Root Metabolism Research Articles

Preinoculation with Bradyrhizobium japonicum enhances the salt tolerance of Glycine max seedlings by regulating polyamine metabolism in roots

Rhizobia are common symbiotic microorganisms in the root system of leguminous plants that can usually provide nitrogen to the host through nitrogen fixation. Studies have shown that rhizobium-preinoculated soybean plants usually exhibit improved salt tolerance, but the underlying mechanism is not fully understood. In this paper, transcriptome sequencing (RNA-seq) revealed that preinoculation with rhizobia affected polyamine (PA) metabolism in soybean roots. The assay of PA contents showed that preinoculation with rhizobia significantly increased the putrescine (Put) content in roots and leaves during short-term salt treatment (0-5d). Long-term salt treatment (5-7d) resulted in a high Put content and significantly increased Spm and Spd contents, resulting in a rapid increase in the Put/(Spd+Spm) ratio (0-5d) and subsequent decrease. Moreover, rhizobium preinoculation of soybean plants resulted in increased contents of conjugated and bound PAs under salt stress. Further transcriptome sequencing, PA contents, PA synthase expression and activity analysis revealed that GmADC may be a key gene related to salt tolerance in rhizobium-preinoculated soybean plants, and the GmADC-overexpressing soybean hairy-root composite plants exhibited less ROS damage, lower Cl-/NO3- ratios and Na+/K+ ratios, and stabilized ion homeostasis. Taken together, preinoculation with rhizobia increased the expression level and enzyme activity of arginine decarboxylase (ADC) in soybean roots, increased the content of Put in roots and leaves, and increased the content of conjugated and bound PAs in soybean plants, thereby alleviating the oxidative and ionic injuries of soybean plants and enhancing the salt tolerance.

Long-term soil warming changes the profile of primary metabolites in fine roots of Norway spruce in a temperate montane forest.

Climate warming poses major threats to temperate forests, but the response of tree root metabolism has largely remained unclear. We examined the impact of long-term soil warming (>14 years, +4°C) on the fine root metabolome across three seasons for 2years in an old spruce forest, using a liquid chromatography-mass spectrometry platform for primary metabolite analysis. A total of 44 primary metabolites were identified in roots (19 amino acids, 12 organic acidsand 13 sugars). Warming increased the concentration of total amino acids and of total sugars by 15% and 21%, respectively, but not organic acids. We found that soil warming and sampling date, along with their interaction, directly influenced the primary metabolite profiles. Specifically, in warming plots, concentrations of arginine, glycine, lysine, threonine, tryptophan, mannose, ribose, fructose, glucoseand oxaloacetic acid increased by 51.4%, 19.9%, 21.5%, 19.3%, 22.1%, 23.0%, 38.0%, 40.7%, 19.8%and 16.7%, respectively. Rather than being driven by single compounds, changes in metabolite profiles reflected a general up- or downregulation of most metabolic pathway network. This emphasises the importance of metabolomics approaches in investigating root metabolic pathways and understanding the effects of climate change on tree root metabolism.

Unlocking nature’s drought resilience: a focus on the parsimonious root phenotype and specialised root metabolism in wild Medicago populations

Abstract Background and aims Crop wild relatives, exposed to strong natural selection, exhibit effective tolerance traits against stresses. While an aggressive root proliferation phenotype has long been considered advantageous for a range of stresses, it appears to be counterproductive under drought due to its high metabolic cost. Recently, a parsimonious root phenotype, metabolically more efficient, has been suggested to be better adapted to semiarid environments, although it is not clear that this phenotype is a trait exhibited by crop wild relatives. Methods Firstly, we analysed the root phenotype and carbon metabolism in four Medicago crop wild relatives adapted to a semiarid environment and compared them with the cultivated M. truncatula Jemalong (A17). Secondly, we exposed the cultivated (probably the least adapted genotype to aridity) and the wild (the most common one in arid zones) M. truncatula genotypes to water deficit. The carbon metabolism response in different parts of their roots was analysed. Results A reduced carbon investment per unit of root length was a common trait in the four wild genotypes, indicative of an evolution towards a parsimonious root phenotype. During the water deficit experiment, the wild M. truncatula showed higher tolerance to drought, along with a superior ability of its taproot to partition sucrose and enhanced capacity of its fibrous roots to maintain sugar homeostasis. Conclusion A parsimonious root phenotype and the spatial specialization of root carbon metabolism represent two important drought tolerance traits. This work provides relevant findings to understand the response of Medicago species roots to water deficit.

A fast solid-phase microextraction scheme for in vivo monitoring of bio-accumulation and bio-transformation of arbidol in living plants

Large quantity of the antiviral drug arbidol is used for resisting virus infection like the Corona Virus Disease 2019 and influenza, resulting in unanticipated environmental pollution. Herein, to investigate the environmental risks of the unanticipated arbidol contamination, a novel in vivo sampling probe was developed based on a bromo-substituted porous organic polymer (Br-POP) and then adopted for tracking the bio-accumulation and bio-transformation of arbidol in living plants by coupling with a nano-electrospray ionization fourier-transform ion cyclotron resonance mass spectrometry (Nano-ESI-FT-ICR-MS) method. The established method showed good extraction performance towards arbidol with limit of detection (LOD) of 0.48 ng g−1, and relative standard deviation (RSD) of single-and multiple- probe of 2.2 and 14 %. Owing to the interactions between the Br-POP and the target analytes, as well as the fast analysis process of Nano-ESI-FT-ICR-MS, <6 min was cost for total sampling and analysis duration, achieving hourly tracking of arbidol and its metabolites in this work. During 21-d in vivo tracking, the concentration of arbidol in living plant stems increased rapidly within 6 h and peaked at 413.93 ± 47.09 ng g−1. Meanwhile, it was found that dissolved organic matters (DOM) had significant effect on arbidol behaviors in living plants, resulting in a decrease of the maximum concentration of arbidol in plant stems (152.70 ± 42.44 ng g−1) and the change of dominant metabolite of arbidol that the S-oxidation rather than N-demethylation product of arbidol was dominant with DOM participation. Additionally, the plant root secretion was found to be significantly altered by arbidol exposure. To summarized, the combination of in vivo SPME and the FT-ICR-MS analysis provide new and important information regarding arbidol contamination and related alternation of plant root metabolism.

Effects of Decabromodiphenyl Ethane and Cadmium Coexposure on Their Bioaccumulation, Oxidative Stress, Root Metabolism, and Rhizosphere Soil Microorganisms in a Soil-Rice System.

Decabromodiphenyl ethane (DBDPE) and cadmium (Cd) are typical pollutants in e-waste, seriously threatening crop growth. This study investigated the bioaccumulation and toxicity mechanisms of DBDPE and Cd in a soil-rice system. The results showed that 50 mg/kg DBDPE could reduce the level of accumulation of Cd in rice roots. DBDPE and Cd induced the antioxidant system (SOD, POD, and MDA) in rice seedlings. The combined exposure reduced the contents of carbohydrates, lipids, amino acids, and organic acids. Phenylalanine and phenylpropanoid metabolisms were identified as the key detoxification metabolic pathways under combined exposure. DBDPE and Cd disrupted the functional cycling of carbon and nitrogen in rhizosphere soil, while Gemmatimonadetes, Actinobacteria, and Bacteroidetes were the key bacterial groups responding to DBDPE and Cd stress. This work provides data for the toxicity risk evaluation of DBDPE and Cd combined exposure to food crops.

Effect of Paenibacillus favisporus CHP14 inoculation on selenium accumulation and tolerance of Pakchoi (Brassica chinensis L.) under exogenous selenite treatments

The effects of Paenibacillus favisporus CHP14 inoculation on selenium (Se) accumulation and Se tolerance of Pakchoi were studied by a pot experiment conducted in greenhouse. The results revealed that the growth traits such as plant height, root length, and biomass were significantly elevated during CHP14 treatment at 0 ∼ 8.0 mg·kg−1 Se(IV) levels. CHP14-inoculated plants accumulated more Se in root and shoot, which were 24.1%∼57.3% and 7.5%∼50.9% higher than those of non-inoculated plants. The contents of leaf nitrogen (N), phosphorus (P), magnesium (Mg), and iron (Fe), as well as the ratio of indoleacetic acid and abscisic acid contents (IAA/ABA) were increased by CHP14 inoculation, and positively associated with photosynthetic pigment contents (p < 0.05). At ≥ 4.0 mg·kg−1 Se(IV) levels, superoxide dismutase, peroxidase, and glutathione peroxidase activities of Pakchoi roots were increased with CHP14 inoculation, by 9.9%∼17.1%, 28.4%∼40.7%, and 7.4%∼15.3%, respectively. Moreover, CHP14 inoculation enhanced ascorbate-glutathione (AsA-GSH) metabolism in roots by upregulating the related enzymes activities and antioxidant contents under excess Se(IV) stress. These findings suggest that CHP14 is beneficial to improve plant growth and enhance Se(IV) resistance of Pakchoi, and can be exploited as potential inoculants for phytoremediation process in Se contaminated soil.

Microbial colonisation rewires the composition and content of poplar root exudates, root and shoot metabolomes

BackgroundTrees are associated with a broad range of microorganisms colonising the diverse tissues of their host. However, the early dynamics of the microbiota assembly microbiota from the root to shoot axis and how it is linked to root exudates and metabolite contents of tissues remain unclear. Here, we characterised how fungal and bacterial communities are altering root exudates as well as root and shoot metabolomes in parallel with their establishment in poplar cuttings (Populus tremula x tremuloides clone T89) over 30 days of growth. Sterile poplar cuttings were planted in natural or gamma irradiated soils. Bulk and rhizospheric soils, root and shoot tissues were collected from day 1 to day 30 to track the dynamic changes of fungal and bacterial communities in the different habitats by DNA metabarcoding. Root exudates and root and shoot metabolites were analysed in parallel by gas chromatography-mass spectrometry.ResultsOur study reveals that microbial colonisation triggered rapid and substantial alterations in both the composition and quantity of root exudates, with over 70 metabolites exclusively identified in remarkably high abundances in the absence of microorganisms. Noteworthy among these were lipid-related metabolites and defence compounds. The microbial colonisation of both roots and shoots exhibited a similar dynamic response, initially involving saprophytic microorganisms and later transitioning to endophytes and symbionts. Key constituents of the shoot microbiota were also discernible at earlier time points in the rhizosphere and roots, indicating that the soil constituted a primary source for shoot microbiota. Furthermore, the microbial colonisation of belowground and aerial compartments induced a reconfiguration of plant metabolism. Specifically, microbial colonisation predominantly instigated alterations in primary metabolism in roots, while in shoots, it primarily influenced defence metabolism.ConclusionsThis study highlighted the profound impact of microbial interactions on metabolic pathways of plants, shedding light on the intricate interplay between plants and their associated microbial communities.2SWtA3_gUD-Xt4Z7N25436Video

Fermentation broth of a novel endophytic fungus enhanced maize salt tolerance by regulating sugar metabolism and phytohormone biosynthesis or signaling

Soil salinization is a major environmental factor that severely affects global agriculture. Root endophytes can enter root cells, and offer various ecological benefits, such as promoting plant growth, improving soil conditions, and enhancing plant resistance. Su100 is a novel strain of endophytic fungus that was characterized from blueberry roots. In this study, we focused on evaluating the effects of Su100 secretion on maize growth. The results demonstrated that maize treated with Su100 fermentation broth (SFB) exhibited significantly stronger salt tolerance than the control. It is worth mentioning that the treated root system not only had an advantage in terms of biomass but also a change in root structure with a significant increase in lateral roots (LRs) compared to the control. Transcriptome analysis combined with hormone content measurements indicated that SFB upregulated the auxin signaling pathway, and also caused alterations in brassinosteroids (BR) and jasmonic acid (JA) biosynthesis and signaling pathways. Transcriptome analyses also indicated that SFB caused significant changes in the sugar metabolism of maize roots. The major changes included: enhancing the conversion and utilization of sucrose in roots; increasing carbon flow to uridine diphosphate glucose (UDPG), which acted as a precursor for producing more cell wall polysaccharides, mainly pectin and lignin; accelerating the tricarboxylic acid cycle, which were further supported by sugar content determinations. Taken together, our results indicated that the enhanced salt tolerance of maize treated with SFB was due to the modulation of sugar metabolism and phytohormone biosynthesis or signaling pathways. This study provided new insights into the mechanisms of action of endophytic fungi and highlighted the potential application of fungal preparations in agriculture.

Metabolic Responses to Excess Manganese in Legumes: Variations in Nitrogen Compounds in Canavalia ensiformis (L.) DC and Cajanus cajan (L.) Millsp

ABSTRACTManganese (Mn) is crucial as a trace element for plant metabolism, but high concentrations in soil can induce symptoms of toxicity. This study aimed to evaluate the metabolism of nitrogen compounds and biomass production in Canavalia ensiformis and Cajanus cajan, clarifying the effects of this metal on nitrogen metabolism. The soil was treated with Mn concentrations of 80, 100, 120, 140, and 160 mg kg−1. Differential responses were observed in the metabolism of nitrogenous compounds between species. C. cajan affected nitrogen metabolism in shoots, roots, and nodules, with significant variations in amino acids, total soluble proteins, ureides, and root biomass concentration. In contrast, C. ensiformis showed stability in the concentrations of compounds, mainly ureides, and proteins, even with increasing doses of Mn in the soil. These findings highlight the importance of nitrogen metabolism in legumes studied as a key aspect for understanding their Mn tolerance mechanisms in soil.

Phosphorus application under continuous wheat-cotton straw retention enhanced cotton root productivity and seedcotton yield by improving the carbohydrate metabolism of root

ContextStraw retention could reduce phosphorus (P) application without decreasing seedcotton yield but related physiological mechanisms were unclear. Cotton root is the first organ to sense the changes in soil environment, and its growth and development, especially carbohydrate metabolism, significantly affected the formation of seedcotton yield. Therefore, it is necessary to explore the responses of cotton root carbohydrate metabolism to straw retention combined with P application. ObjectiveThis study was to investigate the effects of straw retention combined with P application on root carbohydrate metabolism and its relationship with seedcotton yield. MethodsA field experiment (2020–2022) was conducted to evaluate the changes in seedcotton yield, cotton canopy apparent photosynthesis rate (CAP), biomass, root productivity, root carbohydrate contents and related enzyme activities under different straw management [removal (S0), retention (S1)] and P rates (0, 100, 200 kg P2O5 ha−1). ResultsStraw retention and P application both increased seedcotton yield and had a significant interaction effect on it. In the 5th-7th year of straw retention, straw retention reduced 24 %-26 % P application to reach a similar yield of S0 with 100 kg P2O5 ha−1. Analyzing the reasons: (1) Straw retention combined with P application increased cotton CAP, providing adequate assimilates for cotton development; (2) Straw retention combined with P application promoted the utilization of root carbohydrates, thereby increasing root productivity and seedcotton yield. Specifically, compared with S0 without P, S1 combined with P application increased the enzyme activities related to carbohydrate metabolism, especially sucrose synthase (7.6 %-59.4 %) and acid invertase (3.9 %-58.6 %), which reduced sucrose (3.3 %-32.2 %) and starch (4.3 %-28.7 %) contents at the peak boll setting stage. Efficient utilization of sucrose and starch enhanced root productivity, the ratio of root to shoot (R/S) reduced by 2.7 %-21.6 %, while the boll loading of root system (BLR) and boll capacity of root system (BCR) increased by 0.6 %-39.2 % and 3.1 %-50.6 % at the boll opening stage, respectively, favoring the formation of seedcotton yield. Furthermore, when the R/S, BLR, and BCR reached 0.12, 0.81 boll g−1, and 4.33 g g−1, cotton harvested the maximum theoretical yield of 3780, 3774, and 4069 kg ha−1, respectively. ConclusionsStraw retention combined with P application increased root productivity and seedcotton yield by promoting the utilization of root carbohydrates. ImplicationsThis study revealed the internal mechanism for straw retention combined with P application to affect seedcotton yield from the angle of root carbohydrate metabolism and provided a theoretical basis for rationally reducing P fertilizer under straw retention.

Response on root regrowth potential to soil moisture in Sedum species during winter in Særheim, Norway

PurposeThe impact of winter moisture on root metabolism and root integrity has potential consequences for the geographical distribution of drought-adapted succulent species and for their long-term performance on green roofs. The interacting effects of soil characteristics and precipitation frequency on root mortality under winter conditions and the potential to grow new roots in spring were evaluated for six Sedum species under controlled conditions. MethodsTo test for the impact of soil moisture during winter on root regrowth potential in six Sedum species, we used a combination of two substrates with differing water-holding capacity and four contrasting watering regimes. Specially, for the fine and coarse substrates, total pore volume was 42 and 46 %, respectively, and maximum water-holding capacity (i.e. field capacity) was 0.50 and 0.33 kg water per L, respectively. The four watering treatments involved overhead watering to runoff (approx. 10 mm): once every second week, once a week, three times per week and three times per week with 1 cm standing water in trays from January to March 2019. ResultsIt was found that winter soil moisture had no major impact on root mortality or root regrowth potential in spring. Root mortality was not affected by watering frequency and regrowth potential showed no directional response to increased watering frequency, although species-specific responses were involved. Root diameter did not differ between the substrates, but there were some differences between the species. Sedum rupestre had on average the thickest roots (0.17 mm), followed by S. acre, S. anglicum and S. sexangulare (0.15–0.16 mm), while S. album and S. hispanicum had the thinnest roots (0.12–0.13 mm). Moreover, effects of watering frequency on root mortality and regrowth potential were not influenced by soil water-holding capacity across species. We concluded that winter soil moisture had no negative effects on root performance within the range of treatments tested here. ConclusionsRoot response to transient waterlogging or moist but unsaturated soil may not be an important mechanism for determining the survival and distribution of temperate Sedum species during winter.

Rhizosphere effects and microbial N limitations drive the root N limitations in the rhizosphere during secondary succession in a Pinus tabuliformis forest in North China.

Rhizosphere effects (REs) have recently been identified as important regulators of root and microbial nutrient acquisition and are positively involved in nutrient cycling of belowground carbon (C), nitrogen (N), and phosphorus (P). Nutrient conditions of the fine roots and soil N are likely to influence REs. Still, it is unclear how REs of soil nutrients themselves variably impact the supply of nutrients to plants in terms of the responses to soil N due to succession. In this study, we applied both fine roots and extracellular enzymes for vector analysis and stoichiometry of N:P to explore the metabolic limitations of roots and rhizospheric soil microbes and their relationships with REs across five levels of soil N (0, 5, 10, 15, and 20kg N m-2 year-1) along successional age classes of 42, 55, and 65 years in a Pinus tabuliformis forest. Overall, the metabolism of root and rhizospheric soil microbes was mediated by soil N. N limitation of roots initially decreased before increasing, whereas that of microbes demonstrated opposite trends to the N levels owing to competition for inorganic N between them by REs of NO3 --N. However, N limitations of both roots and microbes were alleviated in young stands and increased with succession after the application of N. In addition, root N limitations were manipulated by REs of three different soil N-related indicators, i.e., total N, NH4 +-N, and NO3 --N. Rhizospheric soil microbial N limitation was almost unaffected by REs due to their strong homeostasis but was an important driver in the regulation of root N limitation. Our results indicated that successional age was the most critical driver that directly and indirectly affected root N metabolism. However, the level of N application had a slight effect on root N limitation. Microbial N limitation and variations in the REs of N indicators regulated root N limitation in the rhizosphere. As a result, roots utilized REs to sequester N to alleviate N limitations. Thesefindings contribute to novel mechanistic perspectives on the sustainability of N nutrition by regulating N cycling in a system of plant-soil-microbes in the rhizosphere to adapt to global N deposition or the heterogeneous distribution of bioavailable soil N with succession.

Systemic strategies for cytokinin biosynthesis and catabolism in Arabidopsis roots and leaves under prolonged ammonium nutrition

Cytokinins are growth-regulating plant hormones that are considered to adjust plant development under environmental stresses. During sole ammonium nutrition, a condition known to induce growth retardation of plants, altered cytokinin content can contribute to the characteristic ammonium toxicity syndrome. To understand the metabolic changes in cytokinin pools, cytokinin biosynthesis and degradation were analyzed in the leaves and roots of mature Arabidopsis plants. We found that in leaves of ammonium-grown plants, despite induction of biosynthesis on the expression level, there was no active cytokinin build-up because they were effectively routed toward their downstream catabolites. In roots, cytokinin conjugation was also induced, together with low expression of major synthetic enzymes, resulting in a decreased content of the trans-zeatin form under ammonium conditions. Based on these results, we hypothesized that in leaves and roots, cytokinin turnover is the major regulator of the cytokinin pool and does not allow active cytokinins to accumulate. A potent negative-regulator of root development is trans-zeatin, therefore its low level in mature root tissues of ammonium-grown plants may be responsible for occurrence of a wide root system. Additionally, specific cytokinin enhancement in apical root tips may evoke a short root phenotype in plants under ammonium conditions. The ability to flexibly regulate cytokinin metabolism and distribution in root and shoot tissues can contribute to adjusting plant development in response to ammonium stress.

Multiomics analysis of the effects of manure-borne doxycycline combined with oversized fiber microplastics on pak choi growth and the risk of antibiotic resistance gene transmission

In this study, oversized microplastics (OMPs) were intentionally introduced into soil containing manure-borne doxycycline (DOX). This strategic approach was used to systematically examine the effects of combined OMP and DOX pollution on the growth of pak choi, analyze alterations in soil environmental metabolites, and explore the potential migration of antibiotic resistance genes (ARGs). The results revealed a more pronounced impact of DOX than of OMPs. Slender-fiber OMPs (SF OMPs) had a more substantial influence on the growth of pak choi than did coarse-fiber OMPs (CF OMPs). Conversely, CF OMPs had a more significant effect on the migration of ARGs within the system. When DOX was combined with OMPs, the negative effects of DOX on pak choi growth were mitigated through the synthesis of indole through the adjustment of carbon metabolism and amino acid metabolism in pak choi roots. In this process, Pseudohongiellaceae and Xanthomonadaceae were key bacteria. During the migration of ARGs, the potential host bacterium Limnobacter should be considered. Additionally, the majority of potential host bacteria in the pak choi endophytic environment were associated with tetG. This study provides insights into the intricate interplay among DOX, OMPs, ARGs, plant growth, soil metabolism, and the microbiome.

Factors driving plant diversity in the spontaneous vegetation of the novel ecosystem of post-coal mining spoil heaps and their relationship with soil respiration

The subject of the paper is the analysis of the relationship between spontaneous vegetation diversity and soil respiration in novel post-coal mine ecosystem. In the natural and semi-natural ecosystems, soil respiration process (Rs) is a crucial ecosystem function regulating terrestrial ecosystems’ carbon cycle. Soil respiration depends on the quality and quantity of the soil organic matter (SOM), the soil microbes’ activity, and root metabolism. The listed factors are directly related to the composition diversity of vegetation plant species (biochemistry). For many years, soil respiration parameters have been studied in natural and seminatural vegetation communities and ecosystems. However, there still need to be a greater understanding of the relationship between vegetation plant species diversity and soil respiration as a crucial ecosystem function. Plant species diversity has to be analysed through both the taxonomic diversity and the functional diversity. These approaches reflect the composition, structure, and function of plant species communities. We hypothesise that the diversity of the spontaneous vegetation species composition shapes the amount of soil respiration in a post-coal mine novel ecosystem. The soil respiration differs significantly along the vegetational types driven by habitat gradients and is significantly higher in highly functional richness and dispersion vegetation patches. Contrary to our expectation, soil respiration was the highest in the less diverse vegetation types – both taxonomical and functional evenness were non-significant factors. Only functional dispersion is weakly negative correlated with soil respiration level (SRL).

Response mechanism of Cynodon dactylon to flooding stress based on integrating metabonomics and transcriptomics analysis

Cynodon dactylon, a perennial herbaceous of Poaceae, possessing unique abilities in flooding tolerance and clonal propagation. However, evidences on molecular response mechanism from field are missing. Here, the differential responses of above-ground (stolon) and below-ground (root) organs of C. dactylon under flooding and non-flooding (CK) conditions were compared at the transcriptional and metabolomic levels. Under flooding stress, significant enrichment of differentially expressed genes (DEGs) related to dehydration responses, including cell water homeostasis and ion transmembrane transport were observed in both roots and stolons. The stolons were more sensitive to flooding, while enrichment in energy metabolism in roots were higher, such as the glycolytic process and glycogen biosynthetic process. The DEGs of photosynthesis in stolons were significantly down-regulated compared to roots. Under flooding stress, oxidative phosphorylation (OXPHOS) is inactivated, and the terminal oxidase of the mitochondrial electron transport chain (mtETC), cytochrome c oxidase (COX), is inhibited. Consequently, the expression of pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) involved in fermentative metabolism is upregulated. The combined analysis indicated that phenylalanine, tyrosine, and tryptophan biosynthetic pathways in roots were significantly enriched in the flooding group. In contrast, there was a significant increase in phenylalanine biosynthesis in stolons, and the metabolite phenol exhibited up-regulated expression. In summary, phenylalanine metabolism and phenylalanine biosynthesis are the major responses to flooding stress, indicating the crucial role of these pathways in the flood tolerance of C. dactylon. These findings provide valuable evidence for understanding plant regulatory mechanisms underlying flooding tolerance.

Rhizophagus Irregularis regulates flavonoids metabolism in paper mulberry roots under cadmium stress.

Broussonetia papyrifera is widely found in cadmium (Cd) contaminated areas, with an inherent enhanced flavonoids metabolism and inhibited lignin biosynthesis, colonized by lots of symbiotic fungi, such as arbuscular mycorrhizal fungi (AMF). However, the physiological and molecular mechanisms by which Rhizophagus irregularis, an AM fungus, regulates flavonoids and lignin in B. papyrifera under Cd stress remain unclear. Here, a pot experiment of B. papyrifera inoculated and non-inoculated with R. irregularis under Cd stress was carried out. We determined flavonoids and lignin concentrations in B. papyrifera roots by LC-MS and GC-MS, respectively, and measured the transcriptional levels of flavonoids- or lignin-related genes in B. papyrifera roots, aiming to ascertain the key components of flavonoids or lignin, and key genes regulated by R. irregularis in response to Cd stress. Without R. irregularis, the concentrations of eriodictyol, quercetin and myricetin were significantly increased under Cd stress. The concentrations of eriodictyol and genistein were significantly increased by R. irregularis, while the concentration of rutin was significantly decreased. Total lignin and lignin monomer had no alteration under Cd stress or with R. irregularis inoculation. As for flavonoids- or lignin-related genes, 26 genes were co-regulated by Cd stress and R. irregularis. Among these genes, BpC4H2, BpCHS8 and BpCHI5 were strongly positively associated with eriodictyol, indicating that these three genes participate in eriodictyol biosynthesis and were involved in R. irregularis assisting B. papyrifera to cope with Cd stress. This lays a foundation for further research revealing molecular mechanisms by which R. irregularis regulates flavonoids synthesis to enhance tolerance of B. papyrifera to Cd stress.

Single-cell network analysis reveals gene expression programs for Arabidopsis root development and metabolism

Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated, but related comprehensive gene co-expression network analyses are lacking. We conducted a single-cell gene co-expression network analysis with publicly available scRNA-seq datasets of Arabidopsis roots using a SingleCellGGM algorithm. The analysis identified 149 gene co-expression modules, which we considered to be gene expression programs (GEPs). By examining their spatiotemporal expression, we identified GEPs specifically expressed in major root cell types along their developmental trajectories. These GEPs define gene programs regulating root cell development at different stages and are enriched with relevant developmental regulators. As examples, a GEP specific for the quiescent center (QC) contains 20 genes regulating QC and stem cell niche homeostasis, and four GEPs are expressed in sieve elements (SEs) from early to late developmental stages, with the early-stage GEP containing 17 known SE developmental regulators. We also identified GEPs for metabolic pathways with cell-type-specific expression, suggesting the existence of cell-type-specific metabolism in roots. Using the GEPs, we discovered and verified a columella-specific gene, NRL27, as a regulator of the auxin-related root gravitropism response. Our analysis thus systematically reveals GEPs that regulate Arabidopsis root development and metabolism and provides ample resources for root biology studies.

Cotton adapts to Na2SO4 stress by regulating the metabolic intensity and distribution of metabolites in roots and leaves

Significant Na2SO4 stress severely restricts cotton production in Xinjiang. However, the tolerance mechanism of cotton to Na2SO4 stress is not yet fully understood. This study set up two treatments, normal soil (control, CK) and Na2SO4 stress (Na2SO4, SS), to explore the effects of Na2SO4 stress on the physiological metabolism of cotton leaves and roots. Compared with CK, the total biomass and net photosynthetic stress rate decreased significantly (P < 0.05) by 49.0 and 14.7%, respectively. Additionally, the relative conductivity, malondialdehyde content, superoxide dismutase, peroxidase, and catalase activities of leaves increased significantly by 114.5, 99.8, 160, 16.8, and 117%, respectively. A tandem mass tag (TMT) proteomics analysis identified 319 and 583 differentially expressed proteins in roots and leaves, respectively. They mainly participate in amino acid metabolism, such as alanine, aspartic acid, and glutamate metabolism; histidine metabolism; tyrosine metabolism; tryptophan metabolism; energy metabolism, such as glycolysis; the tricarboxylic acid cycle; phosphorus oxide metabolism; lipid metabolism, such as fatty acid biosynthesis; glycerol phospholipid metabolism; steroid biosynthesis; and steroid hormone biosynthesis. Metabolomic data also showed significant changes in amino acid metabolism, organic acid metabolism, and carbohydrate metabolism in the roots and leaves. Na2SO4 stress inhibited metabolism in cotton roots but promoted metabolism in cotton leaves. Under Na2SO4 stress, cotton may prioritize the use of limited photosynthetic products to maintain the health and life activities of its leaves, while also transporting some organic matter from the leaves to the roots to maintain normal metabolic activity of the roots.

Examining starch metabolism in lotus roots (Nelumbo nucifera Gaertn.) during post-harvest storage at different temperatures

This study explores the impact of postharvest storage temperatures (4 °C and 25 °C) on starch metabolism and textural attributes of glutinous lotus root. While starch metabolism is a well-known factor influencing texture, changes in powdery and sticky qualities have remained unexplored. Our research reveals that storing lotus roots at 4 °C delays water dissipation, amylopectin reduction, and the decline in textural elements such as hardness, adhesiveness, springiness, gumminess, and resilience. Lower temperatures postpone amylopectin reduction and sugar interconversion, thereby preserving the sticky texture. Additionally, they suppress starch formation, delay starch metabolism, and elevate the expression of genes involved in starch metabolism. The correlation between gene expression and root texture indicates the critical role of gene regulation in enzyme activity during storage. Overall, low-temperature storage extends lotus root preservation by regulating metabolite content, enzyme activities, and the corresponding genes involved in starch metabolism, preserving both intrinsic and external root quality.