatment. By running a laboratory-scale column study for nitrogen removal using green sorption media, the variation in composition and concentration of DON can be further linked to the population dynamics of microbial species that dominate the nitrification and denitrification processes. With the varying levels of influent total nitrogen concentration, the efficacy of nitrogen removal via biosorption activated media may be realized at the molecular level with ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry.

Detection of nitrite with a surface-enhanced Raman scattering sensor based on silver nanopyramid array

Nutrient pollution is of worldwide environmental and health concerns due to extensive use of nitrogen fertilizers and release of livestock waste, which induces nitrite compounds in aquatic systems. Herein a surface-enhanced Raman scattering (SERS) sensor is developed for nitrite detection based on coupling between the plasmonic gold nanostars and the silver nanopyramid array. When nitrite is present in the assay, an azo group is formed between the 1-naphthylamine-functionalized silver nanopyramids and the 4-aminothiophenol-functionalized gold nanostars. This not only generates the SERS spectral fingerprint for selective detection, but also creates "hot spots" at the gap between the Au nanostars and the Ag nanopyramids where the azo group is located, amplifying SERS signals remarkably. Finite-difference time-domain (FDTD) simulation shows a SERS enhancement factor of 4 × 10¹⁰ at the "hot spots". As a result, the SERS sensor achieves a limit of detection of 0.6 pg/mL toward nitrite in water, and enables nitrite detection in real-world river water samples. In addition, this sensor eliminates the use of any Raman reporter and any expensive molecular recognition probe such as antibody and aptamer. This highly sensitive, selective and inexpensive SERS sensor has unique advantages over colorimetric, electrochemical and fluorescent devices for small molecule detection.

Soil environment is a key driver of adaptation in Medicago truncatula: new insights from landscape genomics

Spatial differences in environmental selective pressures interact with the genomes of organisms, ultimately leading to local adaptation. Landscape genomics is an emergent research area that uncovers genome-environment associations, thus allowing researchers to identify candidate loci for adaptation to specific environmental variables. In the present study, we used latent factor mixed models (LFMMs) and Moran spectral outlier detection/randomization (MSOD-MSR) to identify candidate loci for adaptation to 10 environmental variables (climatic, soil and atmospheric) among 43 515 single nucleotide polymorphisms (SNPs) from 202 accessions of the model legume Medicago truncatula. Soil variables were associated with a large number of candidate loci identified through both LFMMs and MSOD-MSR. Genes tagged by candidate loci associated with drought and salinity are involved in the response to biotic and abiotic stresses, while those tagged by candidates associated with soil nitrogen and atmospheric nitrogen, participate in the legume-rhizobia symbiosis. Candidate SNPs identified through both LFMMs and MSOD-MSR explained up to 56% of variance in flowering traits. Our findings highlight the importance of soil in driving adaptation in the system and elucidate the basis of evolutionary potential of M. truncatula to respond to global climate change and anthropogenic disruption of the nitrogen cycle.

Genesis, goals and achievements of Long-Term Ecological Research at the global scale: A critical review of ILTER and future directions

Since its founding in 1993 the International Long-term Ecological Research Network (ILTER) has gone through pronounced development phases. The current network comprises 44 active member LTER networks representing 700 LTER Sites and ~80 LTSER Platforms across all continents, active in the fields of ecosystem, critical zone and socio-ecological research. The critical challenges and most important achievements of the initial phase have now become state-of-the-art in networking for excellent science. At the same time increasing integration, accelerating technology, networking of resources and a strong pull for more socially relevant scientific information have been modifying the mission and goals of ILTER. This article provides a critical review of ILTER's mission, goals, development and impacts. Major characteristics, tools, services, partnerships and selected examples of relative strengths relevant for advancing ILTER are presented. We elaborate on the tradeoffs between the needs of the scientific community and stakeholder expectations. The embedding of ILTER in an increasingly collaborative landscape of global environmental observation and ecological research networks and infrastructures is also reflected by developments of pioneering regional and national LTER networks such as SAEON in South Africa, CERN/CEOBEX in China, TERN in Australia or eLTER RI in Europe. The primary role of ILTER is currently seen as a mechanism to investigate ecosystem structure, function, and services in response to a wide range of environmental forcings using long-term, place-based research. We suggest four main fields of activities and advancements for the next decade through development/delivery of a: (1) Global multi-disciplinary community of researchers and research institutes; (2) Strategic global framework and strong partnerships in ecosystem observation and research; (3) Global Research Infrastructure (GRI); and (4) a scientific knowledge factory for societally relevant information on sustainable use of natural resources.

Eco-physiological response of Hypnum cupressiforme Hedw. to increased atmospheric ammonia concentrations in a forest agrosystem

Ammonia (NH₃) emissions are linked to eutrophication, plant toxicity and ecosystem shifts from N to P limitation. Bryophytes are key components of terrestrial ecosystems, yet highly sensitive to N deposition. Hence, physiological responses of mosses may be indicative of NH₃-related impacts, and thus useful to foresee future ecosystem damages and establish atmospheric Critical Levels (CLEs). In this work, samples of Hypnum cupressiforme Hedw. were seasonally collected along a well-defined NH₃ concentration gradient in an oak woodland during a one-year period. We performed a comprehensive evaluation of tissue chemistry, stoichiometry, metabolic enzymes, antioxidant response, membrane damages, photosynthetic pigments, soluble protein content and N and C isotopic fractionation. Our results showed that all the physiological parameters studied (except P, K, Ca and C) responded to the NH₃ gradient in predictable ways, although the magnitude and significance of the response were dependent on the sampling season, especially for enzymatic activities and pigments content. Nutritional imbalances, membrane damages and disturbance of cellular C and N metabolism were found as a consequence to NH₃ exposure, being more affected the mosses more exposed to the barn atmosphere. These findings suggested significant implications of intensive farming for the correct functioning of oak woodlands and highlighted the importance of seasonal dynamics in the study of key physiological processes related to photosynthesis, mosses nutrition and responses to oxidative stress. Finally, tissue N showed the greatest potential for the identification of NH₃-related ecological end points (estimated CLE=3.5μgm^-3), whereas highly scattered physiological responses, although highly sensitive, were not suitable to that end.

Denitrification and Biodiversity of Denitrifiers in a High-Mountain Mediterranean Lake

Wet deposition of reactive nitrogen (Nr) species is considered a main factor contributing to N inputs, of which nitrate ([Formula: see text]) is usually the major component in high-mountain lakes. The microbial group of denitrifiers are largely responsible for reduction of nitrate to molecular dinitrogen (N₂) in terrestrial and aquatic ecosystems, but the role of denitrification in removal of contaminant nitrates in high-mountain lakes is not well understood. We have used the oligotrophic, high-altitude La Caldera lake in the Sierra Nevada range (Spain) as a model to study the role of denitrification in nitrate removal. Dissolved inorganic Nr concentration in the water column of la Caldera, mainly nitrate, decreased over the ice-free season which was not associated with growth of microbial plankton or variations in the ultraviolet radiation. Denitrification activity, estimated as nitrous oxide (N₂O) production, was measured in the water column and in sediments of the lake, and had maximal values in the month of August. Relative abundance of denitrifying bacteria in sediments was studied by quantitative polymerase chain reaction of the 16S rRNA and the two phylogenetically distinct clades nosZI and nosZII genes encoding nitrous oxide reductases. Diversity of denitrifiers in sediments was assessed using a culture-dependent approach and after the construction of clone libraries employing the nosZI gene as a molecular marker. In addition to genera Polymorphum, Paracoccus, Azospirillum, Pseudomonas, Hyphomicrobium, Thauera, and Methylophaga, which were present in the clone libraries, Arthrobacter, Burkholderia, and Rhizobium were also detected in culture media that were not found in the clone libraries. Analysis of biological activities involved in the C, N, P, and S cycles from sediments revealed that nitrate was not a limiting nutrient in the lake, allowed N₂O production and determined denitrifiers' community structure. All these results indicate that denitrification could be a major biochemical process responsible for the N losses that occur in La Caldera lake.

Varying sensitivity of mountainous streamwater base-flow [Formula: see text]concentrations to N deposition in the northern suburbs of Tokyo

Ecosystems of suburban landscapes (i.e., forest, inland water ecosystem) are threatened by high nitrogen (N) loadings derived from urban air pollutants. Forest ecosystems under high chronic N loadings tend to leach more N via streams. In the northern suburbs of Tokyo, N deposition loading on terrestrial ecosystems has increased over the past 30 years. In this region, we investigated nitrate concentrations in 608 independent small forested catchment water samples from northeastern suburbs of Tokyo. The nitrate concentrations varied from 0.07 to 3.31 mg-N L-1 in this region. We evaluated the effects of N deposition and catchment properties (e.g., meteorological and topographic factors, vegetation and soil types) on nitrate concentrations. In the random forest model, simulated N deposition rates from an atmospheric chemistry transportation model explained most of the variance of nitrate concentration. To evaluate the effects of afforestation management in the catchment, we followed a model-based recursive partitioning method (MOB). MOB succeeded in data-driven identification of subgroups with varying sensitivities to N deposition rate by vegetation composition in the catchment. According to MOB, the catchment with dominant coniferous coverage that mostly consisted of plantation with old tree age tended to have strong sensitivity of nitrate concentrations to N deposition loading.

Climate Change Across Seasons Experiment (CCASE): A new method for simulating future climate in seasonally snow-covered ecosystems

Climate models project an increase in mean annual air temperatures and a reduction in the depth and duration of winter snowpack for many mid and high latitude and high elevation seasonally snow-covered ecosystems over the next century. The combined effects of these changes in climate will lead to warmer soils in the growing season and increased frequency of soil freeze-thaw cycles (FTCs) in winter due to the loss of a continuous, insulating snowpack. Previous experiments have warmed soils or removed snow via shoveling or with shelters to mimic projected declines in the winter snowpack. To our knowledge, no experiment has examined the interactive effects of declining snowpack and increased frequency of soil FTCs, combined with soil warming in the snow-free season on terrestrial ecosystems. In addition, none have mimicked directly the projected increase in soil FTC frequency in tall statured forests that is expected as a result of a loss of insulating snow in winter. We established the Climate Change Across Seasons Experiment (CCASE) at Hubbard Brook Experimental Forest in the White Mountains of New Hampshire in 2012 to assess the combined effects of these changes in climate on a variety of pedoclimate conditions, biogeochemical processes, and ecology of northern hardwood forests. This paper demonstrates the feasibility of creating soil FTC events in a tall statured ecosystem in winter to simulate the projected increase in soil FTC frequency over the next century and combines this projected change in winter climate with ecosystem warming throughout the snow-free season. Together, this experiment provides a new and more comprehensive approach for climate change experiments that can be adopted in other seasonally snow-covered ecosystems to simulate expected changes resulting from global air temperature rise.

Short-Term Response of Sasa Dwarf Bamboo to a Change of Soil Nitrogen Fertility in a Forest Ecosystem in Northern Hokkaido, Japan

In forest ecosystems, a change of soil nitrogen (N) cycling after disturbance is regulated by various factors. Sasa dwarf bamboo (hereafter referred to as Sasa) is an understory plant that grows thickly on the forest floor in northern Hokkaido, Japan. However, the ecosystem function of Sasa after disturbances in the soil N cycling is not fully understood. The purpose of this study was to determine the short-term response of Sasa to a change of soil N fertility. Biomass, litterfall, litter decomposition, soil N pool, and N leaching from soil were measured in control, and low- (5 g N m⁻² year⁻¹) and high-N (15 g N m⁻² year⁻¹) addition plots. Sasa immobilized much N as the soil N fertility increased. However, the leaf N concentration in aboveground biomass did not increase, suggesting that the N in leaves was maintained because of the increase of leaf biomass. As a result, the decomposition and mineralization rates of the produced litter before and after N addition were comparable among plots, even though the soil inorganic N fertility increased greatly. These results suggest that immediate response of Sasa to an increase of soil inorganic N mitigates the excess N leaching from soil.

Throughfall and bulk deposition of dissolved organic nitrogen to holm oak forests in the Iberian Peninsula: Flux estimation and identification of potential sources

Deposition of dissolved organic nitrogen (DON) in both bulk precipitation (BD) and canopy throughfall (TF) has been measured for the first time in the western Mediterranean. The study was carried out over a year from 2012 to 2013 at four evergreen holm oak forests located in the Iberian Peninsula: two sites in the Province of Barcelona (Northeastern Spain), one in the Province of Madrid (central Spain) and the fourth in the Province of Navarra (Northern Spain). In BD the annual volume weighted mean (VWM) concentration of DON ranged from 0.25 mg l(-1) in Madrid to 1.14 mg l(-1) in Navarra, whereas in TF it ranged from 0.93 mg l(-1) in Barcelona to 1.98 mg l(-1) in Madrid. The contribution of DON to total nitrogen deposition varied from 34% to 56% in BD in Barcelona and Navarra respectively, and from 38% in Barcelona to 72% in Madrid in TF. Agricultural activities and pollutants generated in metropolitan areas were identified as potential anthropogenic sources of DON at the study sites. Moreover, canopy uptake of DON in Navarra was found in spring and autumn, showing that organic nitrogen may be a supplementary nutrient for Mediterranean forests, assuming that a portion of the nitrogen taken up is assimilated during biologically active periods.