Sugarcane disease recognition through visible and near-infrared spectroscopy using deep learning assisted continuous wavelet transform-based spectrogram.

Utilizing visible and near-infrared (Vis-NIR) spectroscopy in conjunction with chemometrics methods has been widespread for identifying plant diseases. However, a key obstacle involves the extraction of relevant spectral characteristics. This study aimed to enhance sugarcane disease recognition by combining convolutional neural network (CNN) with continuous wavelet transform (CWT) spectrograms for spectral features extraction within the Vis-NIR spectra (380-1400 nm) to improve the accuracy of sugarcane diseases recognition. Using 130 sugarcane leaf samples, the obtained one-dimensional CWT coefficients from Vis-NIR spectra were transformed into two-dimensional spectrograms. Employing CNN, spectrogram features were extracted and incorporated into decision tree, K-nearest neighbour, partial least squares discriminant analysis, and random forest (RF) calibration models. The RF model, integrating spectrogram-derived features, demonstrated the best performance with an average precision of 0.9111, sensitivity of 0.9733, specificity of 0.9791, and accuracy of 0.9487. This study may offer a non-destructive, rapid, and accurate means to detect sugarcane diseases, enabling farmers to receive timely and actionable insights on the crops' health, thus minimizing crop loss and optimizing yields.

Corrigendum: Factors affecting the production of sugarcane yield and sucrose accumulation: suggested potential biological solutions.

[This corrects the article DOI: 10.3389/fpls.2024.1374228.].

Cloning, heterologous expression and characterization of ß-glucosidase deriving from Moniliophthora perniciosa (Stahel) Aime and Phillips Mora.

Β-glucosidase (BGLs) act synergistically with endoglucanases and exoglucanases and then are of great interest for biomass conversion into bioethanol. Thus, the aim of the current study is to produce a recombinant ß-glycosidase from Moniliophtora perniciosa expressed in Escherichia coli cells. Enzyme coding sequence expression was confirmed through Sanger sequencing after using wheat bran (WB) and carboxymethylcellulose (CMC) as fungal growth media. Synthetic gene betaglyc-GH1 with optimized codons for E. coli expression was cloned in pET-28a. ß-glucosidase recombinant (GH1chimera) was purified using a nickel column and its identity was confirmed through mass spectrometry. The recombinant enzyme presented an apparent molecular mass of 53.23 kDa on SDS-PAGE. Recombinant ß-glucosidase has shown hydrolytic activity using p-nitrophenyl-ß-D-glycopyranoside (pNPG) as substrate and maximum activity at pH 4.6 and 65 °C. Thus, the results indicate that the application of the GH1chimera in the hydrolysis of lignocellulosic materials to obtain glucose monomers can be efficient. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-024-04128-x.

CRISPR/Cas technology: fueling the future of Biofuel production with sugarcane.

The objective of present review is to provide a scientific overview of sugarcane as a potential feedstock for biofuel and use of genome editing approach for improvement of industrial and agronomical traits in sugarcane. Sugarcane, a perennial tropical grass with a high biomass index, is a promising feedstock for bioethanol production, and its bagasse, rich in lignocellulosic material, serves as an ideal feedstock for producing second-generation bioethanol. To improve the conversion of sugarcane biomass into biofuels, developing varieties with improved biomass degradability and high biomass and sucrose content is essential. The complex genome architecture and earlier lack of sequence data hindered biotechnological advancements in sugarcane, but recent genome sequence updates offer new opportunities for sugarcane improvement. The first genetically modified sugarcane was developed in 1992 by Bower and Birch using microprojectile bombardment of embryogenic callus. Since then, transgenic techniques have rapidly evolved, leading to the advancement of genome editing technologies. Application of genome editing tools particularly CRISPR/Cas system has been successfully used in sugarcane for editing. Recently, multiple alleles of the magnesium chelatase and acetolactate synthase genes in sugarcane have been successfully edited through multiplexing. Additionally, CRISPR-edited sugarcane varieties with modified cell wall components and increased sucrose content for enhanced bioethanol production have been developed. At the end, the future of CRISPR-edited crops will depend on how well regulatory frameworks adapt to the rapidly evolving technology.

A dual-mode strategy for early detection of sugarcane pokkah boeng disease pathogen: A portable sensing device based on Cross-N DNA framework and MoS2@GDY.

Sucrose, a common sugar primarily derived from sugarcane, is a crucial national strategic resource. However, its yield is significantly affected by various serious diseases, with pokkah boeng disease being one of the most damaging. Therefore, developing a sensitive method for the accurate detection of the pokkah boeng disease pathogen is crucial for ensuring the safety of sugar. This work presents a portable dual-modal detection device, assisted by a smartphone, which is based on MoS2@GDY, Mn3O4@Au nanomenzyme, cross-N DNA framework and Exo III exonuclease-assisted CHA signal amplification technology. The cross-N DNA framework provides many binding sites and is not restricted by AuNPs scattering positions, enhancing the signal output strength of the sensor. Additionally, the detection system incorporates a high-power-density capacitor to further amplify the electrochemical detection signal, increasing sensitivity by 9.1 times. Moreover, the use of electrochemical and colorimetric dual-mode detection effectively avoids mutual interference, reducing the likelihood of false positives from a single signal. Under optimized conditions, the proposed method has a linear range of 0.0001-10,000 pM, and with a detection limit of 6.1 aM (S/N=3). This high-sensitivity, high-reliability portable sensing method shows significant potential for the early detection and real-time on-site monitoring of the pokkah boeng disease pathogen.

Event-based biological pest control: An LMI approach.

This study focuses on the event-triggered control approach for the mathematical model describing the interaction between the sugarcane borer (Diatraea saccharalis) and its egg parasitoid Trichogramma galloi, as well as the combined interaction of Trichogramma galloi and Cotesia flavipes. By employing digital control design, an effective strategy can be devised to minimize the population of natural enemies. Therefore, proposing an event-triggered control mechanism for the sugarcane borer is essential. The primary objective of this study is to develop an event-triggered reliable state feedback controller, ensuring that the states of the sugarcane borer system converge to the desired steady-state equilibrium points. Additionally, this control design significantly reduces control updates and maintains the introduction of natural enemies into the environment. Ultimately, simulations are carried out using sugarcane borer systems to demonstrate the benefits and effectiveness of the proposed event-triggered design technique.

Comparison of Growth and Composition of Black Soldier Fly (Hermetia illucens L.) Larvae Reared on Sugarcane By-Products and Other Substrates.

Black soldier fly larvae (BSFL) can convert organic waste into high-quality biomass. In this study, we tested the potential of sugarcane by-products as a food source for BSFL and compared larval development and nutritional value with some other organic substrates. Seven different substrates were used, including carrot pomace (C), carrot pomace and leftover bread (CB) (50/50), bagasse and vinasse (BV), bagasse and molasses (BM), bagasse, vinasse, and molasses (BVM), a mixture of all the above treatments (MX), and university canteen leftovers (UCLs). The larval weight and length were measured for two weeks from day 5 to 19. Then, the BSFL were harvested and analyzed for dry matter, crude protein, oil, ash, mineral, and fatty acid composition. Larval weight and length varied depending on the feeding substrate provided. University canteen leftovers resulted in the BSFL having at least 18% greater length (17.00 mm) and 56% greater weight (3.15 g) compared to other treatments. The highest amounts of protein (38.9%) and oil (39.06%) were observed in the UCL treatment, while the BV treatment larvae had the highest quantities of ash (28.9%) and dry matter (28.0%). The fatty acid profile of the BSFL revealed three-times-higher levels of saturated fatty acids than unsaturated fatty acids in the UCL treatment and was at least twice as high in other treatments. Overall, the BSFL had the best growth on the UCL substrate, and the combination of bagasse and vinasse (BV) was the most appropriate substrate for BSFL development among the sugarcane by-products.

Exploring the Synergistic Secretome: Insights from Co-Cultivation of Aspergillus brasiliensis and Trichoderma reesei RUT-C30.

The spectrum of enzymes required for complete lignocellulosic waste hydrolysis is too diverse to be secreted by a single organism. An alternative is to employ fungal co-cultures to obtain more diverse and complete enzymatic cocktails without the need to mix enzymes during downstream processing. This study evaluated the co-cultivation of Aspergillus brasiliensis and Trichoderma reesei RUT-C30 in different conditions using sugarcane bagasse as the carbon source. The resulting enzymatic cocktails were characterized according to the impact of strain inoculation time on enzymatic activities and proteome composition. Data revealed that the profile of each enzymatic extract was highly dependent on the order in which the participating fungi were inoculated. Some of the co-cultures exhibited higher enzyme activities compared to their respective monocultures for enzymes such as CMCase, pectinase, ß-glucosidase, and ß-xylosidase. Analysis of the T. reesei RUT-C30 and A. brasiliensis co-culture secretome resulted in the identification of 167 proteins, with 78 from T. reesei and 89 from A. brasiliensis. In agreement with the enzymatic results, proteome analysis also revealed that the timing of inoculation greatly influences the overall secretome, with a predominance of T. reesei RUT-C30 proteins when first inoculated or in simultaneous inoculation.

Optimizing Sugarcane Clonal Propagation In Vitro by Using Calcium Ammonium Nitrate and Ammonium Sulfate.

To replace explosive nitrate-based chemicals in MS medium, this study developed a new, safer, and more cost-effective method using fertilizer-grade calcium ammonium nitrate and ammonium sulfate. This approach replaces ammonium nitrate and potassium nitrate, ensuring both safety and cost efficiency for sugarcane propagation. Six local sugarcane varieties-Zhongtang1 (ZT1), Zhongtang3 (ZT3), Zhongtang6 (ZT6), Guitang42 (GT42), Guitang44 (GT44), and Guiliu 07150 (GT07150)-were used. In the control group (Ck), nitrate ions (NO3-) were 39.28 mM, and ammonium ions (NH4+) were 20.49 mM, with a 2:1 ratio. In the treatment groups, the concentrations of nitrate ions (NO3-) and ammonium ions (NH4+) included treatment 1 (19.69 mM NO3- and 10.3 mM NH4+), treatment 2 (29.54 mM and 15.44 mM), treatment 3 (39.38 mM and 20.59 mM), treatment 4 (49.225 mM and 25.74 mM), treatment 5 (59.07 mM and 30.89 mM), and treatment 6 (68.915 mM and 36.03 mM), respectively, all with the same 2:1 ratio. Fifty bottles per treatment, with three replicates, were used for each sugarcane plantlets treatment. After five subcultures, the optimal ratio was determined by assessing morphological and physiological parameters, nitrogen levels, and SOD enzyme activity. The results indicated that treatment 3 (39.38 mM and 20.59 mM) and treatment 4 (49.225 mM and 25.74 mM) had the best morphological and physiological indicators. The optimal doses of calcium ammonium nitrate and ammonium sulfate were found in treatments 3 and 4, as well as in the control, with no significant difference among them. However, treatment 3, due to its lower dose, was more cost effective. To improve cost efficiency in practical production, it is recommended to use the lower concentration ratio of treatment 3 for plant tissue culture plantlets.

Boron Removal in Aqueous Solutions Using Adsorption with Sugarcane Bagasse Biochar and Ammonia Nanobubbles.

Boron is a naturally occurring trace chemical element. High concentrations of boron in nature can adversely affect biological systems and cause severe pollution to the ecological environment. We examined a method to effectively remove boron ions from water systems using sugarcane bagasse biochar from agricultural waste with NH3 nanobubbles (10% NH3 and 90% N2). We studied the effects of the boron solution concentration, pH, and adsorption time on the adsorption of boron by the modified biochar. At the same time, the possibility of using magnesium chloride and NH3 nanobubbles to enhance the adsorption capacity of the biochar was explored. The carbonization temperature of sugarcane bagasse was investigated using thermogravimetric analysis. It was characterized using XRD, SEM, and BET analysis. The boron adsorption results showed that, under alkaline conditions above pH 9, the adsorption capacity of the positively charged modified biochar was improved under the double-layer effect of magnesium ions and NH3 nanobubbles, because the boron existed in the form of negatively charged borate B(OH)4- anion groups. Moreover, cations on the NH3 nanobubble could adsorb the boron. When the NH3 nanobubbles with boron and the modified biochar with boron could coagulate each other, the boron was removed to a significant extent. Extended DLVO theory was adopted to model the interaction between the NH3 nanobubble and modified biochar. The boron adsorption capacity was 36 mg/g at room temperature according to a Langmuir adsorption isotherm. The adsorbed boron was investigated using FT-IR and XPS analysis. The ammonia could be removed using zeolite molecular sieves and heating. Boron in an aqueous solution can be removed via adsorption with modified biochar with NH3 nanobubbles and MgCl2 addition.

In-field carbon dioxide removal via weathering of crushed basalt applied to acidic tropical agricultural soil.

Enhanced weathering (EW) of silicate rocks such as basalt provides a potential carbon dioxide removal (CDR) technology for combatting climate change. Modelling and mesocosm studies suggest significant CDR via EW but there are few field studies. This study aimed to directly measure in-field CDR via EW of basalt applied to sugarcane on acidic (pH 5.8, 0-0.25 m) Ultisol in tropical northeastern Australia, where weathering potential is high. Coarsely crushed basalt produced as a byproduct of gravel manufacture (<5 mm) was applied annually from 2018 to 2022 at 0 or 50 t ha-1 a-1, incorporated into the soil in 2018 but not in subsequent years. Measurements in 2022 show increased soil pH and extractable Mg and Si at 0-0.25 m depth, indicating significant weathering of the basalt, but showed no increase in crop yield. Soil inorganic carbon content and bicarbonate (HCO3-) flux to deep drainage (1.25 m depth) were measured to quantify CDR in the 2022-2023 wet season (i.e. one year). Soil inorganic carbon was below detection limits. Mean HCO3- flux was 3.15 kmol ha-1 a-1 (±0.40) in the basalt-treated plots and 2.56 kmol ha-1 a-1 (±0.18) in the untreated plots but the difference (0.59 kmol ha-1 a-1 or 0.026 t CO2 ha-1 a-1) was not significant (p = 0.082). Most weathering of the basalt was attributed to acids stronger than carbonic acid. These were, in decreasing order of contribution, surface-bound protons (inherent soil acidity), nitric acid (from nitrification), organic acids, and acids associated with cation uptake by plants. These results indicate in-field CDR via EW of basalt is low where soil and regolith pH is well below the pKa1 of 6.4 for H2CO3. However, increased soil pH, and the consumption of strong acids by weathering will eventually lead to reduced CO2 emission from soil or evasion from rivers, with continued basalt addition.

Textural enhancement and glycemic potency reduction of sugarcane fiber-incorporated white bread with ascorbic acid and xanthan gum.

In this study, ascorbic acid (0.02 % w/w), xanthan (0.75 % or 1.5 % w/w), and their combination have been added into sugarcane fiber (SCF) incorporated (5 % or 10 % w/w) wheat flour-based white breads. The effects of different additives on the physical characteristics, and the in-vitro and in-vivo glycemic potency of breads were evaluated. Addition of xanthan alone and the combination of additives reduced hardness and increased specific volume. SEM images showed that xanthan caused larger, more uneven holes in breadcrumbs due to xanthan's high elasticity and viscosity. FTIR spectrum indicated that the combination of SCF, xanthan, and ascorbic acid resulted in higher ß-turn, lower α-helix protein structures, and lower ratios of α-helix/ß-sheet, indicating a more flexible gluten structure formed. In-vitro digestibility results suggested that all SCF-incorporated breads had a lower glycemic index (GI) value than reference. Samples with 0.02 % (w/w) ascorbic acid and 1.5 % (w/w) xanthan reported the lowest in-vitro and in-vivo GI values.

Impact of thermomechanical pretreatment by twin-screw extrusion on the properties of bio-based materials from sugarcane bagasse obtained by thermocompression.

The aim of this study was to produce binderless materials by thermocompression from lignocellulosic biomass pretreated using twin-screw extrusion. The impact of twin-screw extrusion pretreatment on sugarcane bagasse (SCB) was evaluated, along with the effects of two associated parameters: the liquid-to-solid (L/S) ratio and the screw profile, using three different mechanical shear rates. It was shown that twin-screw extrusion pretreatment resulted in materials with improved properties as compared to those obtained with untreated SCB. The mechanical properties and water resistance of materials obtained after pretreatment were mainly impacted by the screw profile. The flexural modulus increased from 5.3 to 6.1GPa and the flexural strength from 39.0 to 55.5 MPa. Water absorption (WA) from the thermocompressed materials ranged from 25 to 62 %, and thickness swelling (TS) from 24 to 67 %. Materials obtained with a 0.4 L/S ratio had lower flexural strength but the best water resistance. For the same L/S ratio, the use of a more shearing screw profile improved the material properties, especially the water resistance. The best material was produced with pretreated SCB using a 1.25 L/S ratio with the most restrictive screw profile, resulting in materials with a 5.6GPa flexural modulus, 55.5 MPa flexural strength, and WA and TS values of 44 % and 42 %, respectively.

A comparative evaluation of the composition and antioxidant activity of free and bound polyphenols in sugarcane tips.

The sugarcane tip is abundant in phenolic compounds. Previous studies have concentrated on the effects of free polyphenols, while bound polyphenols were overlooked. In this study, the content of bound polyphenols (SPB) (31.9 ± 0.9 mg GAE/g DW) was significantly higher than free polyphenols (SPF) (3.4 ± 0.1 mg GAE/g DW). A total of 44 free and 31 bound phenolics were identified by the UPLC-EIS-QTOF-MS/MS. Moreover, the antioxidant activity of SPB was more pronounced, as evidenced by its higher ABTS+ and DPPH scavenging rates than SPF, which was attributed to the higher tannin content. Furthermore, at all tested concentrations (100 and 200 µg/mL), SPB significantly enhanced the survival and antioxidant enzyme activity of Caenorhabditis elegans (C. elegans), while concurrently reducing ROS levels. High concentrations of SPB even exhibited antioxidant activity comparable to Vitamin C (Vc). The collective findings strongly indicate that SPB holds great potential as an effective antioxidant.

Sequencing vs. amplification for the estimation of allele dosages in sugarcane (Saccharum spp.).

Premise: Detecting single-nucleotide polymorphisms (SNPs) in a cost-effective way is fundamental in any plant breeding pipeline. Here, we compare three genotyping techniques for their ability to reproduce the allele dosage of SNPs of interest in sugarcane (Saccharum spp.). Methods: To identify a reproducible technique to estimate allele dosage for the validation of SNP markers, the correlation between Flex-Seq, kompetitive allele-specific PCR (KASP), and genotyping-by-sequencing and restriction site-associated DNA sequencing (GBS+RADseq) was determined for a set of 76 SNPs. To find alternative methodologies for allele dosage estimation, the KASP and Flex-Seq techniques were compared for the same set of SNPs. For the three techniques, a population of 53 genotypes from the diverse sugarcane panel of the Centro de Investigación de la Caña de Azúcar (Cenicaña), Colombia, was selected. Results: The average Pearson correlation coefficients between GBS+RADseq and Flex-Seq, GBS+RADseq and KASP, and Flex-Seq and KASP were 0.62 ± 0.27, 0.38 ± 0.27, and 0.38 ± 0.30, respectively. Discussion: Flex-Seq reproduced the allele dosages determined using GBS+RADseq with good levels of precision because of its depth of sequencing and ability to target specific positions in the genome. Additionally, Flex-Seq outperformed KASP by allowing the conversion of a higher number of SNPs and a more accurate estimation of the allele dosage. Flex-Seq has therefore become the genotyping methodology of choice for marker validation at Cenicaña.

Premisa: Detectar polimorfismos de un único nucleótido (SNP) de forma costo­efectiva es fundamental en cualquier programa de mejoramiento genético. En este artículo nosotros comparamos tres técnicas de genotipado para medir su habilidad en reproducir las dosis alélicas de SNPs de interés en caña de azúcar (Saccharum spp.). Métodos: Para identificar una técnica reproducible para la estimación de dosis alélicas durante los pasos de validación de marcadores, la correlación entre Flex­Seq, kompetitive allele­specific PCR (KASP), y genotyping­by­sequencing and restriction site­associated DNA sequencing (GBS+RADseq) fue determinada para un set de 76 SNPs. Para identificar metodologías alternativas en la estimación de las dosis alélicas, las tecnologías KASP y Flex­Seq fueron comparadas para el mismo grupo de SNPs. Para las tres técnicas, una población de 53 genotipos fue seleccionados de la población diversa de caña de azúcar del Centro de Investigación de la Caña de Azúcar (Cenicaña), Colombia. Resultados: El promedio del coeficiente de correlación de Pearson entre GBS+RADseq y Flex­Seq, GBS+RADseq y KASP, y Flex­Seq y KASP fue de 0.62 ± 0.27, 0.38 ± 0.27, y 0.38 ± 0.30, respectivamente. Discusión: Flex­Seq reprodujo las dosis alélicas determinadas usando GBS+RADseq con buenos niveles de precisión debido a su profundidad de secuenciación y habilidad de secuenciar posiciones especificas en el genoma. Adicionalmente, Flex­Seq superó a KASP al permitir la conversión de un número mayor de SNPs y al estimar las dosis alélicas de forma más precisa. Flex­Seq por tanto se convierte en la metodología de genotipado de elección para la validación de marcadores en Cenicaña.

Green synthesis of graphene oxide and magnetite nanoparticles and their arsenic removal efficiency from arsenic contaminated soil.

Graphene-based nanomaterials have been proved to be robust sorbents for efficient removal of environmental contaminants including arsenic (As). Biobased graphene oxide (bGO-P) derived from sugarcane bagasse via pyrolysis, GO-C via chemical exfoliation, and magnetite nanoparticles (FeNPs) via green approach using Azadirachta indica leaf extract were synthesized and characterized by Ultraviolet-Visible Spectrophotometer (UV-vis.), Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), mean particle size and Scanning electron microscopy (SEM) along with Energy dispersive spectroscopy (EDX) analysis. Compared to cellulose and hemicellulose, the lignin fraction was less in the precursor material. The GOC, bGO-P and FeNPs displayed maximum absorption at 230, 236, and 374 nm, respectively. FTIR spectrum showed different functional groups (C-OH, C-O-C, COOH and O-H) modifying the surfaces of synthesized materials. Graphene based nanomaterials showed clustered dense flakes of GO-C and thin transparent flakes of bGO-P. Elemental composition by EDX analysis of GO-C (71.26% C and 27.36% O), bGO-P (74.54% C and 24.61% O) and FeNPs (55.61% Fe, 4.1% C and 35.72% O) confirmed the presence of carbon, oxygen, and iron in synthesized nanomaterials. Sorption study was conducted with soil amended with different doses of synthesized nanomaterials (10, 50 and 250 mg) and exposed to 100, 300 and 500 ppm of As. Arsenic concentrations were estimated by colorimetry and atomic absorption spectroscopy (AAS). GO-C, bGO-P, and FeNPs showed substantial As removal efficiency i.e., 81 to 99.3%, 65 to 98.8% and 73.1-89.9%, respectively. Green synthesis of bGO-P and magnetite nanoparticles removed substantial amounts of As compared to GO-C and can be effectively deployed for As removal or immobilization. Higher and medium sorbent doses (250 and 50 mg) exhibited greater As removal and data was best fitted for Freundlich isotherm evidencing favorable sorption. Nevertheless, at low sorbent doses, data was best fitted for both models. Newly synthesized nanomaterials emerged as promising materials for As removal strategy for soil nano-remediation and can be effectively deployed in As contaminated soils.

Biohydrogen production from co-substrates through dark fermentation by bacterial consortium.

Hydrogen is a clean energy carrier that can be used as fuel for fuel cells. Dark fermentative biohydrogen production with other waste biomass needs to be explored as an alternative for sustainable biohydrogen production in future. In this study, lab-scale bioreactor were carried out to produce biohydrogen from co-substrates using bacterial consortium at 37 â„ƒ. For the experimental setup, a 1-L-working-volume reactor was used for biohydrogen production by bacterial monocultures and consortium on co-substrates. A batch experiment was performed at 37 °C with an initial pH of 7.0 and a mixing ratio of 600:300 between dairy whey and sugarcane bagasse. Total solids (TS), volatile solids (VS), total chemical oxygen demand (TCOD), soluble chemical oxygen demand (SCOD), and hydrogen production rate (HPR) were determined from co-substrates during the dark fermentation process. Morphologic changes of biohydrogen producing bacteria binds on co-substrates after the fermentation process were determined using SEM imaging. The bacteria can degrade the substrate when they attach to it causing hole formation and cracked the surface area. The level of biohydrogen production by bacterial consortium was observed and the results revealed a hydrogen production rate of 35.9 mL H2/L/h. In fermentative H2 production, it is quite similar to that of most H2-producing bacteria previously studied, especially that of the bacterial consortium, and this indicates that the attempt to find an outstanding bacterial strain for fermentative H2 production might be very difficult if not impossible.

Meta-analysis of ecological and phylogenetic biomass maturity metrics.

Although a wide variety of biomass sources have been subjected to 16S rRNA gene sequencing, ecological and phylogenetic signatures of maturity have not been identified quantitatively. In this meta-analysis we reanalyzed data from the only published study with publicly available 16S and temperature data (Zhou et al., 2018), and then applied the Zhou results to 705 samples from 13 additional studies. Using the Zhou data, we found that Faith's alpha diversity index correlated inversely with compost temperature and positively with maturity. We also noted a dramatic shift in the ratios of Bacilliota to Acidobacteriota, Planctomycetota, and Pseudomonadota, as samples cooled below 44 °C (p < 0.001). A negative correlation between Bacillota and Pseudomonadota was also observed in all 705 samples that included compost, sugarcane mill mud, anerobic digestates, and vermicompost. Even in the absence of temperature data for the majority of samples, our meta-analysis shows that microbiomes of diverse residuals converged on similar communities that resemble those of soil, regardless of the starting material or residual management process. We propose that approximately < 0.4 log(Bacillota:Pseudomonadota) and > 43 Faith's phylogenetic diversity indices are indicative of maturity of diverse biomass materials destined for land application.

Coexpression Regulation of New and Ancient Genes in the Dynamic Transcriptome Landscape of Stem and Rhizome Development in "Bainianzhe"-An Ancient Chinese Sugarcane Variety Ratooned for Nearly 300 Years.

The sucrose yield in sugarcane largely depends on stem morphology, including length, diameter and sugar content, making sugarcane stem a key trait in breeding. The "Bainianzhe" variety from Songxi County, Fujian Province, possesses both aerial stems and rhizomes, providing a unique model for studying stem development. We performed a spatiotemporal transcriptomic analysis of the base, middle and apical sections of both aerial stems and rhizomes. The analysis categorized transcriptomes by developmental stage-base, middle and apical-rather than environmental differences. Apical segments were enriched with genes related to cell proliferation, while base segments were linked to senescence and fibrosis. Gene regulatory networks revealed key TFs involved in stem development. Orphan genes may be involved in rhizome development through coexpression networks. Plant hormones, especially genes involved in ABA and GAs synthesis, were highly expressed in rhizomes. Thiamine-related genes were also more prevalent in rhizomes. Furthermore, the apical segments of rhizomes enriched in photosynthesis-related genes suggest adaptations to light exposure. Low average temperatures in Songxi have led to unique cold acclimation in Bainianzhe, with rhizomes showing higher expression of genes linked to unsaturated fatty acid synthesis and cold-responsive calcium signalling. This indicates that rhizomes may have enhanced cold tolerance, aiding in the plant's overwintering success.

Complete genome sequences of two Pantoea stewartii strains ATCC 8199 from maize and PSCN1 from sugarcane.

OBJECTIVES: The pathogen of Pantoea stewartii (Ps) is the causal agent of bacterial disease in corn and various graminaceous plants. Ps has two subspecies, Pantoea stewartii subsp. stewartia (Pss) and Pantoea stewartii subsp. indologenes (Psi). This study presents two complete genomes of Ps strains including ATCC 8199 isolated from maize and PSCN1 causing bacterial wilt in sugarcane. The two bacterial genomes information will be helpful for taxonomy analysis in this genus Pantoea at whole-genome levels and accurately discriminated the two subspecies of Pss and Psi. DATA DESCRIPTION: The reference strain ATCC 8199 isolated from maize was purchased from Beijing Biobw Biotechnology Co., Ltd. (China) and the strain of PSCN1 was isolated from sugarcane cultivar YZ08-1095 in Zhanjiang, Guangdong province of China. Two complete genomes were sequenced using Illumina Hiseq (second-generation) and Oxford Nanopore (third-generation) platforms. The genome of the strain ATCC 8199 comprised of 4.78 Mb with an average GC content of 54.03%, along with five plasmids, encoding a total of 4,846 gene with an average gene length of 827 bp. The genome of PSCN1 comprised of 5.03 Mb with an average GC content of 53.78%, along with two plasmids, encoding a total of 4,725 gene with an average gene length of 913 bp. The bacterial pan-genome analysis highlighted the strain ATCC 8199 was clustered into a subgroup with a Pss strain CCUG 26,359 from USA, while the strain PSCN1 was clustered into another subgroup with a Ps strain NRRLB-133 from USA. These findings will serve as a useful resource for further analyses of the evolution of Ps strains and corresponding disease epidemiology worldwide.