Long-term fertilization suppresses rice pathogens by microbial volatile compounds.

Microbial volatile organic compounds (VOCs) can suppress plant pathogens. Although fertilization strongly affects soil microbial communities, the influence of fertilization on microbial VOC-mediated suppression of pathogens has not been elucidated. Soil was sampled from a paddy field that had been subjected to the following treatments for 30 years: a no-fertilizer control, mineral fertilization (NPK), NPK combined with rice straw (NPK + S), NPK combined with chicken manure (70% NPK + 30% M). Then, within a laboratory experiment, pathogens were exposed to VOCs without physical contact to assess the impact of VOCs emitted from paddy soils on in vitro growth of the fungal rice pathogens: Pyricularia oryzae and Rhizoctonia solani. The VOCs emitted from soil reduced the mycelial biomass of P. oryzae and R. solani by 36-51% and 10-30%, respectively, compared to that of the control (no soil; no VOCs emission). Overall, the highest suppression of P. oryzae and R. solani was in the NPK and NPK + S soils, which emitted more quinones, phenols, and low alcohols than NPK + M soils. The abundances of quinones and phenols in the soil air were maximal in the NPK-fertilized soil because the low ratio of dissolved organic carbon and Olsen-P increased the population of key species such as Acidobacteriae, Anaerolineae, and Entorrhizomycetes. The abundance of alcohols was minimum in the NPK + S fertilized soil because the high SOC content decreased the population of Sordariomycetes. In conclusion, mineral fertilization affects bacterial and fungal VOC emissions, thereby suppressing the growth of R. solani and P. oryzae.

Enrichment of beneficial rhizosphere microbes in Chinese wheat yellow mosaic virus-resistant cultivars.

The microbial community within the root system, the rhizosphere closely connected to the root, and their symbiotic relationship with the host are increasingly seen as possible drivers of natural pathogen resistance. Resistant cultivars have the most effective strategy in controlling the Chinese wheat yellow mosaic disease, but the roles of the root and rhizosphere microbial interactions among different taxonomic levels of resistant cultivars are still unknown. Thus, we aimed to investigate whether these microbial community composition and network characteristics are related to disease resistance and to analyze the belowground plant-associated microflora. Relatively high microbial diversity and stable community structure for the resistant cultivars were detected. Comparison analysis showed that some bacterial phyla were significantly enriched in the wheat root or rhizosphere of the resistant wheat cultivar. Furthermore, the root and rhizosphere of the resistant cultivars greatly recruited many known beneficial bacterial and fungal taxa. In contrast, the relative abundance of potential pathogens was higher for the susceptible cultivar than for the resistant cultivar. Network co-occurrence analysis revealed that a much more complex, more mutually beneficial, and a higher number of bacterial keystone taxa in belowground microbial networks were displayed in the resistant cultivar, which may have been responsible for maintaining the stability and ecological balance of the microbial community. Overall, compared with the susceptible cultivar, the resistant cultivar tends to recruit more potential beneficial microbial groups for plant and rhizosphere microbial community interactions. These findings indicate that beneficial rhizosphere microbiomes for cultivars should be targeted and evaluated using community compositional profiles. KEY POINTS: • Different resistance levels in cultivars affect the rhizosphere microbiome.. • Resistant cultivars tend to recruit more potential beneficial microbial groups. • Bacteria occupy a high proportion and core position in the microflora network.

Comparative Genomic Analysis of Two-Component Signal Transduction Systems in Probiotic Lactobacillus casei.

Lactobacillus casei has traditionally been recognized as a probiotic, thus needing to survive the industrial production processes and transit through the gastrointestinal tract before providing benefit to human health. The two-component signal transduction system (TCS) plays important roles in sensing and reacting to environmental changes, which consists of a histidine kinase (HK) and a response regulator (RR). In this study we identified HKs and RRs of six sequenced L. casei strains. Ortholog analysis revealed 15 TCS clusters (HK-RR pairs), one orphan HKs and three orphan RRs, of which 12 TCS clusters were common to all six strains, three were absent in one strain. Further classification of the predicted HKs and RRs revealed interesting aspects of their putative functions. Some TCS clusters are involved with the response under the stress of the bile salts, acid, or oxidative, which contribute to survive the difficult journey through the human gastrointestinal tract. Computational predictions of 15 TCSs were verified by PCR experiments. This genomic level study of TCSs should provide valuable insights into the conservation and divergence of TCS proteins in the L. casei strains.

[Response of Soil Multifunctionality to Reduced Microbial Diversity].

Soil microbial communities play an important role in driving a variety of ecosystem functions and ecological processes and are the primary driving force in maintaining the biogeochemical cycle. It has been observed that soil microbial diversity decreases with land use intensification and climate change in the global background. It is essential to investigate whether the reduction in soil microbial diversity can affect soil multifunctionality. Thus, in this study, the dilution-to-extinction method was used to construct the gradient of soil microbial diversity, combined with high-throughput sequencing to explore the impact of the reduction in bacterial, fungal, and protist diversity on soil multifunctionality. The results showed that the soil microbial alpha diversity (richness and Shannon index) was significantly lower than that of the original soil. Principal coordinate analysis (PCoA) showed that the microbial community structure of original soil was significantly different from that of diluted soil, and the response of bacterial and fungal communities to diluted soil was higher than that of protists. The regression model showed that there was a significant negative linear relationship between the average response value of soil multi-function and the index of microbial diversity, indicating that the change in soil microbial community was the key factor in regulating soil multifunctionality. The regression model showed that there was a significant negative linear relationship between soil multifunctionality and microbial diversity, indicating that the change in soil microbial community was the key factor to regulate soil multi-kinetic energy. Through the aggregated boosted tree analysis (ABT) and regression model, we found that some specific microbial groups, such as the Solacocozyma and Holtermaniella of fungi and Rudaea of bacteria, could significantly promote the change in soil multifunctionality, which showed that key microbial taxa play an indicative role in biological processes. Furthermore, the structural equation model revealed that bacteria could affect soil multifunctionality through the interaction between microbiomes, which was the key biological factor driving the change in soil multifunctionality. This study provided experimental evidence for the impact of soil microbial diversity on soil multifunctionality, and promoted the notion that maintaining a certain diversity of soil microbial community in a single agricultural ecosystem, especially the diversity of key microbial taxa, is of great significance to the sustainable development of ecosystem function in the future.

Microbial community changes in different underground compartments of potato affected yield and quality.

Soil microbial communities are critical to plant health and productivity. Crop-associated microbial diversity may exhibit spatial specificity across regions and soil compartments. However, we lack sound evidence for the impact of variation in soil microbial diversity on plant productivity caused by regional differences. The main aims of this study are to explore the structure and functionality of the belowground (potato tuber surface and rhizosphere) microbial communities in three compartments and assess whether these communities contribute to potato productivity. Significant differences in alpha and beta diversities of belowground microbiota were detected in different compartments and regions, mainly due to differences in available soil nutrients and pH. Changes to microbial diversity between bulk soil and rhizosphere or tuber surface soil were significantly negatively correlated with potato yield and nutrient content and positively correlated with starch content. We further found some bacterial (Mucilaginibacter, Dokdonella, and Salinispora) and fungal (Solicoccozyma, Scytalidium, and Humicola) genera closely associated with potato yield and quality. Aggregated boosted tree prediction revealed that soil physicochemical properties and microbial diversity of tuber surface soil contributed more to potato yield; tuber surface soil bacterial contributed more to potato starch and nutrient content. Our findings provide experimental evidence that the significant differences in soil microbial diversity and specific microbial taxa enrichment may potentially influence crop productivity under soil physicochemical property change scenarios in the agricultural ecosystem. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03167-6.

A K+ channel from salt-tolerant melon inhibited by Na+.

• The possible roles of K(+) channels in plant adaptation to high Na(+) conditions have not been extensively analyzed. Here, we characterize an inward Shaker K(+) channel, MIRK (melon inward rectifying K(+) channel), cloned in a salt-tolerant melon (Cucumis melo) cultivar, and show that this channel displays an unusual sensitivity to Na(+) . • MIRK expression localization was analyzed by reverse-transcription PCR (RT-PCR). MIRK functional analyses were performed in yeast (growth tests) and Xenopus oocytes (voltage-clamp). MIRK-type activity was revealed in guard cells using the patch-clamp technique. • MIRK is an inwardly rectifying Shaker channel belonging to the 'KAT' subgroup and expressed in melon leaves (especially in guard cells and vasculature), stems, flowers and fruits. Besides having similar features to its close homologs, MIRK displays a unique property: inhibition of K(+) transport by external Na(+) . In Xenopus oocytes, external Na(+) affected both inward and outward MIRK currents in a voltage-independent manner, suggesting a blocking site in the channel external mouth. • The degree of MIRK inhibition by Na(+) , which is dependent on the Na(+) /K(+) concentration ratio, is predicted to have an impact on the control of K(+) transport in planta upon salt stress. Expressed in guard cells, MIRK might control Na(+) arrival to the shoots via regulation of stomatal aperture by Na(+) .

[Microbial Carbon Source Metabolic Profile in Rice Rhizosphere and Non-rhizosphere Soils with Different Long-term Fertilization Management].

Rhizosphere and non-rhizosphere soil samples under different long-term fertilization treatments including control without fertilizer (CK), chemical fertilization alone (NPK), rice residues combined with NPK (NPKS), 30% manure plus 70% chemical fertilizers (LOM), and 60% manure plus 40% chemical fertilizers (HOM) were collected from a paddy field in a red soil hilly area in Ningxiang City, Hunan Province, China. The characteristics of microbial carbon utilization in the soils were studied. Results of 18O-H2O tracer analysis showed that both soil microbial biomass carbon content (MBC) and microbial growth rate (CGrowth) were highest in the HOM treatment, whereas they were lowest in CK. In the rhizosphere soil, the highest basal respiration was observed in HOM, and the lowest values were in CK and NPK. Microbial carbon utilization efficiency (CUE) was highest in NPK but lowest in the LOM and HOM treatments. In non-rhizosphere soil, no significant differences between basal respiration and CUE were observed among the fertilization treatments. Results from MicroRespTM showed that the ability of microorganisms to metabolize exogenous carbon sources was higher in non-rhizosphere soil than in rhizosphere soil. The application of organic materials (rice residues or manure) increased the microbial metabolic rate of carboxylic acids, amino acids, and carbohydrates in the order carboxylic acids > amino acids and carbohydrates > complex compounds. Redundancy analysis of the microbial metabolism patterns of various carbon substrates showed that:① CK was well separated from the fertilization treatments; ② NPK was grouped with NPKS, whereas LOM and HOM were grouped together and were separate from NPK and NPKS. This indicates that the fertilization treatments changed the microbial carbon metabolism patterns. The above-mentioned results indicated that the fertilization treatments did not affect microbial CUE and basal respiration. However, exogenous carbon source input (such as root exudates) and the application of organic materials can increase microbial basal respiration, and thus, reduce microbial CUE.

[Transformation and Distribution of Soil Organic Carbon and the Microbial Characteristics in Response to Different Exogenous Carbon Input Levels in Paddy Soil].

The turnover of soil organic carbon (SOC) and the activity of soil microbes can be influenced by exogenous carbon. However, microbial response characteristics of the transformation and distribution of available organic carbon under different levels remain unclear in paddy soils. 13C-labeled glucose was used as a typical available exogenous carbon to simulate indoor culture experiments added at different levels of soil microbial biomass carbon (MBC) (0×MBC, 0.5×MBC, 1×MBC, 3×MBC, and 5×MBC) to reveal the process of C-transformation and distribution. The characteristics of microbial response in the process of exogenous carbon turnover was also monitored. The 96-well microplate fluorescence analysis was adopted to determine the activities of cellobiose hydrolase (CBH) and ß-glucosidase (ß-Glu). The results showed that, in 2 d of incubation, the ratio of labeled glucose carbon to dissolved organic carbon (13C-DOC/DOC) or to SOC (13C-SOC/SOC) was positively correlated with the amount of glucose added. The incorporation of glucose C (13C) into MBC reached the highest value (18.96 mg·kg-1) at 3×MBC treatment but decreased thereafter. The 13C allocation rate was mainly positively correlated with MBC, Olsen-P, and DOC. At 60 d, 13C-DOC, 13C-MBC, and 13C-SOC decreased significantly to less than 0.02 mg·kg-1, 2 mg·kg-1, and 10 mg·kg-1 in soil, and it was positively correlated with the amount of glucose added. Compared with CK, CBH enzyme activity increased significantly after the addition of glucose, and for the 3×MBC treatment it was increased by 22.6 times, which was significantly higher than those of other treatments (P<0.05). However, ß-Glu enzyme activity increased only in the 3×MBC and 5×MBC treatments, wherein it decreased with increasing amounts of added glucose. NH4+-N, pH, ß-Glu, and CBH were the primary factors affecting the distribution rate of 13C. In conclusion, the conversion of exogenous carbon to SOC increased with increased amounts of added organic carbon. This changed the activity of soil enzymes; however, microbial utilization of exogenous carbon may have a saturation threshold. Within the saturation threshold, the conversion rate of organic matter was directly proportional to the amount of added organic matter. When the saturation threshold was exceeded, the conversion rate of organic matter decreased. Therefore, the appropriate addition of exogenous carbon is beneficial, as it can increase SOC in rice fields and improve the quality of the crop growth environment.

[Characterization of Soil Organic Carbon Mineralization Under Different Gradient Carbon Loading in Paddy Soil].

Available carbon is the most active part of the soil carbon pool. It is also the main carbon source of soil microbes and plays an important role in the processes of soil organic carbon mineralization and accumulation. However, the mechanisms are still not clear how soil organic carbon mineralization and its priming effect (PE) are affected by different input levels of readily available carbon, based on the growth requirements of microbes in paddy soil. In this study, an incubation experiment was conducted by adding different levels (0.5, 1, 3, and 5 times of MBC) of exogenous source organic carbon (13C-glucose) to the soil. The mineralization dynamics of labile organic carbon and its priming effect was investigated. The mineralization rate of glucose-C increased significantly with the increasing carbon loading level. The distribution of glucose-C into rapid and slow C pools was also exponentially correlated with the carbon loading (R2=0.99, P<0.05 and R2=0.99, P<0.05, respectively). Negative PE was observed at high carbon loading (3×MBC and 5×MBC); while positive PE was induced by low carbon loading (0.5×MBC and 1×MBC). The cumulative PE was 160.0 mg·kg-1 and 325.1 mg·kg-1, respectively, at the end of the incubation. Redundancy analysis showed that the main factors affecting the cumulative PE were MBC, MBN, and DOC at the initial glucose mineralization stage, while ß-glucosidase, chitinase, and ammonium nitrogen were the main factors at later stages. Therefore, the readily available carbon loading has an important effect on the organic carbon mineralization and PE in paddy soil. Higher carbon loading was good for the accumulation of organic carbon sequestration in paddy soil. This study is of great scientific significance for revealing the activity of organic carbon in paddy fields and for its contribution to the development of sustainable agriculture.

Sludge Biochar Amendment and Alfalfa Revegetation Improve Soil Physicochemical Properties and Increase Diversity of Soil Microbes in Soils from a Rare Earth Element Mining Wasteland.

Long-term unregulated mining of ion-adsorption clays (IAC) in China has resulted in severe ecological destruction and created large areas of wasteland in dire need of rehabilitation. Soil amendment and revegetation are two important means of rehabilitation of IAC mining wasteland. In this study, we used sludge biochar prepared by pyrolysis of municipal sewage sludge as a soil ameliorant, selected alfalfa as a revegetation plant, and conducted pot trials in a climate-controlled chamber. We investigated the effects of alfalfa revegetation, sludge biochar amendment, and their combined amendment on soil physicochemical properties in soil from an IAC mining wasteland as well as the impact of sludge biochar on plant growth. At the same time, we also assessed the impacts of these amendments on the soil microbial community by means of the Illumina Miseq sequences method. Results showed that alfalfa revegetation and sludge biochar both improved soil physicochemical properties and microbial community structure. When alfalfa revegetation and sludge biochar amendment were combined, we detected additive effects on the improvement of soil physicochemical properties as well as increases in the richness and diversity of bacterial and fungal communities. Redundancy analyses suggested that alfalfa revegetation and sludge biochar amendment significantly affected soil microbial community structure. Critical environmental factors consisted of soil available K, pH, organic matter, carbon⁻nitrogen ratio, bulk density, and total porosity. Sludge biochar amendment significantly promoted the growth of alfalfa and changed its root morphology. Combining alfalfa the revegetation with sludge biochar amendment may serve to not only achieve the revegetation of IAC mining wasteland, but also address the challenge of municipal sludge disposal by making the waste profitable.

Biotoxicity and bioavailability of hydrophobic organic compounds solubilized in nonionic surfactant micelle phase and cloud point system.

A recent work has shown that hydrophobic organic compounds solubilized in the micelle phase of some nonionic surfactants present substrate toxicity to microorganisms with increasing bioavailability. However, in cloud point systems, biotoxicity is prevented, because the compounds are solubilized into a coacervate phase, thereby leaving a fraction of compounds with cells in a dilute phase. This study extends the understanding of the relationship between substrate toxicity and bioavailability of hydrophobic organic compounds solubilized in nonionic surfactant micelle phase and cloud point system. Biotoxicity experiments were conducted with naphthalene and phenanthrene in the presence of mixed nonionic surfactants Brij30 and TMN-3, which formed a micelle phase or cloud point system at different concentrations. Saccharomyces cerevisiae, unable to degrade these compounds, was used for the biotoxicity experiments. Glucose in the cloud point system was consumed faster than in the nonionic surfactant micelle phase, indicating that the solubilized compounds had increased toxicity to cells in the nonionic surfactant micelle phase. The results were verified by subsequent biodegradation experiments. The compounds were degraded faster by PAH-degrading bacterium in the cloud point system than in the micelle phase. All these results showed that biotoxicity of the hydrophobic organic compounds increases with bioavailability in the surfactant micelle phase but remains at a low level in the cloud point system. These results provide a guideline for the application of cloud point systems as novel media for microbial transformation or biodegradation.

Screening of lignan patterns in Schisandra species using ultrasonic assisted temperature switch ionic liquid microextraction followed by UPLC-MS/MS analysis.

The ultrasonic assisted temperature-switch ionic liquid microextraction (UATS-ILME) has been successfully applied in extracting of seven lignans from Schisandra. 1-Butyl-3-methylimidazolium tetrafluoroborate ([C4MIM][BF4]) aqueous solution was selected for extracting the target analytes in raw material at 80°C. The lignans were deposited into a single drop by in situ forming 1-butyl-3-methylimidazolium hexafluorophosphate ([C4MIM][PF6]) by cooling down to 0°C and centrifuging for 10min. The extracts were analyzed by ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) in a robust multiple-reaction monitoring (MRM) mode in five minutes. Meanwhile, the proposed method was validated and successfully applied to the determination of seven lignans in twelve Schisandra species. The results indicated that UATS-ILME combined with UPLC-MS/MS is a powerful and practical tool, which has great potential for comprehensive quality control of herbal medicines.

Isolation and characterization of a GS2 gene in melon (Cucumis melo L.) and its expression patterns under the fertilization of different forms of N.

We isolated a novel glutamine synthetase (GS, EC 6.3.1.2) gene M-GS2 (accession: AY773090) by the RACE approach from melon. The full-length cDNA of M-GS2 is 1807 bp and contains a 1296 bp open reading frame (ORF) encoding 432 amino acids. The deduced protein contains conserved structural domains among plant GS2 proteins and shares extensive sequence homology with GS2 enzymes from other higher plants. M-GS2 expresses with specificity in leaf, and identification of a chloroplast transit peptide (cTP) in M-GS2 suggests that it localizes to the chloroplast. As shown by real-time quantitative PCR, distinct forms of nitrogen (N) found in fertilizers transcriptionally regulated M-GS2 differently. Ammonium and nitrate feeding only significantly regulated M-GS2 transcripts in leaf; starving (0.75 mM) or moderate (3.75 mM) N levels dramatically increased M-GS2 transcripts for 1 day, decreasing to a constant low level after 2-3 days, while sufficient N level (7.5 mM) had a minor effect throughout 3 days compared to controls. Glutamate feeding, however, not only significantly regulated M-GS2 transcripts in leaf (decreased initially then increased to higher levels than controls), but also in root, where it was up-regulated continuously. Our results suggested that M-GS2 is the first GS gene cloned and characterized in melon and melon responds to the variations in N fertilization by differentially expressing M-GS2.