Article
Ecology
Ashish B. B. George, Tong Wang, Sergei Maslov
Summary: The dynamics of microbial communities are influenced by competition for resources and cross-feeding. A new model incorporating energetic and thermodynamic constraints reveals that microbial growth can be limited not only by depletion of resources but also by accumulation of byproducts. This model explains the convergence in community structure and function, providing a possible explanation for functional convergence in microbial communities.
Article
Agricultural Engineering
Nathan Innard, James P. J. Chong
Summary: Mixed anaerobic microbial communities play a key role in valorizing waste biomass through anaerobic digestion, and are important in soil and animal microbiomes. Understanding interactions between individual species within these communities is crucial for improving the performance and potential applications of green technology. The challenges associated with assessing the status of anaerobic microbial communities, incorporating measurements into control philosophies, and enhancing their potential to produce higher value products from waste materials are discussed.
BIORESOURCE TECHNOLOGY
(2022)
Review
Environmental Sciences
Anna Christine Trego, Simon Mills, Gavin Collins
Summary: Anaerobic digestion is recognized as a sustainable method for waste management, producing methane-rich biogas. Different specialized granules, including anaerobic and aerobic granules, have opened up new opportunities in wastewater treatment and resource recovery biotechnology. Each type of granule has unique characteristics, biochemical processes, and microbial community compositions.
CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY
(2021)
Article
Agricultural Engineering
Han Wang, Qun Yan, Xiaoqian Zhong, Irini Angelidaki, Ioannis A. Fotidis
Summary: Anaerobic co-digestion is a strategy for increasing methane production, but substrates rich in proteins and lipids can cause a synergetic co-inhibition effect. This study explored the microbial mechanisms behind the co-inhibition effect and found that ammonia played a major role in affecting methanogens. Decreased abundances of certain microorganisms and critical enzymes confirmed the synergetic co-inhibition effect.
BIORESOURCE TECHNOLOGY
(2023)
Article
Environmental Sciences
Gowtham Balasundaram, Rajesh Banu, Sunita Varjani, A. A. Kazmi, Vinay Kumar Tyagi
Summary: This paper provides a comprehensive review of the formation of recalcitrant compounds during feedstocks pretreatment and their detrimental effects on process performance in sustainable energy production. Technologies to mitigate recalcitrant toxicity are also comprehensively discussed.
Article
Agricultural Engineering
Wei Peng, Zhijie Wang, Yinhui Shu, Fan Lu, Hua Zhang, Liming Shao, Pinjing He
Summary: This study assessed the degradation of PBAT/PLA based biopolymer bags during digestion processes, finding no biological degradation after digestion but subsequent aerobic treatment facilitated the degradation of polymers.
BIORESOURCE TECHNOLOGY
(2022)
Article
Agricultural Engineering
Haiquan Dong, Liangchen Yue, Jun Cheng, Rongxin Xia, Junhu Zhou
Summary: Microbial electro-chemical degradation was proposed to enhance methane production from lipids in anaerobic digestion. Applying a voltage strengthened the beta-oxidation of lipids, promoting electron transfer and methane yield. The overall energy conversion efficiency in methane production increased due to microbial electrochemical degradation of lipids.
BIORESOURCE TECHNOLOGY
(2022)
Article
Engineering, Environmental
Valeria Alvarado, Shu-Chien Hsu, Zhuoying Wu, Huichuan Zhuang, Po-Heng Lee, Jeremy S. Guest
Summary: Biological models of anaerobic digestion have been used to test control strategies. This study developed a novel microbial individuality model that identified the importance of homoacetogenesis in anaerobic digestion.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Shah Faisal, Nandini Thakur, Mohammed Jalalah, Farid A. Harraz, Mohammad Sultan Al-Assiri, Irfan Saif, Gohar Ali, Yuanzhang Zheng, El-Sayed Salama
Summary: This review discusses the applications and challenges of lignocellulosic biomass in anaerobic digestion, proposes potential strategies to improve process stability, and delves into the key microbes involved in lignocellulosic biomass degradation.
JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY
(2021)
Article
Environmental Sciences
E. Ortega-Martinez, R. Chamy, D. Jeison
Summary: Thermal hydrolysis as a pre-treatment can enhance hydrolysis rate before anaerobic digestion, but inhibitory compounds and increased liquid fraction colour may be potential drawbacks. This study found that different temperatures led to different outcomes, with a decrease in biogas production rate at 120 degrees C and generation of recalcitrant material at 165 degrees C, causing a decrease in methane potential and COD degradation.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2021)
Article
Environmental Sciences
Zhaodi Guo, Mohammed Jalalah, Saeed A. Alsareii, Farid A. Harraz, Nandini Thakur, El-Sayed Salama
Summary: This study investigated the effects of adding different proportions of biochar on biogas production, volatile fatty acids (VFAs), microbial communities, and enzymes. The results showed that 0.5% biochar significantly increased biogas and VFAs production, and also promoted the abundance of specific bacteria and archaea and the activities of corresponding enzymes under certain conditions.
Article
Environmental Sciences
Lingjiao Kong, Xianyang Shi
Summary: This study investigated the effects of three antibiotic mixtures on the performance, SMPs composition, and microbial community of UASBs. The results showed that antibiotic mixtures decreased the chemical oxygen demand removal efficiency and biogas content of the reactors, and influenced the composition and fluorescence intensity of SMPs. Moreover, antibiotics also had a significant impact on the microbial community structure.
Article
Agricultural Engineering
Yonghua Xu, Xianghui Meng, Yunong Song, Xiaoyi Lv, Yong Sun
Summary: Investigating the effect of butyric acid concentration on anaerobic digestion systems in complex systems is crucial for efficient degradation of butyric acid and improving anaerobic digestion efficiency. In this study, different loadings of butyric acid were added to the anaerobic reactor, and at a high organic loading rate, efficient methane production was achieved with a volumetric biogas production of 1.50 L/(L center dot d) and biogas content between 65% and 75%. Metagenome sequencing revealed changes in the functional flora, indicating significant improvement in the methanogenic capacity of the system.
BIORESOURCE TECHNOLOGY
(2023)
Article
Environmental Sciences
Kongyun Zhu, Lei Zhang, Xuexue Wang, Lan Mu, Changjing Li, Aimin Li
Summary: Norfloxacin inhibits methane production in anaerobic digestion, but the performance and microbial community can recover when the inhibitor is removed. Inhibition of Candidatus_Cloacimonas, Petrimonas, Ercella, Sphaerochaeta and hydrogenotrophic methanogens by NOR is reversible, while inhibition of acetoclastic methanogen Methanosaeta is irreversible.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Energy & Fuels
Gustavo Mockaitis, Guillaume Bruant, Eugenio Foresti, Marcelo Zaiat, Serge R. Guiot
Summary: This study investigates the effect of four different physicochemical pretreatments on anaerobic inoculum for alcohols production. It was found that thermal and acidic-thermal pretreatments selected communities more suitable for acetate and butyrate solventogenesis. The highest concentrations of ethanol and butanol produced were achieved with thermal and acidic-thermal pretreatments. Sequencing data revealed the bacterial genera Pseudomonas, Brevundimonas, and Clostridium as the dominant species selected by these pretreatments.
BIOMASS CONVERSION AND BIOREFINERY
(2022)
Article
Multidisciplinary Sciences
Justin I. Yoo, Patrick S. Daugherty, Michelle A. O'Malley
NATURE COMMUNICATIONS
(2020)
Article
Engineering, Chemical
St. Elmo Wilken, Patrick A. Leggieri, Corey Kerdman-Andrade, Matthew Reilly, Michael K. Theodorou, Michelle A. O'Malley
Review
Microbiology
Luke M. G. Saye, Tejas A. Navaratna, James P. J. Chong, Michelle A. O'Malley, Michael K. Theodorou, Matthew Reilly
Summary: Lignocellulose is a promising feedstock for biofuel production, but pretreatments are needed to overcome its natural recalcitrance. Anaerobic fungi have potential for biofuel production due to their effective ability to hydrolyse lignocellulose and convert it to H-2 and ethanol, as well as produce volatile fatty acid precursors for further conversion.
Article
Microbiology
Stephen P. Lillington, William Chrisler, Charles H. Haitjema, Sean P. Gilmore, Chuck R. Smallwood, Vaithiyalingam Shutthanandan, James E. Evans, Michelle A. O'Malley
Summary: This study used antibodies and imaging tools to investigate the spatial localization patterns of fungal cellulosomes across the life stages of anaerobic fungus Piromyces finnis under different environmental conditions. The findings highlight the impact of cell morphology and regulation of cellulosome production on biomass degradation by anaerobic fungi, providing insights for potential strategies to enhance hydrolytic enzyme yields in fungal cultures.
Review
Biochemical Research Methods
Igor A. Podolsky, Elizabeth E. Schauer, Susanna Seppala, Michelle A. O'Malley
Summary: Efficient utilization of lignocellulosic biomass requires the identification and engineering of new membrane proteins. Recent studies have discovered transporters sourced from anaerobic gut fungi, which enhance xylose transport and enable co-utilization of glucose and xylose. Additionally, fungal cellodextrin transporters have been identified as valuable alternatives for mitigating glucose repression and transporter inhibition.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Patrick A. Leggieri, Corey Kerdman-Andrade, Thomas S. Lankiewicz, Megan T. Valentine, Michelle A. O'Malley
Summary: The study presents a microplate-based method to measure AGF and methanogen concentrations in co-culture, demonstrating significant increases in AGF growth rate and degradation rates in the presence of methanogens. This method allows for direct growth measurements and calculation of metabolic fluxes, essential for understanding rumen metabolism and the impact of co-culture on degradation and production processes.
MICROBIAL CELL FACTORIES
(2021)
Article
Biochemical Research Methods
Justin Yoo, Tejas A. Navaratna, Patrick Kolence, Michelle A. O'Malley
Summary: The directed evolution of proteins is limited by library size and screening ability. The GPCR-FEX platform couples GPCR signaling to expression of a fluoride ion exporter (FEX)-GFP fusion gene, allowing rapid, inexpensive screening of receptor libraries. This platform depletes inactive GPCR variants from the library and enables the rapid engineering of GPCRs, which are important cellular sensors for synthetic biology.
ACS SYNTHETIC BIOLOGY
(2022)
Review
Microbiology
Thomas S. Lankiewicz, Stephen P. Lillington, Michelle A. O'Malley
Summary: Lignocellulosic biorefineries require innovative solutions to reach their full potential, and the discovery of novel lignocellulose-active enzymes could enhance the deconstruction processes. Anaerobic gut fungi, particularly Neocallimastigomycetes, are promising sources for these enzymes due to their extensive carbohydrate-active enzyme content and proficiency in deconstructing complex lignocellulose. Recent progress in understanding Neocallimastigomycetes and their enzymes has been rapid and will continue to expand, especially with advancements in manipulating fungal genomes and expressing fungal enzymes.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2022)
Article
Biotechnology & Applied Microbiology
Jennifer L. Brown, Matthew A. Perisin, Candice L. Swift, Marcus Benyamin, Sanchao Liu, Vasanth Singan, Yu Zhang, Emily Savage, Christa Pennacchio, Igor Grigoriev, Michelle A. O'Malley
Summary: A system for co-cultivation of anaerobic fungi with anaerobic bacteria was established to produce butyrate and butanol from plant biomass. The co-culture formulations consisted of different fungi with the bacterium Clostridium acetobutylicum, and the simultaneous co-culture promoted the production of butyrate up to 30 mM. Two-stage growth slightly promoted solventogenesis and elevated butanol levels. This study demonstrates the potential of a fungal-bacterial co-culture system for biobutanol and bio-butyrate production from lignocellulose.
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Alexey Dementiev, Stephen P. Lillington, Shiyan Jin, Youngchang Kim, Robert Jedrzejczak, Karolina Michalska, Andrzej Joachimiak, Michelle A. O'Malley
Summary: Anaerobic fungi in the guts of large herbivores have genomes with a wide range of carbohydrate-active enzymes (CAZymes), including glycoside hydrolase (GH) family 5 subfamily 4 enzymes. In this study, the structure and kinetics of a GH5 subfamily 4 enzyme (CelD) from Piromyces finnis were characterized. The CelD enzyme showed a modular structure with multiple GH5 domains and fungal dockerin domains. The enzyme exhibited endoglucanase activity and could hydrolyze various substrates. The study also revealed the catalytic mechanism and binding capability of CelD.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Stephen P. Lillington, Matthew Hamilton, Jan-Fang Cheng, Yasuo Yoshikuni, Michelle A. O'Malley
Summary: Anaerobic fungi found in the guts of herbivores have the ability to extract sugars from recalcitrant plant material. These fungi use enzyme complexes called cellulosomes to accelerate biomass hydrolysis. The CotH proteins in these fungi have ATP hydrolysis activity and may contribute to fungal cellulosome assembly and activity.
PROTEIN EXPRESSION AND PURIFICATION
(2023)
Article
Biochemistry & Molecular Biology
Susanna Seppala, Taylor Gierke, Elizabeth E. E. Schauer, Jennifer L. L. Brown, Michelle A. A. O'Malley
Summary: Membrane-embedded transporters play essential roles in cellular functions such as nutrient uptake and waste product extrusion. Multidrug exporters are important for resistance mechanisms and enhancing tolerance to hydrophobic bioproducts in microbial engineering. In this study, we identified small multidrug resistance (SMR) transporters in anaerobic fungi, which have not been reported in eukaryotes before. We demonstrated the potential of these SMR transporters as targets for further characterization by heterologously producing them in the yeast Saccharomyces cerevisiae. These novel anaerobic fungal SMR transporters offer a promising approach to enhance bioproduction in engineered microbial strains.
Article
Multidisciplinary Sciences
Justin I. Yoo, Susanna Seppala, Michelle A. O'Malley
NATURE COMMUNICATIONS
(2020)
Article
Biotechnology & Applied Microbiology
Sean P. Gilmore, Stephen P. Lillington, Charles H. Haitjema, Randall de Groot, Michelle A. O'Malley
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2020)
