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Background and Aims: Understanding microbial compositions and functions in arable soils is crucial for effective agroecosystem management. While many studies have explored this topic, large-scale investigations are lacking, resulting in the absence of consistent and reliable patterns of communities and functions of soil microorganisms. Methods: To address this gap, we performed an integrated analysis of published sequencing data from the soils of three main arable fields: upland, paddy, and paddy-upland rotation. Results: Bacterial diversity (richness, Shannon) was highest in upland soils. Actinobacteria and Planctomycetes were enriched in upland soils, while Proteobacteria, Chloroflexi, and Nitrospirae preferred paddy and paddy-upland rotation soils. Bacteria in upland soils have a greater functional potential to decompose aromatic compounds, as well as for chitinolysis and ureolysis. Methanotrophy, methylotrophy, sulfur-related respiration, and most nitrogen metabolic processes were enriched in paddy fields. Bacteria in upland soils are characterized by increased dormancy potential and a faster response to resource input than those in paddy and paddy-upland rotation soils. Stochastic processes poorly contribute to the bacterial assembly in paddy soils, indicating strong environmental filtering due to anaerobic conditions. The spatial turnover in bacterial community composition was much faster than the functional potential, indicating high functional redundancy, especially in paddy soils. Edaphic factors were the major contributors to bacterial composition, whereas the cropland type influenced the predicted functions. Conclusions: Land use defines microbial composition, functional attributes, and ecological characteristics (e.g., dormancy potential, assembly processes, and functional redundancy). These findings deepen our knowledge of microbial biogeographic patterns in soils of agricultural ecosystems and provide new insights into sustainable cropland management. [ABSTRACT FROM AUTHOR]

Purpose: Agricultural production is facing multiple challenges from global warming. Nitrogen (N) plays an essential role in high-temperature tolerance and crop yield, which may depend on leaf cooling capacity. However, the effects of nitrogen on the leaf temperature response and the regulatory mechanisms of leaf cooling capacity under increased environmental temperature are largely unknown. Methods: Currently, we evaluated the effects of nitrogen on the dynamic change in leaf temperature and the balance between heat dissipation and absorption, which contributes to leaf cooling capacity. Results: The results showed that cucumber plant growth and transpiration rate significantly increased with N supply, while leaf temperature decreased. As the environmental temperature increased, the cucumber leaf temperature and leaf cooling capacity increased, and the leaf cooling capacity improved with the N supply. Leaf temperature was negatively correlated with transpiration rate, and the increased transpiration rate contributed to higher heat dissipation and leaf cooling capacity under a high nitrogen supply. Leaf water content and water potential increased with N supply, which resulted in higher leaf specific heat capacity and heat absorption. However, nitrogen-deficient plants increased the nonstructural carbon content (NSC), structural carbon content (SC), and NSC/SC ratio, thus increasing plant adaptation to environmental stresses. Conclusions: Nitrogen supply improved leaf cooling capacity by increasing the leaf transpiration rate and specific heat capacity, thereby regulating the balance between heat dissipation and absorption. Improving leaf cooling capacity by N supply may be a new strategy to increase plant adaptation to increased environmental temperatures. [ABSTRACT FROM AUTHOR]

Background and aims: It has been confirmed that the declines in arbuscular mycorrhizal fungi (AMF) populations and agroecosystem diversity are largely due to nutrient enrichment caused by fertilization. Replacing chemical-only fertilization with organic fertilization is widely considered a possible approach for maintaining soil biodiversity and a healthy functioning ecosystem. Here we aim to examine the effects of organic fertilizer on AMF occurrence. Methods: We conducted a meta-analysis of 162 field experiments from 54 published studies conducted over the last 20 years. Our dataset included two groups: organic fertilization (OF) vs chemical-only fertilization (CF) and OF vs no fertilization (NF). Results: We found that organic fertilizer increased AM fungal biomass and was less detrimental to AMF richness than mineral-only fertilization. AMF responses to organic fertilizer were generally positive when AMF and host plants had a strong mutualistic symbiosis such as in phosphorus-deficient soil, drought and semi-drought areas, at low latitudes, and at testing sites that contained two or more plant species or included legume. In conditions other than these, the responses were generally negative. Organic carbon input, increased soil phosphorus and the ratio of fertilizer N and P jointly explain the effects of organic fertilizer on AMF occurrence. Conclusions: Our analysis indicates that, although some limiting factors exist, application of organic fertilizer can be an effective practice to protect AM symbiosis from the negative effects of nutrient enrichment in current cropping systems. [ABSTRACT FROM AUTHOR]

Aims: The form of nitrogen (N) supply influences photorespiration in C3 plants, but whether nitrate (NO3−) regulates photorespiration and, if so, the underlying mechanisms for such regulation are still unclear. Methods: Three hydroponic experiments were conducted in a greenhouse to investigate the relationships between leaf NO3− concentrations and photorespiration rates in rice (Oryza sativa L.) genotypes cv. 'Shanyou 63' hybrid indica and 'Zhendao 11' hybrid japonica or using mutants that overexpress NRT2.1 (in cv. 'Nipponbare' inbred japonica). We estimated photorespiratory rate from the CO2 compensation point in the absence of daytime respiration (Γ*) using the biochemical model of photosynthesis. Results: Higher Γ* values under high N level or NO3− were significantly and positively correlated with leaf NO3− concentrations. Further elevating leaf NO3− concentrations by either resuming NO3− nutrition supply after N depletion (in cv. 'Shanyou 63' hybrid indica and 'Zhendao 11' hybrid japonica) or using mutants that overexpress NRT2.1 (in cv. 'Nipponbare' inbred japonica) increased Γ* values. Additionally, the activities of leaf nitrate reductase (Nr) and concentrations of organic acids involving in the tricarboxylic acid (TCA) cycle synchronously changed as environmental conditions were varied. Conclusions: Photorespiration rate is related to the leaf NO3− concentration, and the correlation may links to the photorespiration-TCA derived reductants required for NO3− assimilation. [ABSTRACT FROM AUTHOR]

Aim Trichoderma guizhouense: NJAU 4742 (Tgui) can serve as a promising strain for the development of novel biofertilizers and biofungicides. Plants primed with Tgui via inoculation were investigated to clarify the underlying mechanisms that promote root growth and development and activate the plant innate immune response. Methods: The relative expression of defence-related genes and of genes involved in the auxin signalling pathway in Zea mays and Arabidopsis thaliana was quantified. Scanning electron microscopy (SEM) was performed to visualize the colonization of Tgui in maize roots, and a proteomic approach was used to identify Tgui-derived elicitors. Results: The establishment of Tgui in the rhizosphere of maize leads to the stimulation of the auxin synthesis pathway in maize and subsequently leads to increased plant growth. And the extracellular proteins of Tgui induced systemic resistance (ISR) of maize plants to Fusarium verticillioides (Fv) (Hypocreales, Ascomycota); the ISR of maize plants may be linked to the accumulation of reactive oxygen species (ROS) and increased deposition of callose in maize tissue. Conclusions: Activation of the maize immune response was triggered by the mixture of extracellular proteins secreted by Tgui into the rhizosphere. Our study thereby contributes to a better understanding of the interaction between T. guizhouense and plant roots. [ABSTRACT FROM AUTHOR]

Aims: To investigate the ability of higher nitrogen (N) use efficiency (NUE) in rice production to achieve higher grain yields by optimal N management (OPT). Methods: In 2012 and 2013, four field experiments were conducted in Liyang and Rugao counties, Jiangsu Province, China to investigate the ability of the N-nutrient index (NNI) to mediate the effects of N-free control (CK), farmers' fertilizer practice (FFP), and OPT N management methods on grain yield and NUE through regulating the leaf functions of rice. Results: Compared with FFP, the average rice yield and NUE for OPT were increased, while the N rate was reduced. NNI showed a dynamic change that reached an optimal status in OPT at the harvest stage. N management had a remarkable effect on the leaf area index (LAI), with OPT mitigating the differences between leaf positions, such that basal leaf LAI was improved to compensate for the decreased LAI of the top three leaves. During the grain-filling process, the top three leaves exhibited higher net photosynthesis rate (Pn) and higher grain weights and shorter grain-filling periods of both superior and inferior spikelets in OPT. Based on the contribution of different organs to grain production from the heading to harvest stage, two strategies of yield formation were observed, in which OPT enhanced the dependence on the stems (stem, sheath, and other leaves), while FFP was more dependent on the top three leaves. Conclusions: Our results indicate that optimizing N application improves NNI and leaf functions to increase rice yield and NUE. [ABSTRACT FROM AUTHOR]

Background and aims: The increasing input of anthropogenically-derived nitrogen (N) to ecosystems raises a crucial question: how do N inputs modify the soil microbial stability, and thus affect crop productivity? Methods: Soils from an 8-year rice-wheat rotation experiment with increasing N-input rates were subjected to drying–rewetting (DW) cycles for investigating the resistance and resilience of soil functions, in terms of abundances of genes (potential functions) and activities of enzymes (quantifiable functions), to this stress, and particularly the contribution of resistance and resilience on crop production was evaluated. Results: Although the DW cycles had a stronger effect compared to N fertilization level, the N input was also important in explaining the variation in the resistance and resilience of functional genes and the activities of enzymes involved in C, N and P cycling. Crop yields benefited from both of high resistance and high resilience of soil microbial functions, though the resistance and resilience of soil enzyme activities exhibited a stronger contribution to crop yields compared to the functional genes and the overall contribution strength was conditioned by N input levels. Conclusions: In addition to the well-known direct contribution of N fertilization on crop yields, N input plays an indirect role on crop production via conditioning the resistance and resilience of soil functions in response to repeated DW cycles. [ABSTRACT FROM AUTHOR]

Aims: Plant growth-promoting rhizobacteria (PGPR) substantially improve plant growth and health, but their effects on the succession of rhizosphere microbiota throughout the growth period triggered by pre-inoculation have not yet been considered. Methods: Pepper seedlings cultured from a bio-nursery substrate containing Bacillus velezensis NJAU-Z9 and ordinary nursery substrate were used in this study to evaluate the effects of pre-colonization of a PGPR strain at the seedling stage on yield enhancement. To elucidate the underlying mechanisms involved in the rhizosphere microbiota succession during the whole growth period and their association with yield enhancement, high-throughput sequencing combined with qPCR was conducted. Results: The results showed that, compared to the control without inoculation, pre-inoculation led to a steady yield enhancement in two-season field trials, as well as higher rhizosphere bacterial richness (Chao1) and diversity (Shannon-Wiener). The plant growth stage as the first driving factor, followed by pre-colonization drove the variations of the rhizosphere microbial community composition according to multivariate regression tree analysis and principal coordinate analysis. Variance partitioning analysis (VPA) and Mantel test results showed that the previous plant growth period induced variations in the fungal and bacterial communities at the next stage. Compared to the seedling and flowering stages, the mature-stage microbial community showed a higher degree of explanation of yield enhancement. Additionally, pre-inoculation led to distinctive rhizosphere microbiota succession compared to the control, due to alteration of the initial community. The heat map analysis showed that the rhizosphere microbiota was related to crop yield. In addition to Bacillus velezensis NJAU-Z9, which showed stable abundance in the pepper rhizosphere, stable higher relative abundance of the bacterial genera Sphingomonas, Sphingopyxis, Bradyrhizobium, Chitinophaga, Dyadobacter, Streptomyces, Lysobacter, Pseudomonas and Rhizomicrobium, and the fungal genera Cladorrhinum, Cladosporium and Aspergillus throughout the growth period induced by pre-colonization was associated with yield enhancement. Conclusions: Overall, we conclude that pre-colonization with PGPR changed the initial rhizosphere microbiota and that the plant was triggered to further select distinctive microbes to form unique rhizosphere microbial consortia at the later growth stages, which resulted in plant growth promotion. [ABSTRACT FROM AUTHOR]

Aims: Continuous cropping of watermelon is known to result in the disruption of the rhizospheric bacteria and fungi that contribute to the occurrence of Fusarium wilt disease. However, the underlying changes in microbial composition and function as a response to mono-cropping are less studied. Methods: In this study, differences in composition and potential function of the microbiome between healthy and diseased soils were investigated using MiSeq targeted sequencing and the functional GeoChip array, respectively. Results: Twenty years of continuous watermelon monoculture was found to significantly alter the soil microbial communities by increasing bacterial diversity but decreasing fungal diversity. Compare to bacterial network, fungal co-occurrence networks were less robust and less connected in the monoculture diseased soil. Identified keystone species, belonging to the Proteobacteria, Bacteroidetesand Acidobacteria, were present in both the diseased and healthy soils. Key fungal species from the healthy soil belonged solely within the Ascomycete, while in the diseased soil Basidiomycota were dominant. As such, overall variations in the composition of the soil microbiome are accompanied by changes in the identities of the keystone species when comparing healthy versus diseased soils, further suggesting that soil function may also be altered. Relative abundances of genes associated with the degradation of hemicelluloses and chitin, the Calvin circle, ammonification, stress responses, iron uptake, and nitrogen fixation were significantly higher under long-term monoculture. Particularly, Fusarium spp. relative abundance was positively correlated with the relative abundances of genes involved in adherence, cellular metabolism, and immune evasion which may facilitate pathogen infection of plant roots. Conclusions: In conclusion, these results highlight the significant compositional and functional differences in microbial communities between Fusarium wilt diseased soils and healthy soils under watermelon cultivation. This provides insight into the complex array of microorganisms in soils that suffer from Fusarium disease and illustrates potential directions towards the manipulation of the soil microbiome for suppression of this disease. [ABSTRACT FROM AUTHOR]

Background and aims: Considering the global demands in sustaining agriculture, use of organic amendments is gradually increasing. An improved understanding of the biological process is essential to evaluate the performance of organic amendments on agro-ecosystem.Methods: Soils subjected to different fertilization regimes were collected from a field experiment. Microbial community compositions are assessed with 16S and ITS rRNA gene sequencing and subsequent bioinformatics analysis. Microbial functions are characterized with the geometric mean of the assayed enzyme activities (GMea) and the microbial carbon-use efficiency:nitrogen-use efficiency ratio (CUE:NUE).Results: Compared with the chemically fertilized soil, the GMea significantly increased in organically amended soils. In contrast, the CUE:NUE was highest in chemically treated soil. These changes of microbial functional indicators were associated with shifts in the bacterial and not the fungal community composition, despite the fact that both the bacterial and fungal community compositions were significantly affected by the fertilization regimes. The abundances of specific soil bacterial taxa, especially the genera Luteimonas and Gemmatimona, were enriched by organic amendments. Soil organic carbon emerged as the major determinant of the bacterial community composition.Conclusions: Soil microbial activities and nutrient-use efficiencies were dramatically changed along with the alteration of bacterial community composition. Relatively greater abundance of Luteimonas and Gemmatimona taxa in soils might be useful indicators for soil amelioration. Our research could be helpful to provide better strategies for the maintenance of soil fertility. [ABSTRACT FROM AUTHOR]

Aims: Bio-organic fertilizer and different additives are widely applied to suppress soil-borne diseases. However, how different additives alter bulk soil microflora and thereby induce the healthy rhizospheric microflora remains unclear.Methods: A 3-season field experiment containing four fertilization management programs (chemical fertilizer, organic fertilizer, amino acid organic fertilizer, and bio-organic fertilizer was conducted in a tomato production agroecosystem with high disease incidence to evaluate the induced efficacy. The bacterial and fungal microflora of bulk and rhizosphere soil influenced by different management programs were performed on the Illumina MiSeq platform. Principal coordinate analysis based on the Bray-Curtis distance metric was performed to compare the similarities and differences of the bacterial and fungal community compositions among all soil samples.Results: Soil amended with organic fertilizer, amino acid organic fertilizer, and bio-organic fertilizer progressively and significantly suppressed tomato diseases in comparison with chemical fertilizer, and bio-organic fertilizer presented the best efficacy in all seasons. Interestingly, rhizospheric and bulk soil bacterial and fungal communities of the different fertilization management programs were separated from each other. Six bacterial and 10 fungal rhizospheric genera positively correlated with the same genera observed in bulk soil showing significant relationships with tomato disease incidence were observed, and functional strain SQR9 can be detected in the bulk and rhizosphere soils of bio-organic fertilizer treatments. Additionally, the redundancy analysis results showed the genera in treated chemical fertilizer bulk soil were dominated by Ralstonia and Fusarium, the abundances of which were highest and lowest in treated chemical fertilizer and bio-organic fertilizer rhizosphere, respectively.Conclusions: This study provided insights into soil-borne disease suppression by bulk soil management and confirmed that alterations to the bulk soil microbiota by different organic additives played distinct roles in the formation of rhizospheric soil microflora for the suppression of disease. [ABSTRACT FROM AUTHOR]

Aims: Investigating shifts in soil microbiomes driven by different fertilization regimes would be helpful for lessening the negative effect of monoculture in agricultural systems. Methods: In the present work, we employed MiSeq sequencing to evaluate the response of local microbial communities to three different fertilization regimes, i.e., heavy chemical fertilizer application (CF) and reduced chemical fertilizer applications supplemented with organic (OF) or Trichoderma-enriched organic fertilizer (BF), in a continuous five-season pot experiment on tomato. Results: The CF-treated soil resulted in a bacterial community with the lowest diversity, while the BF-treated soil had the highest diversity level. The OF-treated soil had the lowest diversity in the fungal community, while the CF- and BF-treated soils had higher diversity. Moreover, better plant growth and soil fertility status were obtained in the BF treatment followed by the OF and CF treatments. Conclusions: Compared to the CF and OF regimes, reduced chemical fertilizer plus Trichoderma-enriched organic fertilizer (BF) is the most suitable regime to control microbiome degeneration of monocropped soil and to thus maintain tomato plant growth and health. [ABSTRACT FROM AUTHOR]

Aims: We evaluated the efficacy of biochar application for suppressing bacterial wilt of tomato and identified the potential underlying mechanisms involved in the disease control. Methods: We measured the impact of two different sized biochar (53-120 μm and 380-830 μm) on bacterial wilt incidence in a greenhouse experiment. The efficiency of different sized biochar for the adsorption of tomato root exudates and the pathogen was further examined in vitro. We also quantified the effects of biochar and tomato root exudates on two pathogen virulence factors, chemotaxis, swarming motility and examined the effect of biochar on pathogen root colonization. Results: Fine biochar application (3%; w:w) significantly decreased the bacterial wilt incidence by 19.9%. Biochar with different particle size had similar adsorption capacity for root exudates, while fine biochar was efficient (91%) in pathogen adsorption. Root exudates and fine biochar increased the chemotaxis ability of pathogen, while fine biochar reduced pathogen swarming motility and rhizosphere colonization. Conclusions: Application of fine biochar can significantly decreased bacterial wilt incidence. This was mechanistically explained by biochar ability to 1) adsorb pathogen directly and indirectly via adsorption of root exudates (based on pathogen chemotaxis) and to 2) directly suppress pathogen swarming motility and subsequent root colonization. [ABSTRACT FROM AUTHOR]

Background and aims: Plant growth and photosynthetic ability have been frequently demonstrated to increase with nitrogen (N) supply. N can also promote changes in root water absorption and shoot water status via mechanisms that remain poorly understood. This study aims at investigating the effects of N supply on water absorption. Methods: A hydroponic experiment with two independent rice varieties (cv. 'Shangyou63' hybrid indica and cv. 'Yangdao6' conventional indica, China) supplied by three distinct N levels was performed in a greenhouse. Physiological characteristics were analyzed after a few weeks. Results: Compared to low N supply (20 mg·L), exposure to high N supply (100 mg·L) increased the light-saturated photosynthetic rate ( A) and water use efficiency (WUE) by 17 % and 22 %, respectively, in Shanyou63 and by 43 % and 26 %, respectively, in Yangdao6. The leaf water potential was significantly decreased in Shanyou63 but not in Yangdao6. There were increases in the rate of water uptake and the root hydraulic conductance ( L) under high N supply in both rice cultivars; these changes were accompanied by increased transcription levels of aquaporins (AQPs), decreased aerenchyma formation and root porosity, and decreased root lignin content. Under high N supply, Yangdao6 also exhibited much higher AQP activity, lower aerenchyma and root porosity compared with those of Shanyou63, indicating that Yangdao6 had an increased ability to absorb water compared with that of Shanyou63. Conclusions: The enhanced expression of AQPs and decreased root aerenchyma and lignin contributed to increased water absorption ability under high N supply. In addition, the responses of each of the two rice cultivars (hybrid and conventional) to N supply is related to their water uptake ability, resulting from root porosity and an increase in AQP activity. [ABSTRACT FROM AUTHOR]

Aims: Banana Fusarium wilt disease is caused by the Fusarium oxysporum f. sp. cubense race 4 fungus and is a vast problem for global banana production. Suppressive and conducive soils were analyzed to characterize important microbial populations and soil chemical properties that contribute to disease suppressiveness. Methods: Soil bacteria communities from the two banana orchards with excellent Fusarium disease suppression (suppressive soil) after long-term monoculture and two adjacent banana orchards with serious Fusarium wilt disease (conducive soils) were compared using deep 16S RNA barcode pyrosequencing. Result: Compared to the conducive soils within the same field site, higher ( P < 0.05) richness and diversity indices were observed in both suppressive soils. Moreover, more operational taxonomic units (OTUs) were observed in the two suppressive soils. Hierarchical cluster analyses showed that bacterial community membership and structure in disease-suppressive soils differed from disease-conducive soils. The Acidobacteria phylum was significantly ( P < 0.05) elevated, but Bacteroidetes was significantly ( P < 0.05) reduced in suppressive soils. The Gp4, Gp5, Chthonomonas, Pseudomonas, and Tumebacillus genera were significantly ( P < 0.05) enriched in suppressive soils, but Gp2 was significantly ( P < 0.05) reduced in suppressive soils. Furthermore, the enrichment of Gp5 and Pseudomonas as well as the soil physicochemical properties of available phosphorus were significantly ( P < 0.05) correlated with disease suppression. Conclusions: Naturally disease suppressive soils to banana Fusarium wilt disease harbor unique bacterial communities. [ABSTRACT FROM AUTHOR]

Background and aims: Grafting is commonly used to overcome soil-borne disease but how it affects the root-associated microbiome of concerned crops and the linkage between the microbiome and the resistance of soil-borne disease remain unknown. This study addressed the variation in the microbial activity and bacterial community in the rhizosphere of own-root bottle gourd (rootstock), own-root watermelon, and grafted-root watermelon under field conditions and tried to clarify how bacterial communities in the rhizosphere responded to grafting of watermelon. Methods: Seven types of soil enzyme activities were tested by microplate fluorometric assay, and the root-associated bacterial community was compared using 454 pyrosequencing. Results: Clear distinctions in microbial activity and taxonomic levels between the different treatments were obtained. Compared with grafted-root watermelon, ungrafted watermelon recruited significantly higher beneficial bacterial genera, such as Bacillus spp. and Paenibacillus spp., suggesting the grafted watermelon root could not have the ability to harbor highly beneficial bacteria to exert soil-borne disease resistance. However, a significantly higher Shannon-Wiener index at any reads level was found in the rhizosphere of grafted watermelon compared with ungrafted watermelon. Conclusions: Root-associated bacteria of grafted watermelon possess a broader niche overlap which would provide the potential to exclude the pathogen challenge. We proposed that the grafted watermelon might exert soil-borne disease resistance by maximizing the niche occupancy of rhizosphere rather than by recruiting more beneficial bacteria. [ABSTRACT FROM AUTHOR]

Aims: This research was to study the capacity of Trichoderma harzianum strain SQR-T037 to colonize tomato roots and how this strain and its bio-organic fertilizer stimulate plant growth and increase yields under field conditions. Methods: Field trials were conducted with a reduced application of chemical fertilizer (75 % of the recommended application) plus Trichoderma-enriched bio-organic fertilizer (BF) or organic fertilizer (OF) or Trichoderma spore suspension (SS), while 100 % of the recommended chemical fertilizer (CF) was used as control. Results: Trichoderma SQR-T037 could efficiently colonize tomato roots and soils based on the reverse transcription-quantitative PCR analysis, and significantly stimulate biomass accumulation at an early stage. The 75 % rates of chemical fertilizer coupled with bio-organic fertilizer (BF) produced tomato yields equivalent to those obtained using the 100 % rates of chemical fertilizer (CF), while inoculation with the Trichoderma alone (SS) or supplement with organic fertilizer alone (OF) would cause 11 and 13 % decreases in yield over the control (CF). The efficacy of BF for maintaining a stable tomato yield may be due to the enhanced soil nutrients availability and the increased abundance of soil microflora, including bacteria, fungi, actinomycetes and Trichoderma communities, which had a positive linear correlation in most of the cases revealed by the Pearson correlation analysis. Conclusions: The results of this study imply that the reason by which the bio-organic fertilizer promotes plant growth and increases the tomato yields can be attributed to the enhancement of the rhizospheric microflora, which promotes nutrient activation. Therefore, T. harzianum could be employed in a combination with composts. In this way, the application rate of chemical fertilizers can be practically decreased by 25 % to obtain maximum benefits. [ABSTRACT FROM AUTHOR]

Background and aims: Paenibacillus spp. are widely considered to impact the fertility and health of soil. The aim of this study was to evaluate how different fertilization regimes affect the population size and community structure of Paenibacillus spp. over a long period of time in red soil. Methods: Soil samples were collected from a long-term experiment and were then analyzed using real-time PCR and PCR-DGGE. The correlation analysis, PCA and RDA were used to explore the relationships among Paenibacillus spp. population, community structure and soil properties in different treatments. Results: The pH was seriously decreased only by the application of chemical fertilizer. The largest population of Paenibacillus spp. was found in the soil treated with organic fertilizer application, while the richest diversity was observed in the soil treated only with the chemical fertilizer. The Paenibacillus spp., Paenibacillus alkaliterrae, Paenibacillus campinasensis, and Paenibacillus xylanilyticus were found in all treatments. Paenibacillus castaneae was found in the soil treated with NPK, and Paenibacillus pabuli was specifically observed in the lime-amended treatment. Paenibacillus taichungensis and Paenibacillus prosopidis were detected in the soil treated with only chemical fertilizer. Except for the ammonium and pH, all the tested soil fertility parameters (total C, total N, nitrate, available K and available P) could significantly affect both the Paenibacillus spp. population number and diversity. The soil pH was significantly correlated with Paenibacillus spp. diversity only. Conclusions: Our results indicate that the different long-term fertilization regimes have varied impact on both the Paenibacillus spp. population size and the diversity of the community associated with the soil properties tested. These results can help to enrich the information on the response of beneficial soil microbes to different long-term fertilization regimes. [ABSTRACT FROM AUTHOR]

Aims and background: Soil fertility quality index is a useful indicator that helps to improve sustainable land use management and achieve economical yield in agriculture production. The objectives of this study were to evaluate the changes of soil fertility quality between the 1980s and 2000s in different cropping systems and its significance to crop productivity and sustainability. Methods: We collected all published data on crop yields and soil parameters from 58 long-term experiments in three typical double-cropping systems in China, including maize-wheat (M-W), rice-rice (R-R) and rice-wheat (R-W) cropping systems, and selected seven fertilizer treatments in each experiment, including inorganic fertilizer [nitrogen and phosphorus fertilizer (NP), nitrogen and potassium fertilizer (NK), phosphorus and potassium fertilizer (PK) and balanced mineral fertilizer (NPK)], combined NPK with farmyard manure (NPKM) or crop straw (NPKS), and no fertilizer application (served as control). For comparison, an integrated fertility quality index (IFQI) was used to estimate the variations in soil fertility in different cropping systems. Moreover, the mean production variability index (PVI, %) in each cropping system was calculated to evaluate the stability of crop production. Results: Over cropping systems, the averaged relative yields of PK, NK and NP ranged from 38.0 to 97.4 %, while the mean yields can be increased by 2.4-5.1 % in NPKM, compared to NPK. The mean yields were similar between NPK and NPKS for maize and wheat crops, but the yield was increased by 4.3-10.0 % in NPKS. Among the different treatments, the highest variability of cereal productivity was obtained in NK, PK or Control, while the lowest value was mostly recorded in NPKM or NPKS in these three cropping systems. Relative to the control, the IFQIs in fertilization treatments were increased by 9.4-150.0 %, 6.2-41.5 % and 1.3-17.5 % in M-W, R-W and R-R systems, respectively (except for PK treatment in R-R system). However, changes of IFQI in topsoil differed among fertilizer treatments, and greater increases existed in the treatments receiving organic residues (NPKM and NPKS). Conclusions: The increase in crop yield is exponentially correlated with the increased IFQI over treatments in three cropping systems. Over the treatments and systems, production variability among years is shown to be negatively, linearly related to IFQI ( P < 0.001). Therefore, the high grain yield and low production variability can be simultaneously achieved by increasing soil fertility in all three cropping systems. [ABSTRACT FROM AUTHOR]

Aim: It is necessary to understand the roles of root exudates involved in plant-microbe interactions to inform practical application of beneficial rhizosphere microbial strains. Methods: Colonization of Bacillus amyloliquefaciens SQR9 (isolated from cucumber rhizosphere) and Bacillus subtilis N11 (isolated from banana rhizosphere) of their original host was found to be more effective as compared to the colonization of the non-host plant. Organic acids in the root exudates of the two plants were identified by High performance liquid chromatography (HPLC). The chemotactic response and effects on biofilm formation were assessed for SQR9 and N11 in response to cucumber and banana root exudates, as well as their organic acids components. Results: Citric acid detected exclusively in cucumber exudates could both attract SQR9 and induce its biofilm formation, whereas only chemotactic response but not biofilm formation was induced in N11. Fumaric acid that was only detected in banana root exudates revealed both significant roles on chemotaxis and biofilm formation of N11, while showing only effects on biofilm formation but not chemotaxis of SQR9. Conclusion: The relationship between PGPR strain and root exudates components of its original host might contribute to preferential colonization. This study advances a clearer understanding of the mechanisms relevant to application of PGPR strains in agricultural production. [ABSTRACT FROM AUTHOR]

Aims: Many Trichoderma species are well-known by their ability to promote plant growth and health. However, few studies have been conducted to improve their ability. Laboratory and greenhouse experiments compared the promotion of cucumber growth by the putative mutant Trichoderma harzianum T-E5 versus the wild-type SQR-T037 and bio-organic fertilizers fortified with them. Methods: The putative mutant T-E5 was selected based on plant hormone production in liquid fermentation and then on the effects of T-E5 and SQR-T037 to promote plant growth and colonization of plant roots and rhizosphere soil of cucumber. Results: High-performance liquid chromatography analysis showed that indole acetic acid (IAA) production by T-E5 was enhanced by 30.2 % as compared with SQR-T037. T-E5 treatment statistically increased cucumber plant biomass in soil and hydroponic experiments. Based on TaqMan reverse transcriptase-polymerase chain reaction, the population of T-E5 was almost ten times higher than SQR-T037 in the soil samples at 30 days. The endophytic colonization of roots and stems by the two strains had the same dynamic tendency, but T-E5 was much greater than SQR-T037 at any sampling time. Conclusions: The putative mutant T-E5 enhanced the production of IAA and plant colonization ability, and this improvement had a great potential for further application of T-E5 in crop production. [ABSTRACT FROM AUTHOR]

Aims: Potato bacterial wilt ( Ralstonia solanacearum) is a soil-borne disease that affects the potato plant ( Solanum tuberosum) worldwide and causes serious economic losses in southern China. The objective of this study is to study the effect of bacterial antagonists and bio-organic fertilizers on potato bacterial wilt and rhizosphere soil microbial population. Methods: In the present study, pot and field experiments were conducted to evaluate the LH23 ( Bacillus amyloliquefaciens) and LH36 ( Bacillus subtilis) strains and their derived bio-organic fertilizers (BIO23 and BIO36) as potential biocontrol agents against potato bacterial wilt. Results: BIO23 and BIO36 decreased the incidence of bacterial wilt disease and increased potato yields. In pot experiments, the disease incidence of BIO23 and BIO36 was 8.9 % and 11.1 % respectively, much lower than the control (57.7 %). The biocontrol efficiency of BIO23 was 84.6 %, which was the most successful treatment and BIO36 was the second with a biocontrol efficiency of 80.8 %. The increased percentages of potato yields when compared with the control were 63.5 % (BIO23), 64.7 % (BIO36) 34.8 % (LH23), 33.6 % (LH36) and 20.7 % (OF). The counts of antagonists, bacteria and actinobacteria in the rhizosphere soil were significantly increased in BIO23 and BIO36 treatments, whereas the counts of R. solanacearum and fungi in the soil in the both treatments decreased. In field experiments, 70 days after treatment, the biocontrol efficacies of BIO23 and BIO36 treatments were 92.0 % and 84.0 %, and the yield increases of BIO23 and BIO36 treatments were 42.3 % and 28.8 %, respectively, when compared with the organic fertilizer treatment. In addition, the changes in the microbial populations were the same as those observed in the greenhouse experiment. Conclusions: Potato bacterial wilt could be well controlled by the application bio-organic fertilizer containing a specific antagonist, mainly through the alternation of soil microbial community [ABSTRACT FROM AUTHOR]

Aims: Exudation of organic acid anions is one of the mechanisms responsible for aluminum (Al) tolerance. The plasma membrane (PM) H-ATPase is involved in the exudation of organic acid anions. However, the relationship between organic acid exudation and PM H-ATPase under Al toxicity remains unclear. This study aims to investigate the correlation among Al-induced citrate exudation, PM H-ATPase activity and counterions for citrate release from cluster roots of phosphorus-deficient (−P) white lupin. Methods: Al and various pharmacological agents were applied to incubate the cluster roots of P-deficient white lupin; the citrate exudation rate, PM H-ATPase activity and ion exudation of cluster roots were examined. Results: Citrate exudation from cluster roots of P-deficient white lupin was induced by 50 μM Al treatment within 1.5 h, but no extra increase was found when the duration of Al treatment increased. The PM H-ATPase activity of cluster roots was insensitive to Al treatment, irrespective of Al concentration and duration of Al treatment. Al treatment increased K efflux but not H efflux from cluster roots. After application of pharmacological agents to P-deficient cluster roots under Al treatment or not, vanadate decreased H efflux and increased K efflux, but had no inhibitory effect on citrate exudation; fusicoccin increased H efflux and citrate exudation, but decreased K efflux; tetraethylammonium (TEA) chloride, a K-channel inhibitor, inhibited K efflux and increased H efflux. Conclusions: These results indicate that citrate exudation induced by combined treatment with P-deficiency and Al is independent of PM H-ATPase activity, and is coupled with K efflux, which may compensate H efflux for keeping the charge balance for Al-induced citrate exudation from cluster roots of P-deficient white lupin. [ABSTRACT FROM AUTHOR]

Aims and background: The ability to suppress soil nitrification through the release of nitrification inhibitors from plant roots is termed 'biological nitrification inhibition' (BNI). Earlier, we reported that sorghum roots release higher BNI-activity when grown with NH, but not with NO as N source. Also for BNI release, rhizosphere pH of <5.0 is needed; beyond this, a negative effect on BNI release was observed with nearly 80% loss of BNI activity at pH >7.0. This study is aimed at understanding the inter-functional relationships associated with NH uptake, rhizosphere-pH and plasma membrane H-ATPase (PM H-ATPase) activity in regulating the release of BNIs (biological nitrification inhibitors) from sorghum roots. Methods: Sorghum was grown hydroponically and root exudates were collected from intact plants using a pH-stat system to separate the secondary acidification effects by NH uptake on BNIs release. A recombinant luminescent Nitrosomonas europaea bioassay was used to determine BNI-activity. Root plasma membrane was isolated using a two-phase partitioning system. Hydrolytic H-ATPase activity was determined. Split-root system setup was deployed to understand the localized responses to NH, H-ATPase-stimulator (fusicoccin) or H-ATPase-inhibitor (vanadates) on BNI release by sorghum. Results: Presence of NH in the rhizosphere stimulated the expression of H-ATPase activity and enhanced the release of BNIs from sorghum roots. Fusicoccin, which stimulates H-ATPase activity, also stimulated BNIs release in the absence of NH; vanadate, which suppresses H-ATPase activity, also suppressed the release of BNIs. NH levels (in rhizosphere) positively influenced BNIs release and root H-ATPase activity in the concentration range of 0-1.0 mM, indicating a close relationship between BNI release and root H-ATPase activity with a possible involvement of carrier-mediated transport for the release of BNIs in sorghum. Conclusion: Our results suggest that NH uptake, PM H-ATPase activity, and rhizosphere acidification are functionally inter-connected with BNI release in sorghum. Such knowledge is critical to gain insights into why BNI function is more effective in light-textured, mildly acidic soils compared to other soil types. [ABSTRACT FROM AUTHOR]

Aims: Nitrogen, especially NH, can stimulate the uptake of phosphorus in plants, but the underlying mechanisms have not been clearly elucidated. Because phosphate is taken up via an anion/H co-transport process, we propose that the stimulated uptake of phosphorus by NH versus NO nutrition may be related to the activity of plasma membrane H ATPase. In the present study, we investigated the effect of NH and NO on phosphorus uptake and plasma membrane H ATPase activity in rice. Methods: Rice plants were cultivated in a hydroponic solution with NH or NO. After 15 days of cultivation, phosphorus content was determined. Root plasma membrane was isolated using a two-phase partitioning system and hydrolytic H-ATPase activity was determined by measuring the P concentration after a 30-min hydrolysis reaction. Relative expression of plasma membrane H ATPase genes was analyzed by real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). H ATPase enzyme concentration in the plasma membrane was detected by western blot. For P uptake experiments, rice roots were incubated in the nutrient solution with addition of HPO. Results: P content in both the roots and shoots of rice plants supplemented with NH was significantly higher than P content in plants grown with NO. Plasma membrane H ATPase activity in NH-fed rice roots was significantly higher than that in NO-fed rice roots. Real-time qRT-PCR and western blot results indicated that the higher activity of plasma membrane H ATPase in NH-fed rice roots could be attributed to increased expression of the OSA1, OSA3, OSA7, OSA8 and OSA9 genes and an increase in H ATPase enzyme concentration in the plasma membrane. Results from P uptake experiments showed that rice roots incubated with NH absorbed more P during the four-hour incubation than did rice roots incubated with NO. Vanadate inhibited P uptake in rice roots supplied with NH, while fusicoccin stimulated P uptake under NO nutrition. Conclusions: Taken together, these results suggest an involvement of plasma membrane H ATPase in the stimulated uptake of phosphorus by rice roots supplemented with NH. [ABSTRACT FROM AUTHOR]

Rice grown under anaerobic waterlogged soil condition takes up ammonium as a major source of nitrogen (N). A substantial quantity of nitrate is taken up by rice when aeration conditions prevail. This work compared the physiological and molecular responses of N-depleted rice ( Oryza sativa L. japonica ssp. cv. Wuyunjing) to re-supply of different N sources in a hydroponic system. Expression of six genes known to be related to N uptake and assimilation in roots was analyzed by semi-quantitative reverse transcription polymerase chain reaction (RT-PCR). N starvation increased root growth but decreased shoot biomass and nitrate reductase (NR) activity. In comparison to nitrate as N source, ammonium tended to inhibit root growth but significantly improved shoot growth, total N uptake, and, particularly, the translocation of N to the above ground parts. Replacing half of the ammonium by nitrate in the single ammonium solution increased glutamine synthetase (GS) activity and total N uptake. This replacement enhanced expression of OsAMT1;3 but decreased the expression of OsAMT1;2 in the roots. Likewise, replacing half of the nitrate by ammonium in the single nitrate solution, increased NR activity and expression of an NR gene ( OsNR1) but suppressed expression of OsNRT2 in the roots. Expression of both OsAMT1;1 and a GS gene ( OsGS1;1) was relatively constant and not affected by the N form or starvation in the rice roots. Predominant beneficial effects of dual supply of the two forms of N in comparison with a single form of N either as ammonium or as nitrate might be due to improvement of ammonium uptake due to nitrate presence near the roots and enhanced reduction of nitrate in leaves by ammonium. [ABSTRACT FROM AUTHOR]

Backgrounds and aims: Plant rhizosphere microbiome play crucial roles in plant growth. However, the mechanisms governing the rhizosphere microbiome assembly remain poorly understood. Here, we studied the contributions of sub-communities, referring to the recruited sub-community from bulk soil microbiome (SR) and the released sub-community from endosphere microbiome (ER), to the taxonomical and functional assembly of the rhizosphere microbiome.We transplanted maize seedlings across different soils to identify the origin source of rhizosphere microbial communities. The profiles of rhizosphere microbial communities were acquired using 16S rRNA marker gene sequencing.The amplicon data analyses revealed that, in the reassembled rhizosphere microbial communities after transplanting, the SR and ER sub-communities were distinguished among different soils and the SR sub-communities showed higher bacterial diversity than ER sub-communities. The SR sub-communities dominated the variable selection process, while the ER sub-communities dominated the homogeneous selection process in rhizosphere microbiome assembly. Moreover, we found that specific taxa derived from endosphere play important roles in promoting nitrogen accumulation and reducing nitrogen losses in nitrogen-deficient soil, suggesting that the soil nitrogen level affects the specific taxa from endosphere to rhizosphere to maintain plant nitrogen requirement.Plants could assemble compensatory functional rhizosphere microbiome to guarantee their nutrient requirement in nutrient-deficient soil. Specifically, some taxa derived from endosphere, make great contributions to the functional compensatory assembly in rhizosphere. These findings facilitate our understanding of the assembly mechanisms in rhizosphere, and further soil biological fertility improvement will benefit from isolation and application of these specific functional microbes.Methods: Plant rhizosphere microbiome play crucial roles in plant growth. However, the mechanisms governing the rhizosphere microbiome assembly remain poorly understood. Here, we studied the contributions of sub-communities, referring to the recruited sub-community from bulk soil microbiome (SR) and the released sub-community from endosphere microbiome (ER), to the taxonomical and functional assembly of the rhizosphere microbiome.We transplanted maize seedlings across different soils to identify the origin source of rhizosphere microbial communities. The profiles of rhizosphere microbial communities were acquired using 16S rRNA marker gene sequencing.The amplicon data analyses revealed that, in the reassembled rhizosphere microbial communities after transplanting, the SR and ER sub-communities were distinguished among different soils and the SR sub-communities showed higher bacterial diversity than ER sub-communities. The SR sub-communities dominated the variable selection process, while the ER sub-communities dominated the homogeneous selection process in rhizosphere microbiome assembly. Moreover, we found that specific taxa derived from endosphere play important roles in promoting nitrogen accumulation and reducing nitrogen losses in nitrogen-deficient soil, suggesting that the soil nitrogen level affects the specific taxa from endosphere to rhizosphere to maintain plant nitrogen requirement.Plants could assemble compensatory functional rhizosphere microbiome to guarantee their nutrient requirement in nutrient-deficient soil. Specifically, some taxa derived from endosphere, make great contributions to the functional compensatory assembly in rhizosphere. These findings facilitate our understanding of the assembly mechanisms in rhizosphere, and further soil biological fertility improvement will benefit from isolation and application of these specific functional microbes.Results: Plant rhizosphere microbiome play crucial roles in plant growth. However, the mechanisms governing the rhizosphere microbiome assembly remain poorly understood. Here, we studied the contributions of sub-communities, referring to the recruited sub-community from bulk soil microbiome (SR) and the released sub-community from endosphere microbiome (ER), to the taxonomical and functional assembly of the rhizosphere microbiome.We transplanted maize seedlings across different soils to identify the origin source of rhizosphere microbial communities. The profiles of rhizosphere microbial communities were acquired using 16S rRNA marker gene sequencing.The amplicon data analyses revealed that, in the reassembled rhizosphere microbial communities after transplanting, the SR and ER sub-communities were distinguished among different soils and the SR sub-communities showed higher bacterial diversity than ER sub-communities. The SR sub-communities dominated the variable selection process, while the ER sub-communities dominated the homogeneous selection process in rhizosphere microbiome assembly. Moreover, we found that specific taxa derived from endosphere play important roles in promoting nitrogen accumulation and reducing nitrogen losses in nitrogen-deficient soil, suggesting that the soil nitrogen level affects the specific taxa from endosphere to rhizosphere to maintain plant nitrogen requirement.Plants could assemble compensatory functional rhizosphere microbiome to guarantee their nutrient requirement in nutrient-deficient soil. Specifically, some taxa derived from endosphere, make great contributions to the functional compensatory assembly in rhizosphere. These findings facilitate our understanding of the assembly mechanisms in rhizosphere, and further soil biological fertility improvement will benefit from isolation and application of these specific functional microbes.Conclusions: Plant rhizosphere microbiome play crucial roles in plant growth. However, the mechanisms governing the rhizosphere microbiome assembly remain poorly understood. Here, we studied the contributions of sub-communities, referring to the recruited sub-community from bulk soil microbiome (SR) and the released sub-community from endosphere microbiome (ER), to the taxonomical and functional assembly of the rhizosphere microbiome.We transplanted maize seedlings across different soils to identify the origin source of rhizosphere microbial communities. The profiles of rhizosphere microbial communities were acquired using 16S rRNA marker gene sequencing.The amplicon data analyses revealed that, in the reassembled rhizosphere microbial communities after transplanting, the SR and ER sub-communities were distinguished among different soils and the SR sub-communities showed higher bacterial diversity than ER sub-communities. The SR sub-communities dominated the variable selection process, while the ER sub-communities dominated the homogeneous selection process in rhizosphere microbiome assembly. Moreover, we found that specific taxa derived from endosphere play important roles in promoting nitrogen accumulation and reducing nitrogen losses in nitrogen-deficient soil, suggesting that the soil nitrogen level affects the specific taxa from endosphere to rhizosphere to maintain plant nitrogen requirement.Plants could assemble compensatory functional rhizosphere microbiome to guarantee their nutrient requirement in nutrient-deficient soil. Specifically, some taxa derived from endosphere, make great contributions to the functional compensatory assembly in rhizosphere. These findings facilitate our understanding of the assembly mechanisms in rhizosphere, and further soil biological fertility improvement will benefit from isolation and application of these specific functional microbes. [ABSTRACT FROM AUTHOR]