Search

Abstract Sustainable phosphorus (P) management is essential for ensuring crop production while avoiding environmental damage and the depletion of phosphate rock reserves. Despite local demonstration scale successes, the widespread mobilization of smallholder farmers to adopt sustainable management practices remains a challenge, primarily due to the associated high costs and complicated sampling. Here, we propose a dynamic optimization of soil P status (DOP) approach aimed at managing long-term soil P status within the range of agronomic and environmental soil P thresholds, which facilitates the precise determination of optimal P application rates without the need for frequent soil testing. We evaluate the DOP approach in 35,575 on-farm trials, and the results show that it is agronomically acceptable. Our evaluation extends to estimating future soil P status and P fertilizer inputs across all counties in China for three cereal crops (wheat, rice, and maize). The results indicate that, compared to current practices, the DOP approach can achieve a 47.4% reduction in P fertilizer use without any yield penalty. The DOP approach could become an effective tool for global P management to safeguard food security and enhance environmental sustainability.

Abstract Climate warming threatens global food security by exacerbating pressures on degraded soils under intensive crop production. Conservation agriculture is promoted as a sustainable solution that improves soil health and sustains crop yields in a changing climate, but these benefits may be affected by long-term warming. Here, we investigate the effects of conservation agriculture compared to conventional agriculture on 17 soil properties, microbial diversity and crop yields, during eight-years’ experimental warming. An overall positive effect of warming on soil health over time under conservation agriculture is characterized by linear increases in soil organic carbon and microbial biomass carbon. Warming-triggered shifts in microbial biomass carbon and fungal diversity (saprogen richness) are directly linked to a 9.3% increase in wheat yields over eight years, but only under conservation agriculture. Overall, conservation agriculture results in an average 21% increase in soil health and supports similar levels of crop production after long-term warming compared to conventional agriculture. Our work provides insights into the potential benefits of conservation agriculture for long-term sustainable food production because improved soil health improves resilience to the effects of climate warming.

Deeper understanding of the crosstalk between host cells and Mycobacterium tuberculosis (Mtb) provides crucial guidelines for the rational design of novel intervention strategies against tuberculosis (TB). Mycobacteria possess a unique complex cell wall with arabinogalactan (AG) as a critical component. AG has been identified as a virulence factor of Mtb which is recognized by host galectin-9. Here, we demonstrate that galectin-9 directly inhibited mycobacterial growth through AG-binding property of carbohydrate-recognition domain 2. Furthermore, IgG antibodies with AG specificity were detected in the serum of TB patients. Based on the interaction between galectin-9 and AG, we developed a monoclonal antibody (mAb) screening assay and identified AG-specific mAbs which profoundly inhibit Mtb growth. Mechanistically, proteomic profiling and morphological characterizations revealed that AG-specific mAbs regulate AG biosynthesis, thereby inducing cell wall swelling. Thus, direct AG-binding by galectin-9 or antibodies contributes to protection against TB. Our findings pave the way for the rational design of novel immunotherapeutic strategies for TB control.

Abstract Livestock constitute the world’s largest anthropogenic source of methane (CH4), providing high-protein food to humans but also causing notable climate risks. With rapid urbanization and increasing income levels in China, the livestock sector will face even higher emission pressures, which could jeopardize China’s carbon neutrality target. To formulate targeted methane reduction measures, it is crucial to estimate historical and current emissions on fine geographical scales, considering the high spatial heterogeneity and temporal variability of livestock emissions. However, there is currently a lack of time-series data on city-level livestock methane emissions in China, despite the flourishing livestock industry and large amount of meat consumed. In this study, we constructed a city-level livestock methane emission inventory with dynamic spatial-temporal emission factors considering biological, management, and environmental factors from 2010 to 2020 in China. This inventory could serve as a basic database for related research and future methane mitigation policy formulation, given the population boom and dietary changes.

Tobacco continuous cropping is prevalent in intensive tobacco agriculture but often leads to microbial community imbalance, soil nutrient deficiency, and decreased crop productivity. While the tobacco-rape rotation has demonstrated significant benefits in increasing tobacco yield. Microorganisms play a crucial role in soil nutrient cycling and crop productivity. However, the internal mechanism of tobacco-rape rotation affecting tobacco yield through microbe-soil interaction is still unclear. In this study, two treatments, tobacco continuous cropping (TC) and tobacco-rape rotation (TR) were used to investigate how planting systems affect soil microbial diversity and community structure, and whether these changes subsequently affect crop yields. The results showed that compared with TC, TR significantly increased the Shannon index, Chao1 index, ACE index of bacteria and fungi, indicating increased microbial α-diversity. On the one hand, TR may directly affect the bacterial and fungal community structure due to the specificity of root morphology and root exudates in rape. Compared with TC, TR significantly increased the proportion of beneficial bacterial and fungal taxa while significantly reduced soil-borne pathogens. Additionally, TR enhanced the scale and complexity of microbial co-occurrence networks, promoting potential synergies between bacterial OTUs. On the other hand, TR indirectly changed microbial community composition by improving soil chemical properties and changing microbial life history strategies. Compared with TC, TR significantly increased the relative abundance of copiotrophs while reduced oligotrophs. Notably, TR significantly increased tobacco yield by 39.6% compared with TC. The relationships among yield, microbial community and soil chemical properties indicated that planting systems had the greatest total effect on tobacco yield, and the microbial community, particularly bacteria, had the greatest direct effect on tobacco yield. Our findings highlighted the potential of tobacco-rape rotation to increase yield by both directly and indirectly optimizing microbial community structure.

Abstract China’s rapid increase in mass excreta and its environmental discharge have attracted substantial attention. However, cropland as a main destination of excreta utilization has not been extensively evaluated. Here, a national survey was used to assess the utilization of manure in croplands across China. The data included the inputs of manure nitrogen (N), phosphorus (P), and potassium (K) for cereals, fruits, vegetables, and other crops, along with the manure proportion of total N, P, and K inputs at the county level. The results showed that the manure N, P, and K inputs were 6.85, 2.14, and 4.65 million tons (Mt), respectively, constituting 19.0%, 25.5%, and 31.1% of the total N, P, and K, respectively. The spatial distribution of the manure proportion of total inputs was lower in Eastern China and higher in Western China. The results provide a detailed description of the utilization of manure nutrients in agricultural areas throughout China, which will serve as basic support for policymakers and researchers involved in future agricultural nutrient management in China.

Abstract Background Plant–soil feedback (PSF) has gained increasing interest in agricultural systems. An important question is whether PSF differs between different cropping systems. Few attempts have yet been made to identify the pathogen species involved in negative PSF. Here, we hypothesize that the strength of negative PSF experienced by a crop species is determined by the relative abundance of host-specific soil-borne pathogenic fungi, that is in turn driven by the crop’s relative abundance (in time). Methods We performed a PSF experiment, with different soils originating from three cropping systems in the North China Plain and three crop species (wheat, maize, soybean) in a full factorial design. Soil fungal community composition and relative abundance of fungal (pathogen) species in each treatment was identified by metabarcoding using ITS (Internal Transcribed Spacer) sequencing. Results PSF ranged from negative for wheat, neutral to negative for soybean and neutral to positive for maize, but the former density of a crop in a particular cropping system did not affect the strength of PSF experienced by each of the three. No relationships between fungal pathogen abundance and PSF were found, but we did find a surprisingly large enrichment across steps of the experiment of Chaetomium spp., a known cellulose-degrading fungus. This may be explained by addition of filter paper on the bottom of the pots. Conclusions Our results suggest that the strength of PSF in these crops is not related to the relative abundance of specific fungal pathogens. However, we cannot rule out that our results were affected by the high abundance of one particular cellulose-degrading fungus. This highlights both the need to stop the practice of using filter paper in pot experiments, as well as the relevance of assessing the identity, relative abundance and potential functions of fungal taxa in PSF experiments.

Measurement(s) reactive N loss Technology Type(s) random forest model Sample Characteristic - Environment cropland Sample Characteristic - Location China

Generic approach for rapid prototyping is essential for the progress of synthetic biology. Here the authors modify the cell-free translation system to control protein aggregation and folding and validate the approach by using single conditions for prototyping of various disulfide-constrained polypeptides.

Researchers have previously described the response of crop productivity and greenhouse gas (GHG) emissions to fertilizer nitrogen (N) additions, but they have not determined how to maximize yields while minimizing GHG emissions. We conducted an experiment at 2293 sites with four N levels to simulate both grain yield and yield-scaled GHG emissions in response to the N addition. The yield-scaled GHG emissions decreased by 16% as the N rate increased from treatments without the N addition to the minimum yield-scaled GHG emissions, which was comparable to the values associated with the maximum grain yields. The sites with both high soil productivity and high crop productivity had the highest yield and lowest yield-scaled GHG emissions, with 43% higher yield and 38% lower yield-scaled GHG emissions than sites with low soil and low crop productivity. These findings are expected to enhance evaluations of wheat production and GHG emissions in China, and thereby contribute to addressing disparities in the global food and GHG budget.

The limited available information on variations in yield gaps (differences between actual yields and the theoretically attainable yields) restricts the development of rational strategies to optimize yields and reduce environmental costs. Quantifying the yield potential and the variations in yield gaps will help identify factors that limit yields and will enable a narrowing of the current yield gap. Here, we applied an analytical framework to yield data to identify options for closing the yield gap at the county level. We used a database containing yields for 40 counties and data from 87 representative on-farm experiments in Jilin Province, China, from 2006 to 2008. The yield potential was simulated for each region-year using a Hybrid-Maize model (http://www.hybridmaize.unl.edu/) and weather data. We then conducted a systematic and spatial analysis of actual yields to identify yield gaps at the county level. The simulated average potential yield at 27 representative sites was 15.2 Mg ha−1 (range 8.1–17.6 Mg ha−1) in Jilin Province. The on-farm experiments suggested an attainable potential yield ranging from 8.7 to 16.7 Mg ha−1 across Jilin Province. During this period, the actual maize yield varied between 4.1 and 11.9 Mg ha−1, according to the county-level data. Farmers’ fields, therefore, achieved 52% of the model yield potential and 77% of the attainable potential yield. Widely different amounts of P fertilizer input among farmers contributed significantly to regional variations in YGE. Soil Olsen-P and rainfall were also major factors. The results indicate that there is great potential to substantially increase the maize yield in non-optimal P management regions, such as in the western Jilin Province. Hence, improvements in regional P management strategies, such as at the county level, need to be assessed separately to provide a basis for increasing the actual maize yield.

ABSTRACT Enhancing soil phosphate solubilization is a promising strategy for agricultural sustainability, while little is known about the mechanisms of how microorganisms cope with differing phosphorus availability. Using a combination of genome-resolved metagenomics and amplicon sequencing, we investigated the microbial mechanisms involved in phosphorus cycling under three agricultural treatments in a wheat-maize rotation system and two natural reforestation treatments. Available soil phosphorus was the key factor shaping bacterial and fungal community composition and function across our agricultural and reforestation sites. Membrane-bound quinoprotein glucose dehydrogenase (PQQGDH) and exopolyphosphatases (PPX) governed microbial phosphate solubilization in agroecosystems. In contrast, genes encoding glycerol-3-phosphate transporters (ugpB, ugpC, and ugpQ) displayed a significantly greater abundance in the reforestation soils. The gcd gene encoding PQQGDH was found to be the best determinant for bioavailable soil phosphorus. Metagenome-assembled genomes (MAGs) affiliated with Cyclobacteriaceae and Vicinamibacterales were obtained from agricultural soils. Their MAGs harbored not only gcd but also the pit gene encoding low-affinity phosphate transporters. MAGs obtained from reforestation soils were affiliated with Microtrichales and Burkholderiales. These contain ugp genes but no gcd, and thereby are indicative of a phosphate transporter strategy. Our study demonstrates that knowledge of distinct microbial phosphorus acquisition strategies between agricultural and reforestation soils could help in linking microbial processes with phosphorus cycling. IMPORTANCE The soil microbiome is the key player regulating phosphorus cycling processes. Identifying phosphate-solubilizing bacteria and utilizing them for release of recalcitrant phosphate that is bound to rocks or minerals have implications for improving crop nutrient acquisition and crop productivity. In this study, we combined functional metagenomics and amplicon sequencing to analyze microbial phosphorus cycling processes in natural reforestation and agricultural soils. We found that the phosphorus acquisition strategies significantly differed between these two ecosystems. A microbial phosphorus solubilization strategy dominated in the agricultural soils, while a microbial phosphate transporter strategy was observed in the reforestation soils. We further identified microbial taxa that contributed to enhanced phosphate solubilization in the agroecosystem. These microbes are predicted to be beneficial for the increase in phosphate bioavailability through agricultural practices.

Improving soil organic carbon (SOC) has been considered as a “win-win way” for ensuring high crop productivity and mitigating chemical N input. Improving SOC can achieve higher wheat yield and simultaneously improve nitrogen (N) productivity (defined as kg grain produced per kg total N input from both indigenous and applied N). Two treatments were tested for improving SOC level. The manure treatment involved applying manure for 6 successive years, and the EM treatment involved adding peat and vermiculite once, both combined with optimized in-season N management. The performance of these two systems were compared with a traditional farming system (Control, where only straw was returned each season). N fertilizer input under all three treatments was optimized by in-season N management and was increased by 90.1% and 48.1% under EM and Manure treatments, respectively, as compared with Control. The average wheat yield for the EM and Manure treatments was 9.1 and 9.2 Mg ha–1, respectively, across all three years, which was 18.8% and 19.7% higher, respectively, than that of the Control treatment (7.7 Mg ha–1). The average chemical N application rates for the EM and Manure treatments were 139 and 146 kg ha–1, which were 24.9% and 21.1% lower than those of the Control treatment, respectively. The N productivity was 15.1% and 14.9% which was higher under Manure and EM treatments than that of the Control treatment. The high yield and N productivity were attributed to improved aboveground dry matter and N uptake by wheat, with optimal soil N supply of the root zone. The higher stem number and weight seen in individual plants with increasing SOC resulted in larger spikes and grains at harvest. Our results determined that increasing SOC combined with optimal N management achieve low chemical N input and higher grain yield by increasing productive stems and grains per spike for improving wheat individual growth.

Previous studies have shown that zinc (Zn) accumulation in shoot and grain increased as applied nitrogen (N) rate increased only when Zn supply was not limiting, suggesting a synergistic effect of N on plant Zn accumulation. However, little information is available about the effects of different mineral N sources combined with the presence or absence of Zn on the growth of both shoot and root and nutrient uptake. Maize plants were grown under sand-cultured conditions at three N forms as follows: NO3– nutrition alone, mixture of NO3–/NH4+ with molar ratio of 1:1 (recorded as mixed-N), and NH4+ nutrition alone including zero N supply as the control. These treatments were applied together without or with Zn supply. Results showed that N forms, Zn supply, and their interactions exerted a significant effect on the growth of maize seedlings. Under Zn-sufficient conditions, the dry weight (DW) of shoot, root, and whole plant tended to increase in the order of NH4+ < NO3– < mixed-N nutrition. Compared with NH4+ nutrition alone, mixed-N supply resulted in a 27.4 and 28.1% increase in leaf photosynthetic rate and stomatal conductance, which further resulted in 35.7 and 33.5% of increase in shoot carbon (C) accumulation and shoot DW, respectively. Furthermore, mixed-N supply resulted in a 19.7% of higher shoot C/N ratio vs. NH4+ nutrition alone, which means a higher shoot biomass accumulation, because of a significant positive correlation between shoot C/N ratio and shoot DW (R2 = 0.682***). Additionally, mixed-N supply promoted the greatest root DW, total root length, and total root surface area and synchronously improved the root absorption capacity of N, iron, copper, manganese, magnesium, and calcium. However, the above nutrient uptake and the growth of maize seedlings supplied with NH4+ were superior to either NO3– or mixed-N nutrition under Zn-deficient conditions. These results suggested that combined applications of mixed-N nutrition and Zn fertilizer can maximize plant growth. This information may be useful for enabling integrated N management of Zn-deficient and Zn-sufficient soils and increasing plant and grain production in the future.

Balancing crop productivity with resource use efficiency and beneficial environmental consequences is essential for sustainable agricultural development worldwide. Various strategies and approaches have been proposed and debated, but turning the concept into management practices in the field with measurable outcomes over several scales remains a challenge. An innovative approach, Integrated Soil-Crop System Management (ISSM), for producing more grain with greater nutrient use efficiencies and less environmental pollution is presented. The ISSM approach has been used in China, in field experiments as well as in thousands of farmer fields, to substantially increase the yields of maize, rice and wheat while simultaneously increasing nitrogen use efficiency and reducing environmental footprints. The scientific principle, implementation strategy and procedures of ISSM are discussed and examples of its demonstrated successes at local and regional levels across China are given. Perspectives for further development of ISSM and expanding its potential impact are also proposed and discussed.

Phosphorous (P) fixation in saline soils is a concern worldwide. To investigate optimization strategies for P fertilizer application that improve P use efficiency (PUE) and crop yield in saline soil, in terms of P sources and rates, we conducted a two year field experiment in the coastal saline area of China to investigate the effects of P rates and sources, including superphosphate (SSP), monoammonium phosphate (MAP) and ammonium polyphosphate (APP) on yield, aboveground P uptake, agronomy efficiency (AEP), and soil available P of winter wheat (Triticum aestivum L.). Wheat yield, under the three P sources, increased with P rates and reached a plateau under 20 kg P ha−1 SSP,18 kg P ha−1 MAP, and 17 kg P ha−1 MAP, respectively. The application of SSP increased the wheat yield by 9–11% compared to MAP and APP. The aboveground P uptake of winter wheat under SSP was 14% and 13% higher than MAP and APP, respectively, under the optimal P application rate. The AEP under SSP was higher than the other two P sources under the same P rate. SSP increased the soil Ca2+ concentration by 20–42%, but decreased the Na+ concentration by 14–18% at the P rate of 26 kg P ha−1 in all soil layers, including 0–20, 20–40, 40–60 cm, compared to CK (0 kg P ha−1). The soil Olsen-P concentration under APP was higher than the other P sources. This study suggests that optimizing P sources and rates can improve wheat yield, PUE, and soil quality in the coastal saline soil.

Abstract Growing evidence indicates that climate change has significant impacts on crop production. However, the spatial variability and extent of the impacts on N concentrations in crops have yet to be explicitly described, although N concentration is a critical element of both the nutritional value of food and the planning of appropriate field management procedures. We present multi‐tiered evidence showing that warming increases N concentration in rice and reduces internal N use efficiency (iNUE), thereby increasing N uptake in crops and encouraging greater N fertilizer use. First, we mapped current N concentrations and iNUE for single‐season irrigation paddy rice production in 975 counties across China using data from 1,637 on‐farm experiments and Random Forest regression modeling. Current N concentrations in rice grain and straw have increased with increasing temperatures from northern to southern China. The global meta‐analysis provided further direct evidence that warming increases N concentration in rice. Future warming projections indicate that N concentrations in grain will increase by 5%–9.6% and that iNUE will decrease by 9%–14% under scenarios RCP4.5 and RCP 8.5 although higher CO2 and other factors may also affect N concentrations. Overall, these data demonstrate that N uptake by rice will need to increase by 7.8%–13.6% to maintain current grain yields across China based on warming alone. Our findings indicate that warming associated with increase in N concentration and reduction in iNUE would be expected to encourage N application, raise the urgency of measures to prevent excessive N application, and stronger counteracting measures need to be enacted.

The COVID-19 pandemic brought profound changes to all corners of society and affected people in every aspect of their lives. This survey-based study investigated how household food related matters such as food sourcing and consumption behaviors of 2,126 Chinese consumers in different age groups changed approximately two months into the COVID-19 quarantine. A new food sourcing mechanism, community-based online group grocery-ordering (CoGGO), was widely adopted by households, particularly among the youngest group studied (18-24 years of age). The same group showed a higher confidence in the food supply system during the quarantine and a greater propensity for weight gain while staying-at-home. The more mature age group (≥35 years of age) showed heightened vigilance and awareness, with fewer grocery-shopping trips, a higher tendency for purchasing extra food, and less tendency to waste food. Survey findings of the new food-sourcing mechanism, attitudes to food, and changes in behavior among different age groups provide valuable insights to guide policies and management interventions to address matters pertaining to food supply and distribution, food access and household food security, and food waste reduction.

Synthetic biology holds promise to revolutionize the life sciences and biomedicine via expansion of macromolecular diversity outside the natural chemical space. Use of non-canonical amino acids (ncAAs) via codon reassignment has found diverse applications in protein structure and interaction analysis, introduction of post-translational modifications, production of constrained peptides, antibody-drug conjugates, and novel enzymes. However, simultaneously encoding multiple ncAAs in vivo requires complex engineering and is sometimes restricted by the cell's poor uptake of ncAAs. In contrast the open nature of cell-free protein synthesis systems offers much greater freedom for manipulation and repurposing of the biosynthetic machinery by controlling the level and identity of translational components and reagents, and allows simultaneous incorporation of multiple ncAAs with non-canonical side chains and even backbones (N-methyl, D-, β-amino acids, α-hydroxy acids etc.). This review focuses on the two most used Escherichia coli-based cell-free protein synthesis systems; cell extract- and PURE-based systems. The former is a biological mixture with >500 proteins, while the latter consists of 38 individually purified biomolecules. We delineate compositions of these two systems and discuss their respective advantages and applications. Also, we dissect the translational components required for ncAA incorporation and compile lists of ncAAs that can be incorporated into polypeptides via different acylation approaches. We highlight the recent progress in using unnatural nucleobase pairs to increase the repertoire of orthogonal codons, as well as using tRNA-specific ribozymes for in situ acylation. We summarize advances in engineering of translational machinery such as tRNAs, aminoacyl-tRNA synthetases, elongation factors, and ribosomes to achieve efficient incorporation of structurally challenging ncAAs. We note that, many engineered components of biosynthetic machinery are developed for the use in vivo but are equally applicable to the in vitro systems. These are included in the review to provide a comprehensive overview for ncAA incorporation and offer new insights for the future development in cell-free systems. Finally, we highlight the exciting progress in the genomic engineering, resulting in E. coli strains free of amber and some redundant sense codons. These strains can be used for preparation of cell extracts offering multiple reassignment options.

The ability of Mycobacterium tuberculosis (M. tb) to survive and persist in the host for decades in an asymptomatic state is an important aspect of tuberculosis pathogenesis. Although adaptation to hypoxia is thought to play a prominent role underlying M. tb persistence, how the bacteria achieve this goal is largely unknown. Rv0081, a member of the DosR regulon, is induced at the early stage of hypoxia while Rv3334 is one of the enduring hypoxic response genes. In this study, we uncovered genetic interactions between these two transcription factors. RNA-seq analysis of ΔRv0081 and ΔRv3334 revealed that the gene expression profiles of these two mutants were highly similar. We also found that under hypoxia, Rv0081 positively regulated the expression of Rv3334 while Rv3334 repressed transcription of Rv0081. In addition, we demonstrated that Rv0081 formed dimer and bound to the promoter region of Rv3334. Taken together, these data suggest that Rv0081 and Rv3334 work in the same regulatory pathway and that Rv3334 functions immediately downstream of Rv0081. We also found that Rv3334 is a bona fide regulator of the enduring hypoxic response genes. Our study has uncovered a regulatory pathway that connects the early and the enduring hypoxic response, revealing a transcriptional cascade that coordinates the temporal response of M. tb to hypoxia.

How Mycobacterium tuberculosis (Mtb) escapes autophagy-mediated clearance is poorly understood. Here, Liu et al. show that Mtb-induced MicroRNA-27a targets the ER-associated calcium transporter CACNA2D3, leading to suppression of antimicrobial autophagy and to enhanced intracellular survival of Mtb.

In China, deep tillage (DT; to >20 cm soil depth) has increased crop yields by improving soil properties, while no-tillage (NT) has been recommended to reduce the labor and machinery costs. Local farmers are willing to adopted rotary tillage (RT; harrowing to 10–15 cm depth) for easy management. However, the effects of these tillage management methods on agronomic productivity, greenhouse gas (GHG) emissions, soil organic carbon (SOC) sequestration, and economic return have not been quantified systematically, and their effectiveness remains in question. Here, we present a meta-analysis of the effects of these methods using 665 paired measurements from 144 peer-reviewed studies. The results indicated that DT significantly increased crop yields by 7.5% relative to RT, and even greater increases were observed in regions with low temperatures and with a wheat cropping system. In contrast, NT resulted in a yield reduction of 3.7% relative to RT, however, controlling for the appropriate temperature and long extension duration (>15 yr) could reduce yield losses and even increase the yield. Both DT and NT significantly enhanced SOC sequestration relative to RT. Adoption of DT would lead to both higher total GHG emissions (N2O and CH4) and increased energy costs, while NT reduced GHG emissions. DT management exhibited a positive net profit for all cropping systems; NT decreased the net profit for rice and wheat but increased the profit for maize. Our study highlighted the agronomic, environmental, and economic benefits and trade-offs for the different tillage methods and should enable investors and policymakers to ensure the best tillage management decisions are made depending on the location-specific conditions.

Agriculture in China, which is dominated by millions of smallholders, consumes 30% of global nitrogen (N) fertilizers and results in a high surplus and vast spatial variability of N. Identifying the N-management practices of smallholder farmers is critical to pursuing sustainable agricultural productivity. However, at the national scale, N budgets and spatial distribution based on first-hand data from smallholder farmers are not well characterized. Here, using data collected from a national survey involving 7.3 million farmers from 2005 to 2014, we quantified N budgets, evaluated their spatial variation, and revealed “hotspots” of low N removal and high N surplus for wheat, maize, and rice systems at the county level. The N surplus for cereal crops was 122–140 kg N ha−1, which is equivalent to an annual N surplus of 11.3 megaton (Mt). Chemical N was the most important contributor to the N surplus, while farmers used manure N less than 10% of the total N input. N budgets exhibited vast spatial variation at the county level, and the hotspots contributed to 56% of the total N surplus in China. Targeted efforts for eliminating hotspots could increase N removal by 13–21%, increase N use efficiency to 0.55–0.70, and significantly reduce the N surplus for all counties and crops, by 42%. Based on farmer survey data, our results provide updated estimates of N budgets and highlight hotspots of N surplus for cereal crop systems in China. They provide a benchmark for the development of new agricultural N management policies and technologies in the country.

Overuse of mineral fertilizer has become common at the North China Plain. Simultaneously, more organic manure resources are available for smallholder farmers. In order to increase the use of organic manure and reduce mineral fertilizer applications, a 10-year fertilization experiment with maize took place between 2008 and 2017. We assessed the long-term effects of cattle manure (CM) application and a complete nutrient substitution with mineral fertilizer (MF) at four application levels (3, 6, 9 and 12 t ha−1 CM) on yield, macronutrients (N, P and K) use efficiencies and soil conditions. Results showed that maize yields from CM and MF treatments differed across time and were significantly different in the first year of the experiment to no significant differences with increasing experimental time. In addition, increased MF levels did not result in increased maize yields; this response was different with CM applications. The highest 10-year maize average yield was 7.7 t ha−1 obtained with 9 t ha−1 of CM. Our results also showed that at the lowest application level (3 t ha−1 CM), the partial factor productivity (PFP) and the agronomic efficiency (AE) of all macronutrients were significantly higher with MF than with CM applications. Nevertheless, these differences narrowed with increased fertilizer input levels. The MF and CM recovery efficiency (RE) of N, P and K performed differently. Generally, MF exhibited significantly higher N-RE than CM treatments. CM treatments had significantly higher P-RE, but no K-RE differences were found between CM and MF. Soil available N, P and K significantly increased when fertilizer levels raised. MF treatments exhibited similar levels of soil available N, but lower soil available P and K compared with CM treatments.

Organic fertilizer is an effective substitute for mineral fertilizer that improves crop yield and is environmentally friendly. However, the effects of substitution often vary due to complicated interactions among the organic fertilizer substitution rate (Rs), total nutrient supply, and type of cropping system used. We performed a meta-analysis of 133 maize studies, conducted worldwide, to assess maize yield and environmental performance with substitution of mineral fertilizer with organic fertilizer. At an equivalent nitrogen (N) rate, substituting mineral fertilizer with organic fertilizer increased maize yield by 4.22%, reduced NH3 volatilization by 64.8%, reduced N leaching and runoff by 26.9%, and increased CO2 emissions by 26.8%; however, it had no significant effect on N2O or CH4 emissions. Moreover, substitution with organic fertilizer increased the soil organic carbon sequestration rate by 925 kg C ha−1 yr−1 and decreased the global warming potential by 116 kg CO2 eq ha−1 compared with mineral fertilizer treatment. The net global warming potential after organic fertilizer substitution was −3507 kg CO2 eq ha−1, indicating a net carbon sink. Furthermore, the effect of organic fertilizer substitution varied with the fertilization rate, Rs, and treatment duration. Maize yield and nitrogen use efficiency tended to increase with increasing N application rate following substitution of mineral fertilizer with organic fertilizer. Full substitution reduced N losses more than partial substitution. Further analysis revealed that the yield-optimal Rs for organic N in maize production was 40–60%. Moreover, maize yield and nitrogen use efficiency were further increased after long-term (≥ 3 years) combined use of organic and mineral fertilizers. These findings suggest that rational use of organic and mineral fertilizers improves maize productivity, increases soil organic carbon sequestration, and reduces N and C losses.

As efforts to close crop production yield gaps increase, the need has emerged to identify cost-effective strategies to reduce yield losses through soil improvement. Maize (Zea mays L.) production in coastal saline soil is limited by high salinity and high pH, and a limited number of soil amendment options are available. We performed a field experiment in 2015 and 2016 to evaluate the ability of combined flue gas desulfurization gypsum and furfural residue application (CA) to reduce the maize yield gap and improve soil properties. We carried out the same amendment treatments (CA and no amendment as a control) under moderate (electrical conductivity (EC1:1) ≈ 4 dS m−1) and high (EC1:1 ≈ 6 dS m−1) salinity levels. Averaged over all salinity levels and years, maize yields increased from 32.6% of yield potential in the control to 44.2% with the CA treatments. Post-harvest CA treatment increased the calcium (Ca2+) and soil organic carbon (SOC) contents while decreasing the sodium (Na+) content and pH in the upper soil layer. Corresponding nitrogen, phosphorus, potassium, calcium, and magnesium accumulations in maize were significantly increased, and Na accumulation was decreased in the CA group compared with the control. The economic return associated with CA treatment increased by 215 $ ha−1 at the high salinity level compared with the control, but decreased at the moderate salinity level because of the minor increase in yield. The results of this study provide insight into the reduction of yield gaps by addressing soil constraints.

Understanding the physiological changes associated with high grain yield and high N use efficiency (NUE) is important when increasing the plant density and N rate to develop optimal agronomic management. We tested the hypothesis that high plant densities resulting in crowding stress reduce the ability of plants to use the N supply post-silking, thus decreasing the grain yield and NUE. In 2013 and 2014, a field experiment, with five N-application rates and three plant densities (6.0, 7.5, and 9.0 plants m-2), was conducted in the North China Plain (NCP). The calculated maximum grain yield and agronomic use efficiency (AEN) at a density of 7.5 plants m-2 were 12.4 Mg ha-1 and 39.3 kg kg-1, respectively, which were significantly higher than the values obtained at densities of 6.0 (11.3 Mg ha-1 and 30.2 kg kg-1) and 9.0 plant m-2 (11.7 Mg ha-1 and 27.8 kg kg-1). A high plant density of 9.0 plants m-2 decreased the post-silking N accumulation, leaf N concentration and net photosynthesis, which reduced the post-silking dry matter production, resulting in a low yield and NUE. Although a relatively low grain yield was observed at a density of 9.0 plants m-2, the optimal N rate increased from 150 to 186 kg N ha-1 at a density of 7.5 plants m-2. These results indicate that high plant densities with crowding stress reduce the ability of plants to use soil N during the post-silking period, and high rate of N fertilizer was needed to increase grain yield. We conclude that selecting the appropriate plant density combined with optimal N management could increase grain yields and the NUE in the NCP.

Certain minerals possess structures that convey properties which improve soil quality; however, their application in coastal saline areas has been poorly studied. In this study, we explored the effects of combining mineral amendments on the improvement of wheat yield and soil properties in a two-year field experiment in mildly saline coastal soil areas of the Yellow River Delta, China. Five mineral materials were combined into the following four treatments: zeolite + rock phosphate (ZP), zeolite + silica calcium soil conditioner (ZC), vermiculite + rock phosphate (VP), and vermiculite + medical stone (VS). For all treatments, combined mineral amendments increased wheat yield compared to the control, with similar increases in yield following treatment with VP (45.7%), ZP (43.5%), and ZC (43.6%), and a significantly smaller increase following VS treatment (26.3%). These increases in grain yield were attributed to larger dry matter accumulation and higher grain numbers per ha. Compared to the control, ZP and ZC application substantially reduced soluble magnesium (Mg) and sodium (Na) contents, electrical conductivity (EC), and sodium adsorption ratio (SAR), and increased soil organic carbon (SOC) at a soil depth of 0⁻20 cm. VP application increased soil available phosphorus (P) by 34.7% and soluble potassium (K) by 69.3% at a soil depth of 0⁻20 cm. VS application slightly increased the SOC, total nitrogen (N), available P, and soluble K compared to the control. Overall, these results indicate that combining mineral amendments significantly increases wheat yield and improves soil properties in a saline area. Thus, we recommend the use of mineral amendments in saline coastal areas.

Active crop canopy sensors can be used for non-destructive real-time diagnosis of crop nitrogen (N) status and guiding in-season N management. However, limited studies have compared the performances of two commercially available sensors with three different wavebands: Crop Circle ACS-470 (CC-470) and Crop Circle ACS-430 (CC-430). The objective of this study was to evaluate the performances of CC-470 and CC-430 sensors for estimating winter wheat (Triticum aestivum L.) N status at different measurement heights (40 cm, 70 cm and 100 cm) and growth stages. Results indicated that the canopy reflectance values of CC-470 were more affected by height compared to the CC-430 sensor. The normalized difference red edge (NDRE) and red edge chlorophyll index (CIRE) of CC-430 were stable at the three different measuring heights. The relationships between these indices and the N status indicators were stronger at the Feekes 9–10 stages than the Feekes 6–7 stages for both sensors; however, the CC-430 sensor-based vegetation indices had higher coefficient of determination (R2) values for both stages. It is concluded that the CC-430 sensor is more reliable than CC-470 for winter wheat N status estimation due to its capability of making height-independent measurements. These results demonstrated the importance of considering the influences of height when using active canopy sensors in field measurements.

The transcription regulatory system of Mycobacterium tuberculosis (M. tb) remains incompletely understood. In this study, we have applied the eGLECLUBS algorithm to a group of related prokaryotic genomes for de novo genome-wide prediction of cis-regulatory binding sites (CRBSs) in M. tb H37Rv. The top 250 clusters from our prediction recovered 83.3% (50/60) of all known CRBSs in extracted inter-operonic sequences of this strain. We further demonstrated that the integration of our prediction results with the ChIP-Seq datasets is very effective in identifying true binding sites of TFs. Using electrophoretic mobility shift assays and real-time RT-PCR, we experimentally verified our prediction of CRBSs for Rv0081, an important transcription factor thought to be involved in regulation of M. tb under hypoxia.

The relationships between grain yields and whole-plant accumulation of micronutrients such as zinc (Zn), iron (Fe), manganese (Mn) and copper (Cu) in maize (Zea mays L.) were investigated by studying their reciprocal internal efficiencies (RIEs, g of micronutrient requirement in plant dry matter per Mg of grain). Field experiments were conducted from 2008 to 2011 in North China to evaluate RIEs and shoot micronutrient accumulation dynamics during different growth stages under different yield and nitrogen (N) levels. Fe, Mn and Cu RIEs (average 64.4, 18.1 and 5.3 g, respectively) were less affected by the yield and N levels. ZnRIE increased by 15% with an increased N supply but decreased from 36.3 to 18.0 g with increasing yield. The effect of cultivars on ZnRIE was similar to that of yield ranges. The substantial decrease in ZnRIE may be attributed to an increased Zn harvest index (from 41% to 60%) and decreased Zn concentrations in straw (a 56% decrease) and grain (decreased from 16.9 to 12.2 mg kg-1) rather than greater shoot Zn accumulation. Shoot Fe, Mn and Cu accumulation at maturity tended to increase but the proportions of pre-silking shoot Fe, Cu and Zn accumulation consistently decreased (from 95% to 59%, 90% to 71% and 91% to 66%, respectively). The decrease indicated the high reproductive-stage demands for Fe, Zn and Cu with the increasing yields. Optimized N supply achieved the highest yield and tended to increase grain concentrations of micronutrients compared to no or lower N supply. Excessive N supply did not result in any increases in yield or micronutrient nutrition for shoot or grain. These results indicate that optimized N management may be an economical method of improving micronutrient concentrations in maize grain with higher grain yield.

Sustainable agriculture requires improved phosphorus (P) management to reduce the overreliance on P fertilization. Despite intensive research of root adaptive mechanisms for improving P acquisition, the inherent potential of roots for efficient P acquisition remains unfulfilled, especially in intensive agriculture, while current P management generally focuses on agronomic and environmental concerns. Here, we investigated how levels of soil P affect the inherent potential of maize (Zea mays L.) roots to obtain P from soil. Responses of root morphology, arbuscular mycorrhizal colonization, and phosphate transporters were characterized and related to agronomic traits in pot and field experiments with soil P supply from deficiency to excess. Critical soil Olsen-P level for maize growth approximated 3.2 mg kg(-1), and the threshold indicating a significant environmental risk was about 15 mg kg(-1), which represented the lower and upper levels of soil P recommended in current P management. However, most root adaptations involved with P acquisition were triggered when soil Olsen-P was below 10 mg kg(-1), indicating a threshold for maximum root inherent potential. Therefore, to maintain efficient inherent potential of roots for P acquisition, we suggest that the target upper level of soil P in intensive agriculture should be reduced from the environmental risk threshold to the point maximizing the inherent potential of roots.

The overuse of Nitrogen (N) fertilizers on smallholder farms in rapidly developing countries has increased greenhouse gas (GHG) emissions and accelerated global N consumption over the past 20 years. In this study, a regional N management approach was developed based on the cost of the agricultural response to N application rates from 1,726 on-farm experiments to optimize N management across 12 agroecological subregions in the intensive Chinese smallholder maize belt. The grain yield and GHG emission intensity of this regional N management approach was investigated and compared to field-specific N management and farmers' practices. The regional N rate ranged from 150 to 219 kg N ha(-1) for the 12 agroecological subregions. Grain yields and GHG emission intensities were consistent with this regional N management approach compared to field-specific N management, which indicated that this regional N rate was close to the economically optimal N application. This regional N management approach, if widely adopted in China, could reduce N fertilizer use by more than 1.4 MT per year, increase maize production by 31.9 MT annually, and reduce annual GHG emissions by 18.6 MT. This regional N management approach can minimize net N losses and reduce GHG emission intensity from over- and underapplications, and therefore can also be used as a reference point for regional agricultural extension employees where soil and/or plant N monitoring is lacking.

Understanding the time-course of dry matter (DM) and nitrogen (N) accumulation in terms of yield-trait relationships is essential to simultaneously increase grain yield and synchronize N demand and N supply. We collected 413 data points from 11 field experiments to address patterns of DM and N accumulation with time in relation to grain yield and management of winter wheat in China. Detailed growth analysis was conducted at the Zadok growth stages (GS) 25 (regreening), GS30 (stem elongation), GS60 (anthesis), and GS100 (maturity) in all experiments, including DM and N accumulation. Grain yield averaged 7.3 Mg ha(-1), ranging from 2.1 to 11.2 Mg ha(-1). The percent N accumulation was consistent prior to DM accumulation, while both DM and N accumulation increased continuously with growing time. Both the highest and fastest DM and N accumulations were observed from stem elongation to the anthesis stage. Significant correlations between grain yield and DM and N accumulation were found at each of the four growth stages, although no positive relationship was observed between grain yield and harvest index or N harvest index. The yield increase from 7-9 Mg ha(-1) to >9 Mg ha(-1) was mainly attributed to increased DM and N accumulation from stem elongation to anthesis. Although applying more N fertilizer increased N accumulation during this stage, DM accumulation was not improved, indicating that N fertilizer management and related agronomic management should be intensified synchronously across the wheat growing season to simultaneously achieve high yields and match N demand and N supply.

BACKGROUND: The 10-kDa culture filtrate protein (CFP10) and 6-kDa early-secreted target antigen (ESAT-6) play important roles in mycobacterial virulence and pathogenesis through a 1:1 complex formation (CFP10/ESAT-6 protein, CE protein), which have been used in discriminating TB patients from BCG-vaccinated individuals. The B-cell epitopes of CFP10 and ESAT-6 separately have been analyzed before, however, the epitopes of the CE protein are unclear and the precise epitope in the positions 40 to 62 of ESAT-6 is still unknown. METHODS: In the present study, we searched for the B-cell epitopes of CE protein by using phage-display library biopanning with the anti-CE polyclonal antibodies. The epitopes were identified by sequence alignment, binding affinity and specificity detection, generation of polyclonal mouse sera and detection of TB patient sera. RESULTS: One linear B-cell epitope (KWDAT) consistent with the 162(nd)-166(th) sequence of CE and the 57(th)-61(st) sequence of ESAT-6 protein was selected and identified. Significantly higher titers of E5 peptide-binding antibodies were found in the sera of TB patients compared with those of healthy individuals. CONCLUSION: There was a B-cell epitope for CE and ESAT-6 protein in the position 40 to 62 of ESAT-6. E5 peptide may be useful in the serodiagnosis of tuberculosis, which need to be further confirmed by more sera samples.

BACKGROUND: Mycobacterial culture and identification provide a definitive diagnosis of TB. Culture on Löwenstein-Jensen (L-J) medium is invariably delayed because of the slow growth of M. tuberculosis on L-J slants. Automated liquid culture systems are expensive. A low-cost culturing medium capable of rapidly indicating the presence of mycobacteria is needed. The aim of this study was to develop and evaluate a novel biphasic culture medium for the recovery of mycobacteria from clinical sputum specimens from suspected pulmonary tuberculosis patients. METHODS AND FINDINGS: The biphasic medium consisted of 7 ml units of L-J slant medium, 3 ml units of liquid culture medium, growth indicator and a mixture of antimicrobial agents. The decontamination sediments of sputum specimens were incubated in the biphasic culture medium at 37°C. Mycobacterial growth was determined based on the appearance of red granule sediments and the examination using acid-fast bacilli (AFB). The clinical sputum specimens were cultured in the biphasic medium, on L-J slants and in the Bactec MGIT 960 culture system. Among smear-positive specimens, the mycobacteria recovery rate of the biphasic medium was higher than that of the L-J slants (P0.05). Among smear-negative specimens, the mycobacterial recovery rate of the biphasic medium was higher than that of L-J slants (P

OBJECTIVE: To evaluate the performance of phage amplified biologically assay (PhaB) for detecting tuberculosis (TB) in sputum in the pulmonary tuberculosis (PTB) patients. METHODS: Shanghai Tuberculosis Key Laboratory of Shanghai Pulmonary Hospital participated in the project in collaboration with the laboratories of six hospitals and a total of 1660 eligible participants (1351 PTB patients and 309 non-TB patients) were included in the study. The sputum samples from the participants were detected by smear microscopy, PhaB, and Löwenstein-Jensen (L-J) culture method, respectively. RESULTS: The overall sensitivity of PhaB were higher than that of L-J culture and smear microscopy (p

A lack of basic information on optimal nitrogen (N) management often results in over- or under-application of N fertilizer in small-scale intensive rice farming. Here, we present a new database of N input from a survey of 6611 small-scale rice farmers and rice yield in response to added N in 1177 experimental on-farm tests across eight agroecological subregions of China. This database enables us to evaluate N management by farmers and develop an optimal approach to regional N management. We also investigated grain yield, N application rate, and estimated greenhouse gas (GHG) emissions in comparison to N application and farming practices. Across all farmers, the average N application rate, weighted by the area of rice production in each subregion, was 210 kg ha ^−1 and ranged from 30 to 744 kg ha ^−1 across fields and from 131 to 316 kg ha ^−1 across regions. The regionally optimal N rate (RONR) determined from the experiments averaged 167 kg ha ^−1 and varied from 114 to 224 kg N ha ^−1 for the different regions. If these RONR were widely adopted in China, approximately 56% of farms would reduce their use of N fertilizer, and approximately 33% would increase their use of N fertilizer. As a result, grain yield would increase by 7.4% from 7.14 to 7.67 Mg ha ^−1 , and the estimated GHG emissions would be reduced by 11.1% from 1390 to 1236 kg carbon dioxide (CO _2 ) eq Mg ^−1 grain. These results suggest that to achieve the goals of improvement in regional yield and sustainable environmental development, regional N use should be optimized among N-poor and N-rich farms and regions in China.