Pursuing sustainable productivity with millions of smallholder farmers.

Sustainably feeding a growing population is a grand challenge, and one that is particularly difficult in regions that are dominated by smallholder farming. Despite local successes, mobilizing vast smallholder communities with science- and evidence-based management practices to simultaneously address production and pollution problems has been infeasible. Here we report the outcome of concerted efforts in engaging millions of Chinese smallholder farmers to adopt enhanced management practices for greater yield and environmental performance. First, we conducted field trials across China's major agroecological zones to develop locally applicable recommendations using a comprehensive decision-support program. Engaging farmers to adopt those recommendations involved the collaboration of a core network of 1,152 researchers with numerous extension agents and agribusiness personnel. From 2005 to 2015, about 20.9 million farmers in 452 counties adopted enhanced management practices in fields with a total of 37.7 million cumulative hectares over the years. Average yields (maize, rice and wheat) increased by 10.8-11.5%, generating a net grain output of 33 million tonnes (Mt). At the same time, application of nitrogen decreased by 14.7-18.1%, saving 1.2 Mt of nitrogen fertilizers. The increased grain output and decreased nitrogen fertilizer use were equivalent to US$12.2 billion. Estimated reactive nitrogen losses averaged 4.5-4.7 kg nitrogen per Megagram (Mg) with the intervention compared to 6.0-6.4 kg nitrogen per Mg without. Greenhouse gas emissions were 328 kg, 812 kg and 434 kg CO2 equivalent per Mg of maize, rice and wheat produced, respectively, compared to 422 kg, 941 kg and 549 kg CO2 equivalent per Mg without the intervention. On the basis of a large-scale survey (8.6 million farmer participants) and scenario analyses, we further demonstrate the potential impacts of implementing the enhanced management practices on China's food security and sustainability outlook.

Closing yield gaps in China by empowering smallholder farmers.

Sustainably feeding the world's growing population is a challenge, and closing yield gaps (that is, differences between farmers' yields and what are attainable for a given region) is a vital strategy to address this challenge. The magnitude of yield gaps is particularly large in developing countries where smallholder farming dominates the agricultural landscape. Many factors and constraints interact to limit yields, and progress in problem-solving to bring about changes at the ground level is rare. Here we present an innovative approach for enabling smallholders to achieve yield and economic gains sustainably via the Science and Technology Backyard (STB) platform. STB involves agricultural scientists living in villages among farmers, advancing participatory innovation and technology transfer, and garnering public and private support. We identified multifaceted yield-limiting factors involving agronomic, infrastructural, and socioeconomic conditions. When these limitations and farmers' concerns were addressed, the farmers adopted recommended management practices, thereby improving production outcomes. In one region in China, the five-year average yield increased from 67.9% of the attainable level to 97.0% among 71 leading farmers, and from 62.8% to 79.6% countywide (93,074 households); this was accompanied by resource and economic benefits.

Cooperation between specialized livestock and crop farms can reduce environmental footprints and increase net profits in livestock production.

The rapid specialization of livestock production in China has contributed to spatially decoupled crop and livestock production, leading to various environmental pollution issues. Some regional agro-environmental policies have recently promoted the coupling of specialized crop and livestock farms through cooperation. However, the environmental and economic performances of such cooperation remain unclear. This study investigated multiple environmental footprints of two contrasting production systems: cooperative crop-livestock systems (CCLS) and decoupled specialized livestock systems (DSLS), using survey data of 87 ruminant farms in Northwest China. Results show that farms in CCLS had lower net greenhouse gas (GHG) emissions (12-29%), lower reactive nitrogen (Nr) emissions (21-40%), lower phosphorus footprints (PF) (41-54%), and used less cropland (24-31%) per kg animal product, compared to those in DSLS. The large differences in GHG emissions between the two systems were mainly related to enteric fermentation and resource production (used for feed production). The differences in Nr emissions and PF were mainly related to manure management. Net profits per kg animal product were higher in CCLS (13-35%) than in DSLS, and most profits originated from lower purchasing costs of feed and young livestock. Net profits and environmental footprints were negatively correlated, suggesting an environmental and economic win-win situation for CCLS. The possible obstacles to recoupling specialized crop and livestock farms through cooperation have been discussed, including farm size, contract stability, and local policies. Our study provides science-based evidence to support policymakers and specialized farms to close nutrient loops between crop and livestock production sectors through regional cooperation.

The quality of dissolved organic matter extracted at different times from pig compost and its copper binding capacity based on EEM-PARAFAC.

Dissolved organic matter extracted from compost tea, can be regarded as alternatives to inorganic fertilizers as well to be used as a washing agent for heavy metal polluted soil. However, the composition and quality of compost tea produced under different extraction time are still unknown. The objective of the current study was set to explore the influence of different extraction time (i.e., 6, 12, and 24 h) on the composition, quality, and copper binding capacity of compost tea originated from pig manure compost. The results indicated that the extraction time obviously influenced the phenolic, aromatic carboxylic, and polycyclic aromatic groups of compost tea. In addition, the compost tea undergo the shorter extraction time (i.e., 6 and 12 h) contained more protein and humic-like compositions. Among the all treatments tested herein, the compost tea produced from 12 h extraction time obviously exhibited higher aromaticity, molecular weight, and humification degree than other two treatments. The highest stability constant value (log KM) was observed for the shortest extraction time, i.e., 6.08. According to the quality measures and copper binding capability, shorter extraction times (i.e., 6 and 12 h) would be suggested for compost tea production from pig manure compost.

Energy and Nutrient Recovery from Sewage Sludge and Manure via Anaerobic Digestion with Hydrothermal Pretreatment.

Global expectation for sustainability has prompted the transition of practices in wastewater treatment plants toward not only waste management but also energy and nutrient recovery. It has been shown that low-temperature hydrotherm (HT) treatment can enhance downstream biogas production via anaerobic digestion (AD). Yet, because the application of combined HT and AD is still at an early stage, a systematic understanding of the dynamic speciation evolution of important elements is still lacking. This study investigates energy and nutrient recovery from sewage sludge and swine manure via combined HT-AD treatment. Bench-scale investigation was conducted to evaluate biogas production and understand the dynamic evolution of organic carbon (C) and phosphorus (P) speciation. C and P speciations were characterized using complementary chemical and spectroscopic techniques, including 13C nuclear magnetic resonance (NMR) spectroscopy, P X-ray absorption near edge structure (XANES) spectroscopy, and sequential chemical extraction. Results from this study suggest that low-temperature HT pretreatment can achieve enhanced biogas production for sludge compared to the minimal effect on the biogas production from manure. It also provides guidance for P recovery from liquid digestate and solid residue after the AD process.

Ecological risk of copper and zinc and their different bioavailability change in soil-rice system as affected by biowaste application.

A large amount of organic fertilizer application could be accompanied by soil contamination caused by trace heavy metals. A field experiment was carried out in this study to examine the accumulation and availability of copper (Cu) and zinc (Zn) in soil, and their uptake by rice under continuous application of chicken manure, pig manure and sewage sludge. Results showed that after four years of chicken manure, pig manure and sewage sludge application, the soil Cu accumulation rates were 0.15-1.17 mg kg-1 yr-1, 1.01-4.22 mg kg-1 yr-1 and 0.13-1.15 mg kg-1 yr-1, respectively; Zn accumulation rates were 0.54-5.46 mg kg-1 yr-1, 1.51-9.65 mg kg-1 yr-1 and 1.13-10.47 mg kg-1 yr-1, respectively. Compared to the control, the chicken- and pig manure treatments significantly decreased the DTPA-extractable Cu, but increased the DTPA-extractable Zn in soils; thus decreased the Cu contents in rice grain by 2.2-40.6% and increased the grain Zn by 2.6-30.9%, respectively, with increasing application rates and number of years. The addition of sewage sludge significantly increased bioavailability of Zn in soil and its accumulation in rice, while had limited effect on Cu bioavailability. Results suggested that the continuous application of organic fertilizer with elevated Cu and Zn contents at high application rates can induce their accumulation in soil and affect their bioavailability differently.

Exploring Future Food Provision Scenarios for China.

Developing sustainable food systems is essential, especially for emerging economies, where food systems are changing rapidly and affect the environment and natural resources. We explored possible future pathways for a sustainable food system in China, using multiple environmental indicators linked to eight of the Sustainable Development Goals (SDGs). Forecasts for 2030 in a business as usual scenario (BAU) indicate increases in animal food consumption as well as increased shortages of the land available and the water needed to produce the required food in China. Associated greenhouse gas emissions and nitrogen and phosphorus losses could become 10-42% of global emissions in 2010. We developed three main pathways besides BAU [produce more and better food (PMB), consume and waste less food (CWL), and import more food (IMF)] and analyzed their impacts and contributions to achieving one or more of the eight SDGs. Under these scenarios, the demand for land and water and the emissions of GHG and nutrients may decrease by 7-55% compared to BAU, depending on the pathway followed. A combination of PMB and CWL was most effective, while IMF externalizes impacts to countries exporting to China. Modestly increasing feed or food imports in a selective manner could ease the pressure on natural resources. Our modeling framework allows us to analyze the effects of changes in food production-consumption systems in an integrated manner, and the results can be linked to the eight SDGs. Despite formidable technological, social, educational, and structural barriers that need to be overcome, our study indicates that the ambitious targets of China's new agricultural and environmental strategy appear to be achievable.

Transformation of Phosphorus during (Hydro)thermal Treatments of Solid Biowastes: Reaction Mechanisms and Implications for P Reclamation and Recycling.

Phosphorus (P) is an essential nutrient for all organisms, thus playing unique and critical roles at the food-energy-water nexus. Most P utilized by human activities eventually converges into various solid biowastes, such as crop biomass, animal manures, and sewage sludges. Therefore, integration of efficient P recovery practices into solid biowaste management will not only significantly reduce the dependence on limited geological P resources but also reduce P runoff and related water contamination issues associated with traditional waste management strategies. This study reviews the applications of (hydro)thermal techniques for the treatment of solid biowastes, which can greatly facilitate P recovery in addition to waste volume reduction, decontamination, and energy recovery. Research showed that P speciation (including molecular moiety, complexation state, and mineralogy) can experience significant changes during (hydro)thermal treatments, and are impacted by treatment techniques and conditions. Changes in P speciation and overall properties of the products can alter the mobility and bioavailability of P, and subsequent P reclamation and recycling efficiency of the treatment products. This review summarizes recent progresses in this direction, identifies the challenges and knowledge gaps, and provides a foundation for future research efforts targeting at sustainable management of nutrient-rich biowastes.

In situ stable isotope probing of phosphate-solubilizing bacteria in the hyphosphere.

This study used a [(13)C]DNA stable isotope probing (SIP) technique to elucidate a direct pathway for the translocation of (13)C-labeled photoassimilate from maize plants to extraradical mycelium-associated phosphate-solubilizing bacteria (PSB) that mediate the mineralization and turnover of soil organic phosphorus (P) in the hyphosphere. Inoculation with PSB alone did not provide any benefit to maize plants but utilized the added phytate-P to their own advantage, while inoculation with Rhizophagus irregularis alone significantly promoted shoot biomass and P content compared with the control. However, compared with both sole inoculation treatments, combined inoculation with PSB and R. irregularis in the hyphosphere enhanced organic P mineralization and increased microbial biomass P in the soil. There was no extra benefit to plant P uptake but the hyphal growth of R. irregularis was reduced, suggesting that PSB benefited from the arbuscular mycorrhizal (AM) fungal mycelium and competed for soil P with the fungus. The combination of T-RFLP (terminal restriction fragment length polymorphism) analysis with a clone library revealed that one of the bacteria that actively assimilated carbon derived from pulse-labeled maize plants was Pseudomonas alcaligenes (Pseudomonadaceae) that was initially inoculated into the hyphosphere soil. These results provide the first in situ demonstration of the pathway underlying the carbon flux from plants to the AM mycelium-associated PSB, and the PSB assimilated the photosynthates exuded by the fungus and promoted mineralization and turnover of organic P in the soil.

Grain production versus resource and environmental costs: towards increasing sustainability of nutrient use in China.

Over the past five decades, Chinese grain production has increased 4-fold, from 110 Mt in 1961 to 557 Mt in 2014, with less than 9% of the world's arable land feeding 22% of the world's population, indicating a substantial contribution to global food security. However, compared with developed economies, such as the USA and the European Union, more than half of the increased crop production in China can be attributed to a rapid increase in the consumption of chemicals, particularly fertilizers. Excessive fertilization has caused low nutrient use efficiency and high environmental costs in grain production. We analysed the key requirements underpinning increased sustainability of crop production in China, as follows: (i) enhance nutrient use efficiency and reduce nutrient losses by fertilizing roots not soil to maximize root/rhizosphere efficiency with innovative root zone nutrient management; (ii) improve crop productivity and resource use efficiency by matching the best agronomic management practices with crop improvement; and (iii) promote technology transfer of the root zone nutrient management to achieve the target of high yields and high efficiency with low environmental risks on a broad scale. Coordinating grain production and environmental protection by increasing the sustainability of nutrient use will be a key step in achieving sustainable crop production in Chinese agriculture.

Uptake kinetics and translocation of selenite and selenate as affected by iron plaque on root surfaces of rice seedlings.

MAIN CONCLUSION: Iron plaque on root surfaces greatly influenced selenium uptake and played different roles in selenite and selenate uptake. Iron plaque commonly forms on rice root surfaces under flooded conditions, but little is known about the relationship between iron plaque and selenium (Se) accumulation. Here, we investigate the effects of iron plaque on Se uptake by and translocation within rice (Oryza sativa) seedlings, and the kinetics of selenite and selenate influx into rice roots (with or without iron plaque) were determined in short-term (30 min) experiments. Rice seedlings were planted in nutrient solutions containing different levels of ferrous ion for 3 days and then transplanted into nutrient solutions with selenite or selenate. Se concentrations in iron plaque were positively associated with the amounts of iron plaque in both selenite and selenate treatments and iron plaque had a higher affinity for selenite than selenate. Results showed that iron plaque on root surfaces greatly influenced Se uptake and played different roles in selenite and selenate uptake. The selenite and selenate uptake kinetics results demonstrated that the presence of iron plaque enhanced selenite uptake, but decreased selenate uptake. In addition, root-Se concentrations increased with the increasing amounts of iron plaque, but Se translocation from roots to shoots was reduced with the increasing amounts of iron plaque in the +selenite treatment. Iron plaque significantly influenced selenite uptake and might act as a pool to selenite accumulation in rice plants. However, iron plaque had no significant effect on selenate uptake or even as a barrier to selenate uptake.

Phosphorus recovery from biogas fermentation liquid by Ca-Mg loaded biochar.

Shortage in phosphorus (P) resources and P wastewater pollution is considered as a serious problem worldwide. The application of modified biochar for P recovery from wastewater and reuse of recovered P as agricultural fertilizer is a preferred process. This work aims to develop a calcium and magnesium loaded biochar (Ca-Mg/biochar) application for P recovery from biogas fermentation liquid. The physico-chemical characterization, adsorption efficiency, adsorption selectivity, and postsorption availability of Ca-Mg/biochar were investigated. The synthesized Ca-Mg/biochar was rich in organic functional groups and in CaO and MgO nanoparticles. With the increase in synthesis temperature, the yield decreased, C content increased, H content decreased, N content remained the same basically, and BET surface area increased. The P adsorption of Ca-Mg/biochar could be accelerated by nano-CaO and nano-MgO particles and reached equilibrium after 360min. The process was endothermic, spontaneous, and showed an increase in the disorder of the solid-liquid interface. Moreover, it could be fitted by the Freundlich model. The maximum P adsorption amounts were 294.22, 315.33, and 326.63mg/g. The P adsorption selectivity of Ca-Mg/biochar could not be significantly influenced by the typical pH level of biogas fermentation liquid. The nano-CaO and nano-MgO particles of Ca-Mg/biochar could reduce the negative interaction effects of coexisting ions. The P releasing amounts of postsorption Ca-Mg/biochar were in the order of Ca-Mg/B600>Ca-Mg/B450>Ca-Mg/B300. Results revealed that postsorption Ca-Mg/biochar can continually release P and is more suitable for an acid environment.

Application of a rotation system to oilseed rape and rice fields in Cd-contaminated agricultural land to ensure food safety.

This field experiment analyzed the phytoremediation effects of oilseed rape in moderately cadmium (Cd)-contaminated farmland and the food safety of successive rice in an oilseed rape-rice rotation system. Two oilseed rape cultivars accumulated Cd at different rates. The rapeseed cultivar Zhucang Huazi exhibited high Cd accumulation rates, higher than the legal limit for human consumption (0.2mgkg(-1)); Cd concentrations in the cultivar Chuanyou II-93 were all below the maximum allowed level. Planting oilseed rape increased the uptake of Cd by the successive rice crop compared with a previous fallow treatment. Most Cd concentrations of brown rice were below the maximum allowed level. The phytoextraction efficiency was lower in the moderately Cd-contaminated soil in field experiments. The results suggest screening rice cultivars with lower Cd accumulation can assure the food safety; the mobilization of heavy metals by roots of different plant species should be considered during crop rotation to assure food safety.

[Application of ICP-mS and AFS to detecting heavy metals in phosphorus fertilizers].

In order to investigate heavy metals in phosphorus fertilizers in China, 159 samples of phosphorus fertilizers including imported fertilizers and domestic fertilizers were collected from fertilizer markets, and the contents of heavy metals were determined by ICP-MS and AFS after microwave digestion. The results showed that the phosphorous fertilizers contained certain amount of heavy metals, and there was great variability in the contents of heavy metals. The mean contents of Cd, Cu, Zn, Cr, Pb, Ni, As and Hg were 0. 77, 35.6, 102.7, 24. 1, 16.6, 15.4, 19.4 and 0. 08 mg kg-1 fertilizer, respectively; based on the calculation of P2O5, the mean contents of above heavy metals were 4. 48, 258. 4, 767. 4, 190. 0, 151.3, 134. 5, 155. 8 and 8. 79 mg kg-1 P2 O5, respectively. The contents of heavy metals Cd, Cr, Pb, As and Hg in the tested samples accord with the ecological index of arsenic, cadmium, lead, chromium and mercury for fertilizers (GB/T 23349-2009), with the exception of Cd in one imported sample of diammonium phosphate and As in one sample of mono-ammonium phosphate. Analyzing the contents of heavy metals in imported fertilizers, the Cd contents in imported fertilizers was ranged from 0. 02 to 27. 2 mg kg-1 fertilizer, the mean and median Cd contents in imported fertilizers were 3. 20 and 0. 41 mg kg-1 fertilizer, respectively. And the Cu, Cr and Hg contents in the imported fertilizers were higher than that of domestic fertilizers, the mean contents of Cu, Cr and Hg in imported fertilizers were 39. 4, 26. 6 and 0. 47 mg kg-1 fertilizer, respectively.

Maximizing root/rhizosphere efficiency to improve crop productivity and nutrient use efficiency in intensive agriculture of China.

Root and rhizosphere research has been conducted for many decades, but the underlying strategy of root/rhizosphere processes and management in intensive cropping systems remain largely to be determined. Improved grain production to meet the food demand of an increasing population has been highly dependent on chemical fertilizer input based on the traditionally assumed notion of 'high input, high output', which results in overuse of fertilizers but ignores the biological potential of roots or rhizosphere for efficient mobilization and acquisition of soil nutrients. Root exploration in soil nutrient resources and root-induced rhizosphere processes plays an important role in controlling nutrient transformation, efficient nutrient acquisition and use, and thus crop productivity. The efficiency of root/rhizosphere in terms of improved nutrient mobilization, acquisition, and use can be fully exploited by: (1) manipulating root growth (i.e. root development and size, root system architecture, and distribution); (2) regulating rhizosphere processes (i.e. rhizosphere acidification, organic anion and acid phosphatase exudation, localized application of nutrients, rhizosphere interactions, and use of efficient crop genotypes); and (3) optimizing root zone management to synchronize root growth and soil nutrient supply with demand of nutrients in cropping systems. Experiments have shown that root/rhizosphere management is an effective approach to increase both nutrient use efficiency and crop productivity for sustainable crop production. The objectives of this paper are to summarize the principles of root/rhizosphere management and provide an overview of some successful case studies on how to exploit the biological potential of root system and rhizosphere processes to improve crop productivity and nutrient use efficiency.

Improving crop productivity and resource use efficiency to ensure food security and environmental quality in China.

In recent years, agricultural growth in China has accelerated remarkably, but most of this growth has been driven by increased yield per unit area rather than by expansion of the cultivated area. Looking towards 2030, to meet the demand for grain and to feed a growing population on the available arable land, it is suggested that annual crop production should be increased to around 580 Mt and that yield should increase by at least 2% annually. Crop production will become more difficult with climate change, resource scarcity (e.g. land, water, energy, and nutrients) and environmental degradation (e.g. declining soil quality, increased greenhouse gas emissions, and surface water eutrophication). To pursue the fastest and most practical route to improved yield, the near-term strategy is application and extension of existing agricultural technologies. This would lead to substantial improvement in crop and soil management practices, which are currently suboptimal. Two pivotal components are required if we are to follow new trajectories. First, the disciplines of soil management and agronomy need to be given increased emphasis in research and teaching, as part of a grand food security challenge. Second, continued genetic improvement in crop varieties will be vital. However, our view is that the biggest gains from improved technology will come most immediately from combinations of improved crops and improved agronomical practices. The objectives of this paper are to summarize the historical trend of crop production in China and to examine the main constraints to the further increase of crop productivity. The paper provides a perspective on the challenge faced by science and technology in agriculture which must be met both in terms of increased crop productivity but also in increased resource use efficiency and the protection of environmental quality.

Integrated soil-crop system management: reducing environmental risk while increasing crop productivity and improving nutrient use efficiency in China.

During the past 47 yr (1961-2007), Chinese cereal production has increased by 3.2-fold, successfully feeding 22% of the global human population with only 9% of the world's arable land, but at high environmental cost and resource consumption. Worse, crop production has been stagnant since 1996 while the population and demand for food continue to rise. New advances for sustainability of agriculture and ecosystem services will be needed during the coming 50 yr to reduce environmental risk while increasing crop productivity and improving nutrient use efficiency. Here, we advocate and develop integrated soil-crop system management (ISSM). In this approach, the key points are (i) to take all possible soil quality improvement measures into consideration, (ii) to integrate the utilization of various nutrient resources and match nutrient supply to crop requirements, and (iii) to integrate soil and nutrient management with high-yielding cultivation systems. Recent field experiments have shed light on how ISSM can lead to significant increases in crop yields while increasing nutrient use efficiency and reducing environmental risk.

Liraglutide-induced structural modulation of the gut microbiota in patients with type 2 diabetes mellitus.

Accumulating evidence has suggested the importance of gut microbiota in the development of type 2 diabetes mellitus (T2DM). In the present study, 40 patients with T2DM were treated with liraglutide for 4 months. Feces samples and clinical characteristics were collected from these 40 T2DM patients before and after the liraglutide treatment. The diversity and composition of gut microbiota in the two groups were determined by sequencing the V4 region of bacterial 16S rRNA genes. Meanwhile, blood glucose, insulin, hemoglobin A1c (HbA1c), and lipid metabolism were also measured in the pre- and post-liraglutide-treatment groups. We find that Baseline HbA1c was associated with liraglutide treatment response (R 2 = 0.527, ß =  - 0.726, p < 0.0001). After adjusted for baseline HbA1c, blood urea nitrogen was associated with liraglutide treatment response. Besides, our results showed reduced gut microbial alpha diversity, different community structure distribution and altered microbial interaction network in patients treated with liraglutide. The liner discriminant analysis (LDA) effect size (LEfSe) analysis showed that 21 species of bacteria were abundant in the pre-liraglutide-treatment group and 15 species were abundant in the post-liraglutide-treatment group. In addition, we also find that Megamonas were significantly correlated with older age, diabetes duration and diabetic retinopathy, Clostridum were significantly correlated with family history of diabetes and Oscillospira were significantly correlated with both diabetic retinopathy and diabetic peripheral neuropathy. Functional analysis based on Kyoto Encyclopedia of Genes and Genomes (KEGG) and cluster of orthologous groups (COG) annotations enriched three KEGG metabolic pathways and six functional COG categories in the post-liraglutide-treatment group. In conclusion, our research suggests that baseline HbA1c, blood urea nitrogen and gut microbiota are associated with the liraglutide treatment applied on patients with T2DM. These findings may contribute to the beneficial effects of liraglutide against diabetes.

Prediction of Minimal Inhibitory Concentration of Meropenem Against Klebsiella pneumoniae Using Metagenomic Data.

Minimal inhibitory concentration (MIC) is defined as the lowest concentration of an antimicrobial agent that can inhibit the visible growth of a particular microorganism after overnight incubation. Clinically, antibiotic doses for specific infections are determined according to the fraction of MIC. Therefore, credible assessment of MICs will provide a physician valuable information on the choice of therapeutic strategy. Early and precise usage of antibiotics is the key to an infection therapy. Compared with the traditional culture-based method, the approach of whole genome sequencing to identify MICs can shorten the experimental time, thereby improving clinical efficacy. Klebsiella pneumoniae is one of the most significant members of the genus Klebsiella in the Enterobacteriaceae family and also a common non-social pathogen. Meropenem is a broad-spectrum antibacterial agent of the carbapenem family, which can produce antibacterial effects of most Gram-positive and -negative bacteria. In this study, we used single-nucleotide polymorphism (SNP) information and nucleotide k-mers count based on metagenomic data to predict MICs of meropenem against K. pneumoniae. Then, features of 110 sequenced K. pneumoniae genome data were combined and modeled with XGBoost algorithm and deep neural network (DNN) algorithm to predict MICs. We first use the XGBoost classification model and the XGBoost regression model. After five runs, the average accuracy of the test set was calculated. The accuracy of using nucleotide k-mers to predict MICs of the XGBoost classification model and XGBoost regression model was 84.5 and 89.1%. The accuracy of SNP in predicting MIC was 80 and 81.8%, respectively. The results show that XGBoost regression is better than XGBoost classification in both nucleotide k-mers and SNPs to predict MICs. We further selected 40 nucleotide k-mers and 40 SNPs with the highest correlation with MIC values as features to retrain the XGBoost regression model and DNN regression model. After 100 and 1,000 runs, the results show that the accuracy of the two models was improved. The accuracy of the XGBoost regression model for k-mers, SNPs, and k-mers & SNPs was 91.1, 85.2, and 91.3%, respectively. The accuracy of the DNN regression model was 91.9, 87.1, and 91.8%, respectively. Through external verification, some of the selected features were found to be related to drug resistance.

Enhanced adsorption of Cu(II) and Zn(II) from aqueous solution by polyethyleneimine modified straw hydrochar.

Heavy metals removal from aqueous phase by adsorption technique has recently attracted a considerable interest. Although various adsorbing materials have been developed, introducing more functional groups is considered as the most efficient way to promote the adsorption capacity of the selected adsorbent. However, this approach is usually limited in costly modification precursor and unguaranteed loading efficacy. In this study, waste corn straw was converted to adsorbent precursor by hydrothermal carbonization. The obtained hydrochar (HC) was chemically activated before being modified by polyethyleneimine (PEI). Multiple analysis methods including Scanning Electron Microscopy, Fourier Transform Infrared analysis, and X-ray Photoelectron Spectroscopy analysis verified the alkali activated hydrochar (alkali-HC) was more efficacy to enhance PEI grafting than acid activation. Based on this, the modified HC materials obtained a better adsorption performance. The sorption process of Cu(II) and Zn(II) on the acid-PEI-HC, alkali-PEI-HC, and pristine HC fitted the pseudo second order kinetic and Freundlich model well, and was dominated by chemisorption. Among these adsorbents, the adsorption capacity of alkali-PEI-HC to metal ions was the maximum, which was 207.6 mg/g to Zn(II) and 56.1 mg/g to Cu(II) at 298 K. Regeneration tests showed a result of no less than 60% of its removal capacity was achieved after five cycles. Therefore, alkali-PEI-HC performed as a promising composite sorbent for metal ions. In addition, the study described here has provided a new basis for the utilization of hydrochar (1.08 kWh kg-1) derived from agricultural resources as a promising adsorbent precursor.