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Passionfruit (Passiflora edulis) is a significant fruit crop in the commercial sector, owing to its high nutritional and medicinal value. The advent of high-throughput genomics sequencing technology has led to the publication of a vast amount of passionfruit omics data, encompassing complete genome sequences and transcriptome data under diverse stress conditions. To facilitate the efficient integration, storage, and analysis of these large-scale datasets, and to enable researchers to effectively utilize these omics data, we developed the first passionfruit genome database (PGD). The PGD platform comprises a diverse range of functional modules, including a genome browser, search function, heatmap, gene expression patterns, various tools, sequence alignment, and batch download, thereby providing a user-friendly interface. Additionally, supplementary practical tools have been developed for the PGD, such as gene family analysis tools, gene ontology (GO) terms, a pathway enrichment analysis, and other data analysis and mining tools, which enhance the data's utilization value. By leveraging the database's robust scalability, the intention is to continue to collect and integrate passionfruit omics data in the PGD, providing comprehensive and in-depth support for passionfruit research. The PGD is freely accessible via http://passionfruit.com.cn. [ABSTRACT FROM AUTHOR]

Microbial communities and associated enzymes that hydrolyze lignocellulose in the presence of lignin decomposition products are important for industrial and environmental bioconversion processes. The aims of this study were to identify microorganisms capable of decomposing lignocellulose and tolerating lignin decomposition products under high-solids and thermophilic conditions, and to elucidate potential mechanisms of tolerance. High-solids incubations were conducted to enrich for thermophilic communities that decompose Douglas fir. Bacterial and fungal communities were determined using 16S rRNA and ITS region gene sequencing, and PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was applied to predict genes involved in lignocellulose degradation and tolerance to lignin decomposition products. Lignin decomposition increased with enrichment of specific microorganisms. The dominant bacterium identified with enrichment was from the genus Rubrobacter while the dominant fungus was from the genus Talaromyces . Bacteria containing predicted genes associated with lignin degradation and tolerance to breakdown products were identified. These included organisms from the genus Rubrobacter , and families Beijerinckiaceae and Xanthomonadaceae . The dominant bacteria and fungi identified may be promising sources of enzymes that degrade lignocellulose and genes that confer tolerance to lignin decomposition products. [ABSTRACT FROM AUTHOR]

Microorganisms involved in biomass deconstruction are an important resource for organic waste recycling and enzymes for lignocellulose bioconversion. The goals of this study were to examine the impact of nitrogen amendment on microbial community restructuring, secretion of xylanases and endoglucanases, and potential for biomass deconstruction. Communities were cultivated aerobically at 55 °C on green waste (GW) amended with varying levels of NH 4 Cl. Bacterial and fungal communities were determined using 16S rRNA and ITS region gene sequencing and PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was applied to predict relative abundance of genes involved in lignocellulose hydrolysis. Nitrogen amendment significantly increased secretion of xylanases and endoglucanases, and microbial activity; enzyme activities and cumulative respiration were greatest when nitrogen level in GW was between 4.13–4.56 wt% (g/g), but decreased with higher nitrogen levels. The microbial community shifted to one with increasing potential to decompose complex polymers as nitrogen increased with peak potential occurring between 3.79–4.45 wt% (g/g) nitrogen amendment. The results will aid in informing the management of nitrogen level to foster microbial communities capable of secreting enzymes that hydrolyze recalcitrant polymers in lignocellulose and yield rapid decomposition of green waste. [ABSTRACT FROM AUTHOR]

Chemical and physical pretreatment of biomass is a critical step in the conversion of lignocellulose to biofuels and bioproducts. Ionic liquid (IL) pretreatment has attracted significant attention due to the unique ability of certain ILs to solubilize some or all components of the plant cell wall. However, these ILs inhibit not only the enzyme activities but also the growth and productivity of microorganisms used in downstream hydrolysis and fermentation processes. While pretreated biomass can be washed to remove residual IL and reduce inhibition, extensive washing is costly and not feasible in large-scale processes. IL-tolerant microorganisms and microbial communities have been discovered from environmental samples and studies begun to elucidate mechanisms of IL tolerance. The discovery of IL tolerance in environmental microbial communities and individual microbes has lead to the proposal of molecular mechanisms of resistance. In this article, we review recent progress on discovering IL-tolerant microorganisms, identifying metabolic pathways and mechanisms of tolerance, and engineering microorganisms for IL tolerance. Research in these areas will yield new approaches to overcome inhibition in lignocellulosic biomass bioconversion processes and increase opportunities for the use of ILs in biomass pretreatment. [ABSTRACT FROM AUTHOR]

Abstract: Sugar beet pulp (SBP) as received has a fairly high moisture content of 75–85%, which makes SBP storage a challenge. Ensilage was studied over 90days and was found to effectively preserve SBP without lactic acid bacterium inoculation. Higher packing density yielded a slightly better silage quality. Ensilage improved sugar yield upon enzymatic hydrolysis of ensiled SBP washed with water. However, neither washing nor sterilization improved ethanol production from ensiled SBP using Escherichia coli KO11, suggesting ensiled SBP could be used directly in fermentation. The ethanol yield from ensiled SBP was nearly 50% higher than raw SBP. Fed-batch fermentation obtained approximately 30% higher ethanol yield than batch. Fed-batch could also be carried out at 12% solid loading with a 50% lower enzyme dosage compared to batch at the same solid loading, indicating opportunities to improve the economics of SBP conversion into liquid fuels. [Copyright &y& Elsevier]

Abstract: Ensiling was investigated for the long-term storage of Sugar Beet Pulp (SBP). Eight strains of lactic acid bacteria (LAB) and a non-inoculated control were screened based on their ability to rapidly reduce pH, produce a large amount of lactic acid and inhibit undesirable fermentations. Lactobacillus brevis B-1836 (LAB #120), Lactobacillus fermentum NRRL B-4524 (LAB #137) and a non-inoculated control were selected for further research to determine the effects of LAB inoculation level and packing density on SBP silage quality and sugar yield upon enzymatic hydrolysis. Both SBP preservation and prevention of cellulose and hemicellulose loss were better when SBP was treated with LAB #137 compared to LAB #120 and the non-inoculated control. Additionally, the ensiling process was found to significantly improve the enzymatic digestibility of SBP by as much as 35%. The results suggest that ensiling may be a promising technology for SBP stabilization and pretreatment for bioconversion to products. [ABSTRACT FROM AUTHOR]

Abstract: Leaching was studied for its application in extracting inorganic and organic constituents from fresh fermented grape pomace, air-dried fermented grape pomace and air-dried sugar beet pulp. Samples of each feedstock were leached in water at ambient temperature for 30 or 120min at dry solid-to-liquid ratios of 1/20 and 1/50kg/L. Leaching removed 82% of sodium, 86% of potassium, and 76% of chlorine from sugar beet pulp, and reduced total ash concentration in air-dry fermented grape pomace from 8.2% to 2.9% of dry matter, 8.2% to 4.4% in fresh fermented grape pomace, and 12.5% to 5.4% in sugar beet pulp. Glycerol (7–11mg/dry g), ethanol (131–158mg/dry g), and acetic acid (24–31mg/dry g) were also extracted from fermented grape pomace. These results indicate that leaching is a beneficial pretreatment step for improving the quality of food processing residues for thermochemical and biochemical conversion. [Copyright &y& Elsevier]

Abstract: Sugar beet pulp (SBP) is the residue of beet sugar processing and is a promising feedstock for fuel ethanol production. Response surface methodology was used to investigate the effects of temperature, acid concentration and solid loading on dilute sulfuric acid pretreatment and enzymatic hydrolysis of SBP. Mass balances on cellulose, hemicellulose, pectin, and protein were performed and sugar degradation products such as 5-hydroxymethylfurfural (HMF), furfural and acetic acid were monitored. Scanning electron microscopy was used to study changes in the physical structure of SBP upon pretreatment. Acid pretreatment increased the enzymatic digestibility of SBP from 33% (raw) to 93% (treated). Pretreatment at optimum conditions (temperature=120°C, acid concentration=0.66% and solid loading=6%) resulted in 93% enzymatic hydrolysis yield and 62% total reducing sugar yield. The ethanol yield from pretreated SBP under the optimum conditions was 0.4g ethanol/g dry matter in a simultaneous saccharification and fermentation (SSF) process employing Escherichia coli KO11. [Copyright &y& Elsevier]

We characterised the virus-derived small interfering RNAs (vsiRNA) of bamboo mosaic virus (Ba-vsiRNAs) and its associated satellite RNA (satRNA)-derived siRNAs (satsiRNAs) in a bamboo plant ( Dendrocalamus latiflorus) by deep sequencing. Ba-vsiRNAs and satsiRNAs of 21-22 nt in length, with both (+) and (-) polarity, predominated. The 5′-terminal base of Ba-vsiRNA was biased towards A, whereas a bias towards C/U was observed in sense satsiRNAs, and towards A in antisense satsiRNAs. A large set of bamboo genes were identified as potential targets of Ba-vsiRNAs and satsiRNAs, revealing RNA silencing-based virus-host interactions in plants. Moreover, we isolated and characterised new isolates of bamboo mosaic virus (BaMV; 6,350 nt) and BaMV-associated satRNA (satBaMV; 834 nt), designated BaMV-MAZSL1 and satBaMV-MAZSL1, respectively. [ABSTRACT FROM AUTHOR]

The complete genome sequences of three isolates of bamboo mosaic virus (BaMV) from mainland China were determined and compared to those of BaMV isolates from Taiwan. Sequence analysis showed that isolate BaMV-JXYBZ1 from Fuzhou shares 98 % nucleotide sequence identity with BaMV-YTHSL14 from nucleotides 2586 to 6306, and more than 94 % nucleotide sequence identity with BaMV-MUZHUBZ2 in other regions. Recombination and phylogenetic analyses indicate that BaMV-JXYBZ1 is a recombinant with one recombination breakpoint. To our knowledge, this is the first report of a BaMV recombinant worldwide. [ABSTRACT FROM AUTHOR]