Dictyophora indusiata and Bacillus aryabhattai improve sugarcane yield by endogenously associating with the root and regulating flavonoid metabolism.

Introduction: Endophytes play a significant role in regulating plant root development and facilitating nutrient solubilization and transportation. This association could improve plant growth. The present study has uncovered a distinct phenotype, which we refer to as "white root", arising from the intricate interactions between endophytic fungi and bacteria with the roots in a sugarcane and bamboo fungus (Dictyophora indusiata) intercropping system. Methods: We investigated the mechanisms underlying the formation of this "white root" phenotype and its impact on sugarcane yield and metabolism by metabarcoding and metabolome analysis. Results and Discussion: Initial analysis revealed that intercropping with D. indusiata increased sugarcane yield by enhancing the number of viable tillers compared with bagasse and no input control. Metabarcoding based on second-generation and third-generation sequencing indicated that D. indusiate and Bacillus aryabhattai dominates the fungal and bacterial composition in the "white root" phenotype of sugarcane root. The coexistence of D. indusiata and B. aryabhattai as endophytes induced plant growth-promoting metabolites in the sugarcane root system, such as lysoPC 18:1 and dihydrobenzofuran, probably contributing to increased sugarcane yield. Furthermore, the association also enhanced the metabolism of compounds, such as naringenin-7-O-glucoside (Prunin), naringenin-7-O-neohesperidoside (Naringin)*, hesperetin-7-O-neohesperidoside (Neohesperidin), epicatechin, and aromadendrin (Dihydrokaempferol), involved in flavonoid metabolism during the formation of the endophytic phenotype in the sugarcane root system. These observations suggest that the "white root" phenotype promotes sugarcane growth by activating flavonoid metabolism. This study reports an interesting phenomenon where D. indusiata, coordinate with the specific bacteria invade, forms a "white root" phenotype with sugarcane root. The study also provides new insights into using D. indusiata as a soil inoculant for promoting sugarcane growth and proposes a new approach for improve sugarcane cultivation.

A Highly Integrated Lab-on-a-CMOS Platform for Real-Time Monitoring of E. Coli Growth Kinetics.

Existing miniaturized and cost-effective solutions for bacterial growth monitoring usually require offline incubators with constant temperature to culture the bio-samples prior to measurement. Such a separated sample preparation and detection scheme requires extensive human intervention, risks contamination, and suffers from poor temporal resolution. To achieve integrated sample preparation and real-time bacterial growth monitoring, this article presents a lab-on-a-CMOS platform incorporates an optical sensor array, temperature sensor array, micro-heaters, and readout circuits. Escherichia coli's (E. coli) optimum growth temperature of 37 °C is achieved through a heat regulation system consisting of two micro-heaters and an on-chip temperature sensor array. A photodiode array with an in-pixel capacitive trans-impedance amplifier to reduce inter-pixel cross-coupling is designed to extract the optical information during bacterial growth. To balance the footprint, power consumption, and quantization speed, a 10 b column successive-approximation register (SAR)/single-slope (SS) dual-mode analog-to-digital converter (ADC) is designed to digitize the temperature and optical signals. Fabricated in a standard 0.18 um CMOS process, the proposed platform can regulate the sample temperature to 37 +/- 0.2/0.3 °C within 32 mins. Enabled by an on-chip heat regulation system and photodetectors, the prototype demonstrates a real-time monitoring of bacterial growth kinetics and antibiotic responses. Minute-level temporal resolution is achieved as this proposed platform is free of extensive and time-consuming human intervention. The proposed platform can be viably used in contamination sensitive applications such as antibiotic tests, stem cell cultures, and organ-on-chips.

Morchella esculenta cultivation in fallow paddy fields and drylands affects the diversity of soil bacteria and soil chemical properties.

The properties of paddy field (DT) and dry land (HD) soil and food production can be enhanced by the cultivation of Morchella esculenta (ME) during the fallow period. However, whether ME cultivation affects the soil health and microbial diversity of paddy fields and drylands during the cultivation period remains unclear, and this has greatly limited the wider use of this cultivation model. Here, we analyzed the soil chemical properties and bacterial diversity (via metabarcoding sequencing) of DT and HD soils following ME cultivation. Our findings indicated that ME cultivation could enhance soil health. The content of soil phosphorus and potassium (K) was increased in DT soil under ME cultivation, and the K content was significantly higher in HD soil than in DT soil under ME cultivation. ME cultivation had a weak effect on alpha diversity, and ME cultivation affected the abundance of some genera of soil bacteria. The cultivation of ME might reduce the methane production capacity of DT soil and enhance the nitrogen cycling process of HD soil based on the results of functional annotation analysis. Network analysis and correlation analysis showed that Gemmatimonas, Bryobacter, and Anaeromyxobacter were the key bacterial genera regulating soil chemical properties in DT soil under ME cultivation, and Bryobacter, Bacillus, Streptomyces, and Paenarthrobacter were the key taxa associated with the accumulation of K in HD soil. The results of our study will aid future efforts to further improve this cultivation model.

Soil chemistry, metabarcoding, and metabolome analyses reveal that a sugarcane-Dictyophora indusiata intercropping system can enhance soil health by reducing soil nitrogen loss.

Introduction: Greater amounts of fertilizer are applied every year to meet the growing demand for food. Sugarcane is one of the important food sources for human beings. Methods: Here, we evaluated the effects of a sugarcane-Dictyophora indusiata (DI) intercropping system on soil health by conducting an experiment with three different treatments: (1) bagasse application (BAS process), (2) bagasse + DI (DIS process), and (3) the control (CK). We then analyzed soil chemistry, the diversity of soil bacteria and fungi, and the composition of metabolites to clarify the mechanism underlying the effects of this intercropping system on soil properties. Results and discussion: Soil chemistry analyses revealed that the content of several soil nutrients such as nitrogen (N) and phosphorus (P) was higher in the BAS process than in the CK. In the DIS process, a large amount of soil P was consumed by DI. At the same time, the urease activity was inhibited, thus slowing down the loss of soil in the DI process, while the activity of other enzymes such as ß-glucosidase and laccase was increased. It was also noticed that the content of lanthanum and calcium was higher in the BAS process than in the other treatments, and DI did not significantly alter the concentrations of these soil metal ions. Bacterial diversity was higher in the BAS process than in the other treatments, and fungal diversity was lower in the DIS process than in the other treatments. The soil metabolome analysis revealed that the abundance of carbohydrate metabolites was significantly lower in the BAS process than in the CK and the DIS process. The abundance of D(+)-talose was correlated with the content of soil nutrients. Path analysis revealed that the content of soil nutrients in the DIS process was mainly affected by fungi, bacteria, the soil metabolome, and soil enzyme activity. Our findings indicate that the sugarcane-DIS intercropping system can enhance soil health.

Genome, transcriptome, and metabolome analyses provide new insights into the resource development in an edible fungus Dictyophora indusiata.

Dictyophora indusiata (Vent. Ex Pers.) Fisch. (DI) is an edible and medicinal fungus widely used in East Asian countries. However, during DI cultivation, the formation of fruiting bodies cannot be regulated, which leads to yield and quality losses. The present study performed a combined genome, transcriptome, and metabolome analysis of DI. Using Nanopore and Illumina sequencing approaches, we created the DI reference genome, which was 67.32 Mb long with 323 contigs. We identified 19,909 coding genes on this genome, of which 46 gene clusters were related to terpenoid synthesis. Subsequent transcriptome sequencing using five DI tissues (cap, indusia, mycelia, stipe, and volva) showed high expression levels of genes in the cap, indicating the tissue's importance in regulating the fruiting body formation. Meanwhile, the metabolome analysis identified 728 metabolites from the five tissues. Mycelium was rich in choline, while volva was rich in dendronobilin; stipe had monosaccharides as the primary component, and the cap was the main source of indole acetic acid (IAA) synthesis. We confirmed the importance of tryptophan metabolism for DI fruiting body differentiation based on KEGG pathway analysis. Finally, the combined multiomics analysis identified three new genes related to IAA synthesis of the tryptophan metabolic pathway in the cap, which may regulate DI fruiting body synthesis and improve DI quality. Thus, the study's findings expand our understanding of resource development and the molecular mechanisms underlying DI development and differentiation. However, the current genome is still a rough draft that needs to be strengthened.

Sugarcane Wax Metabolites and Their Toxicity to Silkworms.

Sugarcane wax has the potential to be utilized as a novel natural insecticide, which could help to reduce the large yield losses caused by agricultural pests. By employing the gas chromatography-mass spectrometry (GC-MS) approach, we conducted a study to analyze the composition of epicuticular wax from the rind of the sugarcane variety YT71210. A total of 157 metabolites, categorized into 15 classes, were identified, with naphthalene, a metabolite with insect-resistant properties, being the most prevalent. The feeding trial experiment suggested that sugarcane wax is toxic to silkworms by impacting the internal organs. Intestinal microbial diversity analysis suggested that the abundance of Enterococcus genus was significantly increased in both ordure and gut of silkworm after wax treatment. The results indicated that the feeding of wax has an adverse effect on the gut microbial composition of silkworms. Our findings lay a foundation for the efficacy of sugarcane waxes as a valuable natural insecticide and for the prediction of promising sugarcane varieties with insect resistance.

Assessment of the rhizosphere fungi and bacteria recruited by sugarcane during smut invasion.

Whip smut is one of the most serious and widely spread sugarcane diseases. Plant-associated microbes play various roles in conferring advantages to the host plant. Understanding the microbes associated with sugarcane roots will help develop strategies for the biocontrol of smut. Therefore, the present study explored microbe-mediated sugarcane response to smut invasion via 16S rRNA and ITS metabarcoding survey of the rhizosphere soils of resistant and susceptible sugarcane varieties. The bacterial and fungal diversity in the rhizosphere soils differed between the resistant and susceptible varieties. The bacterial genera Sphingomonas, Microcoleus_Es-Yyy1400, Marmoricola, Reyranella, Promicromonospora, Iamia, Phenylobacterium, Aridibacter, Actinophytocola, and Edaphobacter and one fungal genus Cyphellophora were found associated with smut resistance in sugarcane. Detailed analysis revealed that the majority of bacteria were beneficial, including the actinomycete Marmoricola and Iamia and Reyranella with denitrification activity. Analysis of bacterial network interaction showed that three major groups interacted during smut invasion. Meanwhile, seven of these genera appeared to interact and promote each other's growth. Finally, functional annotation based on the Functional Annotation of Prokaryotic Taxa (FAPROTAX) database predicted that the abundant bacteria are dominated by oxygenic photoautotrophy, photoautotrophy, and phototrophy functions, which may be related to smut resistance in sugarcane. The present study thus provides new insights into the dynamics of the sugarcane rhizosphere microbial community during smut invasion.

A high-throughput lipidomics and transcriptomic approach reveals novel compounds from sugarcane linked with promising therapeutic potential against COVID-19.

Sugarcane (Saccharum ssp., Poaceae) provides enormous metabolites such as sugars, lipid, and other dietary metabolites to humans. Among them, lipids are important metabolites that perform various functions and have promising pharmacological value. However, in sugarcane, few studies are focusing on lipidomics and few lipid compounds were reported, and their pharmacological values are not explored yet. The transcriptomic and widely targeted lipidomics approach quantified 134 lipid compounds from the rind of six sugarcane genotypes. These lipid compounds include 57 fatty acids, 30 lysophosphatidylcholines, 23 glycerol esters, 21 lysophosphatidylethanolamines, 2 phosphatidylcholines, and 1 sphingolipid. Among them, 119 compounds were first time reported in sugarcane rind. Seventeen lipids compounds including 12 fatty acids, 2 glycerol lipids, LysoPC 16:0, LysoPE 16:0, and choline alfoscerate were abundantly found in the rind of sugarcane genotypes. From metabolic and transcriptomic results, we have developed a comprehensive lipid metabolic pathway and highlighted key genes that are differentially expressed in sugarcane. Several genes associated with α-linolenic acid and linoleic acid biosynthesis pathways were highly expressed in the rind of the ROC22 genotype. ROC22 has a high level of α-linolenic acid (an essential fatty acid) followed by ROC16. Moreover, we have explored pharmacological values of lipid compounds and found that the 2-linoleoylglycerol and gingerglycolipid C have strong binding interactions with 3CLpro of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) and these compounds can be utilized against SARS-CoV-2 as therapeutic agents. The transcriptome, metabolome, and bioinformatics analysis suggests that the sugarcane cultivars have a diversity of lipid compounds having promising therapeutic potential, and exploring the lipid metabolism will help to know more compounds that have promising cosmetic and pharmacological value.

Metabarcoding and Metabolome Analyses Reveal Mechanisms of Leymus chinensis Growth Promotion by Fairy Ring of Leucocalocybe mongolica.

Fairy rings are a unique ecological phenomenon caused by the growth of the fungal mycelium in the soil. Fairy rings formed by Leucocalocybe mongolica (LM) are generally distributed in the Mongolian Plateau, where they promote plant growth without fertilization and alleviate fertilizer use. We previously investigated the soil factors regulating growth promotion in a fairy ring ecosystem; however, the aspects of the plant (Leymus chinensis, LC) that promote growth have not been explored. Therefore, the present study investigated the endophyte diversity and metabolome of LC in an LM fairy ring ecosystem. We analyzed the leaf and root samples of LC from the DARK (FR) and OUT (CK) zones. The fairy rings significantly improved the fungal diversity of roots and leaves and the bacterial diversity of leaves in the FR zone. Ralstonia was the dominant bacteria detected in the LC leaves. In addition, Marasmius, another fairy ring fungal genus, was also detected with a high abundance in the roots of the FR zone. Furthermore, widely targeted metabolome analysis combined with KEGG annotation identified 1011 novel metabolites from the leaves and roots of LC and seven pathways significantly regulated by the fairy ring in the FR zone. The fairy ring ecosystem significantly downregulated the flavonoid metabolism in the leaves and roots of LC. The correlation analysis found Ralstonia is a potential regulatory factor of flavonoid biosynthesis in LC. In addition, salicylic acid and jasmonic acid were found upregulated in the leaves, probably related to Marasmius enrichment. Thus, the study details plant factors associated with enhanced growth in an LM fairy ring ecosystem. These findings lay a theoretical foundation for developing the fairy ring ecosystem in an agricultural system.

A Novel Design Nomogram for Optimization of Micro Search Coil Magnetometer for Energy Monitoring in Smart Buildings.

In this paper, a new analytical method to achieve the maximum signal-to-noise ratio (SNR) of a micro search coil magnetometer (µSCM) is presented. A planar spiral inductor was utilized to miniaturize conventional bulky search coil magnetometers. First, dimensional analysis was applied to identify three dimensionless parameters for the µSCM's key performance indices (sensitivity (Se), noise, and SNR). The effect of the parameters on the µSCM's performance was carefully investigated, and a novel 4D nomogram was developed. Furthermore, an SNR analysis considering noise sources of a low-noise amplifier was performed. By combining the results from the nomogram and the effect of the noise sources from the amplifier circuit, optimum values for the dimensionless parameters were calculated. According to the calculation results, the dominant noise source varied with an increase in the track width ratio to the outer diameter. Seven different samples were fabricated by a single-mask lithography process. The sensitivity of 1612 mV/mT was demonstrated at a 50 Hz input magnetic field, which was better than the previous µSCM (Se = 6.5 mV/mT) by more than 2 orders of magnitude. Finally, one of the fabricated µSCMs was employed to measure the online power consumption of a personal computer while different types of software were running.

Soil Chemical Properties, Metabolome, and Metabarcoding Give the New Insights into the Soil Transforming Process of Fairy Ring Fungi Leucocalocybe mongolica.

A unique ecological landscape distributed in the Mongolian Plateau, called fairy rings, caused by the growth of the fungus Leucocalocybe mongolica (LM) in the soil could promote plant growth without fertilization. Therefore, this landscape can alleviate fertilizer use and has excellent value for agricultural production. The previous studies only investigated several parameters of the fairy rings, such as soil microbial diversity and some soil chemical properties, thus conclusions based on the studies on fairy rings lack comprehension. Therefore, the present study systematically investigated the chemical properties, metabolome, and metabarcoding of LM-transformed soil. We analyzed fairy ring soils from DARK (FR) and OUT (CK) zone correlated growth promotion with ten soil chemical properties, including N, nitrate-N, inorganic-P, cellulose, available boron, available sulfur, Fe, Mn, Zn, and Cu, which were identified as important markers to screen fairy ring landscapes. Metabolomics showed that the accumulation of 17 carbohydrate-dominated metabolites was closely associated with plant growth promotion. Finally, metabarcoding detected fungi as the main components affecting soil conversion. Among the various fungi at the family level, Lasiosphaeriaceae, unidentified_Auriculariales_sp, and Herpotrichiellaceae were markers to screen fairy ring. Our study is novel and systematically reveals the fairy ring soil ecology and lists the key factors promoting plant growth. These findings lay a theoretical foundation for developing the fairy ring landscape in an agricultural system.

Transcriptomic and Widely Targeted Metabolomic Approach Identified Diverse Group of Bioactive Compounds, Antiradical Activities, and Their Associated Genes in Six Sugarcane Varieties.

Sugarcane is cultivated mainly for its high sucrose content but it can also produce many metabolites with promising antioxidant potential. However, very few studies have been reported on the biosynthesis of metabolites in sugarcane to date. In this study, we have identified a wide range of amino acids and organic acids in the rind of six sugarcane varieties by the LC-MS/MS method. A total number of 72 amino acids and 55 organic acid compounds were characterized; among these, 100 were reported for the first time. Moreover, 13 amino acids and seven organic acids were abundantly distributed in all varieties tested and considered major amino acids and organic acids in sugarcane. The variety Taitang134 (F134) showed the highest content of total amino acids, whereas the varieties ROC16 and Yuetang93/159 (YT93/159) had maximum content of organic acids. The amino acids of the rind extract presented higher antioxidant capacity than the organic acids of the rind extract. In addition, the transcriptomic and metabolic integrated analysis highlighted some candidate genes associated with amino acid biosynthesis in sugarcane. We selected a transcription factor gene, MYB(t), and over-expressed it in Arabidopsis. The transgenic plants showed a higher accumulation of amino acids with higher antiradical activity compared with the wild-type Arabidopsis plants. Thus, we characterize a wide range of amino acids and organic acids and their antiradical activities in different sugarcane varieties and present candidate genes that can be potentially valuable for the genetic improvement of metabolites in sugarcane bagasse.

LC-MS/MS-based metabolomics approach revealed novel phytocompounds from sugarcane rind with promising pharmacological value.

BACKGROUND: Sugarcane provides many secondary metabolites for the pharmacological and cosmetic industries. Secondary metabolites, such as phenolic compounds, flavonoids, and anthocyanins, have been studied, but few reports focus on the identification of alkaloid and non-alkaloid phytocompounds in sugarcane. RESULTS: In this study, we identified 40 compounds in total from the rinds of cultivated sugarcane varieties (including eight alkaloids, 24 non-alkaloids, and eight others) by using the liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach. Among these compounds, 31 were novel and are reported for the first time in sugarcane. Some alkaloids such as 3-indoleacrylic acid, N,N-dimethyl-5-methoxytryptamine, tryptamine, 6-hydroxynicotinic acid, and 6-deoxyfagomine are identified the first time in sugarcane rind. Four alkaloids such as trigonelline, piperidine, 3-indoleacrylic acid, and 6-deoxyfagomine are found abundantly in sugarcane rind and these compounds have promising pharmaceutical value. Some phytocompounds such as choline and acetylcholine (non-alkaloid compounds) were most common in the rind of ROC22 and Yuetang93/159 (YT93/159). Hierarchical cluster analysis and principal component analysis revealed that the ROC22, Taitang172 (F172), and Yuetang71/210 (YT71/210) varieties were quite similar in alkaloid composition when compared with other sugarcane varieties. We have also characterized the biosynthesis pathway of sugarcane alkaloids. The rind of F172, ROC22, and YT71/210 showed the highest total alkaloid content, whereas the rind of ROC16 revealed a minimum level. Interestingly, the rind extract from YT71/210 and F172 showed maximum antioxidant activity, followed by ROC22. CONCLUSION: Our results showed the diversity of alkaloid and non-alkaloid compounds in the rind of six cultivated sugarcanes and highlighted the promising phytocompounds that can be extracted, isolated, and utilized by the pharmacological industry. © 2022 Society of Chemical Industry.

Antioxidant Metabolites in Primitive, Wild, and Cultivated Citrus and Their Role in Stress Tolerance.

The genus Citrus contains a vast range of antioxidant metabolites, dietary metabolites, and antioxidant polyphenols that protect plants from unfavorable environmental conditions, enhance their tolerance to abiotic and biotic stresses, and possess multiple health-promoting effects in humans. This review summarizes various antioxidant metabolites such as organic acids, amino acids, alkaloids, fatty acids, carotenoids, ascorbic acid, tocopherols, terpenoids, hydroxycinnamic acids, flavonoids, and anthocyanins that are distributed in different citrus species. Among these antioxidant metabolites, flavonoids are abundantly present in primitive, wild, and cultivated citrus species and possess the highest antioxidant activity. We demonstrate that the primitive and wild citrus species (e.g., Atalantia buxifolia and C. latipes) have a high level of antioxidant metabolites and are tolerant to various abiotic and biotic stresses compared with cultivated citrus species (e.g., C. sinensis and C. reticulata). Additionally, we highlight the potential usage of citrus wastes (rag, seeds, fruit peels, etc.) and the health-promoting properties of citrus metabolites. Furthermore, we summarize the genes that are involved in the biosynthesis of antioxidant metabolites in different citrus species. We speculate that the genome-engineering technologies should be used to confirm the functions of candidate genes that are responsible for the accumulation of antioxidant metabolites, which will serve as an alternative tool to breed citrus cultivars with increased antioxidant metabolites.

The Divergent Roles of the Rice bcl-2 Associated Athanogene (BAG) Genes in Plant Development and Environmental Responses.

Bcl-2-associated athanogene (BAG), a group of proteins evolutionarily conserved and functioned as co-chaperones in plants and animals, is involved in various cell activities and diverse physiological processes. However, the biological functions of this gene family in rice are largely unknown. In this study, we identified a total of six BAG members in rice. These genes were classified into two groups, OsBAG1, -2, -3, and -4 are in group I with a conserved ubiquitin-like structure and OsBAG5 and -6 are in group Ⅱ with a calmodulin-binding domain, in addition to a common BAG domain. The BAG genes exhibited diverse expression patterns, with OsBAG4 showing the highest expression level, followed by OsBAG1 and OsBAG3, and OsBAG6 preferentially expressed in the panicle, endosperm, and calli. The co-expression analysis and the hierarchical cluster analysis indicated that the OsBAG1 and OsBAG3 were co-expressed with primary cell wall-biosynthesizing genes, OsBAG4 was co-expressed with phytohormone and transcriptional factors, and OsBAG6 was co-expressed with disease and shock-associated genes. ß-glucuronidase (GUS) staining further indicated that OsBAG3 is mainly involved in primary young tissues under both primary and secondary growth. In addition, the expression of the BAG genes under brown planthopper (BPH) feeding, N, P, and K deficiency, heat, drought and plant hormones treatments was investigated. Our results clearly showed that OsBAGs are multifunctional molecules as inferred by their protein structures, subcellular localizations, and expression profiles. BAGs in group I are mainly involved in plant development, whereas BAGs in group II are reactive in gene regulations and stress responses. Our results provide a solid basis for the further elucidation of the biological functions of plant BAG genes.

An Optical and Temperature Assisted CMOS ISFET Sensor Array for Robust E. Coli Detection.

Both bacterial viability and concentration are significant metrics for bacterial detection. Existing miniaturized and cost-effective single-mode sensor, pH or optical, can only be skilled at detecting single information viability or concentration. This paper presents an inverter-based CMOS ion-sensitive-field-effect-transistor (ISFET) sensor array, featuring bacterial pH detection which is an indicator of viability. The proposed design realizes pH detection using the native passivation layer of CMOS process as a sensing layer and configuring an inverter-based front-end as a capacitive feedback amplifier. This sensor array is assisted by temperature sensing and optical detection which reveals bacterial concentration. The optical detection is enabled using the leakage current of a reset switch as a response to a light source. While in reset mode, the inverter-based amplifier works as a temperature sensor that could help to reduce temperature influences on pH and optical detection. All the functionalities are realized using one single inverter-based amplifier, resulting in a compact pixel structure and largely relaxed design complexity for the sensor system. Fabricated in 0.18 µm standard CMOS process, the proposed CMOS sensor array system achieves an amplified pH sensitivity of 221 mV/pH, an improved sensor resolution of 0.03 pH through systematic noise optimization, a linear optical response, and a maximum temperature error of 0.69 °C. The sensing capabilities of the proposed design are demonstrated through on-chip Escherichia coli (E. coli) detection. This study may be extended to a rapid and cost-effective platform that renders multiple information of bacterial samples.

Grassland fairy rings of Leucocalocybe mongolica represent the center of a rich soil microbial community.

BACKGROUND: The ecological phenomenon of fungal fairy rings is usually found in grasslands and caused by the growth of specific fairy ring fungi in soil. The fairy rings are classified into three zones (DARK, DEAD, and OUT), and they have the potential to increase crop yield. Among these fairy rings, distinct characteristics of type I fairy rings can be seen in the rings formed by Leucocalocybe mongolica (LM). Our studies addressed changes in the soil microbial structure due to LM fairy rings to enhance understand of this ecological phenomenon. METHODS: In the present study, we report the soil microbial analysis results (fungi and bacteria), including those of metabarcoding (16s rRNA, ITS), microbial quantity, and metagenomics surveys of soils collected from various fairy ring zones, of 6 LM fairy rings. All sampling sites cover the grasslands of Mongolian Plateau in China. RESULTS: First, we found through metabarcoding surveys that the difference in microbial diversity is relatively less in bacteria and that the abundance of fairy ring fungi (LM) is relatively high in DEAD zones. We also identified eight bacterial and fungal families, including Sphingobacteriaceae and Sphingomonadaceae that were enriched within the soils of fairy ring zones. Second, we found that the abundance of soil bacteria in the DEAD zones is sharply increased along with the growth of fairy ring fungi (LM). Third, we found through shotgun sequencing that fairy ring-infected zones, DARK and DEAD, exhibit greater genetic diversity than OUT zones. Finally, we showed that the fairy ring ecosystem is the center for a rich grassland microbial community. CONCLUSIONS: The reported data can improve our understanding of type I fairy rings and will be further insightful to the research on crop production.

Analyses of transcriptomes and the first complete genome of Leucocalocybe mongolica provide new insights into phylogenetic relationships and conservation.

In this study, we report a de novo assembly of the first high-quality genome for a wild mushroom species Leucocalocybe mongolica (LM). We performed high-throughput transcriptome sequencing to analyze the genetic basis for the life history of LM. Our results show that the genome size of LM is 46.0 Mb, including 26 contigs with a contig N50 size of 3.6 Mb. In total, we predicted 11,599 protein-coding genes, of which 65.7% (7630) could be aligned with high confidence to annotated homologous genes in other species. We performed phylogenetic analyses using genes form 3269 single-copy gene families and showed support for distinguishing LM from the genus Tricholoma (L.) P.Kumm., in which it is sometimes circumscribed. We believe that one reason for limited wild occurrences of LM may be the loss of key metabolic genes, especially carbohydrate-active enzymes (CAZymes), based on comparisons with other closely related species. The results of our transcriptome analyses between vegetative (mycelia) and reproductive (fruiting bodies) organs indicated that changes in gene expression among some key CAZyme genes may help to determine the switch from asexual to sexual reproduction. Taken together, our genomic and transcriptome data for LM comprise a valuable resource for both understanding the evolutionary and life history of this species.

Novel Insights into Anthocyanin Metabolism and Molecular Characterization of Associated Genes in Sugarcane Rinds Using the Metabolome and Transcriptome.

Saccharum officinarum (sugarcane) is the fifth major cultivated crop around the world. Sugarcane rind is a promising source for anthocyanin pigments; however, limited information is available on the anthocyanin and its biosynthesis in sugarcane rinds. In this study, we have quantified 49 compounds including 6 flavonoids and 43 anthocyanins in the rind of 6 sugarcane cultivars by using LCMS/MS approach. Thirty of them were quantified for the first time in sugarcane. The 43 anthocyanins included 10 cyanidin (Cya), 11 pelargonidin (Pel), 9 peonidin (Peo), 5 malvidin (Mal), 4 delphinidin (Del), and 4 petunidin (Pet) metabolites. High contents of Cya derivatives were observed in the rind of YT71/210 (dark purple rind), such as cya-3-O-(6-O-malonyl)-glu 1283.3 µg/g and cya-3-O-glu 482.67 µg/g followed by ROC22 (red rind) 821.3 µg/g and 409 µg/g, respectively, whereas the YT93/159 (green rind) showed a minimum level of these compounds. Among six cultivars, ROC22 rind has high levels of Peo derivatives such as peo-3-O-glu (197 µg/g), peo-3-O-(6-O-malonyl)-glu (69 µg/g) and peo-3-O-(6-O-p-coumaryl)-glu (55.17 µg/g). The gene expression analysis revealed that some genes, including a MYB(t) gene, were highly associated with the color phenotype. Thus, we cloned and overexpressed the gene in Arabidopsis and found the pinkish brown color in the hypocotyl of all transgenic lines compared with the wild type. Hence, we have quantified a wide range of anthocyanins in major sugarcane cultivars, reported many new anthocyanins for the first time, and concluded that Cya and Peo derivatives are the major contributing factor of dissimilar colors in sugarcane. The finding and the verification of a novel MYB gene involved in anthocyanin biosynthesis have demonstrated that our study was very valuable for gene discovery and genetic improvement of sugarcane cultivars to harvest high anthocyanin contents.

A High Offset Distribution Tolerance High Resolution ISFET Array With Auto-Compensation for Long-Term Bacterial Metabolism Monitoring.

This paper presents a CMOS ion-sensitive-field-effect-transistor (ISFET) array with superior offset distribution tolerance, resolution and linearity for long-term bacterial metabolism monitoring. A floating gate ISFET is adopted as the sensing front end to maximize ion sensitivity and support ultra-long-term measurement. To solve the DC offset issue induced by trapped chargers and drifts in each ISFET sensor, a complementary readout scheme with column offset compensation is proposed. P-type and N-type source followers are combined to cover a wide range of input DC offsets while maintaining small area and high linearity. The DC offset is digitally compensated during signal readout to facilitate global amplification and quantization. Fabricated in 0.18 µm standard CMOS process, the ISFET array can tolerate an offset distribution beyond power supply with a linear pH-to-output response. Due to high ion sensitivity and low circuit noise, the whole system achieves a high resolution of 0.017 pH. The proposed ISFET system has successfully demonstrated an accurate pH monitoring of normal Escherichis coli growth for 11 hours and its response to antibiotics, showing long-term bacterial metabolism monitoring capability.