Quantification and enzyme targets of fatty acid amides from duckweed root exudates involved in the stimulation of denitrification

Nitrogen-loss and carbon-footprint reduction by plant-rhizosphere exudates

Low-carbon approaches to agriculture constitute a pivotal measure to address the challenge of global climate change. In agroecosystems, rhizosphere exudates are significantly involved in regulating the nitrogen (N) cycle and facilitating belowground chemical communication between plants and soil microbes to reduce direct and indirect emissions of greenhouse gases (GHGs) and control N runoff from cultivated sites into natural water bodies. Here, we discuss specific rhizosphere exudates from plants and microorganisms and the mechanisms by which they reduce N loss and subsequent N pollution in terrestrial and aquatic environments, including biological nitrification inhibitors (BNIs), biological denitrification inhibitors (BDIs), and biological denitrification promoters (BDPs). We also highlight promising application scenarios and challenges in relation to rhizosphere exudates in terrestrial and aquatic environments.

Antibacterial Activity and Mechanism of Three Root Exudates from Mulberry Seedlings against Ralstonia pseudosolanacearum

Bacterial wilt is a significant soil-borne disease that poses a threat to mulberry production yield and quality of agricultural production worldwide. However, the disease resistance mechanisms dependent on root exudates are not well understood. In this present study, we investigated the antibacterial mechanisms of the main active substances (erucamide, oleamide, and camphor bromide) present in mulberry root exudates (MRE) against Ralstonia pseudosolanacearum (Rp), the causal agent of bacterial wilt. Our findings revealed that these three active substances inhibited the growth activity of Rp by affecting the cell morphology and extracellular polysaccharide content, as well as triggering a burst of reactive oxygen species. The active substances induced oxidative stress, leading to a decrease in Rp growth. Additionally, the expression levels of key genes in the hrp gene cluster (hrpB, hrpX, and hrpF) and other virulence-related genes (such as ripAW, ripAE, Rs5-4819, Rs5-4374, ace, egl3, and pehB) were significantly reduced upon treatment with the active substances. Further pathogenicity experiments demonstrated that root exudates (at a concentration of 1.5 mg·mL-1) delayed or slowed down the occurrence of bacterial wilt in mulberry. These findings provide valuable insight into the antimicrobial mechanisms of MRE against Rp and lay a theoretical foundation for the development and application of biocontrol agents to control mulberry bacterial wilt.

Self-assembled electrochemically active biofilms doped with carbon nanotubes: Electron exchange efficiency and cytotoxicity evaluation

Thick electrochemically active biofilms (EABs) will lead to insufficient extracellular electron transfer (EET) rate because of the limitation of both substrate diffusion and electron exchange. Herein, carbon nanotubes (CNTs)-doped EABs are developed through self-assembly. The highly conductive biofilms (internal resistance of ∼211 Ω) are efficiently enriched at CNTs dosage of 1 g L-1, with the stable power output of 0.568 W m-2 over three months. The embedded CNTs can act as electron tunnel to accelerate the EET rate in thick biofilm. Self-charging/discharging experiments and Nernst-Monod model stimulation demonstrate a higher net charge storage capacity (0.15 C m-2) and more negative half-saturation potential (-0.401 V) for the hybrid biofilms than that of the control (0.09 C m-2, and -0.378 V). Enzyme activity tests and the observation of confocal laser scanning microscopy by live/dead staining show a nearly negligible cytotoxicity of CNTs, and non-targeted metabonomics analysis reveals fourteen differential metabolites that do not play key roles in microbial central metabolic pathways according to KEGG compound database. The abundance of typical exoelectrogens Geobacter sp. is 2-fold of the control, resulting in a better bioelectrocatalytic activity. These finding provide a possible approach to prolong electron exchange and power output by developing a hybrid EABs doped with conductive material.

Innate Root Exudates Contributed to Contrasting Coping Strategies in Response to Ralstonia solanacearum in Resistant and Susceptible Tomato Cultivars

Tomato cultivars with contrasting resistance to pathogens regulate root exudates differentially in response to Ralstonia solanacearum attacks. However, strategies using innate root exudates against infection remain unknown. This study analyzed the innate root exudates of two tomato cultivars and their functions in regulating R. solanacearum infection. The innate root exudates differed between the two cultivars. Astaxanthin released from resistant plants inhibited colonization by R. solanacearum but promoted motility, while neferine released from susceptible plants suppressed motility and colonization. The secretion of astaxanthin in resistant tomatoes promoted the growth of biocontrol fungi in soil and reduced the abundance of pathogenic fungi. Neferine secreted by the susceptible cultivar inhibited the relative abundance of the bacterial-biocontrol-related Bacillus genus, indirectly reducing the soil's immune capacity. This study revealed contrasting strategies using root exudates in resistant and susceptible tomato cultivars to cope with R. solanacearum infection, providing a basis for breeding disease-resistant cultivars.

Arbuscular mycorrhizal fungi impact the production of alkannin/shikonin and their derivatives in Alkanna tinctoria Tausch. grown in semi-hydroponic and pot cultivation systems

Introduction

Alkanna tinctoria Tausch. is a medicinal plant well-known to produce important therapeutic compounds, such as alkannin/shikonin and their derivatives (A/Sd). It associates with arbuscular mycorrhizal fungi (AMF), which are known, amongst others beneficial effects, to modulate the plant secondary metabolites (SMs) biosynthesis. However, to the best of our knowledge, no study on the effects of AMF strains on the growth and production of A/Sd in A. tinctoria has been reported in the literature.

Methods

Here, three experiments were conducted. In Experiment 1, plants were associated with the GINCO strain Rhizophagus irregularis MUCL 41833 and, in Experiment 2, with two strains of GINCO (R. irregularis MUCL 41833 and Rhizophagus aggregatus MUCL 49408) and two native strains isolated from wild growing A. tinctoria (R. irregularis and Septoglomus viscosum) and were grown in a semi-hydroponic (S-H) cultivation system. Plants were harvested after 9 and 37 days in Experiment 1 and 9 days in Experiment 2. In Experiment 3, plants were associated with the two native AMF strains and with R. irregularis MUCL 41833 and were grown for 85 days in pots under greenhouse conditions. Quantification and identification of A/Sd were performed by HPLC-PDA and by HPLC-HRMS/MS, respectively. LePGT1, LePGT2, and GHQH genes involved in the A/Sd biosynthesis were analyzed through RT-qPCR.

Results

In Experiment 1, no significant differences were noticed in the production of A/Sd. Conversely, in Experiments 2 and 3, plants associated with the native AMF R. irregularis had the highest content of total A/Sd expressed as shikonin equivalent. In Experiment 1, a significantly higher relative expression of both LePGT1 and LePGT2 was observed in plants inoculated with R. irregularis MUCL 41833 compared with control plants after 37 days in the S-H cultivation system. Similarly, a significantly higher relative expression of LePGT2 in plants inoculated with R. irregularis MUCL 41833 was noticed after 9 versus 37 days in the S-H cultivation system. In Experiment 2, a significant lower relative expression of LePGT2 was observed in native AMF R. irregularis inoculated plants compared to the control.

Discussion

Overall, our study showed that the native R. irregularis strain increased A/Sd production in A. tinctoria regardless of the growing system used, further suggesting that the inoculation of native/best performing AMF is a promising method to improve the production of important SMs.

Root exudate-derived compounds stimulate the phosphorus solubilizing ability of bacteria

Low phosphorus (P) availability in soils is a major challenge for sustainable food production, as most soil P is often unavailable for plant uptake and effective strategies to access this P are limited. Certain soil occurring bacteria and root exudate-derived compounds that release P are in combination promising tools to develop applications that increase phosphorus use efficiency in crops. Here, we studied the ability of root exudate compounds (galactinol, threonine, and 4-hydroxybutyric acid) induced under low P conditions to stimulate the ability of bacteria to solubilize P. Galactinol, threonine, and 4-hydroxybutyric acid were incubated with the P solubilizing bacterial strains Enterobacter cloacae, Pseudomonas pseudoalcaligenes, and Bacillus thuringiensis under either inorganic (calcium phosphate) or organic (phytin) forms of plant-unavailable P. Overall, we found that the addition of individual root exudate compounds did not support bacterial growth rates. However, root exudates supplemented to the different bacterial appeared to enhance P solubilizing activity and overall P availability. Threonine and 4-hydroxybutyric acid induced P solubilization in all three bacterial strains. Subsequent exogenous application of threonine to soils improved the root growth of corn, enhanced nitrogen and P concentrations in roots and increased available levels of potassium, calcium and magnesium in soils. Thus, it appears that threonine might promote the bacterial solubilization and plant-uptake of a variety of nutrients. Altogether, these findings expand on the function of exuded specialized compounds and propose alternative approaches to unlock existing phosphorus reservoirs of P in crop lands.

Response of Rhizosphere Bacterial Communities to Near-Natural Forest Management and Tree Species within Chinese Fir Plantations

Near-natural forest management plays an important role in the maintenance of the long-term productivity and soil fertility of plantations. We conducted high-throughput absolute quantitative sequencing of 16S rRNA genes to compare the structures and diversity of rhizosphere soil bacterial communities among a pure Chinese fir (Cunninghamia lanceolata) plantation (S), a Cunninghamia lanceolata-Castanopsis hystrix-Michelia hedyosperma mixed plantation (SHX), and a Cunninghamia lanceolata-Castanopsis fissa mixed plantation (SD). The results revealed that near-natural forest management improved the rhizosphere soil properties of Chinese fir, especially the phosphorus content. Rhizosphere soil bacterial communities of Chinese fir in SHX and SD contained higher total absolute abundances and more unique operational taxonomic units (OTUs) than the pure plantation forest. Planctomycetes and Actinobacteria were abundant in SD, and Actinobacteria were enriched in SHX. The tree species also had an impact on the rhizosphere soil bacterial communities. For the rhizosphere soils of different tree species of SHX, the available phosphorus (AP) content of the rhizosphere of Chinese fir significantly surpassed those of Castanopsis hystrix and Michelia hedyosperma. Bacteria related to nitrogen fixing, such as Burkholderiales and Rhizobiales, were more abundant in Chinese fir in SD than in Castanopsis fissa. Acdiobacteria and Proteobacteria underpinned the differences found in the compositions of soil bacteria. The pH and soil organic matter were key variables influencing the rhizosphere soil bacterial communities. Our results demonstrated that in Chinese fir plantations, 12 years of near-natural management of introduced broad-leaved tree species can drive alterations of the physicochemical characteristics, bacterial community structure, and composition of rhizosphere soil, with tree species identity further influencing the rhizosphere soil bacterial community. IMPORTANCE Near-natural forest management is an important way to change the soil fertility decline and productivity reduction of pure Chinese fir plantations. At present, many detailed studies have been carried out on the impact of near-natural forest management on Chinese fir plantations at home and abroad. However, there are still few studies on the response of rhizosphere bacterial communities to near-natural forest management. Our study determined absolute quantities of Chinese fir rhizosphere bacterial communities in different mixed patterns. The results underscore the importance of near-natural forest management for Chinese fir plantation rhizosphere bacterial communities and provide new information on soil factors that affect rhizosphere bacterial communities in South China.

Characteristics of nitrogen distribution and its response to microecosystem changes in green infrastructure with different woody plants

With the acceleration of urbanization, N pollution in rainfall runoff has become the primary cause of eutrophication. In order to control N pollution in rainfall runoff, green infrastructure (GI) has been widely implemented. However, little is known about the process through which plants, especially woody plants, affect N distribution and the microecosystem in GI. Limited information suggests that woody plants mainly affect N distribution and alter the microecosystem through the influence of their roots. Therefore, laboratory tests were conducted to investigate the roles of the taproot plant Sophora japonica and the fibrous root plant Malus baccata and the resultant changes at the microecosystem level regarding N removal in a column-scale GI. After one year of growth, analysis of the morphological traits of the roots revealed that the average root length and diameter of S. japonica were approximately 2.3 and 1.8 times greater than those of M. baccata, respectively. An investigation of microbial diversity revealed that in comparison to the control GI system without plants, the GI systems with S. japonica and M. baccata hosted 45.68% and 59.88% more Actinobacteria, respectively. Further, the soil urease (S-UE) activities in the GI systems with S. japonica and M. baccata were 13.6% and 98.8% higher than that in the control, respectively, and the soil acid protease (S-ALPT) activities were 20.5% and 25.4% higher than that in the control, respectively. Compared to the control and the S. japonica GI system, the NH₃-N content in the soil of the M. baccata GI was 94.4% and 15.2% lower, respectively, and the NO₃-N content was 57.3% and 12.7% lower, respectively. The M. baccata GI system had the lowest NH₃-N and NO₃-N contents because it was most abundant in Actinobacteria and Arthrobacter and had the highest S-UE and S-ALPT activities. The results may be useful for improving N removal in GI containing different woody plants, and by extension for improving control of N pollution from rainfall runoff.

Fosthiazate inhibits root-knot disease and alters rhizosphere microbiome of Cucumis melo var. saccharinus

Root-knot nematodes especially Meloidogyne spp. are considered as most destructive obligate parasites that substantially reduce crop yield and quality. Fosthiazate is an efficient organothiophosphate chemical with nematicidal activity against Meloidogyne spp. The present study aimed to analyze the efficacy of fosthiazate against root-knot disease in Cucumis melo var. saccharinus and its potential effects on rhizosphere microbiome and metabolites. The fosthiazate (40%) was applied two times by spraying on the day of transplanting and during the pollination period (after 31 days). Samples from treatment (fosthiazate 40%: MF) and control groups (untreated plants; MCK) were analysed through metagenomic and metabolomic profiling of rhizospheres. Results revealed that root-knot index of the MF group (9.26 ± 1.28) was significantly (p < 0.05) lower than the MCK group (22.06 ± 0.71) with a control effect of 57.85% after 31 days of the first spray, whereas fosthiazate efficacy reduced to 31.87% after 38 days of second application with significantly (p < 0.05) different root-knot index values (MF: 56 ± 1.43 and; MCK: 82.26 ± 3.87). However, Cucumis melo var. saccharinus fruit yield in both groups (MCK: 21.1 ± 0.9 and MF: 21.53 ± 0.85) showed no differences (p > 0.05). Metagenomic profiling revealed Proteobacteria, Acidobacteriota, and Firmicutes as predominant phyla and Bacillus, Sphingomonas, and Acidibacter as predominant genera in rhizosphere soil samples of both MF and MCK groups. Further, a t-test revealed higher differential enrichment of Firmicutes at phylum level and Bacillus at genus level in MF than MCK. Metabolomic profiling of rhizospheric soil revealed a total of six differential metabolites (p < 0.05), four of them (Sucrose, Hexaonic acid 1, (Z)-9-Octadecenamide 1, and Hexadecanamide) were up-regulated in MF group, whereas two of them (2,3,4-Trihydroxy-3-(Hydroxymethyl) Butanol and Sulfurous acid, 2, ethylhexylundecyl ester) were down-regulated in CK group. Our study concluded that fosthiazate exhibits a better control over the rook-knot disease in the short term and resulted in trackable changes in rhizosphere microbiome and metabolome.

A Plant Worthy of Further Study-Volatile and Non-Volatile Compounds of Portenschlagiella ramosissima (Port.) Tutin and Its Biological Activity

New and detailed data are presented on the phytochemical composition of the volatile and non-volatile organic compounds of the Mediterranean endemic species Portenschlagiella ramosissima (Port.) Tutin. Both the essential oil and hydrosol were obtained from the air-dried plant by hydrodistillation and analyzed by gas chromatography-mass spectrometry. The volatile compounds from the fresh and air-dried plants and from the hydrosol were isolated for the first time by headspace solid-phase microextraction using two fibres of different polarity. The benzene derivative group was the predominant group in all samples, with myristicin being the most abundant component of all. The non-volatile compounds of the methanol extract were analyzed by ultra-high-performance liquid chromatography-high-resolution mass spectrometry with electrospray ionisation, and three flavonoid glycosides, one anthocyanidin glycoside, and lipid derivatives were detected. Both the chemical composition and biological activities of this plant have been described in a very limited number of publications, making it an interesting source for further study. The antiphytoviral activity of the essential oil and hydrosol showed that both extracts significantly reduced the number of lesions on the leaves of local host plants infected with tobacco mosaic virus. Moderate antiproliferative activity of the methanol extract was detected in three cancer cell lines, cervical cancer cell line, human colon cancer cell line and human osteosarcoma cell line, using the MTS-based cell proliferation assay. Based on the results, we highlight this plant as a new source of bioactive compounds and natural phytotherapeutic agent that deserves further investigation.

Mining Small Molecules from Teredinibacter turnerae Strains Isolated from Philippine Teredinidae

Endosymbiotic relationship has played a significant role in the evolution of marine species, allowing for the development of biochemical machinery for the synthesis of diverse metabolites. In this work, we explore the chemical space of exogenous compounds from shipworm endosymbionts using LC-MS-based metabolomics. Priority T. turnerae strains (1022X.S.1B.7A, 991H.S.0A.06B, 1675L.S.0A.01) that displayed antimicrobial activity, isolated from shipworms collected from several sites in the Philippines were cultured, and fractionated extracts were subjected for profiling using ultrahigh-performance liquid chromatography with high-resolution mass spectrometry quadrupole time-of-flight mass analyzer (UHPLC-HRMS QTOF). T. turnerae T7901 was used as a reference microorganism for dereplication analysis. Tandem MS data were analyzed through the Global Natural Products Social (GNPS) molecular networking, which resulted to 93 clusters with more than two nodes, leading to four putatively annotated clusters: lipids, lysophosphatidylethanolamines, cyclic dipeptides, and rhamnolipids. Additional clusters were also annotated through molecular networking with cross-reference to previous publications. Tartrolon D cluster with analogues, turnercyclamycins A and B; teredinibactin A, dechloroteredinibactin, and two other possible teredinibactin analogues; and oxylipin (E)-11-oxooctadec-12-enoic acid were putatively identified as described. Molecular networking also revealed two additional metabolite clusters, annotated as lyso-ornithine lipids and polyethers. Manual fragmentation analysis corroborated the putative identification generated from GNPS. However, some of the clusters remained unclassified due to the limited structural information on marine natural products in the public database. The result of this study, nonetheless, showed the diversity in the chemical space occupied by shipworm endosymbionts. This study also affirms the use of bioinformatics, molecular networking, and fragmentation mechanisms analysis as tools for the dereplication of high-throughput data to aid the prioritization of strains for further analysis.

Long-term continuous mono-cropping of Macadamia integrifolia greatly affects soil physicochemical properties, rhizospheric bacterial diversity, and metabolite contents

Macadamia integrifolia is the most economically important Proteaceae crop known for its edible nuts. The present study was conducted to examine the effect of continuous cultivation (for 1, 5, and 20 years) of M. integrifolia on soil quality, bacterial diversity, and metabolites. Soil rhizospheres from three different Macadamia rhizosphere orchards, 1-year monoculture orchard (CK), 5-year monoculture orchard (Y5), and 20-year monoculture orchard (Y20), were analyzed through metagenomic and metabolomic profiling. The soil physicochemical properties, including organic matter, and available nutrients (P, N, and K) were first increased significantly (p &lt; 0.05) from the CK to the Y5 group and then decreased (p &lt; 0.05) from the Y5 to the Y20 group. The soil pH continuously decreased (p &lt; 0.05) over time from CK to Y20. Metagenomic profiling revealed that Actinobacteria, Acidobacteria, and Proteobacteria were the top three abundant phyla with their inconsistent relative abundance patterns from CK to Y20 (CK: 23.76%, Y5: 34. 06%, and Y20: 31.55%), (CK: 13.59%, Y5: 18.59%, and Y20: 21.35%), and (CK: 27.59%, Y5: 15.98%, and Y20: 17.08%), respectively. Furthermore, the Y5 rhizospheres had a higher number of beneficial bacterial genera belonging to Proteobacteria and Actinobacteria than the Y20 rhizospheres. The KEGG annotation analysis revealed that cellular processes, organism systems, metabolism, and genetic information were the most enriched functional categories. CAZy database screening indicated the highest enrichment of glycoside hydrolases following the glycoside transferases and carbohydrate-binding modules. Differential metabolite analysis revealed the highest number of metabolites (11) in the Y5 group than in the Y20 group (6). It is concluded that continuous monoculture of M. integrifolia improves the soil physicochemical properties, bacterial diversity, and metabolite contents in short-term planted orchards which, however, are deteriorated in long-term planted orchards.

Phytoremediation performance of three traditional ornamental hydrophytes and the structure of their rhizosphere microorganism populations

The use of phytoremediation technology in urban and rural landscapes can permit both aesthetic and water purification functions to be achieved sustainably. Here, the ability of three ornamental aquatic plant species (Lythrum salicaria L., Sagittaria trifolia L., and Typha orientalis C. Presl) to remove nutrients from simulated contaminated water over 35 days and the structure of their rhizosphere microorganism populations were evaluated to examine their potential to be used for landscape phytoremediation as well as determine the mechanism of nutrient removal. L. salicaria had the highest nutrient removal ability (86.91-96.96% removal efficiency of total nitrogen and 46.04-66.70% removal efficiency of total phosphorus). The population structure of rhizosphere microorganisms was mainly affected by plant species and not the nutrient level of the water body according to principal coordinates analysis and non-metric multi-dimensional scaling. Betaproteobacteriales and Chitinophagales were highly correlated with the content of nutrients in water according to redundancy analysis. The accumulation of the two orders by L. salicaria and higher biomass might explain the stronger removal ability of L. salicaria. The findings of this study indicate that these plants could enhance urban and rural water landscape design; our results also shed new light on the mechanism of phytoremediation by rhizosphere microorganisms.

Effects of Litter and Root Manipulations on Soil Bacterial and Fungal Community Structure and Function in a Schrenk's Spruce (Picea schrenkiana) Forest

Soil microorganisms are the key driver of the geochemical cycle in forest ecosystem. Changes in litter and roots can affect soil microbial activities and nutrient cycling; however, the impact of this change on soil microbial community composition and function remain unclear. Here, we explored the effects of litter and root manipulations [control (CK), doubled litter input (DL), litter removal (NL), root exclusion (NR), and a combination of litter removal and root exclusion (NI)] on soil bacterial and fungal communities and functional groups during a 2-year field experiment, using illumina HiSeq sequencing coupled with the function prediction platform of PICRUSt and FUNGuild. Our results showed that litter and root removal decreased the diversity of soil bacteria and fungi (AEC, Shannon, and Chao1). The bacterial communities under different treatments were dominated by the phyla Proteobacteria, Acidobacteria, and Actinomycetes, and NL and NR reduced the relative abundance of the first two phyla. For the fungal communities, Basidiomycetes, Ascomycota, and Mortierellomycota were the dominant phyla. DL increased the relative abundance of Basidiomycetes, while NL and NR decreased the relative abundance of Ascomycota. We also found that litter and root manipulations altered the functional groups related to the metabolism of cofactors and vitamins, lipid metabolism, biosynthesis of other secondary metabolites, environmental adaptation, cell growth, and death. The functional groups including ectomycorrhizal, ectomycorrhizal-orchid mycorrhizal root-associated biotrophs and soil saprotrophs in the fungal community were also different among the different treatments. Soil organic carbon (SOC), pH, and soil water content are important factors driving changes in bacterial and fungal communities, respectively. Our results demonstrate that the changes in plant detritus altered the soil microbial community structure and function by affecting soil physicochemical factors, which provides important data for understanding the material cycle of forest ecosystems under global change.

Biocontrol potential and antifungal mechanism of a novel Streptomyces sichuanensis against Fusarium oxysporum f. sp. cubense tropical race 4 in vitro and in vivo

Most commercial banana cultivars are highly susceptible to Fusarium wilt caused by soilborne fungus Fusarium oxysporum f. sp. cubense (Foc), especially tropical race 4 (TR4). Biological control using antagonistic microorganism has been considered as an alternative method to fungicide. Our previous study showed that Streptomyces sp. SCA3-4 ^T had a broad-spectrum antifungal activity from the rhizosphere soil of Opuntia stricta in a dry hot valley. Here, the sequenced genome of strain SCA3-4 ^T contained 6614 predicted genes with 72.38% of G + C content. A polymorphic tree was constructed using the multilocus sequence analysis (MLSA) of five house-keeping gene alleles (atpD, gyrB, recA, rpoB, and trpB). Strain SCA3-4 ^T formed a distinct clade with Streptomyces mobaraensis NBRC 13819 ^T with 71% of bootstrap. Average nucleotide identity (ANI) values between genomes of strain SCA3-4 ^T and S. mobaraensis NBRC 13819 ^T was 85.83% below 95-96% of the novel species threshold, and named after Streptomyces sichuanensis sp. nov. The type strain is SCA3-4 ^T (= GDMCC 4.214 ^T = JCM 34964 ^T). Genomic analysis revealed that strain SCA3-4 ^T contained 36 known biosynthetic gene clusters of secondary metabolites. Antifungal activity of strain SCA3-4 ^T was closely associated with the production of siderophore and its extracts induced the apoptosis of Foc TR4 cells. A total of 12 potential antifungal metabolites including terpenoids, esters, acid, macrolides etc. were obtained by the gas chromatography-mass spectrometry (GC-MS). Greenhouse experiment indicated that strain SCA3-4 ^T could significantly inhibit infection of Foc TR4 in the roots and corms of banana seedlings and reduce disease index. Therefore, strain SCA3-4 ^T is an important microbial resource for exploring novel natural compounds and developing biopesticides to manage Foc TR4. KEY POINTS: • Strain SCA3-4 ^T was identified as a novel species of Streptomyces. • Siderophore participates in the antifungal regulation. • Secondary metabolites of strain SCA3-4 ^T improves the plant resistance to Foc TR4.

Stigmasterol root exudation arising from Pseudomonas inoculation of the duckweed rhizosphere enhances nitrogen removal from polluted waters

Rhizospheric microorganisms such as denitrifying bacteria are able to affect 'rhizobioaugmention' in aquatic plants and can help boost wastewater purification by benefiting plant growth, but little is known about their effects on the production of plant root exudates, and how such exudates may affect microorganismal nitrogen removal. Here, we assess the effects of the rhizospheric Pseudomonas inoculant strain RWX31 on the root exudate profile of the duckweed Spirodela polyrrhiza, using gas chromatography/mass spectrometry. Compared to untreated plants, inoculation with RWX31 specifically induced the exudation of two sterols, stigmasterol and β-sitosterol. An authentic standard assay revealed that stigmasterol significantly promoted nitrogen removal and biofilm formation by the denitrifying bacterial strain RWX31, whereas β-sitosterol had no effect. Assays for denitrifying enzyme activity were conducted to show that stigmasterol stimulated nitrogen removal by targeting nitrite reductase in bacteria. Enhanced N removal from water by stigmasterol, and a synergistic stimulatory effect with RWX31, was observed in open duckweed cultivation systems. We suggest that this is linked to a modulation of community composition of nirS- and nirK-type denitrifying bacteria in the rhizosphere, with a higher abundance of Bosea, Rhizobium, and Brucella, and a lower abundance of Rubrivivax. Our findings provide important new insights into the interaction of duckweed with the rhizospheric bacterial strain RWX31 and their involvement in the aquatic N cycle and offer a new path toward more effective bio-formulations for the purification of N-polluted waters.

Return of the Lemnaceae: duckweed as a model plant system in the genomics and postgenomics era

The aquatic Lemnaceae family, commonly called duckweed, comprises some of the smallest and fastest growing angiosperms known on Earth. Their tiny size, rapid growth by clonal propagation, and facile uptake of labeled compounds from the media were attractive features that made them a well-known model for plant biology from 1950 to 1990. Interest in duckweed has steadily regained momentum over the past decade, driven in part by the growing need to identify alternative plants from traditional agricultural crops that can help tackle urgent societal challenges, such as climate change and rapid population expansion. Propelled by rapid advances in genomic technologies, recent studies with duckweed again highlight the potential of these small plants to enable discoveries in diverse fields from ecology to chronobiology. Building on established community resources, duckweed is reemerging as a platform to study plant processes at the systems level and to translate knowledge gained for field deployment to address some of society's pressing needs. This review details the anatomy, development, physiology, and molecular characteristics of the Lemnaceae to introduce them to the broader plant research community. We highlight recent research enabled by Lemnaceae to demonstrate how these plants can be used for quantitative studies of complex processes and for revealing potentially novel strategies in plant defense and genome maintenance.

Identification and characterization of proteins, lipids, and metabolites in two organic fertilizer products derived from different nutrient sources

The biochemical composition of organic fertilizers largely determines their nutrient supply characteristics following soil application as well as their potential impact on soil microbial communities. Yet, limited information is available regarding the biochemical composition of organic fertilizers derived from different nutrient sources. Here, we qualitatively analyzed the presence and abundance of proteins, lipids, and metabolites in a liquid fish fertilizer (LFF) product and a type of granular organic fertilizer (GOF) commonly used in organic vegetable production, using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Our results suggest that the presence and abundance of proteins, lipids, and metabolites differ greatly between GOF and LFF. The qualitative analysis shows LFF as a rich source of metabolites, while complex proteins and long-chain saturated fatty acids are dominant in GOF. The degree of biochemical composition complexity may help explain the varying impacts of different types of organic fertilizers on nutrient availability, soil health, and environmental quality.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s13765-021-00625-2.

Isolation and Identification of Antibacterial Bioactive Compounds From Bacillus megaterium L2

Bacterial metabolites exhibit a variety of biologically active compounds including antibacterial and antifungal activities. It is well known that Bacillus is considered to be a promising source of bioactive secondary metabolites. Most plant pathogens have an incredible ability to mutate and acquire resistance, causing major economic losses in the agricultural field. Therefore, it is necessary to use the natural antibacterial compounds in microbes to control plant pathogens. This study was conducted to investigate the bio-active compounds of Bacillus megaterium L2. According to the activity guidance of Agrobacterium tumefaciens T-37, Erwinia carotovora EC-1 and Ralstonia solanacearum RS-2, five monomeric compounds, including erucamide (1), behenic acid (2), palmitic acid (3), phenylacetic acid (4), and β-sitosterol (5), were fractionated and purified from the crude ethyl acetate extract of B. megaterium. To our knowledge, all compounds were isolated from the bacterium for the first time. To understand the antimicrobial activity of these compounds, and their minimum inhibitory concentrations (MICs) (range: 0.98∼500 μg/mL) were determined by the broth microdilution method. For the three tested pathogens, palmitic acid exhibited almost no antibacterial activity (>500 μg/mL), while erucamide had moderate antibacterial activity (MIC = 500 μg/mL). Behenic acid showed MICs of 250 μg/mL against T-37 and RS-2 strains with an antibacterial activity. β-sitosterol showed significant antimicrobial activity against RS-2. β-sitosterol showed remarkable antimicrobial activity against RS-2 with an MIC of 15.6 μg/mL. In addition, with the antimicrobial activity, against T-37 (62.5 μg/mL) and against EC-1 (125 μg/mL) and RS-2 (15.6 μg/mL) strains notably, phenylacetic acid may be interesting for the prevention and control of phytopathogenic bacteria. Our findings suggest that isolated compounds such as behenic acid, β-sitosterol, and phenylacetic acid may be promising candidates for natural antimicrobial agents.

Community dynamics of duckweed-associated bacteria upon inoculation of plant growth-promoting bacteria

Plant growth-promoting bacteria (PGPB) have recently been demonstrated as a promising agent to improve wastewater treatment and biomass production efficiency of duckweed hydrocultures. With a view to their reliable use in aqueous environments, this study analysed the plant colonization dynamics of PGPB and the ecological consequences for the entire duckweed-associated bacterial community. A PGPB strain, Aquitalea magnusonii H3, was inoculated to duckweed at different cell densities or timings in the presence of three environmental bacterial communities. The results showed that strain H3 improved duckweed growth by 11.7–32.1% in five out of nine experiments. Quantitative-PCR and amplicon sequencing analyses showed that strain H3 successfully colonized duckweed after 1 and 3 d of inoculation in all cultivation tests. However, it significantly decreased in number after 7 d, and similar bacterial communities were observed on duckweed regardless of H3 inoculation. Predicted metagenome analysis suggested that genes related to bacterial chemotactic motility and surface attachment systems are consistently enriched through community assembly on duckweed. Taken together, strain H3 dominantly colonized duckweed for a short period and improved duckweed growth. However, the inoculation of the PGPB did not have a lasting impact due to the strong resilience of the natural duckweed microbiome.

GFP Scaffold-Based Engineering for the Production of Unbranched Very Long Chain Fatty Acids in Escherichia coli With Oleic Acid and Cerulenin Supplementation

Currently, very long chain fatty acids (VLCFAs) for oleochemical, pharmaceutical, cosmetic, or food applications are extracted from plant or marine organism resources, which is associated with a negative environmental impact. Therefore, there is an industrial demand to develop sustainable, microbial resources. Due to its ease of genetic modification and well-characterized metabolism, Escherichia coli has established itself as a model organism to study and tailor microbial fatty acid biosynthesis using a concerted genetic engineering approach. In this study, we systematically implemented a plant-derived (Arabidopsis thaliana) enzymatic cascade in Escherichia coli to enable unbranched VLCFA biosynthesis. The four Arabidopsis thaliana membrane-bound VLCFA enzymes were expressed using a synthetic expression cassette. To facilitate enzyme solubilization and interaction of the synthetic VLCFA synthase complex, we applied a self-assembly GFP scaffold. In order to initiate VLCFA biosynthesis, external oleic acid and cerulenin were supplemented to cultures. In this context, we detected the generation of arachidic (20:0), cis-11-eicosenoic (20:1) and cis-13-eicosenoic acid (20:1).

Floating duckweed mitigated ammonia volatilization and increased grain yield and nitrogen use efficiency of rice in biochar amended paddy soils

Biochar (BC) potentially accelerates ammonia (NH₃) volatilization from rice paddy soils. In this regard, however, application the floating duckweed (FDW) to biochar-amended soil to control the NH₃ volatilization is not studied up-to-date. Therefore, the impacts of BC application with and without FDW on the NH₃ and nitrous oxide (N₂O) emissions, NUE and rice grain yield were evaluated in a soil columns experiment. We repacked soil columns with Hydragric Anthrosol and Haplic Acrisol treated in triplicates with Urea, Urea + BC and Urea + BC + FDW. Total NH₃ losses from Hydragric Anthrosol and Haplic Acrisol were 15.2-33.2 kg N ha^-1 and 19.6-39.7 kg N ha^-1, respectively. Urea + BC treatment recorded 25.6-43.7% higher (p < 0.05) NH₃ losses than Urea treatment, attributing to higher pH value of floodwater. Floating duckweed decreased soil pH and therefore significantly reduced (p < 0.05) the NH₃ volatilizations from the two soils by 50.6-54.2% over Urea + BC and by 34.2-38.0% over Urea treatment. Total N₂O emissions from Hydragric Anthrosol and Haplic Acrisol were 1.19-3.42 kg N ha^-1 and 0.67-2.08 kg N ha^-1, respectively. Urea + BC treatment increased N₂O emissions by 58.8-68.7% and Urea + BC + FDW treatment further increased N₂O emission by 187.4-210.4% over Urea treatment. Higher ammonium content of the topsoil, explained the N₂O increases in the Urea + BC and Urea + BC + FDW treatments. Urea + BC slightly reduced the rice grain yield and NUE, while the Urea + BC + FDW promoted both rice yield and NUE. Our data indicate that co-application of FDW along with BC in paddy soil could mitigate the NH₃ volatilization and enhance the rice grain yield and NUE.

Comparative metabolomics of temperature sensitive resistance to wheat streak mosaic virus (WSMV) in resistant and susceptible wheat cultivars

In order to evaluate wheat resistance to wheat streak mosaic virus (WSMV) at low temperature and resistance breakdown at high temperature, metabolic profile of WSMV-resistant (R) and susceptible (S) wheat cultivars were analyzed. Metabolites were detected by UPLC-QTOF/MS in leaves of R and S plants challenged with WSMV at 20 °C and 32 °C, 24, 48 and 72 h post inoculation (hpi). WSMV and mock inoculated plants were used for discriminating the most significant metabolites and metabolic pathways affected at those temperatures. At 24 hpi/20 °C and 48 hpi/20 °C, the most important metabolites in R plants were coumarins, a limited number of lipids, and unknown compounds, while at 72 hpi/20 °C, in addition to coumarins, alkaloids and several amino acids were increased. Compared to 24 and 48 hpi, at 72hpi, in R plants most metabolic pathways were up-regulated at 20 °C. These resistance-related specific pathways included amino acid metabolism, lipid metabolism and alkaloids pathways. Also, several pathways were up-regulated at 32 °C.These combined heat stress and pathogen related pathways, included lipid metabolism and amino acid metabolism. Some carbohydrate metabolism pathways were considered as heat stress related pathways and could be associated with resistance breakdown. On the other hand, the increased expression of lipid compounds, especially 24 hpi at 32 °C in R plant, can be attributed to plant adaptation to combined stressors such as pathogen and high temperature. Increased susceptibility of R plants at 32 °C coincided with a down-regulated expression of components of signal transduction pathways or in a decreased level of metabolites related to this pathway, especially at a later time after infection, leading to decreased metabolite signaling. Decrease of signaling compounds under combined stress is a possible outcome of deactivating WSMV specific signaling networks leading to compatible response in R plants. The significance of these findings considering the recent increase of global temperature and the challenge of breakdown of temperature sensitive resistance to some plant viruses is discussed.

Effects of antibiotics on nitrogen uptake of four wetland plant species grown under hydroponic culture

To investigate the effects of antibiotics on nitrogen removal and uptake by wetland plants, four typical macrophyte species, Cyperus alternifolius L., Typha angustifolia L., Lythrum salicaria L., and Acorus calamus L., were grown in hydroponic cultivation systems and fed wastewater polluted with 10 μg L^-1 Ofloxacin (OFL) and Tetracycline (TET). Biomass production, nitrogen mass concentration, chlorophyll content, root exudates, and nitrogen removal efficiency of hydroponic cultivation were investigated. The results indicated that in all hydroponic systems, NH₄⁺-N was entirely removed from the hydroponic substrate within 1 day and plant nitrogen accumulation was the main role of the removed NO₃^-. OFL and TET stimulated the accumulation of biomass and nitrogen of A. calamus but significantly inhibited the NO₃^--N removal ability of L. salicaria (98.6 to 76.2%) and T. augustifolia (84.3 to 40.2%). This indicates that A. calamus may be a good choice for nitrogen uptake in wetlands contaminated with antibiotics. OFL and TET improved the concentrations of total organic carbon (TOC), total nitrogen (TN), organic acid, and soluble sugars in root exudates, especially for oxalic acid. Considering the significant correlation between TOC of root exudates and nitrogen removal efficiency, the TOC of root exudates may be an important index for choosing macrophytes to maintain nitrogen removal ability in wetlands contaminated with antibiotics.

Food Authentication: Small-Molecule Profiling as a Tool for the Geographic Discrimination of German White Asparagus

For the first time, a non-targeted metabolomics approach by means of ultraperformance liquid chromatography coupled to electrospray quadruple time-of-flight mass spectrometry was chosen for the discrimination of geographical origins of white asparagus samples ( Asparagus officinalis). Over a period of four harvesting periods (4 years), approximately 400 asparagus samples were measured. Initially, four different liquid chromatography-mass spectrometry methods were used to detect as many metabolites as possible and to assess which method is most suitable. The most relevant marker compounds were linked to the influence of different plant stress parameters and climate effects. Some of the samples were also analyzed by isotope-ratio mass spectrometry (IRMS), which is the current gold standard for the discrimination of the geographical origin of asparagus. In summary, the analysis of the metabolome was proven to be quite suitable to determine the geographical origin of asparagus and seems to provide better interpretable results than IRMS studies.

Unraveling the metabolic response of Brassica oleracea exposed to Xanthomonas campestris pv. campestris

BACKGROUND

Brassica crops together with cereals represent the basis of world supplies. Due to their importance, the production losses caused by Xanthomonas campestris pv. campestris (Xcc) infection represent a high economic impact. Understanding molecular and biochemical mechanisms of plants is essential to develop resistant crops with durable protection against diseases. In this regard, metabolomics has emerged as a valuable technology to provide an overview of the biological status of a plant exposed to a disease. This study investigated the dynamic changes in the metabolic profile of Brassica oleracea plants during an Xcc infection from leaves collected at five different days post infection using a mass spectrometry approach.

RESULTS

Results showed that Xcc infection causes dynamic changes in the metabolome of B. oleracea. Moreover, induction/repression pattern of the metabolites implicated in the response follows a complex dynamics during infection progression, indicating a complex temporal response. Specific metabolic pathways such as alkaloids, coumarins or sphingolipids are postulated as promising key role candidates in the infection response.

CONCLUSION

This work tries to decipher the changes produced on Brassica crops metabolome under Xcc infection and represents a step forward in the understanding of B. oleracea-Xcc interaction. © 2018 Society of Chemical Industry.

13-Docosenamide release by bacteria in response to glucose during growth-fluorescein quenching and clinical application

Our investigations on extracellular biochemical events to find readily and sensitively detectable/measurable molecular targets for developing easier, simpler, and quicker diagnostic methods and tools for bacterial pathogens led to the observation that bacteria grown in the presence of glucose produced a compound capable of quenching fluorescein. Under the experimental conditions, among various sugars, glucose was found to induce maximum amount of the quencher when Escherichia coli was grown in presence of 50 mM glucose in rarified LB. The release of quencher closely following bacterial growth significantly from fourth hour after moderate inoculation. This fluorescein-quencher was purified using TLC and HPLC and identified using GC-MS as 13-docosenamide or erucamide, originally known as plant lipid, is a neuroactive compound in human and animals. Fluorescence and UV-absorption spectral analysis showed that the compound formed stable adduct with fluorescein in the ground state. Commercial 13-docosonamide enabled quantitation of the compound produced in micromolar quantities during glucose utilization from the medium. Twenty-seven different commonly encountered bacteria, pathogens or otherwise, could produce the quencher. A simple microplate-based growth monitoring method was developed exploiting quenching as an easily and readily measurable signal, either using a reader or an imager. While 13-docosenamide release by bacteria may be relevant in host-bacteria interactions, especially when growing under conditions that provide glucose, the new approach with inexpensive reagents can provide a new antibiogram technique.

Biological nitrification inhibition by rice root exudates and its relationship with nitrogen-use efficiency

Microbial nitrification in soils is a major contributor to nitrogen (N) loss in agricultural systems. Some plants can secrete organic substances that act as biological nitrification inhibitors (BNIs), and a small number of BNIs have been identified and characterized. However, virtually no research has focused on the important food crop, rice (Oryza sativa). Here, 19 rice varieties were explored for BNI potential on the key nitrifying bacterium Nitrosomonas europaea. Exudates from both indica and japonica genotypes were found to possess strong BNI potential. Older seedlings had higher BNI abilities than younger ones; Zhongjiu25 (ZJ25) and Wuyunjing7 (WYJ7) were the most effective genotypes among indica and japonica varieties, respectively. A new nitrification inhibitor, 1,9-decanediol, was identified, shown to block the ammonia monooxygenase (AMO) pathway of ammonia oxidation and to possess an 80% effective dose (ED₈₀ ) of 90 ng μl^-1 . Plant N-use efficiency (NUE) was determined using a ¹⁵ N-labeling method. Correlation analyses indicated that both BNI abilities and 1,9-decanediol amounts of root exudates were positively correlated with plant ammonium-use efficiency and ammonium preference. These findings provide important new insights into the plant-bacterial interactions involved in the soil N cycle, and improve our understanding of the BNI capacity of rice in the context of NUE.