Article
Agricultural Engineering
Meera Christopher, Athiraraj Sreeja-Raju, Meena Sankar, Digambar Vitthal Gokhale, Ashok Pandey, Rajeev K. Sukumaran
Summary: Improving ligninase activity of the hypercellulolytic fungus Penicillium janthinellum NCIM 1366 may help enhance hydrolysis efficiency. Additionally, larger pore sizes and higher crystallinity of substrates positively influence enzyme penetration and processive hydrolysis, contributing to improved hydrolysis efficiency. A correlation analysis identified 41 proteins, including 20 CAZymes, as primary drivers of cellulase activity in Penicillium janthinellum NCIM 1366.
BIORESOURCE TECHNOLOGY
(2022)
Review
Microbiology
Hayat Hage, Marie-Noelle Rosso
Summary: Fungi play a crucial role in the postindustrial era by reducing CO2 emissions and optimizing waste utilization. They utilize carbohydrate-active enzymes to process plant waste, contributing to both CO2 assimilation and emissions.
Article
Biochemistry & Molecular Biology
Shuang Hu, Rui Zhu, Xing-Ye Yu, Bao-Teng Wang, Hong-Hua Ruan, Feng-Jie Jin
Summary: Recent studies have focused on the degradation of plant cell wall polysaccharides by fungal extracellular enzymes. In this study, a strain of Penicillium oxalicum with strong xylanase-producing ability was isolated and its genome was sequenced. The analysis revealed the presence of various carbohydrate-active enzymes (CAZymes) encoding genes involved in the degradation of plant cell wall components, particularly cellulose and hemicellulose.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Marion Coluccia, Ludovic Besaury
Summary: Through bioinformatics analysis, we found that the Acidobacteria phylum has a high abundance and diversity of carbohydrate-active enzyme families and secreted peptidase families, which play important roles in the degradation of plant biomass, explaining the high abundance of Acidobacteria in the environment.
MOLECULAR GENETICS AND GENOMICS
(2023)
Article
Agricultural Engineering
Shuai Zhao, Rong-Ming Mai, Ting Zhang, Xiang-Zhao Feng, Wen-Tong Li, Wen-Xuan Wang, Xue-Mei Luo, Jia-Xun Feng
Summary: Genetic engineering can effectively improve the production of plant-biomass degrading enzymes by fungi. In this study, the transcription repressor CxrC and the translational elongation factor eEF1A were identified as key targets for enhancing enzyme production. Manipulating these genes resulted in significantly higher enzyme production.
BIORESOURCE TECHNOLOGY
(2022)
Article
Microbiology
Ruba A. Ashy, Rewaa S. Jalal, Hana S. Sonbol, Mashael D. Alqahtani, Fatmah O. Sefrji, Sahar A. Alshareef, Fatimah M. Alshehrei, Haneen W. Abuauf, Lina Baz, Manal A. Tashkandi, Israa J. Hakeem, Mohammed Y. Refai, Aala A. Abulfaraj
Summary: The study aimed to investigate the genes encoding CAZymes and other KEGG enzymes in the phageome of soil rhizosphere of M. oleifera. The abundance of these genes was higher in the rhizospheric microbiome than in the bulk soil. Detected viral families include Potyviridae and Caudoviricetes, which are mainly associated with bacterial genera Pseudomonas, Streptomyces, and Mycobacterium.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Dae Yeon Kim, Myoung-Jun Jang, Youn-Jin Park, Jae Yoon Kim
Summary: Lentinula edodes is an edible mushroom rich in polysaccharides, glucan, and lentinan, known for its unique flavor. This study examined the morphological changes and global gene expression patterns of L. edodes under blue light, revealing differences in pileus diameter growth and stipe length under different light sources. Upregulated genes related to lignocellulose, CAZyme, and transcription factors were identified in response to blue light, contributing to a better understanding of fruit body development and complex carbohydrate metabolism in mushroom-breeding programs.
APPLIED SCIENCES-BASEL
(2021)
Article
Biotechnology & Applied Microbiology
Xiao-Ming Pang, Di Tian, Ting Zhang, Lu-Sheng Liao, Cheng-Xi Li, Xue-Mei Luo, Jia-Xun Feng, Shuai Zhao
Summary: This study found that GNG-1 modulates the expression of genes encoding PBDEs and sporulation-related activators in Penicillium oxalicum. Further research showed that CxrB can indirectly regulate the transcription levels of key amylase genes.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Food Science & Technology
Jiayu Zhou, Weifeng Gong, Tingting Tu, Jiaqi Zhang, Xiaoshuang Xia, Luning Zhao, Xinghua Zhou, Yun Wang
Summary: In this study, the researchers identified 212 and 268 candidate effector protein genes of P. expansum during infection of apple fruits by using RNA-Seq analysis and computational prediction. One of the candidate genes, Peclg, was induced significantly during the pathogen-host interaction. Knockout of Peclg gene resulted in reduced conidial production and germination, increased sensitivity to salt stress, SDS and Congo red, and decreased pathogenicity and infectious growth on apple fruits.
Article
Biochemistry & Molecular Biology
Lakshan Paudel, Bashu Dev Pardhe, So-Ra Han, Jun Hyuck Lee, Tae-Jin Oh
Summary: The genomic analysis of Streptomyces sp. KCCM12257 identified 233 CAZyme genes, with a predominant glycosyl hydrolase family. Among them, a new chitosanase (MDI5907146) of GH46 family was characterized, which showed activity towards colloidal chitosan. The enzyme hydrolyzes colloidal chitosan into monoacetyl chitobiose and exhibits optimum activity at pH 6.5 and 40 degrees C.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biotechnology & Applied Microbiology
Bo Ma, Yuan-Ni Ning, Cheng-Xi Li, Di Tian, Hao Guo, Xiao-Ming Pang, Xue-Mei Luo, Shuai Zhao, Jia-Xun Feng
Summary: Mitogen-activated protein kinase (MAPK) cascades are highly conserved and play important roles in various cellular processes in fungi. In Penicillium oxalicum, a deletion of the gene Fus3/Kss1-like PoxMK1 resulted in a significant reduction in cellulase and plant-biomass-degrading enzyme (PBDE) production, as well as altered vegetative growth and pigment biosynthesis. Comparative transcriptomic and phosphoproteomic analyses provided new insights into the regulation of PBDE gene expression in fungi.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Maria Soledad Vela Gurovic, Marina Lucia Diaz, Cristian Andres Gallo, Julian Dietrich
Summary: A phylogenomic study using various bioinformatic tools identified a high rate of misidentified Streptomyces albus genomes in GenBank. The pangenome of the confirmed S. albus genomes was almost closed, showing conservation in enzymes related to lignocellulose degradation. The core genome of S. albus revealed a high potential for discovering novel bioactive metabolites and regulatory genomic elements related to lignocellulose deconstruction.
MOLECULAR GENETICS AND GENOMICS
(2021)
Article
Agronomy
Meiqiu Xu, Esa Abiso Godana, Solairaj Dhanasekaran, Xiaoyun Zhang, Qiya Yang, Lina Zhao, Hongyin Zhang
Summary: Penicillium expansum causes economic losses by causing blue mold disease in pears during storage and transportation. The defense mechanisms of pears against P. expansum are not well understood, limiting the progress in control strategies. This study used transcriptome and proteome approaches to evaluate the defense mechanisms of pears against P. expansum and identified significantly enriched genes/proteins related to metabolic processes and plant hormones. The findings contribute to the development of strategies for controlling fungal diseases.
POSTHARVEST BIOLOGY AND TECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Jan H. Nagel, Michael J. Wingfield, Bernard Slippers
Summary: The genomes of Botryosphaeriaceae fungi are rich in carbohydrate-active enzymes, proteases, lipases, and secondary metabolic biosynthetic gene clusters compared to other Dothideomycete genomes. These genomes also have moderate to high GC contents and low levels of repetitive DNA. The abundance of secreted hydrolytic enzymes and secondary metabolite biosynthetic gene clusters in the genomes of Botryosphaeria, Macrophomina, Lasiodiplodia, and Neofusicoccum suggest similarities to necrotrophic plant pathogens and endophytes of woody plants.
Article
Chemistry, Applied
Yalan Wu, Yufang Gao, Xiaodong Zheng, Ting Yu, Fujie Yan
Summary: This study found that GlcNAc significantly improved the antagonistic efficacy of Kluyveromyces marxianus against Penicillium expansum by increasing biocontrol-related enzymes and stress-resistant substances. GlcNAc also enhanced the antioxidative-related enzyme activities and proliferative capacity of K. marxianus, contributing to its environmental adaptability and stress resistance.
Review
Agricultural Engineering
Xinxin Li, Adiphol Dilokpimol, Mirjam A. Kabel, Ronald P. de Vries
Summary: Fungi are important polysaccharide degraders in nature, and they can diversify their carbohydrate-active enzyme combinations to survive in different ecological habitats. This review summarizes the current knowledge on substrate specificity of xylanolytic enzymes and the diversity of enzyme sets in fungi, and reviews the industrial applications of fungal xylanolytic enzymes.
BIORESOURCE TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Nancy Coconi Linares, Xinxin Li, Adiphol Dilokpimol, Ronald P. de Vries
Summary: The fungus Penicillium subrubescens has more alpha-L-arabinofuranosidase-encoding genes compared to other Penicillia, with nine ABFs from GH families GH51, GH54, and GH62 showing highly diverse specificity and activity levels. However, the substrate preference of the enzymes did not correlate with the expression of the corresponding genes, suggesting a complex regulatory system governing L-arabinose release from plant biomass by P. subrubescens.
Article
Biochemistry & Molecular Biology
Adiphol Dilokpimol, Bart Verkerk, Xinxin Li, Annie Bellemare, Mathieu Lavallee, Matthias Frommhagen, Emilie Normolle Underlin, Mirjam A. Kabel, Justin Powlowski, Adrian Tsang, Ronald P. de Vries
Summary: In this study, ten novel fungal CE1 enzymes from different subfamilies were heterologously produced and screened for their activity towards model and complex plant biomass substrates. The study found CE1 enzymes with dual feruloyl/acetyl xylan esterase (FXE) activity, expanding the substrate specificity. These new FXEs from CE1 can efficiently release both feruloyl and acetyl residues from feruloylated xylan, making them potentially valuable components in industrial enzyme cocktails for plant biomass degradation.
Article
Biochemical Research Methods
Xinxin Li, Dimitrios Kouzounis, Mirjam A. Kabel, Ronald P. de Vries, Adiphol Dilokpimol
Summary: Efficient bioconversion of agro-industrial side streams requires a wide range of enzyme activities. This study focused on the GH30 family of enzymes and identified novel enzyme activities within this diverse family. A phylogenetic tree was constructed, showing that GH30 enzymes cluster into four subfamilies with distinct polysaccharide specificities and high potential for the production of short non-digestible di- and oligosaccharides.
Article
Biotechnology & Applied Microbiology
Jiali Meng, Zoltan Nemeth, Mao Peng, Erzsebet Fekete, Sandra Garrigues, Anna Lipzen, Vivian Ng, Emily Savage, Yu Zhang, Igor Grigoriev, Miia R. Makela, Levente Karaffa, Ronald P. de Vries
Summary: In this study, the interaction between GalX, GalR, and AraR in the catabolism of d-galactose and l-arabinose was investigated in filamentous fungi. The results clearly demonstrated that GalX, GalR, and AraR co-regulate the catabolism of d-galactose in Aspergillus nidulans, with GalX playing a prominent role in gene regulation and AraR compensating for the absence of GalR and/or GalX.
MICROBIAL BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Mila Marinovic, Marcos Di Falco, Maria Victoria Aguilar Pontes, Andras Gorzsas, Adrian Tsang, Ronald P. de Vries, Miia R. Makela, Kristiina Hilden
Summary: The unique ability of basidiomycete white rot fungi to degrade all components of plant cell walls makes them essential in the global carbon cycle. This study analyzed the proteomes of two closely related white rot fungi during cultivation on solid spruce wood, revealing specific enzymes produced during the degradation process. These findings provide valuable insights into enzyme production in nature and their potential use in biotechnological applications.
Article
Biochemical Research Methods
Felipe Andres Venegas, Sanna Koutaniemi, Sandra M. J. Langeveld, Annie Bellemare, Sun-Li Chong, Adiphol Dilokpimol, Michael J. Lowden, Kristiina S. Hilden, Juan Francisco Leyva-Illades, Miia R. Makela, Thi Thanh My Pham, Mao Peng, Mark A. Hancock, Yun Zheng, Adrian Tsang, Maija Tenkanen, Justin Powlowski, Ronald P. de Vries
Summary: Acetyl esterases are important enzymes for fungi to degrade plant biomass. This study identified four CE16 members in the genome of Aspergillus niger NRRL3, showing diverse substrate specificity. One of the enzymes (HaeA) demonstrated activity on various oligosaccharides, making it a promising candidate for biotechnological applications.
Article
Biochemistry & Molecular Biology
Jiali Meng, Miia R. Maekelae, Ronald P. de Vries
Summary: In this study, an l-arabitol transporter, LatA, was identified in Aspergillus niger. It was found that LatA only imports l-arabitol and is regulated by the arabinanolytic transcriptional activator AraR. Deletion of latA can increase l-arabitol production, indicating its potential for improving l-arabitol-producing cell factories. Phylogenetic analysis showed that homologs of LatA are widely conserved in fungi.
Article
Microbiology
Jiajia Li, Tania Chroumpi, Sandra Garrigues, Roland S. Kun, Jiali Meng, Sonia Salazar-Cerezo, Maria Victoria Aguilar-Pontes, Yu Zhang, Sravanthi Tejomurthula, Anna Lipzen, Vivian Ng, Chaevien S. Clendinen, Nikola Tolic, Igor Grigoriev, Adrian Tsang, Miia R. Makela, Berend Snel, Mao Peng, Ronald P. de Vries
Summary: Fungi play a critical role in the global carbon cycle by degrading plant polysaccharides to small sugars and metabolizing them as carbon and energy sources. This study mapped the sugar metabolic network of Aspergillus niger to other fungi species and found that the diversity of sugar metabolism is correlated with taxonomic distance. Integrative analysis of transcriptome, proteome, and metabolome confirmed these results and provided a valuable resource for rational metabolic engineering.
Article
Microbiology
Mao Peng, Sander Bervoets, Thommas Chin-A-Woeng, Zoraide Granchi, Kristiina Hilden, Miia R. Makela, Ronald P. de Vries
Summary: The study compared the transcriptome profiles of two white-rot wood-decay fungi, Trametes pubescens and Phlebia centrifuga, under different temperature and carbon source conditions. The results showed that both fungi exhibited different molecular responses to different environmental conditions, with Trametes pubescens expressing more genes related to lignin modification and Phlebia centrifuga showing stronger ability to adapt to temperature fluctuations.
MICROBIOLOGICAL RESEARCH
(2023)
Article
Microbiology
Roland S. Kun, Sonia Salazar-Cerezo, Mao Peng, Yu Zhang, Emily Savage, Anna Lipzen, Vivian Ng, Igor V. Grigoriev, Ronald P. de Vries, Sandra Garrigues
Summary: This study deepened the understanding of the storage polysaccharide regulators AmyR and InuR in Aspergillus niger by assessing the phenotypes and transcriptomic data of different strains under various culture conditions. The results showed that AmyR has a minor contribution to sucrose and inulin utilization when InuR is active, and deletion of amyR in the Delta inuR background strain resulted in pronounced growth reduction on both substrates, particularly in solid cultures. Overall, the study highlights the importance of culture conditions in accurately studying the role of transcription factors in filamentous fungi.
Article
Microbiology
Jiajia Li, Ad Wiebenga, Anna Lipzen, Vivian Ng, Sravanthi Tejomurthula, Yu Zhang, Igor V. Grigoriev, Mao Peng, Ronald P. de Vries
Summary: This study systematically compared the genomic content and transcriptional dynamics of carbohydrate-active enzymes (CAZymes) in six taxonomically distant fungal species during growth on nine monosaccharides. It identified considerable genomic variation and remarkable transcriptomic diversity of CAZymes, implying the preferred carbon source of these fungi and their different methods of transcription regulation.
Article
Agricultural Engineering
Li Xu, Jiajia Li, Victor M. Gonzalez Ramos, Christina Lyra, Ad Wiebenga, Igor V. Grigoriev, Ronald P. de Vries, Miia R. Makela, Mao Peng
Summary: This study presents a comparative analysis of sugar transporters (STs) in four filamentous fungi, revealing their diversity at the genomic/transcriptomic level and showing complex regulation patterns. The findings provide valuable insights into the function of STs and their potential applications in metabolic engineering.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Yinping Xiang, Meiying Jia, Rui Xu, Jialu Xu, Lele He, Haihao Peng, Weimin Sun, Dongbo Wang, Weiping Xiong, Zhaohui Yang
Summary: This study investigated the impact of the non-antibiotic pharmaceutical carbamazepine on antibiotic resistance genes (ARGs) during anaerobic digestion. The results showed that carbamazepine induced the enrichment of ARGs and increased the abundance of bacteria carrying these genes. It also facilitated microbial aggregation and intercellular communication, leading to an increased frequency of ARGs transmission. Moreover, carbamazepine promoted the acquisition of ARGs by pathogens and elevated their overall abundance.
BIORESOURCE TECHNOLOGY
(2024)
Review
Agricultural Engineering
Weixin Zhao, Tianyi Hu, Hao Ma, Dan Li, Qingliang Zhao, Junqiu Jiang, Liangliang Wei
Summary: This review summarizes the effects and potential mechanisms of biochar on microbial behavior in AD systems. The addition of biochar has been found to promote microbial colonization, alleviate stress, provide nutrients, and enhance enzyme activity. Future research directions include targeted design of biochar, in-depth study of microbial mechanisms, and improved models.
BIORESOURCE TECHNOLOGY
(2024)
Review
Agricultural Engineering
Christina Karmann, Anna Magrova, Pavel Jenicek, Jan Bartacek, Vojtech Kouba
Summary: This review assesses nitrogen removal technologies in reject water treatment, highlighting the differences in environmental impacts and economic benefits. Partial nitritation-anammox shows potential for economic benefits and positive environmental outcomes when operated and controlled properly.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Wei-Hao Huang, Ying-Ju Chang, Duu-Jong Lee
Summary: This study modified pinecone biochar with layered double hydroxide (LDH) to enhance its adsorption capacity for heavy metal and phosphate ions. The LDH-biochar showed significantly improved adsorption capacities for Pb2+ and phosphate, and a slight increase for Cu2+ and Co2+. The LDH layer enhanced the adsorption through various mechanisms.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Chao Song, Fanfan Cai, Shuang Yang, Ligong Wang, Guangqing Liu, Chang Chen
Summary: This paper developed a machine learning model to predict the biochemical methane potential during anaerobic digestion. Model analysis identified lignin content, organic loading, and nitrogen content as key attributes for methane production prediction. For feedstocks with high cellulose content, early methane production is lower but can be improved by prolonging digestion time. Moreover, lignin content exceeding a certain value significantly inhibits methane production.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Sang Min Lee, Ju Young Lee, Ji-Sook Hahn, Seung-Ho Baek
Summary: This study successfully developed an efficient platform strain using Yarrowia lipolytica for the bioconversion of renewable resources into adipic acid, achieving a remarkable increase in production level.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Sefkan Kendir, Matthias Franzreb
Summary: This study presents a novel approach using magnetic separation to efficiently harvest freshwater microalgae, Chlorella vulgaris. By combining pH-induced calcium phosphate precipitation with cheap natural magnetite microparticles, harvesting efficiencies up to 98% were achieved in the model medium.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Ishaq Kariim, Ji-Yeon Park, Wajahat Waheed Kazmi, Hulda Swai, In-Gu Lee, Thomas Kivevele
Summary: The impact of reaction temperature, residence time, and ethanol: acetone on the energy compositions and yield enhancement of biocrudes was investigated. The results showed that under appropriate conditions, biocrudes with high energy and low oxygen content can be obtained, indicating a high potential for utilization.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Xiyue Zhang, Xiyao Li, Liang Zhang, Yongzhen Peng
Summary: Intermittent aeration is an innovative approach to enhance nitrogen removal in low carbon-to-nitrogen ratio municipal sewage, providing an efficient strategy for the continuous plug-flow AOA process.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Xu Yang, Mahmoud Mazarji, Mengtong Li, Aohua Li, Ronghua Li, Zengqiang Zhang, Junting Pan
Summary: This study investigated the impact of magnetite on the nitrogen cycle of pig manure biostabilisation. The addition of magnetite increased N2O emissions and decreased NH3 emissions during composting. It also increased the total nitrogen content but should be considered for its significant increase in N2O emissions in engineering practice.
BIORESOURCE TECHNOLOGY
(2024)
Review
Agricultural Engineering
Ty Shitanaka, Haylee Fujioka, Muzammil Khan, Manpreet Kaur, Zhi-Yan Du, Samir Kumar Khanal
Summary: The market value of microalgae has exponentially increased in the past two decades, thanks to their applications in various industries. However, the supply of high-value microalgal bioproducts is limited due to several factors, and strategies are being explored to overcome these limitations and improve microalgae production, thus increasing the availability of algal-derived bioproducts in the market.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Martin Kerner, Thorsten Wolff, Torsten Brinkmann
Summary: The efficiency of using enriched CO2 from flue gas for large-scale production of green microalgae has been studied. The results show that the use of membrane devices and static mixers can effectively improve the CO2 recovery rate and maintain the suitable pH and temperature during cultivation, achieving a more economical and sustainable microalgae production.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Rui Ma, Ji Li, Rd Tyagi, Xiaolei Zhang
Summary: This review summarizes the microorganisms capable of using CO2 and CH4 to produce PHAs, illustrating the production process, factors influencing it, and discussing optimization techniques. It identifies the challenges and future prospects for developing economically viable PHAs production using GHGs as a carbon source.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Bing Wang, Peng Zhang, Xu Guo, Xu Bao, Junjie Tian, Guomin Li, Jian Zhang
Summary: The addition of zeolite in the co-composting of chicken manure and straw significantly reduced the emissions of ammonia and N2O, and increased the nitrate content. Zeolite also promoted the abundance of nitrification genes and inhibited the expression of denitrification genes.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Rohit Dey, Franziska Ortiz Tena, Song Wang, Josef Martin Messmann, Christian Steinweg, Claudia Thomsen, Clemens Posten, Stefan Leu, Matthias S. Ullrich, Laurenz Thomsen
Summary: This study investigated the operation of a 1000L microalgae-based membrane photobioreactor system for continuous secondary wastewater treatment. The research focused on a green microalgae strain called Desmodesmus sp. The study aimed to understand key trends and optimization strategies by conducting experiments in both summer and winter seasons. The findings showed that maintaining low cell concentrations during periods of light inhibition was beneficial for nutrient uptake rates. Effective strategies for enhancing algae-based wastewater treatment included cell mass recycling and adjusting dilution rates based on light availability.
BIORESOURCE TECHNOLOGY
(2024)
