Search

Laboratory tests and greenhouse experiments were carried out to investigate the abilities of Bacillus subtilis Y-IVI to promote plant growth and to colonize the rhizosphere and interior tissues of muskmelon. Laboratory tests showed that B. subtilis Y-IVI can produce indole acetic acid, siderophores, and ammonia. The inoculation of soil with green fluorescent protein-tagged Y-IVI (GY-IVI) significantly increased plant shoot and root dry weights as compared with the non-inoculated soils. The inoculation of soil with B. subtilis GY-IVI maintained approximately 10 colony-forming units (cfu) of GY-IVI per gram of dry rhizosphere soil for 1 month. The GY-IVI recovered from the interior of crowns and roots in the inoculated soil were 10 and 10 cfu g dry weight, respectively, suggesting that GY-IVI acted as an endophyte. In the present study, we combined the two important growth promotion ingredients, colonization ability and growth promotion metabolites produced by biological agents, to investigate B. subtilis Y-IVI's promotion effects on muskmelon growth. [ABSTRACT FROM AUTHOR]

n experiment was planned to evaluate the behavior of Paenibacillus polymyxa SQR-21 under differential iron availability. P. polymyxa was grown under three differential iron conditions (0, 2, 20 μM). Iron starvation slowed bacterial growth and at all iron levels, pH of liquid culture was decreased, but maximum decrease was observed at highest iron level. Cell surface ferrireductase activity decreased as culture aged, while extracellular Fe-reducing activity constantly increased. Hydroxamates type siderophores production was increased with the decrease in iron levels. Numerous cellular proteins were expressed by P. polymyxa in the range of 5-140 kDa and several of them showed conspicuous differential iron regulation. P. polymyxa seems to have more than one type of iron acquisition mechanism including gradual release of organic acids, cell surface ferrireductases, extracellular reductants, and secretion of low molecular weight hydroxamates chelators. This article is the first to report the kinetic study of P. polymyxa under differential iron availability. The information provided here gives initial information about the iron uptake mechanism of P. polymyxa. [ABSTRACT FROM AUTHOR]

To study the effects of local nitrogen supply on water and nutrient absorption, French bean ( Phaseolus vulgaris L.) plants were grown in a split root system. Five treatments supplied with different nitrogen forms were compared: homogeneous nitrate (NN) and homogenous ammonium (AA) supply, spatially separated supply of nitrate and ammonium (NA), half of the root system supplied with N-free nutrient solution, the other half with either nitrate (N0) or ammonium (A0). The results showed that 10 d after onset of treatments, root dry matter (DM) in the nitrate-supplied vessels treated with NA was more than two times higher than that in the ammonium-supplied vessels. Water uptake from the nitrate-supplied vessels treated with NA was 281% higher than under ammonium supply. In treatments N0 and A0, the local supply of N resulted in clearly higher root DM, and water uptake from the nitrate-supplied vessels was 82% higher than in the -N vessels. However, in A0 plants, water uptake from the -N nutrient solution was 129% higher than from the ammonium-supplied vessels. This indicates a compensatory effect, which resulted in almost identical rates of total water uptake of treatments AA and A0, which had comparable shoot DM and leaf area. Ammonium supply reduced potassium and magnesium absorption. Water uptake was positively correlated with N, Mg and K uptake. [ABSTRACT FROM AUTHOR]

Warming and precipitation anomalies affect terrestrial carbon balance partly through altering microbial eco-physiological processes (e.g., growth and death) in soil. However, little is known about how such processes responds to simultaneous regime shifts in temperature and precipitation. We used the 18O-water quantitative stable isotope probing approach to estimate bacterial growth in alpine meadow soils of the Tibetan Plateau after a decade of warming and altered precipitation manipulation. Our results showed that the growth of major taxa was suppressed by the single and combined effects of temperature and precipitation, eliciting 40-90% of growth reduction of whole community. The antagonistic interactions of warming and altered precipitation on population growth were common (~70% taxa), represented by the weak antagonistic interactions of warming and drought, and the neutralizing effects of warming and wet. The members in Solirubrobacter and Pseudonocardia genera had high growth rates under changed climate regimes. These results are important to understand and predict the soil microbial dynamics in alpine meadow ecosystems suffering from multiple climate change factors. [ABSTRACT FROM AUTHOR]

Organic carbon availability in soil is crucial for shaping microbial communities, yet, uncertainties persist concerning microbial adaptations to carbon levels and the ensuing ecological and evolutionary consequences. We investigated organic carbon metabolism, antibiotic resistance, and virus-host interactions in soils subjected to 40 y of chemical and organic fertilization that led to contrasting carbon availability: carbon-poor and carbon-rich soils, respectively. Carbon-poor soils drove the enrichment of putative genes involved in organic matter decomposition and exhibited specialization in utilizing complex organic compounds, reflecting scramble competition. This specialization confers a competitive advantage of microbial communities in carbon-poor soils but reduces their buffering capacity in terms of organic carbon metabolisms, making them more vulnerable to environmental fluctuations. Additionally, in carbon-poor soils, viral auxiliary metabolic genes linked to organic carbon metabolism increased host competitiveness and environmental adaptability through a strategy akin to "piggyback the winner." Furthermore, putative antibiotic resistance genes, particularly in low-abundance drug categories, were enriched in carbon-poor soils as an evolutionary consequence of chemical warfare (i.e., interference competition). This raises concerns about the potential dissemination of antibiotic resistance from conventional agriculture that relies on chemical-only fertilization. Consequently, carbon starvation resulting from long-term chemical-only fertilization increases microbial adaptations to competition, underscoring the importance of implementing sustainable agricultural practices to mitigate the emergence and spread of antimicrobial resistance and to increase soil carbon storage. [ABSTRACT FROM AUTHOR]

Microbial interactions affect community stability and niche spaces in all ecosystems. However, it is not clear what factors influence these interactions, leading to changes in species fitness and ecological niches. Here, we utilized 16 monocultures and their corresponding pairwise co-cultures to measure niche changes among 16 cultivable bacterial species in a wide range of carbon sources, and we used resource availability as a parameter to alter the interactions of the synthetic bacterial community. Our results suggest that metabolic similarity drives niche deformation between bacterial species. We further found that resource limitation resulted in increased microbial inhibition and more negative interactions. At high resource availability, bacteria exhibited little inhibitory potential and stronger facilitation (in 71% of cases), promoting niche expansion. Overall, our results show that metabolic similarity induces different degrees of resource competition, altering pairwise interactions within the synthetic community and potentially modulating bacterial niches. This framework may lay the basis for understanding complex niche deformation and microbial interactions as modulated by metabolic similarity and resource availability. [ABSTRACT FROM AUTHOR]

While bacterial diversity is beneficial for the functioning of rhizosphere microbiomes, multi-species bioinoculants often fail to promote plant growth. One potential reason for this is that competition between different species of inoculated consortia members creates conflicts for their survival and functioning. To circumvent this, we used transposon insertion mutagenesis to increase the functional diversity within Bacillus amyloliquefaciens bacterial species and tested if we could improve plant growth promotion by assembling consortia of highly clonal but phenotypically dissimilar mutants. While most insertion mutations were harmful, some significantly improved B. amyloliquefaciens plant growth promotion traits relative to the wild-type strain. Eight phenotypically distinct mutants were selected to test if their functioning could be improved by applying them as multifunctional consortia. We found that B. amyloliquefaciens consortium richness correlated positively with plant root colonization and protection from Ralstonia solanacearum phytopathogenic bacterium. Crucially, 8-mutant consortium consisting of phenotypically dissimilar mutants performed better than randomly assembled 8-mutant consortia, suggesting that improvements were likely driven by consortia multifunctionality instead of consortia richness. Together, our results suggest that increasing intra-species phenotypic diversity could be an effective way to improve probiotic consortium functioning and plant growth promotion in agricultural syste [ABSTRACT FROM AUTHOR]

Division of labor, where subpopulations perform complementary tasks simultaneously within an assembly, characterizes major evolutionary transitions of cooperation in certain cases. Currently, the mechanism and significance of mediating the interaction between different cell types during the division of labor, remain largely unknown. Here, we investigated the molecular mechanism and ecological function of a policing system for optimizing the division of labor in Bacillus velezensis SQR9. During biofilm formation, cells differentiated into the extracellular matrix (ECM)-producers and cheater-like nonproducers. ECM-producers were also active in the biosynthesis of genomic island-governed toxic bacillunoic acids (BAs) and self-resistance; while the nonproducers were sensitive to this antibiotic and could be partially eliminated. Spo0A was identified to be the co-regulator for triggering both ECM production and BAs synthesis/immunity. Besides its well-known regulation of ECM secretion, Spo0A activates acetyl-CoA carboxylase to produce malonyl-CoA, which is essential for BAs biosynthesis, thereby stimulating BAs production and self-immunity. Finally, the policing system not only excluded ECM-nonproducing cheater-like individuals but also improved the production of other public goods such as protease and siderophore, consequently, enhancing the population stability and ecological fitness under stress conditions and in the rhizosphere. This study provides insights into our understanding of the maintenance and evolution of microbial cooperation. [ABSTRACT FROM AUTHOR]

The article presents a study on the significant role of an unidentified allele of the nitrate transporter gene OsNRT2.3 in maintaining high yield and high nitrogen use efficiency under high temperatures. Topics discussed include the structure of small RNA and OsNRT2.3a/b transcription, and the implications of the study for breeding rice varieties with higher grain yield and lower nitrogen fertilizer input.

The practice of growing agricultural crops in rows results in larger soil nematode populations in the root-associated soil than in the bulk soil between the rows. Fertilisers applied to improve grain yield generally increase the abundance of nematode communities in agricultural soils. The objective of this study was to compare total nematode density and four dominant genera in the root-associated and bulk soils of paddy rice and upland wheat receiving organic and mineral fertilisers. Dominant nematode genera accounted for 80% of all nematodes and represented four trophic groups. There was greater total nematode density and a higher enrichment index (El) but less nematode diversity (H') and a lower structure index (SI) in the root-associated soil than bulk soil of upland wheat. By contrast, nematode abundance, diversity and ecological indices were similar in the root-associated and bulk soils of the paddy rice. Soil nematode communities were affected significantly and consistently by fertilisation in upland wheat and paddy rice phases. More herbivore Hirschmanniella were present with mineral fertiliser than in the non-fertilised control. Straw-based organic fertilisers increased the abundance of bacterivore Eucephalobus. The lack of interaction between rhizosphere effect and fertilisation indicated that crop-growing conditions (different species and water regimes) were more influential on nematode communities and not consistently impacted by short-term organic and mineral fertilisation in the rice-wheat agroecosystem. [ABSTRACT FROM AUTHOR]

Organic manures may contain high levels of arsenic (As) due to the use of As-containing growth-promoting substances in animal feed. To develop a bioremediation strategy to remove As from organic waste, Bacillus subtilis 168, a bacterial strain which can grow at high temperature but is unable to methylate and volatilize As, was genetically engineered to express the arsenite S-adenosylmethionine methyltransferase gene (CmarsM) from the thermophilic alga Cyanidioschyzon merolae. The genetically engineered B. subtilis 168 converted most of the inorganic As in the medium into dimethylarsenate and trimethylarsine oxide within 48 h and volatized substantial amounts of dimethylarsine and trimethylarsine. The rate of As methylation and volatilization increased with temperature from 37 to 50°C. When inoculated into an As-contaminated organic manure composted at 50°C, the modified strain significantly enhanced As volatilization. This study provides a proof of concept of using genetically engineered microorganisms for bioremediation of As-contaminated organic waste during composting. [ABSTRACT FROM AUTHOR]

Organic manures may contain high levels of arsenic (As) due to the use of As-containing growth-promoting substances in animal feed. To develop a bioremediation strategy to remove As from organic waste, Bacillus subtilis 168, a bacterial strain which can grow at high temperature but is unable to methylate and volatilize As, was genetically engineered to express the arsenite S-adenosylmethionine methyltransferase gene (CmarsM) from the thermophilic alga Cyanidioschyzon merolae. The genetically engineered B. subtilis 168 converted most of the inorganic As in the medium into dimethylarsenate and trimethylarsine oxide within 48 h and volatized substantial amounts of dimethylarsine and trimethylarsine. The rate of As methylation and volatilization increased with temperature from 37 to 50°C. When inoculated into an As-contaminated organic manure composted at 50°C, the modified strain significantly enhanced As volatilization. This study provides a proof of concept of using genetically engineered microorganisms for bioremediation of As-contaminated organic waste during composting. [ABSTRACT FROM AUTHOR]

Bacteria have evolved multiple signal transduction systems that permit an adaptation to changing environmental conditions. Chemoreceptor-based signaling cascades are very abundant in bacteria and are among the most complex signaling systems. Currently, our knowledge on the molecular features that determine signal recognition at chemoreceptors is limited. Chemoreceptor McpA of Bacillus velezensis SQR9 has been shown to mediate chemotaxis to a broad range of different ligands. Here we show that its ligand binding domain binds directly 13 chemoattractants. We provide support that organic acids and amino acids bind to the membrane-distal and membrane-proximal module of the dCache domain, respectively, whereas binding of sugars/sugar alcohols occurred at both modules. Structural biology studies combined with site-directed mutagenesis experiments have permitted to identify 10 amino acid residues that play key roles in the recognition of multiple ligands. Residues in membrane-distal and membrane-proximal regions were central for sensing organic acids and amimo acids, respectively, whereas all residues participated in sugars/sugar alcohol sensing. Most characterized chemoreceptors possess a narrow and well-defined ligand spectrum. We propose here a sensing mechanism involving both dCache modules that allows the integration of very diverse signals by a single chemoreceptor. [ABSTRACT FROM AUTHOR]

Bacillus sp. strains that are beneficial to plants are widely used in commercial biofertilizers and biocontrol agents for sustainable agriculture. Generally, functional Bacillus strains are applied as single-strain communities since the principles of synthetic microbial consortia constructed with Bacillus strains remain largely unclear. Here, we demonstrated that the mutual compatibility directly affects the survival and function of two-member consortia composed of Bacillus velezensis SQR9 and FZB42 in the rhizosphere. A mutation in the global regulator Spo0A of SQR9 markedly reduced the boundary phenotype (appearance of a visible boundary line at the meeting point of two swarms) with wild-type FZB42, and the combined use of the SQR9(Î"spo0A) mutant and FZB42 improved biofilm formation, root colonization, and the production of secondary metabolites that are beneficial to plants. Furthermore, alleviation of antagonistic interactions of two-member Bacillus consortia improved its beneficial effects to cucumber in a greenhouse experiment. Our results provide evidence that social interactions among bacteria could be an influencing factor for achieving a desired community-level function. [ABSTRACT FROM AUTHOR]

Agricultural production continues to be constrained by a number of biotic and abiotic factors that can reduce crop yield quantity and quality. Potassium (K) is an essential nutrient that affects most of the biochemical and physiological processes that influence plant growth and metabolism. It also contributes to the survival of plants exposed to various biotic and abiotic stresses. The following review focuses on the emerging role of K in defending against a number of biotic and abiotic stresses, including diseases, pests, drought, salinity, cold and frost and waterlogging. The availability of K and its effects on plant growth, anatomy, morphology and plant metabolism are discussed. The physiological and molecular mechanisms of K function in plant stress resistance are reviewed. This article also evaluates the potential for improving plant stress resistance by modifying K fertilizer inputs and highlights the future needs for research about the role of K in agriculture. [ABSTRACT FROM AUTHOR]

In North America, one of the most important root diseases of Poa and Festuca turf is summer patch, caused by Magnaporthe poae. Detection and identification of M. poae in infected roots by conventional culture-based methods is difficult and time consuming, typically taking 3 wk or longer to accomplish. In this study, a culture-independent, TaqMan real-time PCR assay was developed for the detection of M. poae from the roots of fungicide-treated and non-treated Kentucky bluegrass (Poa pratensis) turf. The assay was validated with the target pathogen, closely related fungal species and a number of other microorganisms that inhabit the same host and soil environment. This assay was more sensitive (could detect as little as 3.88 pg genomic DNA of M. poae), rapid and accurate compared to direct microscopic observation and isolation on a selective medium. The real-time PCR detection results corresponded closely to visual assessments of disease severity in the field. Utilization of this assay in diagnostic laboratories will enable turfgrass managers to more quickly and effectively detect and potentially reduce fungicide usage through early and accurate identification of the pathogen. [ABSTRACT FROM AUTHOR]

The family Magnaporthaceae contains devastating fungal cereal and grass pathogens, such as Magnaporthe oryzae (rice blast fungus, formerly known as M. grisea), M. poae (summer patch pathogen of turf grasses) and Gaeumannomyces graminis (take-all fungus of various cereals and grasses), which are popular model organisms in fungal biology and host-pathogen interaction studies. Despite their ecological and economic importance, the phylogenetic relationships among the constituent species remain ambiguous due to the lack of convincing morphological characters and paucity of molecular data for the majority of the non-model species in the family. In this study our multilocus phylogeny suggests that both Magnaporthe and Gaeumannomyces are polyphyletic genera. The phylogeny also provides insights into fungal biology and pathogenesis. Magnaporthe oryzae formed a basal clade, while M. poae and M. rhizophila formed another well supported clade with G. incrustans and G. graminis. The basal species infect both root and aerial parts of the plant host, while the aerial infection capacity seems to be lost in the taxa of the latter clade. The phylogeny is corroborated by evolution of the anamorphs and a cAMP-dependent protein kinase (CPKA) gene. Magnaporthe oryzae produces Pyricularia, while taxa in the latter clade all. produce Phialophora-like anamorphs. CPKA is present in animals and many fungal lineages with various functions. In M. oryzae CPKA is essential for the formation of functional appressoria for leaf penetration. In root-infecting G. graminis var. tritici and M. poae however only non-functional CPKA homologous pseudogenes were found in their genomes. The study indicates that anamorphic and ecological features are more informative than the teleomorphic characters in defining monophyletic groups among these taxa. [ABSTRACT FROM AUTHOR]

Abstract: The effects of four metal ions (Ca2+, Ni2+, Mn2+ and Cu2+) were evaluated on growth and production of antifungal compounds by Paenibacillus polymyxa SQR-21 and a quadratic predictive model was developed using response surface methodology (RSM). The results revealed, Mn2+ and Ni2+ showed most positive synergistic interactive affect on production of antifungal compounds followed by the positive interactive synergistic affect of Cu2+ and Ni2+ and then Mn2+ and Cu2+. While the interactive effect of Ca2+ with all other three metals inhibited the production of antifungal compounds. The Mn2+ (P =0.0384), Ni2+ (P =0.0004) and Cu2+ (P =0.0117) significantly affected the production of antifungal compounds while the effect of Ca2+ (P =0.1851) was less significant. The maximum growth (OD600 =1.55) was obtained at 500 (0), 125 (0), 100 (−2) and 37.5 (0) μM levels and the maximum size of inhibition zone (31mm) was measured at 400 (−1), 150 (1), 400 (1) and 25μM (−1) levels of Ca2+, Mn2+, Ni2+ and Cu2+, respectively. The RSM model provided an easy and effective way to determine the interactive effect of metal ions on production of antifungal compounds by P. polymyxa SQR-21 so that optimum media recipes can be developed to produce maximum amounts of antifungal compounds under laboratory and commercial fermentation conditions. [Copyright &y& Elsevier]

The uptake of nitrogen (N) by roots is known to change with supply in a manner that suggests that the N status of plants is somehow sensed and can feedback to regulate this process. The most abundant source of N in soils for crops is nitrate. Uptake systems for nitrate, ammonium, and amino acids are present in the roots of most plants including crops. As nitrate is assimilated via conversion to nitrite, then ammonium into amino acids, it has been suggested that the internal pools of amino acids within plants may indicate nitrogen status by providing a signal that can regulate nitrate uptake by the plant. In support of this idea, both nitrate and ammonium influx and transporter transcript were shown to decrease in root tissue treated with exogenously applied amino acids. Several different amino acids have been tested for their effects on influx and transcription and glutamine was most effective. The feedback regulation occurs by changing the expression of transporters, but may also involve the post-translational modification of proteins. For example, some of the cytoplasmic enzymes responsible for nitrate assimilation are regulated by phosphorylation and binding of a 14-3-3 protein. The effects of treating plants with glutamine have been examined, first to identify the uptake of the amino acid and then to measure tissue nitrate reductase activity and cellular pools of nitrate. These results are reviewed in terms of feedback regulation and the putative cell sensing systems for N status including a possible specific role for cytosolic nitrate. [ABSTRACT FROM PUBLISHER]

A long-term field experiment, started in 1983, was carried out on a clay loam soil (Ferric/Haplic Luvisols, FAO) in Jurong Agricultural Institute, Jiangsu Province, China, to study changes of organic carbon (C) and nitrogen (N) pools in the topsoil under a rice/wheat rotation system. Treatments included conventional tillage (CT) and no tillage (NT) combined with various fertilizer treatments. The fertilizer treatments were control (no fertilizer), chemical fertilizer only, straw plus chemical fertilizer, and pig manure plus chemical fertilizer. With the exception of the control treatment, all treatments received the same level (in kg ha-1) of N (150), phosphorus (P) (50), and potassium (K) (155). Results showed that soil organic C, N, and microbial biomass carbon (MBC) and nitrogen (MBN) were higher in the top 5 cm layer after 18 years of no tillage than that under CT, whereas the reverse trend was observed in 5 to 10- and 10 to 20-cm layers. The application of organic manures with a reduced amount of commercial chemical fertilizer increased the content of soil organic C, total and available N, and MBC and MBN compared to the treatment with inorganic fertilizer alone. Organic C and total N contents of soils from different treatments were found in the order of pig manure plus inorganic fertilizer>straw plus inorganic fertilizer>inorganic fertilizer>control. Microbial biomass C and MBN showed a similar trend to organic C and total N. These results indicate that a combination of NT and application of pig manure is the best way to sustain soil fertility in the experiment. [ABSTRACT FROM AUTHOR]

The size of tissue amino acid pools in plants may indicate nitrogen status and provide a signal that can regulate nitrate uptake and assimilation. The effects of treating barley roots with glutamine have been examined, first to identify the transport system for the uptake of the amino acid and then to measure root NR activity and cellular pools of nitrate. Treating N replete roots with glutamine elicited a change in the cell membrane potential and the size of this response was concentration dependent. In addition, the size of the electrical change depended on the previous exposures of the root to glutamine and was lost after a few cycles of treatment. Whole root tissue pools of glutamine and phenylalanine increased when roots were incubated in a nutrient solution containing 10 mM nitrate and 1 mM glutamine. Treating roots with 1 mM glutamine increased cytosolic nitrate activity from 3 mM to 7 mM and this change peaked after 2 h of treatment. Parallel measurements of root nitrate reductase activity during treatment with 1 mM glutamine showed a decrease. These measurements provide evidence for feedback regulation on NR activity that result in changes in cytosolic nitrate activity. After 6 h in glutamine both root NR activity and cytosolic nitrate activity returned to pretreatment values, while tissue concentrations of glutamine and phenylalanine remained elevated. The data are discussed in terms of the mechanisms that are most likely to be responsible for the changes in cytosolic nitrate. [ABSTRACT FROM PUBLISHER]

Bacillus amyloliquefaciens NJN-6 produces volatile compounds (VOCs) that inhibit the grovrth and spore germination of Fusarium oxysporum f. sp. cúbense. Among the total of 36 volatile compounds detected, 11 compounds completely inhibited fungal growth. The antifungal activity of these compounds suggested that VOCs can play important roles over short and long distances in the suppression oí Fusarium oxysporum. [ABSTRACT FROM AUTHOR]

Cerato-platanins (CPs) form a family of fungal small-secreted cysteine-rich proteins (SSCPs) and are of particular interest not only because of their surface activity but also their abundant secretion by fungi. We performed an evolutionary analysis for 283 CPs from 157 fungal genomes with the focus on the opportunistic plant-beneficial and mycoparasitic fungus Trichoderma. Our results revealed the long evolutionary history of CPs in Dikarya fungi that have undergone several events of lateral gene transfer and gene duplication. Three genes were maintained in the core genome of Trichoderma, while some species have up to four CP encoding genes. All Trichoderma CPs evolve under stabilizing natural selection pressure. The functional analysis of CPs in T. guizhouense and T. harzianum revealed that only EPL1 is active at all stages of the development but plays a minor role in interactions with other fungi and bacteria. The deletion of this gene results in increased colonization of tomato roots by Trichoderma spp. Similarly, the biochemical tests of the heterologously produced EPL1 by Pichia pastoris support the above claims. Based on the obtained results, we conclude that the function of CPs is probably linked to their surfactant properties and the ability to modify the hyphosphere of submerged mycelium and thus facilitate the nutritional versatility of fungi. The effector-like properties do not sufficiently describe the diversity and evolution of these proteins in fungi as they are also maintained, duplicated, or laterally transferred in the genomes of non-herbivore fungi. [ABSTRACT FROM AUTHOR]

Even though bacteria are important in determining plant growth and health via volatile organic compounds (VOCs), it is unclear how these beneficial effects emerge in multi-species microbiomes. Here we studied this using a model plant–bacteria system, where we manipulated bacterial community richness and composition and determined the subsequent effects on VOC production and VOC-mediated pathogen suppression and plant growth-promotion. We assembled VOC-producing bacterial communities in different richness levels ranging from one to 12 strains using three soil-dwelling bacterial genera (Bacillus, Paenibacillus and Pseudomonas) and investigated how the composition and richness of bacterial community affect the production and functioning of VOCs. We found that VOC production correlated positively with pathogen suppression and plant growth promotion and that all bacteria produced a diverse set of VOCs. However, while pathogen suppression was maximized at intermediate community richness levels when the relative amount and the number of VOCs were the highest, plant growth promotion was maximized at low richness levels and was only affected by the relative amount of plant growth-promoting VOCs. The contrasting effects of richness could be explained by differences in the amount and number of produced VOCs and by opposing effects of community productivity and evenness on pathogen suppression and plant-growth promotion along the richness gradient. Together, these results suggest that the number of interacting bacterial species and the structure of the rhizosphere microbiome drive the balance between VOC-mediated microbe–pathogen and microbe–plant interactions potentially affecting plant disease outcomes in natural and agricultural ecosystems. [ABSTRACT FROM AUTHOR]

Decomposition of crop residues in soil is mediated by microorganisms whose activities vary with fertilization. The complexity of active microorganisms and their interactions utilizing residues is impossible to disentangle without isotope applications. Thus, 13C-labeled rice residues were employed, and DNA stable-isotope probing (DNA-SIP) combined with high-throughput sequencing was applied to identify microbes active in assimilating residue carbon (C). Manure addition strongly modified microbial community compositions involved in the C flow from rice residues. Relative abundances of the bacterial genus Lysobacter and fungal genus Syncephalis were increased, but abundances of the bacterial genus Streptomyces and fungal genus Trichoderma were decreased in soils receiving mineral fertilizers plus manure (NPKM) compared to levels in soils receiving only mineral fertilizers (NPK). Microbes involved in the flow of residue C formed a more complex network in NPKM than in NPK soils because of the necessity to decompose more diverse organic compounds. The fungal species (Jugulospora rotula and Emericellopsis terricola in NPK and NPKM soils, respectively) were identified as keystone species in the network and may significantly contribute to residue C decomposition. Most of the fungal genera in NPKM soils, especially Chaetomium, Staphylotrichum, Penicillium, and Aspergillus, responded faster to residue addition than those in NPK soils. This is connected with the changes in the composition of the rice residue during degradation and with fungal adaptation (abundance and activity) to continuous manure input. Our findings provide fundamental information about the roles of key microbial groups in residue decomposition and offer important cues on manipulating the soil microbiome for residue utilization and C sequestration in soil. [ABSTRACT FROM AUTHOR]

Nitrogen (N) is one of the most important elements that has a central impact on plant growth and yield. N is also widely involved in plant stress responses, but its roles in host-pathogen interactions are complex as each affects the other. In this review, we summarize the relationship between N nutrition and plant disease and stress its importance for both host and pathogen. From the perspective of the pathogen, we describe how N can affect the pathogen’s infection strategy, whether necrotrophic or biotrophic. N can influence the deployment of virulence factors such as type III secretion systems in bacterial pathogen or contribute nutrients such as gamma-aminobutyric acid to the invader. Considering the host, the association between N nutrition and plant defence is considered in terms of physical, biochemical and genetic mechanisms. Generally, N has negative effects on physical defences and the production of anti-microbial phytoalexins but positive effects on defence-related enzymes and proteins to affect local defence as well as systemic resistance. N nutrition can also influence defence via amino acid metabolism and hormone production to affect downstream defence-related gene expression via transcriptional regulation and nitric oxide (NO) production, which represents a direct link with N. Although the critical role of N nutrition in plant defences is stressed in this review, further work is urgently needed to provide a comprehensive understanding of how opposing virulence and defence mechanisms are influenced by interacting networks. [ABSTRACT FROM AUTHOR]

Climate change is predicted to alter precipitation and drought patterns, which has become a global concern as evidence accumulates that it will affect ecosystem services. Disentangling the ability of soil multiple-functions to withstand this stress multifunctionality resistance) is a crucial topic for assessing the stability and adaptability of agroecosystems. Presently, we explored the effects of nutrient-addition on multifunctionality resistance to drying-wetting cycles, and evaluated the importance of microbial functional capacity (characterized by the abundances of genes involved in carbon, nitrogen and phosphorus cycles) for this resistance. The multifunctionality of soils treated with nitrogen (N) and straw showed a higher resistance to drying-wetting cycles compared to non-amended soils. Microbial functional capacity displayed a positive linear relationship with multifunctionality resistance. Random forest analysis showed that the abundances of archeal amoA associated with nitrification), nosZ and narG (denitrification) genes were major predictors of multifunctionality resistance in soils without straw addition. In contrast, major predictors of multifunctionality resistance in straw amended soils were the abundances of GH51 (xylan degradation) and fungcbhIF (cellulose degradation) genes. Structural equation modeling further demonstrated the large direct contribution of carbon (C)- and N-cycling related gene abundances to multifunctionality resistance. The modeling further elucidated the positive effects of microbial functional capacity on this resistance, which was mediated potentially by high soil fungi:bacteria ratio, dissolved organic C content, and low pH. Present work suggests that nutrient management of agroecosystems can buffer negative impacts on ecosystem functioning caused by climate-change associated increase in drying-wetting cycles via enriching functional capacity of microbial communities. [ABSTRACT FROM AUTHOR]

The rhizosphere colonization by plant growth-promoting rhizobacterium (PGPR) along plant roots facilitates the ability of PGPRs to promote plant growth and health. Thus, an understanding of the molecular mechanisms of the root colonization process by plant-beneficial Bacillus strains is essential for the use of these strains in agriculture. Here we observed that an sfp gene mutant of a plant-growth-promoting rhizobacterium, Bacillus velezensis SQR9 was unable to form normal biofilm architecture, and differential protein expression was observed by proteomic analysis. A minor wall teichoic acid (WTA) biosynthetic protein, GgaA, was decreased over 4-fold in the Δsfp mutant, and impairment of ggaA gene postponed biofilm formation and decreased cucumber root colonization capabilities. In addition, we provide evidence that the major WTA biosynthetic enzyme, GtaB, involved in both biofilm formation and root colonization. The deficiency in biofilm formation of the ΔgtaB mutant may be due to an absence of UDP-glucose, which is necessary for the synthesis of biofilm matrix exopolysaccharides (EPS). These observations provide insights into the root colonization process by a plant-beneficial Bacillus strain, which help to improve its application as a biofertilizer. [ABSTRACT FROM AUTHOR]

Bacillus velezensis SQR9 (former B. amyloliquefaciens SQR9) is a plantgrowth- promoting rhizobacterium (PGPR) that promotes plant growth and health. The colonization of PGPR strains along plant roots is a prerequisite for them to execute their specific functions. However, one problem of microbial introduction in practice is that the applied PGPR strains do not always successfully colonize the rhizosphere. In Bacillus spp., two-component signal transduction system (TCS) DegS/U regulates flagellar motility, biofilm formation and antibiotic production. Phosphorylation of DegU by DegS is positively affected by DegQ protein. In this study, we constructed a xylose-inducible degQ genetically engineered strain SQR9XYQ to improve the biocontrol activity. The results from in vitro, root in situ, greenhouse experiments and RT-qPCR studies demonstrate that (i) the phosphorylation of DegU in SQR9XYQ can be gradually activated by xylose, which is a component of both cucumber and tomato root exudates, and (ii) biofilm formation, antibiotic expression, colonization activity, and biocontrol efficiency were improved in SQR9XYQ compared with the wild-type strain SQR9. These results suggest that colonization trait is important to biocontrol strains for maintenance of plant health. [ABSTRACT FROM AUTHOR]

Diversity-invasion resistance relationships are often variable and sensitive to environmental conditions such as resource availability. Resource stoichiometry, the relative concentration of different elements in the environment, has been shown to have strong effects on the physiology and interactions between different species. Yet, its role for diversity-invasion resistance relationships is still poorly understood. Here, we explored how the ratio of nitrogen (N) and phosphorus affects the productivity and invasion resistance of constructed microbial communities by a plant pathogenic bacterium, Ralstonia solanacearum. We found that resource stoichiometry and species identity effects affected the invasion resistance of communities. Both high N concentration and resident community diversity constrained invasions, and two resident species, in particular, had strong negative effects on the relative density of the invader and the resident community productivity. While resource stoichiometry did not affect the mean productivity of the resident community, it favoured the growth of two species that strongly constrained invasions turning the slope of productivity-invasion resistance relationship more negative. Together our findings suggest that alterations in resource stoichiometry can change the community resistance to invasions by having disproportionate effects on species growth, potentially explaining changes in microbial community composition under eutrophication. [ABSTRACT FROM AUTHOR]

Efficient biofilm formation and root colonization capabilities facilitate the ability of beneficial plant rhizobacteria to promote plant growth and antagonize soilborne pathogens. Biofilm formation by plant-beneficial Bacillus strains is triggered by environmental cues, including oxygen deficiency, but the pathways that sense these environmental signals and regulate biofilm formation have not been thoroughly elucidated. In this study, we showed that the ResDE two-component regulatory system in the plant growth-promoting rhizobacterium Bacillus amyloliquefaciens strain SQR9 senses the oxygen deficiency signal and regulates biofilm formation. ResE is activated by sensing the oxygen limitation-induced reduction of the NAD+/ NADH pool through its PAS domain, stimulating its kinase activity, and resulting in the transfer of a phosphoryl group to ResD. The phosphorylated ResD directly binds to the promoter regions of the qoxABCD and ctaCDEF operons to improve the biosynthesis of terminal oxidases, which can interact with KinB to activate biofilm formation. These results not only revealed the novel regulatory function of the ResDE two-component system but also contributed to the understanding of the complicated regulatory network governing Bacillus biofilm formation. This research may help to enhance the root colonization and the plant-beneficial efficiency of SQR9 and other Bacillus rhizobacteria used in agriculture. IMPORTANCE Bacillus spp. are widely used as bioinoculants for plant growth promotion and disease suppression. The exertion of their plant-beneficial functions is largely dependent on their root colonization, which is closely related to their biofilm formation capabilities. On the other hand, Bacillus is the model bacterium for biofilm study, and the process and molecular network of biofilm formation are well characterized (B. Mielich-Süss and D. Lopez, Environ Microbiol 17:555-565, 2015, https://doi .org/10.1111/1462-2920.12527; L. S. Cairns, L. Hobley, and N. R. Stanley-Wall, Mol Microbiol 93:587-598, 2014, https://doi.org/10.1111/mmi.12697; H. Vlamakis, C. Aguilar, R. Losick, and R. Kolter, Genes Dev 22:945-953, 2008, https://doi.org/10.1101/gad .1645008; S. S. Branda, A. Vik, L. Friedman, and R. Kolter, Trends Microbiol 13:20-26, 2005, https://doi.org/10.1016/j.tim.2004.11.006; C. Aguilar, H. Vlamakis, R. Losick, and R. Kolter, Curr Opin Microbiol 10:638-643, 2007, https://doi.org/10.1016/j.mib.2007.09 .006; S. S. Branda, J. E. González-Pastor, S. Ben-Yehuda, R. Losick, and R. Kolter, Proc Natl Acad Sci U S A 98:11621-11626, 2001, https://doi.org/10.1073/pnas.191384198). However, the identification and sensing of environmental signals triggering Bacillus biofilm formation need further research. Here, we report that the oxygen deficiency signal inducing Bacillus biofilm formation is sensed by the ResDE two-component regulatory system. Our results not only revealed the novel regulatory function of the ResDE two-component regulatory system but also identified the sensing system of a biofilmtriggering signal. This knowledge can help to enhance the biofilm formation and root colonization of plant-beneficial Bacillus strains and also provide new insights of bacterial biofilm formation regulation. [ABSTRACT FROM AUTHOR]

Xylanase with a high thermostability will satisfy the needs of raising the temperature of hydrolysis to improve the rheology of the broth in industry of biomass conversion. In this study, a xylanase gene (xyn10A), predicted to encode a hydrolase domain of GH10, a linker region and a CBM1 domain, was cloned from a superior lignocellulose degrading strain Aspergillus fumigatus Z5 and successfully expressed in Pichia pastoris X33. Xyn10A has a specific xylanase activity of 34.4 U mg-1, and is optimally active at 90 °C and pH 6.0. Xyn10A shows quite stable at pHs ranging from 3.0 to 11.0, and keeps over 40% of xylanase activity after incubation at 70 °C for 1 h. Removal of CBM1 domain has a slight negative effect on its thermostability, but the further cleavage of linker region significantly decreased its stability at high temperature. The transfer of CBM1 and linker region to another GH10 xylanase can help to increase the thermostability. In addition, hydrolase domains between the two Xyn10A proteins naturally formed a dimer structure, which became more thermostable after removing the CBM1 or/and linker region. This thermostable Xyn10A is a suitable candidate for the highly efficient fungal enzyme cocktails for biomass conversion. [ABSTRACT FROM AUTHOR]

Carbon sequestration in paddy soils through organic fertilization is of great importance for soil quality improvement in subtropical Asia. This study explored the effect of oxalate extractable iron oxides (Feo) on soil organic carbon (SOC) sequestration in response to different fertilization treatments. Soil samples were collected from 0- to 10-cm, 10- to 20-cm, and 20- to 40-cm depth intervals in June 2016 after a wheat (Triticum aestivum L.) harvest. This study involved five treatments: control with no fertilizer (CK), chemical fertilizer (NPK), 50% chemical fertilizer plus manure (NPKM), 100% chemical fertilizer plus straw (NPKS), and 30% chemical fertilizer plus manure organic-inorganic compound fertilizer (NPKMOI). Organic fertilization significantly (P < 0.05) increased the SOC content and the Feo concentration compared with chemical fertilization alone. The specific C mineralization rate (SCMR, rate per unit SOC) increased with increasing soil depths, suggesting that SOC at the 20- to 40-cm depth was more labile than that from 0 to 20 cm. The percentage of SOC present as microbial biomass carbon (MBC) was significantly (P < 0.001) positively correlated with SCMR, indicating that soil microorganisms influenced the potential SOC mineralization. Furthermore, the alternation of drying and wetting in paddy soils drives the biogeochemical cycles of iron and SOC, during which organic fertilization promotes the accumulation of Feo possibly by forming organo-iron complexes as indicated by the higher Feo content in NPKM than in NPK. The Feo was significantly (P < 0.001) positively correlated with SOC and the percentage of aromatic C, indicating that Feo may play an important role in preserving SOC, especially the aromatic compounds. Therefore, the enhancement of Feo by organic fertilization, especially organic manure that is enriched in aromatic compounds, improved the SOC sequestration potential in the rice (Oryza sativa)-wheat rotation system. [ABSTRACT FROM AUTHOR]

* Background and Aims Fusarium wilt is primarily a soil-borne disease and results in yield loss and quality decline in cucumber (Cucumis sativus). The main symptom of fusarium wilt is the wilting of entire plant, which could be caused by a fungal toxin(s) or blockage of water transport. To investigate whether this wilt arises from water shortage, the physiological responses of hydroponically grown cucumber plants subjected to water stress using polyethylene glycol (PEG, 6000) were compared with those of plants infected with Fusarium oxysporum f. sp. cucumerinum (FOC). * Methods Parameters reflecting plant water status were measured 8 d after the start of treatment. Leaf gas exchange parameters and temperature were measured with a LI-COR portable open photosynthesis system and by thermal imaging. Chlorophyll fluorescence and chloroplast structures were assessed by imaging pulse amplitude-modulated fluorometry and transmission electron microscopy, respectively. * Key Results Cucumber water balance was altered after FOC infection, with decreased water absorption and hydraulic conductivity. However, the responses of cucumber leaves to FOC and PEG differed in leaf regions. Under water stress, measures of lipid peroxidation (malondialdehyde) and chlorophyll fluorescence indicated that the leaf edge was more seriously injured, with a higher leaf temperature and disrupted leaf water status compared with the centre. Here, abscisic acid (ABA) and proline were negatively correlated with water potential. In contrast, under FOC infection, membrane damage and a higher temperature were observed in the leaf centre while ABA and proline did not vary with water potential. Cytologically, FOC-infected cucumber leaves exhibited circular chloroplasts and swelled starch grains in the leaf centre, in which they again differed from PEG-stressed cucumber leaves. * Conclusions This study illustrates the non-causal relationship between fusarium wilt and water transport blockage. Although leaf wilt occurred in both water stress and FOC infection, the physiological responses were different, especially in leaf spatial distribution. [ABSTRACT FROM AUTHOR]

Ethylene increases root cortical aerenchyma formation in maize (Zea mays L.), rice (Oryza sativa L.) and other species. To further investigate the effects of nitrate, ammonium and water stress on ethylene production and aerenchyma formation in roots, two lowland rice cultivars (Shanyou 63, hybrid indica, and Yangdao 6, inbred indica) were cultured hydroponically with 10% (w/v) polyethylene glycol to simulate water stress. Water stress decreased shoot biomass, stomatal conductivity and leaf water potential in cultivars fed with nitrate but not with ammonium. Water stress induced more aerenchyma formation in cultivars fed with nitrate rather than ammonium, and increased cortical aerenchyma was found in Yangdao 6. Endogenous ethylene production by roots increased significantly under water stress in plants fed with nitrate rather than ammonium. Exogenous ethylene stimulated root cortical aerenchyma formation. Expression of the ethylene biosynthesis gene 1-aminocyclo-propane-1-carboxylic acid (ACC) synthase (ACS5) was greater in roots fed with nitrate rather than ammonium in the presence and absence of water stress. The expression of ethylene signalling pathway genes involved in programmed cell death (lesion-simulating disease (L.S.D.)1.1 and L.S.D.2; enhanced disease susceptibility (EDS) and phytoalexin-deficient (PAD4)) were regulated by the N form and water stress. In plants of cultivars fed with ammonium, L.S.D.1.1 expression increased under water stress, whereas L.S.D.2, EDS and PAD4 expression decreased. In conclusion, nitrate increases ethylene production and cortical aerenchyma formation in roots of water-stressed lowland rice. However, ammonium increased L.S.D.1.1 expression in water-stressed roots, and decreased ACS5, EDS and PAD4 expression, which would inhibit ethylene production and aerenchyma formation. [ABSTRACT FROM AUTHOR]

Cucumber Fusarium wilt, induced by Fusarium oxysporum f. sp. cucumerinum (FOC), causes severe losses in cucumber yield and quality. Nitrogen (N), as the most important mineral nutrient for plants, plays a critical role in plant-pathogen interactions. Hydroponic assays were conducted to investigate the effects of different N forms (NH4+ vs. NO3-) and supply levels (low, 1 mM; high, 5 mM) on cucumber Fusarium wilt. The NO3--fed cucumber plants were more tolerant to Fusarium wilt compared with NH4+-fed plants, and accompanied by lower leaf temperature after FOC infection. The disease index decreased as the NO3- supply increased but increased with the NH4+ level supplied. Although the FOC grew better under high NO3- in vitro, FOC colonization and fusaric acid (FA) production decreased in cucumber plants under high NO3- supply, associated with lower leaf membrane injury. There was a positive correlation between the FA content and the FOC number or relative membrane injury. After the exogenous application of FA, less FA accumulated in the leaves under NO3- feeding, accompanied with a lower leaf membrane injury. In conclusion, higher NO3- supply protected cucumber plants against Fusarium wilt by suppressing FOC colonization and FA production in plants, and increasing the plant tolerance to FA. [ABSTRACT FROM AUTHOR]

To analyze the effect of nitrogen form on salt stress, we studied the response of two different plant species, canola (Brassica napus L.), a dicotyledon which prefers NO3 - nutrition, and rice (Oryza sativa L.), a monocotyledon which prefers NH4 + nutrition, to salt stress under NO3 - (NN) and NH4 + (AN) nutrition. Salt stress was simulated by the addition of 150 and 100mM NaCl to NN (NNS) and AN (ANS) in canola and rice seedlings, respectively. Salt stress induced reductions of shoot and root biomass that were more drastic under ANS. A higher Na+ content was obtained in NNS than in ANS. The impact of Na+ on the reduction of biomass (Δbiomass/Na+) was 162, 181, 230 and 245% higher in canola root, canola shoot, rice root and rice shoot in ANS than in NNS, respectively. In both canola and rice seedlings, the ratio of leaf Na+ content in apoplasts to symplasts ([Na+]apo/[Na+]sym) was higher in NNS than in ANS. Also, in canola seedlings, the ratio of apoplast Na+ in the leaf edge to the leaf center ([Na+]LE/[Na+]LC) was 18 times higher in NNS than in ANS. Our results illustrate that the confinement of Na+ in the canola leaf edge, as well as the restriction of Na+ in leaf apoplasts of canola and rice seedlings, protect cells from suffering Na+ stress and contribute to the higher tolerance of NO3 --fed plants. [ABSTRACT FROM AUTHOR]

Salt stress reduces plant growth and is now becoming one of the most important factors restricting agricultural productivity. Inoculation of plant growth-promoting rhizobacteria (PGPR) has been shown to confer plant tolerance against abiotic stress, but the detailed mechanisms of how this occurs remain unclear. In this study, hydroponic experiments indicated that the PGPR strain Bacillus amyloliquefaciens SQR9 could help maize plants tolerate salt stress. After exposure to salt stress for 20 days, SQR9 significantly promoted the growth of maize seedlings and enhanced the chlorophyll content compared with the control. Additional analysis showed that the involved mechanisms could be the enhanced total soluble sugar content for decreasing cell destruction, improved peroxidase/catalase activity and glutathione content for scavenging reactive oxygen species, and reduced Na+ levels in the plant to decrease Na+ toxicity. These physiological appearances were further confirmed by the upregulation of RBCS, RBCL, H+-PPase, HKT1, NHX1, NHX2 and NHX3, as well as downregulation of NCED expression, as determined by quantitative reverse transcription-polymerase chain reaction. However, SQR9 counteracted the increase of abscisic acid in response to salt stress. In summary, these results show that SQR9 confers plant salt tolerance by protecting the plant cells and managing Na+ homeostasis. Hence, it can be used in salt stress prone areas, thereby promoting agricultural production. [ABSTRACT FROM AUTHOR]

Fusarium wilt causes severe yield losses in cash crops. Nitrogen plays a critical role in the management of plant disease; however, the regulating mechanism is poorly understood. Using biochemical, physiological, bioinformatic and transcriptome approaches, we analyzed how nitrogen forms regulate the interactions between cucumber plants and Fusarium oxysporum f. sp. cucumerinum (FOC). Nitrate significantly suppressed Fusarium wilt compared with ammonium in both pot and hydroponic experiments. Fewer FOC colonized the roots and stems under nitrate compared with ammonium supply. Cucumber grown with nitrate accumulated less fusaric acid (FA) after FOC infection and exhibited increased tolerance to chemical FA by decreasing FA absorption and transportation in shoots. A lower citrate concentration was observed in nitrate-grown cucumbers, which was associated with lower MATE (multidrug and toxin compound extrusion) family gene and citrate synthase (CS) gene expression, as well as lower CS activity. Citrate enhanced FOC spore germination and infection, and increased disease incidence and the FOC population in ammonium- treated plants. Our study provides evidence that nitrate protects cucumber plants against F. oxysporum by decreasing root citrate exudation and FOC infection. Citrate exudation is essential for regulating disease development of Fusarium wilt in cucumber plants. [ABSTRACT FROM AUTHOR]

Aquaporins, major intrinsic proteins (MIPs) present in the plasma and intracellular membranes, facilitate the transport of small neutral molecules across cell membranes in higher plants. Recently, progress has been made in understanding the mechanisms of aquaporin subcellular localization, transport selectivity, and gating properties. Although the role of aquaporins in maintaining the plant water status has been addressed, the interactions between plant aquaporins and mineral nutrients remain largely unknown. This review highlights the roles of various aquaporin orthologues in mineral nutrient uptake and transport, as well as the regulatory effects of mineral nutrients on aquaporin expression and activity, and an integrated link between aquaporins and mineral nutrient metabolism was identified. [ABSTRACT FROM AUTHOR]

Cellular pH homeostasis is fundamental for life, and all cells adapt to maintain this balance. In plants, the chemical form of nitrogen supply, nitrate and ammonium, is one of the cellular pH dominators. We report that the rice nitrate transporter OsNRT2.3 is transcribed into two spliced isoforms with a natural variation in expression ratio. One splice form, OsNRT2.3b is located on the plasma membrane, is expressed mainly in the phloem, and has a regulatory motif on the cytosolic side that acts to switch nitrate transport activity on or off by a pH-sensing mechanism. High OsNRT2.3b expression in rice enhances the pH-buffering capacity of the plant, increasing N, Fe, and P uptake. In field trials, increased expression of OsNRT2.3b improved grain yield and nitrogen use efficiency (NUE) by 40%. These results indicate that pH sensing by the rice nitrate transporter OsNRT2.3b is important for plant adaption to varied N supply forms and can provide a target for improving NUE. [ABSTRACT FROM AUTHOR]

Microbial arsenic (As) methylation and volatilization are important processes controlling the As biogeochemical cycle in paddy soils. To further understand these processes, we isolated a novel bacterial strain, SM-1, from an As-contaminated paddy soil. SM-1 showed strong As methylation and volatilization abilities, converting almost all arsenite (10 µM) to dimethylarsenate and trimethylarsenic oxide in the medium and trimethylarsine gas into the headspace within 24 h, with trimethylarsine accounting for nearly half of the total As. On the basis of the 16S rRNA sequence, strain SM-1 represents a new species in a new genus within the family Cytophagaceae. Strain SM-1 is abundant in the paddy soil and inoculation of SM-1 greatly enhanced As methylation and volatilization in the soil. An arsenite methyltransferase gene (ArarsM) was cloned from SM-1. When expressed in Escherichia coli, ArArsM conferred the As methylation and volatilization abilities to E. coli and increased its resistance to arsenite. The high As methylation and volatilization abilities of SM-1 are likely attributed to an efficient ArArsM enzyme coupled with low arsenite efflux. These results suggest that strain SM-1 plays an important role in As methylation and volatilization in the paddy soil and has a great potential for As bioremediation. [ABSTRACT FROM AUTHOR]

Our previous studies demonstrated that chloroplastic CO2 concentration (Cc) is not sufficient under high-nitrogen (N) supply in rice plants. In this research, we studied how aquaporins- (AQPs) mediated Cc under different N-supply levels. A hydroponic experiment was conducted in a greenhouse with three different N levels (low N, 0.71 mM; intermediate N, 2.86 mM; and high N, 7.14 mM) in a rice cultivar (Oryza sativa cv. Shanyou 63) and with an ospip1;1 mutant (Oryza sativa cv. Nipponbare). The photosynthetic nitrogen-use efficiency (PNUE) decreased with increasing leaf-N content. Under high-N supply, the estimated Cc was significantly lower than the theoretical Cc and the specific Rubisco activity (carboxylation efficiency/Rubisco content, CE/Rubisco) decreased, because of a decrease of relative CO2 diffusion conductance (total CO2 diffusion conductance/leaf-N content, gt/N) in mesophyll cells. Real Time Quantitative PCR (Q-RT-PCR) showed that most OsPIP1s and OsPIP2s expression were downregulated under the high-N supply. Furthermore, Cc and gm decreased in the ospip1;1 mutant line compared with that of the wild-type plant. It was concluded that under high-N supply, the decreased PNUE was associated with non-sufficient Cc, mediated by AQP in mesophyll conductance. [ABSTRACT FROM AUTHOR]

SIZ1-mediated SUMOylation regulates hormone signaling as well as abiotic and biotic stress responses in plants. Here, we investigated the expression profile of OsSIZ1 in rice using quantitative reverse transcription-PCR (qRT-PCR) and pOsSIZ1-GUS transgenic plants, and the function of OsSIZ1 in the responses to phosphate and nitrogen using a reverse genetics approach. OsSIZ1 is constitutively expressed throughout the vegetative and reproductive growth of rice, with stronger promoter activities in vascular bundles of culms. ossiz1 mutants had shorter primary roots and adventitious roots than wild-type plants, suggesting that OsSIZ1 is associated with the regulation of root system architecture. Total phosphorus (P) and phosphate (Pi) concentrations in both roots and shoots of ossiz1 mutants were significantly increased irrespective of Pi supply conditions compared with the wild type. Pi concentration in the xylem sap of ossiz1 mutants was significantly higher than that of the wild type under a Pi-sufficient growth regime. Total nitrogen (N) concentrations in the most detected tissues of ossiz1 mutants were significantly increased compared with the wild type. Analysis of mineral contents in ossiz1 mutants indicated that OsSIZ1 functions specifically in Pi and N responses, not those of other nutrients examined, in rice. Further, qRT-PCR analyses revealed that the expression of multiple genes involved in Pi starvation signaling and N transport and assimilation were altered in ossiz1 mutants. Together, these results suggested that OsSIZ1 may act as a regulator of the Pi (N)-dependent responses in rice. [ABSTRACT FROM AUTHOR]

Traditionally farmers in China have relied on organic manures to build the organic matter content in soil and to fertilise crops for both human and livestock consumption. However, with requirements to increase food production, the use of relatively cheap inorganic fertilisers has increased, and manure nutrients are not always used to their potential. In addition, farms of all sizes and even biogas plants, often lack the basic infrastructure to manage manures; poor containment facilities often result in untreated manures being discharged directly into watercourses, whilst transportation of manures to the field and land spreading is often not mechanised and relies on availability of suitable labour. There is already clear evidence of overuse of nutrients in some parts of China and this is causing undesirable impacts on the environment. With the increasing demand for livestock products from a burgeoning population and changes in dietary preferences towards animal protein, greater quantities of manure nutrients will be generated in the next twenty years, especially in peri-urban concentrated animal feeding operations and intensive farms. It is essential that China addresses the infrastructural, research and communication challenges to ensure that manures are integrated into nutrient planning at the field, farm and regional level to safeguard the environment, reduce the requirement for inorganic fertiliser production and use, and improve farmer incomes. This paper reviews the current manure management practices, both nationally and, where appropriate, at a regional scale, and assesses what barriers currently prevent efficient manure nutrient utilisation in China. We then address the future challenges for manure nutrient management in China, before summarising key gaps in knowledge and communication with implications for research and policy. [ABSTRACT FROM AUTHOR]

Background: Bacillus amyloliquefaciens SQR9 is a plant growth-promoting rhizobacteria (PGPR) with outstanding abilities to enhance plant growth and to control soil-borne diseases. Root exudates is known to play important roles in plant-microbe interactions. To explore the rhizosphere interactions and plant-beneficial characteristics of SQR9, the complete genome sequence as well as the transcriptome in response to maize root exudates under biofilm-forming conditions were elucidated. Results: Maize root exudates stimulated SQR9 biofilm formation in liquid culture, which is known to be positively correlated with enhanced root colonization. Transcriptional profiling via RNA-sequencing of SQR9 under static conditions indicated that, at 24 h post-inoculation, root exudates stimulated the expression of metabolism-relevant genes, while at 48 h post-inoculation, genes related to extracellular matrix production (tapA-sipW-tasA operon) were activated by root exudates. The individual components in maize root exudates that stimulated biofilm formation included glucose, citric acid, and fumaric acid, which either promoted the growth of SQR9 cells or activated extracellular matrix production. In addition, numerous groups of genes involved in rhizosphere adaptation and in plant-beneficial traits, including plant polysaccharide utilization, cell motility and chemotaxis, secondary antibiotics synthesis clusters, and plant growth promotion-relevant, were identified in the SQR9 genome. These genes also appeared to be induced by the maize root exudates. Conclusions: Enhanced biofilm formation of B. amyloliquefaciens SQR9 by maize root exudates could mainly be attributed to promoting cell growth and to inducing extracellular matrix production. The genomic analysis also highlighted the elements involved in the strain's potential as a PGPR. This study provides useful information for understanding plant-rhizobacteria interactions and hence for promoting the agricultural applications of this strain. [ABSTRACT FROM AUTHOR]

Background: The plant growth-promoting rhizobacteria (PGPR) strain Bacillus amyloliquefaciens SQR9, isolated from the cucumber rhizosphere, protects the host plant from pathogen invasion and promotes plant growth through efficient root colonization. The phytohormone indole-3-acetic acid (IAA) has been suggested to contribute to the plant-growth-promoting effect of Bacillus strains. The possible IAA synthetic pathways in B. amyloliquefaciens SQR9 were investigated in this study, using a combination of chemical and genetic analysis. Results: Gene candidates involved in tryptophan-dependent IAA synthesis were identified through tryptophan response transcriptional analysis, and inactivation of genes ysnE, dhaS, yclC, and yhcX in SQR9 led to 86, 77, 55, and 24 % reductions of the IAA production, respectively. The genes patB (encoding a conserved hypothetical protein predicted to be an aminotransferase), yclC (encoding a UbiD family decarboxylase), and dhaS (encoding indole 3-acetaldehyde dehydrogenase), which were proposed to constitute the indole-3-pyruvic acid (IPyA) pathway for IAA biosynthesis, were separately expressed in SQR9 or co-expressed as an entire IAA synthesis pathway cluster in SQR9 and B. subtilis 168, all these recombinants showed increased IAA production. These results suggested that gene products of dhaS, patB, yclB, yclC, yhcX and ysnE were involved in IAA biosynthesis. Genes patB, yclC and dhaS constitute a potential complete IPyA pathway of IAA biosynthesis in SQR9. Conclusions: In conclusion, biosynthesis of IAA in B. amyloliquefaciens SQR9 occurs through multiple pathways. [ABSTRACT FROM AUTHOR]

Background: Bacillus amyloliquefaciens SQR9 is a plant growth-promoting rhizobacteria (PGPR) with outstanding abilities to enhance plant growth and to control soil-borne diseases. Root exudates is known to play important roles in plant-microbe interactions. To explore the rhizosphere interactions and plant-beneficial characteristics of SQR9, the complete genome sequence as well as the transcriptome in response to maize root exudates under biofilm-forming conditions were elucidated. Results: Maize root exudates stimulated SQR9 biofilm formation in liquid culture, which is known to be positively correlated with enhanced root colonization. Transcriptional profiling via RNA-sequencing of SQR9 under static conditions indicated that, at 24 h post-inoculation, root exudates stimulated the expression of metabolism-relevant genes, while at 48 h post-inoculation, genes related to extracellular matrix production (tapA-sipW-tasA operon) were activated by root exudates. The individual components in maize root exudates that stimulated biofilm formation included glucose, citric acid, and fumaric acid, which either promoted the growth of SQR9 cells or activated extracellular matrix production. In addition, numerous groups of genes involved in rhizosphere adaptation and in plant-beneficial traits, including plant polysaccharide utilization, cell motility and chemotaxis, secondary antibiotics synthesis clusters, and plant growth promotion-relevant, were identified in the SQR9 genome. These genes also appeared to be induced by the maize root exudates. Conclusions: Enhanced biofilm formation of B. amyloliquefaciens SQR9 by maize root exudates could mainly be attributed to promoting cell growth and to inducing extracellular matrix production. The genomic analysis also highlighted the elements involved in the strain’s potential as a PGPR. This study provides useful information for understanding plant-rhizobacteria interactions and hence for promoting the agricultural applications of this strain. [ABSTRACT FROM AUTHOR]

Continuous cropping with banana results in an enrichment of Fusarium oxysporum f. sp. cubense race 4 (FOC) in soil, causing the soil-borne disease Fusarium wilt. Crop rotation has been an effective method of controlling various soil-borne diseases. However, no information is currently available concerning variations in soil microbial community structure in banana crop rotations. Thus, the influence of two-year crop rotation systems of pineapple-banana and maize-banana on the population density of FOC and soil microbial community structure was investigated to identify which rotation system is more effective in FOC suppression and differences in microbial community composition among different rotations. Bacterial and fungal communities were interrogated by pyrosequencing of the 16 S RNA gene and the internal transcribed spacer (ITS) region. The pineapple-banana rotation was more effective than maize-banana in reducing FOC abundances and suppressing Fusarium wilt disease incidence. Allelopathic effects of pineapple root exudates on FOC were not observed. Greater fungal community variations than bacterial were identified between the two rotation systems, suggesting that fungal communities may play a more important role in regulating FOC abundances. Furthermore, in the pineapple-banana rotation, Acidobacteria, Planctomycetes, Chloroflexi phyla, Gp1, Gp2 and Burkholderia bacterial genera increased while the fungal phyla Basidiomycota, (esp. Gymnopilus) increased and Sordariomycetes decreased. Such changes may be important microbial factors in the decrease in FOC. [ABSTRACT FROM AUTHOR]

Background: Plant biomass, the most abundant natural material on earth, represents a vast source of food and energy in nature. As the main component of plant biomass, xylan is a complex polysaccharide comprising a linear β(1,4)-linked backbone of xylosyl residues substituted by acetyl, arabinosyl, glucuronysyl and 4-O-methylglucuronycyl residues. Results: Aspergillus fumigatus Z5 is an efficient plant biomass depolymerization fungus. In this study, its crude xylanolytic enzymes were characterized and identified by two-dimensional gel electrophoresis (2-DE). The optimal temperature for the crude xylanases was close to 60 °C, the highest xylanase activity was achieved at pH ranged from 3 to 6, and the crude xylanases also showed a very broad region of pH (3-11) stability. The maximal xylanase activity of 21.45 U ⋅ ml-1 was observed in the fourth day of cultivation at 50 °C and 150 rpm with 2 % xylan as the sole carbon source. Zymogram analysis indicated that there were more than seven secreted proteins with xylanase activity. In the crude enzyme, two major endoxylanases, five cellulases and several associated enzymes were identified to be involved in the hydrolysis of polysaccharides. Of the total 13 xylanase genes in the Z5 genome, 11 were observed using q-PCR to be induced by xylan, one of which, An endo-1,4-β-xylanase with a low secretion level, was also expressed and characterized. The final hydrolysis products of xylan by crude enzyme mainly consisted of xylobiose. Conclusions: This study provides a comprehensive understanding of the depolymerization of xylan by Z5 and will help to design enzymatic strategies for plant biomass utilization. [ABSTRACT FROM AUTHOR]