Transformation of the Nitrogen Cycle: Recent Trends, Questions, and Potential Solutions

Transcriptome analysis of nitrogen-efficient rice over-expressing alanine aminotransferase

Crop plants require nitrogen for key macromolecules, such as DNA, proteins and metabolites, yet they are generally inefficient at acquiring nitrogen from the soil. Crop producers compensate for this low nitrogen utilization efficiency by applying nitrogen fertilizers. However, much of this nitrogen is unavailable to the plants as a result of microbial uptake and environmental loss of nitrogen, causing air, water and soil pollution. We engineered rice over-expressing alanine aminotransferase (AlaAT) under the control of a tissue-specific promoter that showed a strong nitrogen use efficiency phenotype. In this study, we examined the transcriptome response in roots and shoots to the over-expression of AlaAT to provide insights into the nitrogen-use-efficient phenotype of these plants. Transgenic and control rice plants were grown hydroponically and the root and shoot gene expression profiles were analysed using Affymetrix Rice GeneChip microarrays. Transcriptome analysis revealed that there was little impact on the transgenic transcriptome compared with controls, with 0.11% and 0.07% differentially regulated genes in roots and shoots, respectively. The most up-regulated transcripts, a glycine-rich cell wall (GRP) gene and a gene encoding a hypothetical protein (Os8823), were expressed in roots. Another transgenic root-specific up-regulated gene was leucine rich repeat (LRR). Genes induced in the transgenic shoots included GRP, LRR, acireductone dioxygenase (OsARD), SNF2 ATP-translocase and a putative leucine zipper transcription factor. This study provides a genome-wide view of the response to AlaAT over-expression, and elucidates some of the genes that may play a role in the nitrogen-use-efficient phenotype.

Leaching and utilization of nitrogen during a spring wheat catch crop succession

An experiment covering a 2-yr spring wheat (Triticum aestivum L.) catch crop succession was conducted in lysimeters to account for the losses of N due to leaching. We sought to relate these losses to the N uptake of the main crop and to integrate the estimated N loss and uptake into a balance. The non-winter hardy catch crops [yellow mustard (Sinapis alba L.), Phacelia (Phacelia tanacetifolia Benth), and sunflower (Helianthus annuus L.)] as well as bare soil fallow were studied at low and high N input levels of 4 and 29 g N m(-2) yr(-1), respectively. Catch crops allowed for an effective reduction of N leaching of 0.33 to 1.67 g N m(-2) yr(-1) compared to fallow. Reductions in N leaching were achieved mainly by avoiding the fallow period during autumn and winter while the catch crop species grown had little impact. During the spring wheat growing season, N leaching losses were highest after yellow mustard, the most effective catch crop for the entire crop succession. A balance of N indicated that the reductions in N leaching exerted by the catch crops did not result in a higher overall utilization of N by spring wheat. Thus, the efficacy shown by catch crops in reducing N leaching during growth is relatively lower when considering the entire crop succession. In addition, the N saved by growing catch crops does not increase N utilization by succeeding spring wheat.

Nitrous oxide emission by aquatic macrofauna

A large variety of aquatic animals was found to emit the potent greenhouse gas nitrous oxide when nitrate was present in the environment. The emission was ascribed to denitrification by ingested bacteria in the anoxic animal gut, and the exceptionally high N(2)O-to-N(2) production ratio suggested delayed induction of the last step of denitrification. Filter- and deposit-feeding animal species showed the highest rates of nitrous oxide emission and predators the lowest, probably reflecting the different amounts of denitrifying bacteria in the diet. We estimate that nitrous oxide emission by aquatic animals is quantitatively important in nitrate-rich aquatic environments like freshwater, coastal marine, and deep-sea ecosystems. The contribution of this source to overall nitrous oxide emission from aquatic environments might further increase because of the projected increase of nitrate availability in tropical regions and the numeric dominance of filter- and deposit-feeders in eutrophic ecosystems.

Reducing environmental risk by improving N management in intensive Chinese agricultural systems

Excessive N fertilization in intensive agricultural areas of China has resulted in serious environmental problems because of atmospheric, soil, and water enrichment with reactive N of agricultural origin. This study examines grain yields and N loss pathways using a synthetic approach in 2 of the most intensive double-cropping systems in China: waterlogged rice/upland wheat in the Taihu region of east China versus irrigated wheat/rainfed maize on the North China Plain. When compared with knowledge-based optimum N fertilization with 30-60% N savings, we found that current agricultural N practices with 550-600 kg of N per hectare fertilizer annually do not significantly increase crop yields but do lead to about 2 times larger N losses to the environment. The higher N loss rates and lower N retention rates indicate little utilization of residual N by the succeeding crop in rice/wheat systems in comparison with wheat/maize systems. Periodic waterlogging of upland systems caused large N losses by denitrification in the Taihu region. Calcareous soils and concentrated summer rainfall resulted in ammonia volatilization (19% for wheat and 24% for maize) and nitrate leaching being the main N loss pathways in wheat/maize systems. More than 2-fold increases in atmospheric deposition and irrigation water N reflect heavy air and water pollution and these have become important N sources to agricultural ecosystems. A better N balance can be achieved without sacrificing crop yields but significantly reducing environmental risk by adopting optimum N fertilization techniques, controlling the primary N loss pathways, and improving the performance of the agricultural Extension Service.

Uptake of organic nitrogen by plants

Languishing for many years in the shadow of plant inorganic nitrogen (N) nutrition research, studies of organic N uptake have attracted increased attention during the last decade. The capacity of plants to acquire organic N, demonstrated in laboratory and field settings, has thereby been well established. Even so, the ecological significance of organic N uptake for plant N nutrition is still a matter of discussion. Several lines of evidence suggest that plants growing in various ecosystems may access organic N species. Many soils display amino acid concentrations similar to, or higher than, those of inorganic N, mainly as a result of rapid hydrolysis of soil proteins. Transporters mediating amino acid uptake have been identified both in mycorrhizal fungi and in plant roots. Studies of endogenous metabolism of absorbed amino acids suggest that L- but not D-enantiomers are efficiently utilized. Dual labelled amino acids supplied to soil have provided strong evidence for plant uptake of organic N in the field but have failed to provide information on the quantitative importance of this process. Thus, direct evidence that organic N contributes significantly to plant N nutrition is still lacking. Recent progress in our understanding of the mechanisms underlying plant organic N uptake may open new avenues for the exploration of this subject.

On the fate of anthropogenic nitrogen

This article provides a synthesis of literature values to trace the fate of 150 Tg/yr anthropogenic nitrogen applied by humans to the Earth's land surface. Approximately 9 TgN/yr may be accumulating in the terrestrial biosphere in pools with residence times of ten to several hundred years. Enhanced fluvial transport of nitrogen in rivers and percolation to groundwater accounts for approximately 35 and 15 TgN/yr, respectively. Greater denitrification in terrestrial soils and wetlands may account for the loss of approximately 17 TgN/yr from the land surface, calculated by a compilation of data on the fraction of N(2)O emitted to the atmosphere and the current global rise of this gas in the atmosphere. A recent estimate of atmospheric transport of reactive nitrogen from land to sea (NO(x) and NH(x)) accounts for 48 TgN/yr. The total of these enhanced sinks, 124 TgN/yr, is less than the human-enhanced inputs to the land surface, indicating areas of needed additional attention to global nitrogen biogeochemistry. Policy makers should focus on increasing nitrogen-use efficiency in fertilization, reducing transport of reactive N to rivers and groundwater, and maximizing denitrification to its N(2) endproduct.

The microbial nitrogen cycle

This special issue highlights several recent discoveries in the microbial nitrogen cycle including the diversity of nitrogen-fixing bacteria in special habitats, distribution and contribution of aerobic ammonium oxidation by bacteria and crenarchaea in various aquatic and terrestrial ecosystems, regulation of metabolism in nitrifying bacteria, the molecular diversity of denitrifying microorganisms and their enzymes, the functional diversity of freshwater and marine anammox bacteria, the physiology of nitrite-dependent anaerobic methane oxidation and the degradation of recalcitrant organic nitrogen compounds. Simultaneously the articles in this issue show that many questions still need to be addressed, and that the microbes involved in catalyzing the nitrogen conversions still harbour many secrets that need to be disclosed to fully understand the biogeochemical nitrogen cycle, and make future predictions and global modelling possible.