Synthetic nitrogen fertilizers deplete soil nitrogen: a global dilemma for sustainable cereal production

Validation of QTL mapping and transcriptome profiling for identification of candidate genes associated with nitrogen stress tolerance in sorghum

BACKGROUND

Quantitative trait loci (QTLs) detected in one mapping population may not be detected in other mapping populations at all the time. Therefore, before being used for marker assisted breeding, QTLs need to be validated in different environments and/or genetic backgrounds to rule out statistical anomalies. In this regard, we mapped the QTLs controlling various agronomic traits in a recombinant inbred line (RIL) population in response to Nitrogen (N) stress and validated these with the reported QTLs in our earlier study to find the stable and consistent QTLs across populations. Also, with Illumina RNA-sequencing we checked the differential expression of gene (DEG) transcripts between parents and pools of RILs with high and low nitrogen use efficiency (NUE) and overlaid these DEGs on to the common validated QTLs to find candidate genes associated with N-stress tolerance in sorghum.

RESULTS

An F₇ RIL population derived from a cross between CK60 (N-stress sensitive) and San Chi San (N-stress tolerant) inbred sorghum lines was used to map QTLs for 11 agronomic traits tested under different N-levels. Composite interval mapping analysis detected a total of 32 QTLs for 11 agronomic traits. Validation of these QTLs revealed that of the detected, nine QTLs from this population were consistent with the reported QTLs in earlier study using CK60/China17 RIL population. The validated QTLs were located on chromosomes 1, 6, 7, 8, and 9. In addition, root transcriptomic profiling detected 55 and 20 differentially expressed gene (DEG) transcripts between parents and pools of RILs with high and low NUE respectively. Also, overlay of these DEG transcripts on to the validated QTLs found candidate genes transcripts for NUE and also showed the expected differential expression. For example, DEG transcripts encoding Lysine histidine transporter 1 (LHT1) had abundant expression in San Chi San and the tolerant RIL pool, whereas DEG transcripts encoding seed storage albumin, transcription factor IIIC (TFIIIC) and dwarfing gene (DW2) encoding multidrug resistance-associated protein-9 homolog showed abundant expression in CK60 parent, similar to earlier study.

CONCLUSIONS

The validated QTLs among different mapping populations would be the most reliable and stable QTLs across germplasm. The DEG transcripts found in the validated QTL regions will serve as future candidate genes for enhancing NUE in sorghum using molecular approaches.

Effects of intensive and alternative production systems on the technological and quality parameters of rapeseed seed (Brassica napus L. 'Siska')

BACKGROUND

Organic production is widely assumed to affect quality and nutritional parameters of arable crops. A field experiment was started in 2009 following integrated (INT), organic (ORG) and biodynamic (BD) production standards for wheat, maize and rapeseed production. With resort to standard analytical procedures and chemometrics, compositional parameters of Brassica napus L. 'Siska' seed (water, protein, oil and glucosinolate content) by non-destructive near-infrared spectroscopy (NIRS), and fatty acid composition determined by gas chromatography, were assessed.

RESULTS

The BD and ORG production systems positively influenced oleic fatty acid and oil content in comparison to INT, which had higher levels of protein and water content (19.8% and 4.7%, respectively), as well as linolenic (3.8%), gadoleic (12.6%) and hexadecadienoic (15.5%) fatty acids. Increases in the listed parameters were linked to mineral fertilizer application in the INT production system. With principal component analysis (PCA) the INT samples were clearly differentiated. The PCA results were influenced by differences in linolenic, gadoleic and behenic fatty acid levels as well as protein and water content.

CONCLUSION

Because quality parameters in rapeseed are increased in alternative production systems, production with an understanding of the soil processes and yield formation presents an opportunity for ORG and BD farmers. © 2016 Society of Chemical Industry.

Transcriptome and metabolite analysis identifies nitrogen utilization genes in tea plant (Camellia sinensis)

Applied nitrogen (N) fertilizer significantly increases the leaf yield. However, most N is not utilized by the plant, negatively impacting the environment. To date, little is known regarding N utilization genes and mechanisms in the leaf production. To understand this, we investigated transcriptomes using RNA-seq and amino acid levels with N treatment in tea (Camellia sinensis), the most popular beverage crop. We identified 196 and 29 common differentially expressed genes in roots and leaves, respectively, in response to ammonium in two tea varieties. Among those genes, AMT, NRT and AQP for N uptake and GOGAT and GS for N assimilation were the key genes, validated by RT-qPCR, which expressed in a network manner with tissue specificity. Importantly, only AQP and three novel DEGs associated with stress, manganese binding, and gibberellin-regulated transcription factor were common in N responses across all tissues and varieties. A hypothesized gene regulatory network for N was proposed. A strong statistical correlation between key genes’ expression and amino acid content was revealed. The key genes and regulatory network improve our understanding of the molecular mechanism of N usage and offer gene targets for plant improvement.

The Combination of Trichoderma harzianum and Chemical Fertilization Leads to the Deregulation of Phytohormone Networking, Preventing the Adaptive Responses of Tomato Plants to Salt Stress

Plants have evolved effective mechanisms to avoid or reduce the potential damage caused by abiotic stresses. In addition to biocontrol abilities, Trichoderma genus fungi promote growth and alleviate the adverse effects caused by saline stress in plants. Morphological, physiological, and molecular changes were analyzed in salt-stressed tomato plants grown under greenhouse conditions in order to investigate the effects of chemical and biological fertilizations. The application of Trichoderma harzianum T34 to tomato seeds had very positive effects on plant growth, independently of chemical fertilization. The application of salt stress significantly changed the parameters related to growth and gas-exchange rates in tomato plants subject to chemical fertilization. However, the gas-exchange parameters were not affected in unfertilized plants under the same moderate saline stress. The combined application of T34 and salt significantly reduced the fresh and dry weights of NPK-fertilized plants, while the opposite effects were detected when no chemical fertilization was applied. Decaying symptoms were observed in salt-stressed and chemically fertilized plants previously treated with T34. This damaged phenotype was linked to significantly higher intercellular CO2 and slight increases in stomatal conductance and transpiration, and to the deregulation of phytohormone networking in terms of significantly lower expression levels of the salt overlay sensitivity 1 (SOS1) gene, and the genes involved in signaling abscisic acid-, ethylene-, and salicylic acid-dependent pathways and ROS production, in comparison with those observed in salt-challenged NPK-fertilized plants.

Maximum soil organic carbon storage in Midwest U.S. cropping systems when crops are optimally nitrogen-fertilized

Nitrogen fertilization is critical to optimize short-term crop yield, but its long-term effect on soil organic C (SOC) is uncertain. Here, we clarify the impact of N fertilization on SOC in typical maize-based (Zea mays L.) Midwest U.S. cropping systems by accounting for site-to-site variability in maize yield response to N fertilization. Within continuous maize and maize-soybean [Glycine max (L.) Merr.] systems at four Iowa locations, we evaluated changes in surface SOC over 14 to 16 years across a range of N fertilizer rates empirically determined to be insufficient, optimum, or excessive for maximum maize yield. Soil organic C balances were negative where no N was applied but neutral (maize-soybean) or positive (continuous maize) at the agronomic optimum N rate (AONR). For continuous maize, the rate of SOC storage increased with increasing N rate, reaching a maximum at the AONR and decreasing above the AONR. Greater SOC storage in the optimally fertilized continuous maize system than in the optimally fertilized maize-soybean system was attributed to greater crop residue production and greater SOC storage efficiency in the continuous maize system. Mean annual crop residue production at the AONR was 22% greater in the continuous maize system than in the maize-soybean system and the rate of SOC storage per unit residue C input was 58% greater in the monocrop system. Our results demonstrate that agronomic optimum N fertilization is critical to maintain or increase SOC of Midwest U.S. cropland.

QTL Mapping by Whole Genome Re-sequencing and Analysis of Candidate Genes for Nitrogen Use Efficiency in Rice

Nitrogen is a major nutritional element in rice production. However, excessive application of nitrogen fertilizer has caused severe environmental pollution. Therefore, development of rice varieties with improved nitrogen use efficiency (NUE) is urgent for sustainable agriculture. In this study, bulked segregant analysis (BSA) combined with whole genome re-sequencing (WGS) technology was applied to finely map quantitative trait loci (QTL) for NUE. A key QTL, designated as qNUE6 was identified on chromosome 6 and further validated by Insertion/Deletion (InDel) marker-based substitutional mapping in recombinants from F₂ population (NIL-13B4 × GH998). Forty-four genes were identified in this 266.5-kb region. According to detection and annotation analysis of variation sites, 39 genes with large-effect single-nucleotide polymorphisms (SNPs) and large-effect InDels were selected as candidates and their expression levels were analyzed by qRT-PCR. Significant differences in the expression levels of LOC_Os06g15370 (peptide transporter PTR2) and LOC_Os06g15420 (asparagine synthetase) were observed between two parents (Y11 and GH998). Phylogenetic analysis in Arabidopsis thaliana identified two closely related homologs, AT1G68570 (AtNPF3.1) and AT5G65010 (ASN2), which share 72.3 and 87.5% amino acid similarity with LOC_Os06g15370 and LOC_Os06g15420, respectively. Taken together, our results suggested that qNUE6 is a possible candidate gene for NUE in rice. The fine mapping and candidate gene analysis of qNUE6 provide the basis of molecular breeding for genetic improvement of rice varieties with high NUE, and lay the foundation for further cloning and functional analysis.

Identification of QTL Associated with Nitrogen Uptake and Nitrogen Use Efficiency Using High Throughput Genotyped CSSLs in Rice (Oryza sativa L.)

Nitrogen (N) availability is a major factor limiting crop growth and development. Identification of quantitative trait loci (QTL) for N uptake (NUP) and N use efficiency (NUE) can provide useful information regarding the genetic basis of these traits and their associated effects on yield production. In this study, a set of high throughput genotyped chromosome segment substitution lines (CSSLs) derived from a cross between recipient 9311 and donor Nipponbare were used to identify QTL for rice NUP and NUE. Using high throughput sequencing, each CSSL were genotyped and an ultra-high-quality physical map was constructed. A total of 13 QTL, seven for NUP and six for NUE, were identified in plants under hydroponic culture with all nutrients supplied in sufficient quantities. The proportion of phenotypic variation explained by these QTL for NUP and NUE ranged from 3.16-13.99% and 3.76-12.34%, respectively. We also identified several QTL for biomass yield (BY) and grain yield (GY), which were responsible for 3.21-45.54% and 6.28-7.31%, respectively, of observed phenotypic variation. GY were significantly positively correlated with NUP and NUE, with NUP more closely correlated than NUE. Our results contribute information to NUP and NUE improvement in rice.

Mineral vs. Organic Amendments: Microbial Community Structure, Activity and Abundance of Agriculturally Relevant Microbes Are Driven by Long-Term Fertilization Strategies

Soil management is fundamental to all agricultural systems and fertilization practices have contributed substantially to the impressive increases in food production. Despite the pivotal role of soil microorganisms in agro-ecosystems, we still have a limited understanding of the complex response of the soil microbiota to organic and mineral fertilization in the very long-term. Here, we report the effects of different fertilization regimes (mineral, organic and combined mineral and organic fertilization), carried out for more than a century, on the structure and activity of the soil microbiome. Organic matter content, nutrient concentrations, and microbial biomass carbon were significantly increased by mineral, and even more strongly by organic fertilization. Pyrosequencing revealed significant differences between the structures of bacterial and fungal soil communities associated to each fertilization regime. Organic fertilization increased bacterial diversity, and stimulated microbial groups (Firmicutes, Proteobacteria, and Zygomycota) that are known to prefer nutrient-rich environments, and that are involved in the degradation of complex organic compounds. In contrast, soils not receiving manure harbored distinct microbial communities enriched in oligotrophic organisms adapted to nutrient-limited environments, as Acidobacteria. The fertilization regime also affected the relative abundances of plant beneficial and detrimental microbial taxa, which may influence productivity and stability of the agroecosystem. As expected, the activity of microbial exoenzymes involved in carbon, nitrogen, and phosphorous mineralization were enhanced by both types of fertilization. However, in contrast to comparable studies, the highest chitinase and phosphatase activities were observed in the solely mineral fertilized soil. Interestingly, these two enzymes showed also a particular high biomass-specific activities and a strong negative relation with soil pH. As many soil parameters are known to change slowly, the particularity of unchanged fertilization treatments since 1902 allows a profound assessment of linkages between management and abiotic as well as biotic soil parameters. Our study revealed that pH and TOC were the majors, while nitrogen and phosphorous pools were minors, drivers for structure and activity of the soil microbial community. Due to the long-term treatments studied, our findings likely represent permanent and stable, rather than transient, responses of soil microbial communities to fertilization.

Glutamine synthetase in Durum Wheat: Genotypic Variation and Relationship with Grain Protein Content

Grain protein content (GPC), is one of the most important trait in wheat and its characterized by a very complex genetic control. The identification of wheat varieties with high GPC (HGPC), as well as the characterization of central enzymes involved in these processes, are important for more sustainable agricultural practices. In this study, we focused on Glutamine synthetase (GS) as a candidate to study GPC in wheat. We analyzed GS expression and its enzymatic activity in different tissues and phenological stages in 10 durum wheat genotypes with different GPC. Although each genotype performed quite differently from the others, both because their genetic variability and their adaptability to specific environmental conditions, the highest GS activity and expression were found in genotypes with HGPC and vice versa the lowest ones in genotypes with low GPC (LGPC). Moreover, in genotypes contrasting in GPC bred at different nitrogen regimes (0, 60, 140 N Unit/ha) GS behaved differently in diverse organs. Nitrogen supplement increased GS expression and activity in roots of all genotypes, highlighting the key role of this enzyme in nitrogen assimilation and ammonium detoxification in roots. Otherwise, nitrogen treatments decreased GS expression and activity in the leaves of HGPC genotypes and did not affect GS in the leaves of LGPC genotypes. Finally, no changes in GS and soluble protein content occurred at the filling stage in the caryopses of all analyzed genotypes.

Polymer Coated Urea in Turfgrass Maintains Vigor and Mitigates Nitrogen's Environmental Impacts

Polymer coated urea (PCU) is a N fertilizer which, when added to moist soil, uses temperature-controlled diffusion to regulate N release in matching plant demand and mitigate environmental losses. Uncoated urea and PCU were compared for their effects on gaseous (N₂O and NH₃) and aqueous (NO₃^-) N environmental losses in cool season turfgrass over the entire PCU N-release period. Field studies were conducted on established turfgrass sites with mixtures of Kentucky bluegrass (Poa pratensis L.) and perennial ryegrass (Lolium perenne L.) in sand and loam soils. Each study compared 0 kg N ha^-1 (control) to 200 kg N ha^-1 applied as either urea or PCU (Duration 45CR®). Application of urea resulted in 127–476% more evolution of measured N₂O into the atmosphere, whereas PCU was similar to background emission levels from the control. Compared to urea, PCU reduced NH₃ emissions by 41–49% and N₂O emissions by 45–73%, while improving growth and verdure compared to the control. Differences in leachate NO₃^- among urea, PCU and control were inconclusive. This improvement in N management to ameliorate atmospheric losses of N using PCU will contribute to conserving natural resources and mitigating environmental impacts of N fertilization in turfgrass.

The Genetics of Nitrogen Use Efficiency in Crop Plants

In the past 50 years, the application of synthetic nitrogen (N) fertilizer to farmland resulted in a dramatic increase in crop yields but with considerable negative impacts on the environment. New solutions are therefore needed to simultaneously increase yields while maintaining, or preferably decreasing, applied N to maximize the nitrogen use efficiency (NUE) of crops. In this review, we outline the definition of NUE, the selection and development of NUE crops, and the factors that interact with NUE. In particular, we emphasize the challenges of developing crop plants with enhanced NUE, using more classical genetic approaches based on utilizing existing allelic variation for NUE traits. The challenges of phenotyping, mapping quantitative trait loci (QTLs), and selecting candidate genes for NUE improvement are described. In addition, we highlight the importance of different factors that lead to changes in the NUE components of nitrogen uptake efficiency (NUpE) and nitrogen utilization efficiency (NUtE).

The core root microbiome of sugarcanes cultivated under varying nitrogen fertilizer application

Diazotrophic bacteria potentially supply substantial amounts of biologically fixed nitrogen to crops, but their occurrence may be suppressed by high nitrogen fertilizer application. Here, we explored the impact of high nitrogen fertilizer rates on the presence of diazotrophs in field-grown sugarcane with industry-standard or reduced nitrogen fertilizer application. Despite large differences in soil microbial communities between test sites, a core sugarcane root microbiome was identified. The sugarcane root-enriched core taxa overlap with those of Arabidopsis thaliana raising the possibility that certain bacterial families have had long association with plants. Reduced nitrogen fertilizer application had remarkably little effect on the core root microbiome and did not increase the relative abundance of root-associated diazotrophs or nif gene counts. Correspondingly, low nitrogen fertilizer crops had lower biomass and nitrogen content, reflecting a lack of major input of biologically fixed nitrogen, indicating that manipulating nitrogen fertilizer rates does not improve sugarcane yields by enriching diazotrophic populations under the test conditions. Standard nitrogen fertilizer crops had improved biomass and nitrogen content, and corresponding soils had higher abundances of nitrification and denitrification genes. These findings highlight that achieving a balance in maximizing crop yields and minimizing nutrient pollution associated with nitrogen fertilizer application requires understanding of how microbial communities respond to fertilizer use.

Suppression of soil nitrification by plants

Nitrification, the biological oxidation of ammonium to nitrate, weakens the soil's ability to retain N and facilitates N-losses from production agriculture through nitrate-leaching and denitrification. This process has a profound influence on what form of mineral-N is absorbed, used by plants, and retained in the soil, or lost to the environment, which in turn affects N-cycling, N-use efficiency (NUE) and ecosystem health and services. As reactive-N is often the most limiting in natural ecosystems, plants have acquired a range of mechanisms that suppress soil-nitrifier activity to limit N-losses via N-leaching and denitrification. Plants' ability to produce and release nitrification inhibitors from roots and suppress soil-nitrifier activity is termed 'biological nitrification inhibition' (BNI). With recent developments in methodology for in-situ measurement of nitrification inhibition, it is now possible to characterize BNI function in plants. This review assesses the current status of our understanding of the production and release of biological nitrification inhibitors (BNIs) and their potential in improving NUE in agriculture. A suite of genetic, soil and environmental factors regulate BNI activity in plants. BNI-function can be genetically exploited to improve the BNI-capacity of major food- and feed-crops to develop next-generation production systems with reduced nitrification and N2O emission rates to benefit both agriculture and the environment. The feasibility of such an approach is discussed based on the progresses made.

Adoption of nitrogen-efficient technologies by u.s. Corn farmers

Anthropogenically introduced nitrogen (N) has compromised environmental quality, but it is an essential element for crop production, particularly corn production. Increasing N use efficiency by adopting eco-innovations such as N soil testing, plant tissue testing, and N transformation inhibitors can ameliorate this problem. Data from the 2010 USDA Agricultural Resource Management Survey of corn producers was used to examine the factors affecting adoption of these practices. Twenty-one percent of the 1840 corn farmers had adopted N soil testing, 3% had adopted plant tissue testing, and 10% had adopted N inhibitors. A multivariate probit regression found significant results for each category of explanatory variable that was examined. Among the findings was the importance of information source for N recommendations. Farmers who did not obtain external recommendations were less likely to adopt all three practices than farmers who received recommendations from a crop consultant. Those who received recommendations from fertilizer dealers were less likely to adopt N soil testing and plant tissue testing. All regions were more likely to adopt N soil testing than the Midwest, and warmer regions were less likely to adopt B transformation inhibitors. Those who adopted conservation tillage were more likely to adopt plant tissue testing and N inhibitors, and those who received conservation payments were more likely to adopt N soil testing and plant tissue testing. Adoption of conservation tillage was also associated with the adoption of several other technologies. Implications for research and educational programs are discussed.

TOND1 confers tolerance to nitrogen deficiency in rice

Nitrogen (N), the most important mineral nutrient for plants, is critical to agricultural production systems. N deficiency severely affects rice growth and decreases rice yields. However, excessive use of N fertilizer has caused severe pollution to agricultural and ecological environments. The necessity of breeding of crops that require lower input of N fertilizer has been recognized. Here we identified a major quantitative trait locus on chromosome 12, Tolerance Of Nitrogen Deficiency 1 (TOND1), that confers tolerance to N deficiency in the indica cultivar Teqing. Sequence verification of 75 indica and 75 japonica cultivars from 18 countries and regions demonstrated that only 27.3% of cultivars (41 indica cultivars) contain TOND1, whereas 72.7% of cultivars, including the remaining 34 indica cultivars and all 75 japonica cultivars, do not harbor the TOND1 allele. Over-expression of TOND1 increased the tolerance to N deficiency in the TOND1-deficient rice cultivars. The identification of TOND1 provides a molecular basis for breeding rice varieties with improved grain yield despite decreased input of N fertilizers.

Collaboration between grass seedlings and rhizobacteria to scavenge organic nitrogen in soils

Plants require nitrogen (N) to make proteins, nucleic acids and other biological molecules. It is widely accepted that plants absorb inorganic forms of N to fill their needs. However, recently it has become clear that plants also have the capacity to absorb organic N from soils. In this paper we describe a new kind of symbiosis involving seed-vectored rhizobacteria and grasses that is targeted at enhancing acquisition of organic N from soils. Our proposal is based on results of experiments on seedlings of grass species Festuca arundinacea Schreb., Lolium perenne L. and Poa annua L. that suggest: (i) seed-vectored rhizobacteria colonize seedling roots and influence their development; (ii) reactive oxygen secretion by seedling roots plays a role in organic N procurement by denaturing microbial proteins in the vicinity of roots (daytime activity); and (iii) plant root and microbial proteases degrade denatured proteins prior to absorption by roots (night-time activity). This research involved the following types of studies: (i) seedling root development experiments with and without rhizobacteria on a variety of substrates in agarose media and (ii) isotopic N-tracking experiments to evaluate the absorption into seedlings of N obtained from degradation of proteins. We hypothesize that grasses, in particular, are adapted to scavenge organic N from soils through application of this 'oxidative nitrogen scavenging' symbiosis with rhizobacteria, and their soil-permeating root systems. This newly discovered symbiosis in grass species could lead to new ways to cultivate and manage grasses to enhance efficiency of N utilization and reduce applications of inorganic fertilizers.

Nitrogen acquisition in Agave tequilana from degradation of endophytic bacteria

Plants form symbiotic associations with endophytic bacteria within tissues of leaves, stems, and roots. It is unclear whether or how plants obtain nitrogen from these endophytic bacteria. Here we present evidence showing nitrogen flow from endophytic bacteria to plants in a process that appears to involve oxidative degradation of bacteria. In our experiments we employed Agave tequilana and its seed-transmitted endophyte Bacillus tequilensis to elucidate organic nitrogen transfer from ¹⁵N-labeled bacteria to plants. Bacillus tequilensis cells grown in a minimal medium with ¹⁵NH₄Cl as the nitrogen source were watered onto plants growing in sand. We traced incorporation of ¹⁵N into tryptophan, deoxynucleosides and pheophytin derived from chlorophyll a. Probes for hydrogen peroxide show its presence during degradation of bacteria in plant tissues, supporting involvement of reactive oxygen in the degradation process. In another experiment to assess nitrogen absorbed as a result of endophytic colonization of plants we demonstrated that endophytic bacteria potentially transfer more nitrogen to plants and stimulate greater biomass in plants than heat-killed bacteria that do not colonize plants but instead degrade in the soil. Findings presented here support the hypothesis that some plants under nutrient limitation may degrade and obtain nitrogen from endophytic microbes.

Nodule performance within a changing environmental context

Global climate models predict that future environmental conditions will see alterations in temperature, water availability and CO2 concentration ([CO2]) in the atmosphere. Climate change will reinforce the need to develop highly productive crops. For this purpose it is essential to identify target traits conditioning plant performance in changing environments. N2 fixing plants represent the second major crop of agricultural importance worldwide. The current review provides a compilation of results from existing literature on the effects of several abiotic stress conditions on nodule performance and N2 fixation. The environmental factors analysed include water stress, salinity, temperature, and elevated [CO2]. Despite the large number of studies analysing [CO2] effects in plants, frequently they have been conducted under optimal growth conditions that are difficult to find in natural conditions where different stresses often occur simultaneously. This is why we have also included a section describing the current state of knowledge of interacting environmental conditions in nodule functioning. Regardless of the environmental factor considered, it is evident that some general patterns of nodule response are observed. Nodule carbohydrate and N compound availability, together with the presence of oxygen reactive species (ROS) have proven to be the key factors modulating N2 fixation at the physiological/biochemical levels. However, with the exception of water availability and [CO2], it should also be considered that nodule performance has not been characterised in detail under other limiting growth conditions. This highlights the necessity to conduct further studies considering these factors. Finally, we also observe that a better understanding of these metabolic effects of changing environment in nodule functioning would require an integrated and synergistic investigation based on widely used and novel protocols such as transcriptomics, proteomics, metabolomics and stable isotopes.

Low nitrogen fertilization adapts rice root microbiome to low nutrient environment by changing biogeochemical functions

Reduced fertilizer usage is one of the objectives of field management in the pursuit of sustainable agriculture. Here, we report on shifts of bacterial communities in paddy rice ecosystems with low (LN), standard (SN), and high (HN) levels of N fertilizer application (0, 30, and 300 kg N ha⁻¹, respectively). The LN field had received no N fertilizer for 5 years prior to the experiment. The LN and HN plants showed a 50% decrease and a 60% increase in biomass compared with the SN plant biomass, respectively. Analyses of 16S rRNA genes suggested shifts of bacterial communities between the LN and SN root microbiomes, which were statistically confirmed by metagenome analyses. The relative abundances of Burkholderia, Bradyrhizobium and Methylosinus were significantly increased in root microbiome of the LN field relative to the SN field. Conversely, the abundance of methanogenic archaea was reduced in the LN field relative to the SN field. The functional genes for methane oxidation (pmo and mmo) and plant association (acdS and iaaMH) were significantly abundant in the LN root microbiome. Quantitative PCR of pmoA/mcrA genes and a ¹³C methane experiment provided evidence of more active methane oxidation in the rice roots of the LN field. In addition, functional genes for the metabolism of N, S, Fe, and aromatic compounds were more abundant in the LN root microbiome. These results suggest that low-N-fertilizer management is an important factor in shaping the microbial community structure containing key microbes for plant associations and biogeochemical processes in paddy rice ecosystems.

Long-term fate of nitrate fertilizer in agricultural soils

Increasing diffuse nitrate loading of surface waters and groundwater has emerged as a major problem in many agricultural areas of the world, resulting in contamination of drinking water resources in aquifers as well as eutrophication of freshwaters and coastal marine ecosystems. Although empirical correlations between application rates of N fertilizers to agricultural soils and nitrate contamination of adjacent hydrological systems have been demonstrated, the transit times of fertilizer N in the pedosphere-hydrosphere system are poorly understood. We investigated the fate of isotopically labeled nitrogen fertilizers in a three-decade-long in situ tracer experiment that quantified not only fertilizer N uptake by plants and retention in soils, but also determined to which extent and over which time periods fertilizer N stored in soil organic matter is rereleased for either uptake in crops or export into the hydrosphere. We found that 61-65% of the applied fertilizers N were taken up by plants, whereas 12-15% of the labeled fertilizer N were still residing in the soil organic matter more than a quarter century after tracer application. Between 8-12% of the applied fertilizer had leaked toward the hydrosphere during the 30-y observation period. We predict that additional exports of (15)N-labeled nitrate from the tracer application in 1982 toward the hydrosphere will continue for at least another five decades. Therefore, attempts to reduce agricultural nitrate contamination of aquatic systems must consider the long-term legacy of past applications of synthetic fertilizers in agricultural systems and the nitrogen retention capacity of agricultural soils.

Mineral constituents profile of biochar derived from diversified waste biomasses: implications for agricultural applications

The wide distribution and high heterogeneity of different elements in biochars derived from diverse feedstocks make it difficult to regulate their application in soil and to evaluate the maximum potential contribution of the nutrients and trace metals as well as the potential risk of toxic metals. This study classified 20 biochars, covering six typical categories, into three clusters according to their similarity and distance on nutrients and minerals using cluster analysis. Four principle components (PC) were extracted using factor analysis to reduce dimension and clearly characterize the mineral profile of these biochars. The contribution of each group of elements in the PCs to every cluster was clarified. PC1 had a high loading for Mg, Cu, Zn, Al, and Fe; PC2 was related to N, K, and Mn; and PC3 and PC4 mainly represented P and Ca. Cluster 1 included bone dregs and eggshell biochars with PC3 and PC4 as the main contributors. Cluster 2 included waterweeds and waste paper biochars, which were close to shrimp hull and chlorella biochars, with the main contributions being from PC2 and PC4. Cluster 3 included biochars with PC1 as the main contributor. At a soil biochar amendment rate of 50 t ha, the soil nutrients were significantly elevated, whereas the rise in toxic metals was negligible compared with Class I of the China Environmental Quality Standards for Soil. Biochar can potentially supply soil nutrients and trace metals, and different cluster biochars can be applied appropriately to different soils so that excessive or deficient nutrient and metal applications can be avoided.

Engineering nitrogen use efficient crop plants: the current status

In the last 40 years the amount of synthetic nitrogen (N) applied to crops has risen drastically, resulting in significant increases in yield but with considerable impacts on the environment. A requirement for crops that require decreased N fertilizer levels has been recognized in the call for a 'Second Green Revolution' and research in the field of nitrogen use efficiency (NUE) has continued to grow. This has prompted a search to identify genes that improve the NUE of crop plants, with candidate NUE genes existing in pathways relating to N uptake, assimilation, amino acid biosynthesis, C/N storage and metabolism, signalling and regulation of N metabolism and translocation, remobilization and senescence. Herein is a review of the approaches taken to determine possible NUE candidate genes, an overview of experimental study of these genes as effectors of NUE in both cereal and non-cereal plants and the processes of commercialization of enhanced NUE crop plants. Patents issued regarding increased NUE in plants as well as gene pyramiding studies are also discussed as well as future directions of NUE research.

Legumes can increase cadmium contamination in neighboring crops

Legumes are widely used in many cropping systems because they share their nitrogen fixation products and phosphorus mobilization activities with their neighbors. In the current study, however, we showed that co-cultivation with legumes increased cadmium (Cd) contamination in the adjacent crops. Both field and mesocosm experiments indicated that legumes increased Cd levels in edible parts and shoots of four neighboring crops and five maize varieties tested, regardless of the Cd levels in the soil. This enhanced Cd accumulation in crops was attributed to root interactions that alter the rhizosphere environment. Co-cultivation with legumes reduced soil pH, which somewhat increased the exchangeable forms of Cd. Our results have demonstrated the inevitable increases in Cd levels of crops as a direct result of co-cultivation with legumes even under situations when these levels are below the permissible threshold. With this new revelation, we need to consider carefully the current cropping systems involving legumes and perhaps to re-design the current and future cropping systems in view of avoiding food contamination by Cd.

Assessing nitrification and denitrification in a paddy soil with different water dynamics and applied liquid cattle waste using the ¹⁵N isotopic technique

Using livestock wastewater for rice production in paddy fields can remove nitrogen and supplement the use of chemical fertilizers. However, paddy fields have complicated water dynamics owing to varying characteristics and would influence nitrogen removal through nitrification followed by denitrification. Quantification of nitrification and denitrification is of great importance in assessing the influence of water dynamics on nitrogen removal in paddy fields. In this study, nitrification and nitrate reduction rates with different water dynamics after liquid cattle waste application were evaluated, and the in situ denitrification rate was determined directly using the (15)N isotopic technique in a laboratory experiment. A significant linear regression correlation between nitrification and the nitrate reduction rate was observed and showed different regression coefficients under different water dynamics. The regression coefficient in the continuously flooded paddy soil was higher than in the drained-reflooded paddy soil, suggesting that nitrate would be consumed faster in the flooded paddy soil. However, nitrification was limited and the maximum rate was only 13.3 μg Ng(-1)day(-1) in the flooded paddy soil with rice plants, which limited the supply of nitrate. In contrast, the drained-reflooded paddy soil had an enhanced nitrification rate up to 56.8 μg Ng(-1)day(-1), which was four times higher than the flooded paddy soil and further stimulated nitrate reduction rates. Correspondingly, the in situ denitrification rates determined directly in the drained-reflooded paddy soil ranged from 5 to 1035 mg Nm(-2)day(-1), which was higher than the continuously flooded paddy soil (from 5 to 318 mg Nm(-2)day(-1)) during the vegetation period. The nitrogen removal through denitrification accounted for 38.9% and 9.9% of applied nitrogen in the drained-reflooded paddy soil and continuously flooded paddy soil, respectively.

Carbon and nitrogen stocks and nitrogen mineralization in organically managed soils amended with composted manures

The use of composted manures and of legumes in crop rotations may control the quality and quantity of soil organic matter and may affect nutrient retention and recycling. We studied soil organic C and N stocks and N mineralization in organically and conventionally managed dryland arable soils. We selected 13 extensive organic fields managed organically for 10 yr or more as well as adjacent fields managed conventionally. Organic farmers applied composted manures ranging from 0 to 1380 kg C ha yr and incorporated legumes in crop rotations. In contrast, conventional farmers applied fresh manures combined with slurries and/or mineral fertilizers ranging from 200 to 1900 kg C ha yr and practiced a cereal monoculture. Despite the fact that the application of organic C was similar in both farming systems, organically managed soils showed higher C and similar N content and lower bulk density than conventionally managed soils. Moreover, organic C stocks responded to the inputs of organic C in manures and to the presence of legumes only in organically managed soils. In contrast, stocks of organic N increased with the inputs of N or C in both farming systems. In organically managed soils, organic N stocks were less mineralizable than in conventional soils. However, N mineralization in organic soils was sensitive to the N fixation rates of legumes and to application rate and C/N ratio of the organic fertilizers.

Heterologous expression of ATG8c from soybean confers tolerance to nitrogen deficiency and increases yield in Arabidopsis

Nitrogen is an essential element for plant growth and yield. Improving Nitrogen Use Efficiency (NUE) of crops could potentially reduce the application of chemical fertilizer and alleviate environmental damage. To identify new NUE genes is therefore an important task in molecular breeding. Macroautophagy (autophagy) is an intracellular process in which damaged or obsolete cytoplasmic components are encapsulated in double membraned vesicles termed autophagosomes, then delivered to the vacuole for degradation and nutrient recycling. One of the core components of autophagosome formation, ATG8, has been shown to directly mediate autophagosome expansion, and the transcript of which is highly inducible upon starvation. Therefore, we postulated that certain homologs of Saccharomyces cerevisiae ATG8 (ScATG8) from crop species could have potential for NUE crop breeding. A soybean (Glycine max, cv. Zhonghuang-13) ATG8, GmATG8c, was selected from the 11 family members based on transcript analysis upon nitrogen deprivation. GmATG8c could partially complement the yeast atg8 mutant. Constitutive expression of GmATG8c in soybean callus cells not only enhanced nitrogen starvation tolerance of the cells but accelerated the growth of the calli. Transgenic Arabidopsis over-expressing GmATG8c performed better under extended nitrogen and carbon starvation conditions. Meanwhile, under optimum growth conditions, the transgenic plants grew faster, bolted earlier, produced larger primary and axillary inflorescences, eventually produced more seeds than the wild-type. In average, the yield was improved by 12.9%. We conclude that GmATG8c may serve as an excellent candidate for breeding crops with enhanced NUE and better yield.

Greenhouse gas emissions and plant characteristics from soil cultivated with sunflower (Helianthus annuus L.) and amended with organic or inorganic fertilizers

Agricultural application of wastewater sludge has become the most widespread method of disposal, but the environmental effects on soil, air, and crops must be considered. The effect of wastewater sludge or urea on sunflower's (Helianthus annuus L.) growth and yield, the soil properties, and the resulting CO(2) and N(2)O emissions are still unknown. The objectives of this study were to investigate: i) the effect on soil properties of organic or inorganic fertilizer added to agricultural soil cultivated with sunflower, ii) how urea or wastewater sludge increases CO(2) and N(2)O emissions from agricultural soil over short time periods, and iii) the effect on plant characteristics and yield of urea or wastewater sludge added to agricultural soil cultivated with sunflower. The sunflower was fertilized with wastewater sludge or urea or grown in unamended soil under greenhouse conditions while plant and soil characteristics, yield, and greenhouse gas emissions were monitored. Sludge and urea modified some soil characteristics at the onset of the experiment and during the first two months but not thereafter. Some plant characteristics were improved by sludge. Urea and sludge treatments increased the yield at similar rates, while sludge-amended soil significantly increased N(2)O emissions but not CO(2) emissions compared to the other amended or unamended soils. This implies that wastewater sludge increased the biomass and/or the yield; however, from a holistic point of view, using wastewater sludge as fertilizer should be viewed with concern.

Role of nitrogen fertilization in sustaining organic matter in cultivated soils

Soil organic matter (SOM) is essential for sustaining food production and maintaining ecosystem services and is a vital resource base for storing C and N. The impact of long-term use of synthetic fertilizer N on SOM, however, has been questioned recently. Here we tested the hypothesis that long-term application of N results in a decrease in SOM. We used data from 135 studies of 114 long-term experiments located at 100 sites throughout the world over time scales of decades under a range of land-management and climate regimes to quantify changes in soil organic carbon (SOC) and soil organic nitrogen (SON). Published data of a total of 917 and 580 observations for SOC and SON, respectively, from control (unfertilized or zero N) and N-fertilized treatments (synthetic, organic, and combination) were analyzed using the SAS mixed model and by meta-analysis. Results demonstrate declines of 7 to 16% in SOC and 7 to 11% in SON with no N amendments. In soils receiving synthetic fertilizer N, the rate of SOM loss decreased. The time-fertilizer response ratio, which is based on changes in the paired comparisons, showed average increases of 8 and 12% for SOC and SON, respectively, following the application of synthetic fertilizer N. Addition of organic matter (i.e., manure) increased SOM, on average, by 37%. When cropping systems fluctuated between flooding and drying, SOM decreased more than in continuous dryland or flooded systems. Flooded rice ( L.) soils show net accumulations of SOC and SON. This work shows a general decline in SOM for all long-term sites, with and without synthetic fertilizer N. However, our analysis also demonstrates that in addition to its role in improving crop productivity, synthetic fertilizer N significantly reduces the rate at which SOM is declining in agricultural soils, worldwide.

The Campesino-to-Campesino agroecology movement of ANAP in Cuba: social process methodology in the construction of sustainable peasant agriculture and food sovereignty

Agroecology has played a key role in helping Cuba survive the crisis caused by the collapse of the socialist bloc in Europe and the tightening of the US trade embargo. Cuban peasants have been able to boost food production without scarce and expensive imported agricultural chemicals by first substituting more ecological inputs for the no longer available imports, and then by making a transition to more agroecologically integrated and diverse farming systems. This was possible not so much because appropriate alternatives were made available, but rather because of the Campesino-a-Campesino (CAC) social process methodology that the National Association of Small Farmers (ANAP) used to build a grassroots agroecology movement. This paper was produced in a 'self-study' process spearheaded by ANAP and La Via Campesina, the international agrarian movement of which ANAP is a member. In it we document and analyze the history of the Campesino-to-Campesino Agroecology Movement (MACAC), and the significantly increased contribution of peasants to national food production in Cuba that was brought about, at least in part, due to this movement. Our key findings are (i) the spread of agroecology was rapid and successful largely due to the social process methodology and social movement dynamics, (ii) farming practices evolved over time and contributed to significantly increased relative and absolute production by the peasant sector, and (iii) those practices resulted in additional benefits including resilience to climate change.