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Genome-wide characterization of miRNA and siRNA pathways in the parasitoid wasp Pteromalus puparum
XIAO Shan, FANG Qi, LIU Ming-ming, ZHANG Jiao, WANG Bei-bei, YAN Zhi-chao, WANG Fang, David W. STANLEY, YE Gong-yin
2022, 21 (4): 1106-1115.   DOI: 10.1016/S2095-3119(20)63465-7
Abstract136)      PDF in ScienceDirect      
microRNAs (miRNAs) and small interfering RNAs (siRNAs) are small non-coding RNAs (ncRNAs) that trigger RNA interference (RNAi) in eukaryotic organisms.  The biogenesis pathways for these ncRNAs are well established in Drosophila melanogaster, Aedes aegypti, Bombyx mori and other insects, but lacking in hymenopteran species, particularly in parasitoid wasps.  Pteromalus puparum is a parasitoid of pupal butterflies.  This study identified and analyzed two pathways by interrogating the P. puparum genome.  All core genes of the two pathways are present in the genome as a single copy, except for two genes in the siRNA pathway, R2D2 (two copies) and Argonaute-2 (three).  Conserved domain analyses showed the protein structures in P. puparum were similar to cognate proteins in other insect species.  Phylogenetic analyses of hymenopteran Dicer and Argonaute genes suggested that the siRNA pathway-related genes evolved faster than those in the miRNA pathway.  The study found a decelerated evolution rate of P. puparum Dicer-2 with respect to Dicer-1, which was contrary to other hymenopterans.  Expression analyses revealed high mRNA levels for all miRNA pathway genes in P. puparum adults and the siRNA related genes were expressed in different patterns.  The findings add valuable new knowledge of the miRNA and siRNA pathways and their regulatory actions in parasitoid wasps.
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Does poverty-alleviation-based industry development improve farmers’ livelihood capital?
LIU Ming-yue, FENG Xiao-long, WANG San-gui, ZHONG Yu
2021, 20 (4): 915-926.   DOI: 10.1016/S2095-3119(20)63449-9
Abstract206)      PDF in ScienceDirect      
Targeted poverty alleviation is a unique approach adopted in China to help achieve the vision of a moderately prosperous society in all aspects and the “Chinese Dream”.  Industrial development as a means of poverty alleviation is an integral part of the “Five-pronged Poverty Alleviation Measures” Project of targeted poverty alleviation, and a critical foundation for other poverty alleviation measures.  In this study, a comprehensive evaluation method was used to measure farmers’ livelihood based on the framework of sustainable livelihood.  Specifically, the effects of industrial development on farmers’ livelihood capital were estimated by employing the propensity score matching combined with the difference-in-differences (PSM-DID) approach.  Findings suggest that industrial development had a significantly positive effect on the livelihood capital of farmers.  Industrial development can significantly enhance farmers’ human, social and financial capital, while it cannot significantly affect the natural and physical capital.  Industrial development had heterogeneous effects on farmers’ livelihood capital, more efficiently impacting on the non-poor than the poor.  The effects on farmers’ livelihood capital varied across regions, with Guizhou experiencing a larger effect than Sichuan.  However, the effect was insignificant for farmers in Gansu.  To improve farmers’ livelihood capital, it is necessary to take measures to strengthen their human capital, promote the innovation of financial products, and make good use of their social capital; it is also essential to strengthen the support of industrial development to the poor. 
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Assembly and co-occurrence patterns of rare and abundant bacterial sub-communities in rice rhizosphere soil under short-term nitrogen deep placement
LI Gui-long, WU Meng, LI Peng-fa, WEI Shi-ping, LIU Jia, JIANG Chun-yu, LIU Ming, LI Zhong-pei
2021, 20 (12): 3299-3311.   DOI: 10.1016/S2095-3119(20)63462-1
Abstract133)      PDF in ScienceDirect      
Nitrogen (N) deep placement has been found to reduce N leaching and increase N use efficiency in paddy fields.  However, relatively little is known how bacterial consortia, especially abundant and rare taxa, respond to N deep placement, which is critical for understanding the biodiversity and function of agricultural ecosystem.  In this study, Illumina sequencing and ecological models were conducted to examine the diversity patterns and underlying assembly mechanisms of abundant and rare taxa in rice rhizosphere soil under different N fertilization regimes at four rice growth stages in paddy fields.  The results showed that abundant and rare bacteria had distinct distribution patterns in rhizosphere samples.  Abundant bacteria showed ubiquitous distribution; while rare taxa exhibited uneven distribution across all samples.  Stochastic processes dominated community assembly of both abundant and rare bacteria, with dispersal limitation playing a more vital role in abundant bacteria, and undominated processes playing a more important role in rare bacteria.  The N deep placement was associated with a greater influence of dispersal limitation than the broadcast N fertilizer (BN) and no N fertilizer (NN) treatments in abundant and rare taxa of rhizosphere soil; while greater contributions from homogenizing dispersal were observed for BN and NN in rare taxa.  Network analysis indicated that abundant taxa with closer relationships were  usually more likely to occupy the central position of the network than rare taxa.  Nevertheless, most of the keystone species were rare taxa and might have played essential roles in maintaining the network stability.  Overall, these findings highlighted that the ecological mechanisms and co-occurrence patterns of abundant and rare bacteria in rhizosphere soil under N deep placement.
 
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Bacterial diversity and community composition changes in paddy soils that have different parent materials and fertility levels
MA Xin-ling, LIU Jia, CHEN Xiao-fen, LI Wei-tao, JIANG Chun-yu, WU Meng, LIU Ming, LI Zhong-pei
2021, 20 (10): 2797-2806.   DOI: 10.1016/S2095-3119(20)63364-0
Abstract188)      PDF in ScienceDirect      
Parent materials and the fertility levels of paddy soils are highly variable in subtropical China.  Bacterial diversity and community composition play pivotal roles in soil ecosystem processes and functions.  However, the effects of parent material and fertility on bacterial diversity and community composition in paddy soils are unclear.  The key soil factors driving the changes in bacterial diversity, community composition, and the specific bacterial species in soils that are derived from different parent materials and have differing fertility levels are unknown.  Soil samples were collected from paddy fields in two areas with different parent materials (quaternary red clay or tertiary sandstone) and two levels of fertility (high or low).  The variations in bacterial diversity indices and communities were evaluated by 454 pyrosequencing which targeted the V4–V5 region of the 16S rRNA gene.  The effects of parent material and fertility on bacterial diversity and community composition were clarified by a two-way ANOVA and a two-way PERMANOVA.  A principal coordinate analysis (PCoA), a redundancy analysis (RDA), and multivariate regression trees (MRT) were used to assess changes in the studied variables and identify the factors affecting bacterial community composition.  Co-occurrence network analysis was performed to find correlations between bacterial genera and specific soil properties, and a statistical analysis of metagenomic profiles (STAMP) was used to determine bacterial genus abundance differences between the soil samples.  The contributions made by parent material and soil fertility to changes in the bacterial diversity indices were comparable, but soil fertility accounted for a larger part of the shift in bacterial community composition than the parent material.  Soil properties, especially soil texture, were strongly associated with bacterial diversity.  The RDA showed that soil organic carbon (SOC) was the primary factor influencing bacterial community composition.  A key threshold for SOC (25.5 g kg–1) separated low fertility soils from high fertility soils.  The network analysis implied that bacterial interactions tended towards cooperation and that copiotrophic bacteria became dominant when the soil environment improved.  The STAMP revealed that copiotrophic bacteria, such as Massilia and Rhodanobacter, were more abundant in the high fertility soils, while oligotrophic bacteria, such as Anaerolinea, were dominant in low fertility soils.  The results showed that soil texture played a role in bacterial diversity, but nutrients, especially SOC, shaped bacterial community composition in paddy soils with different parent materials and fertility levels.
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Alginate oligosaccharides preparation, biological activities and their application in livestock and poultry 
LIU Ming, LIU Lei, ZHANG Hong-fu, YI Bao, Nadia EVERAERT
2021, 20 (1): 24-34.   DOI: 10.1016/S2095-3119(20)63195-1
Abstract149)      PDF in ScienceDirect      
Alginate oligosaccharides (AOS), belonging to the class of functional marine oligosaccharides, are low-molecular polymers linked by β-1,4-mannuronic acid (M) and α-1,4-guluronic acid (G), which could be classically obtained by enzymatic hydrolysis of alginate. With low viscosity and good water solubility, as well as anti-oxidant, immune regulation, anti-bacterial and anti-inflammatory activities, AOS have been widely used in medical science and functional food, green agriculture and other fields. As new bio-feed additives, AOS have broad potential applications in animal husbandry. In this review, the sources of alginate, chemical structure and preparation methods of AOS, and their biological activities and application in livestock and poultry are summarized. We expect this review could contribute to lay a foundation of application and further research for AOS in livestock and poultry.
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Identification and gene mapping of the starch accumulation and premature leaf senescence mutant ossac4 in rice
ZHU Mao-di, CHEN Xin-long, ZHU Xiao-yan, XING Ya-di, DU Dan, ZHANG Ying-ying, LIU Ming-ming, ZHANG Qiu-li, LU Xin, PENG Sha-sha, HE Guang-hua, ZHANG Tian-quan
2020, 19 (9): 2150-2164.   DOI: 10.1016/S2095-3119(19)62814-5
Abstract140)      PDF in ScienceDirect      
The rice mutant ossac4 (starch accumulating 4) was raised from seeds of the rice (Oryza sativa L.) indica maintainer line Xinong 1B treated with ethyl methanesulfonate.  The distal and medial portions of the second leaf displayed premature senescence in the ossac4 mutant at the four-leaf stage.  Physiological and biochemical analysis, and cytological examination revealed that the ossac4 mutant exhibited the premature leaf senescence phenotype.  At the four-leaf stage, the leaves of the ossac4 mutant exhibited significantly increased contents of starch compared with those of the wild type (WT).  Quantitative real-time PCR analysis showed that the expression levels of photosynthesis-associated genes were down-regulated and the expression levels of glucose metabolism-associated genes were abnormal.  Genetic analysis indicated that the ossac4 mutation was controlled by a single recessive nuclear gene.  The OsSAC4 gene was localized to a 322.7-kb interval between the simple-sequence repeat marker XYH11-90 and the single-nucleotide polymorphism marker SNP5300 on chromosome 11.  The target interval contained 20 annotated genes.  The present results demonstrated that ossac4 represents a novel starch accumulation and premature leaf senescence mutant, and lays the foundation for cloning and functional analysis of OsSAC4.
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Optimize nitrogen fertilization location in root-growing zone to increase grain yield and nitrogen use efficiency of transplanted rice in subtropical China
WU Meng, LIU Ming, LIU Jia, LI Wei-tao, JIANG Chun-yu, LI Zhong-pei
2017, 16 (09): 2073-2081.   DOI: 10.1016/S2095-3119(16)61544-7
Abstract891)      PDF in ScienceDirect      
The optimized nitrogen fertilization location differs in different rice-growing regions.  We optimized nitrogen deep-point application in root-growing zone (NARZ) for transplanted rice in subtropical China.  Field plot experiments were conducted over two years (2014–2015) in a double-rice cropping system to evaluate the effects of nitrogen (N) fertilizer location on grain yield and N use efficiency (NUE).  Four different nitrogen deep-point application methods (DN) were compared with traditional broadcast application (BN) using granular urea.  The results showed that grain yield,  recovery efficiency of N (REN), agronomic efficiency of N (AEN), and partial factor productivity of N (PFPN) significantly increased 10.3–63.4, 13.7–56.7, 24.7–201.9 and 10.2–63.4%, respectively, in DN treatment compared to BN, respectively.  We also find that DN treatments increased grain yield as well as grain N content, and thus grain quality, in comparison with conventional BN treatment.  Correlation analysis indicated that significant improvement in grain yield and NUE mainly resulted from increases in productive panicle number and grain N content.  In our proposed NARZ method, granular urea should be placed 0 to 5 cm around the rice seeding at a 12-cm depth druing rice transplanting.  In NARZ, balanced application of N, P and K further improved grain yield and NUE over treatments with a single N deep-point application.  High N uptake by the rice plant did not cause significant soil fertility depletion, demonstrating that this method could guarantee sustainable rice production.    
 
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6-Benzylaminopurine treatment maintains the quality of Chinese chive (Allium tuberosum Rottler ex Spreng.) by enhancing antioxidant enzyme activity
JIA Li-e, LIU Sheng, DUAN Xiao-ming, ZHANG Chao, WU Zhan-hui, LIU Ming-chi, GUO Shao-gui, ZUO Jin-hua, WANG Li-bin
2017, 16 (09): 1968-1977.   DOI: 10.1016/S2095-3119(17)61663-0
Abstract698)      PDF in ScienceDirect      
Chinese chive usually develops an off-flavor after a short storage time.  To explore effective ways to maintain the postharvest quality of Chinese chive, the effect of exogenous application of 6-benzylaminopurine (6-BA) on postharvest quality and antioxidant activity of chive was evaluated, and the mechanism of the physiological responses of chive to 6-BA treatment was explored.  Chives were sprayed for 10 min with 100, 300, or 500 mg L–1 6-BA or with alkaline solution as the control, then stored at (2±1)°C with a relative humidity (RH) of 80–85%.  We found that 300 mg L–1 6-BA significantly delayed yellowing and chlorophyll degradation, maintained the total phenolic and flavonoid content, and improved the activities of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD).  In conclusion, we identified exogenous application of 6-BA as an effective method for maintaining postharvest quality of Chinese chive.  In addition, our finding that the activities of antioxidant enzymes increase in response to exogenous 6-BA provides new insights into the mechanism of cytokinin-based postharvest fresh-keeping. 
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Soil N transformation and microbial community structure as affected by adding biochar to a paddy soil of subtropical China
LI Ming, LIU Ming, LI Zhong-pei, JIANG Chun-yu, WU Meng
2016, 15 (1): 209-219.   DOI: 10.1016/S2095-3119(15)61136-4
Abstract2068)      PDF in ScienceDirect      
We have had little understanding on the effects of different types and quantities of biochar amendment on soil N transformation process and the microbial properties. In this study, various biochars were produced from straw residues and wood chips, and then added separately to a paddy soil at rates of 0.5, 1 and 2% (w/w). The effects of biochar application on soil net N mineralization and nitrification processes, chemical and microbial properties were examined in the laboratory experiment. After 135 d of incubation, addition of straw biochars increased soil pH to larger extent than wood biochars. The biochar-amended soils had 37.7, 7.3 and 227.6% more soil organic carbon (SOC), available P and K contents, respectively, than the control soil. The rates of net N mineralization and nitrification increased significantly as biochars quantity rose, and straw biochars had greater effect on N transformation rate than wood biochars. Soil microbial biomass carbon increased by 14.8, 45.5 and 62.5% relative to the control when 0.5, 1 and 2% biochars (both straw- and wood-derived biochars), respectively, were added. Moreover, biochars amendments significantly enhanced the concentrations of phospholipid fatty acids (PLFAs), as the general bacteria abundance increased by 161.0% on average. Multivariate analysis suggested that the three rice straw biochar (RB) application levels induced different changes in soil microbial community structure, but there was no significant difference between RB and masson pine biochar (MB) until the application rate reached 2%. Our results showed that biochars amendment can increase soil nutrient content, affect the N transformation process, and alter soil microbial properties, all of which are biochar type and quantity dependent. Therefore, addition of biochars to soil may be an appropriate way to disposal waste and improve soil quality, while the biochar type and addition rate should be taken into consideration before its large-scale application in agro-ecosystem.
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Effect of Different Rice-Crab Coculture Modes on Soil Carbohydrates
YAN Ying, LIU Ming-da, YANG Dan, ZHANG Wei, AN Hui, WANG Yao-jing, XIE Hong-tu
2014, 13 (3): 641-647.   DOI: 10.1016/S2095-3119(13)60722-4
Abstract1601)      PDF in ScienceDirect      
Traditional agricultural systems have contributed to food and livelihood security. Rice-crab coculture (RC) is an important eco-agricultural process in rice production in northern China. Recognizing the soil fertility in RC may help develop novel sustainable agriculture. Soil carbohydrates are important factors in determining soil fertility in different culture modes. In this study, soil carbohydrates were analyzed under three different culture modes including rice monoculture (RM), conventional rice-crab coculture (CRC) and organic rice-crab coculture (ORC). Results showed that the contents of soil organic carbon and carbohydrates were significantly higher in the ORC than those in RM. The increasing effect was greater with increased organic manure. Similar tendency was found in CRC, but the overall effect was less pronounced compared with ORC. Carbohydrates were more sensitive to RC mode and manure amendment than soil organic carbon. Compare to RM, the (Gal+Man)/(Ara+Xyl) ratio decreased in all the RC modes, indicating a relative enrichment in plant-derived carbohydrates due to the input of crab feed and manure. While the increasing (Gal+Man)/(Ara+Xyl) ratio in ORC modes with increased organic manure suggested that crab activity and metabolism induced microbially derived carbohydrates accumulation. The lower GluN/MurA ratio in ORC indicated an enhancement of bacteria contribution to SOM turnover in a short term. The findings reveal that the ORC mode could improve the quantity and composition of soil carbohydrates, effectively, to ensure a sustainable use of paddy soil.
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Effect of Intensive Inorganic Fertilizer Application on Microbial Properties in a Paddy Soil of Subtropical China
LIU Ming, Klemens Ekschmitt, ZHANG Bin, Stephanie I J Holzhauer, LI Zhong-pei, ZHANG Tao-lin , Sabine Rauch
2011, 10 (11): 1758-1764.   DOI: 10.1016/S1671-2927(11)60175-2
Abstract2538)      PDF in ScienceDirect      
A field experiment with rice-rice rotation was conducted since 2002 in southeast China for investigating the response of soil microbial properties to intensive nitrogen fertilizer application. The tested soil was a subtropical paddy soil derived from Quaternary red clay. Differences between treatments existed in different application rates of urea when the experiment was designed. Urea was applied in five rates, i.e., 0, 0.5, 1, 1.5, and 2 U, equivalent to 0, 0.5, 1, 1.5, and 2 times the local average amount of urea application (900 kg urea ha-1 yr-1, equivalent to 414 kg N ha-1 yr-1). In 2007, soil total nitrogen, available nitrogen, and soil organic carbon contents were increased by 10.2-27.9, 8.0-16.0, and 10.2-30.6%, respectively, in treatments with urea application rates of 0.5 to 2 U compared to control (0 U). Microbial biomass carbon and nitrogen were also increased by 3.1-30.8 and 1.3-13.9%, respectively, in treatments with urea application. Basal respiration in treatments with urea input were 9.4-29.1% higher than that in control. However, changes of bacterial functional diversity had different trends. Urea fertilization enhanced bacterial functional diversity until treatment of 1 U, but re-decreased it from treatment of 1.5 U. Principal components analysis indicated that there were intimate relationships among soil organic matter, nitrogen nutrient, microbial biomass, and respiration. Nevertheless, microbial diversity was related to soil moisture contents after urea application. We conclude here that the application of N fertilizer improved soil microbial biomass and respiratory activity. But, microbial diversity was reduced when excessive urea was applied in the tested paddy soil.
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