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Liang J, Zhang R, Chang J, Chen L, Nabi M, Zhang H, Zhang G, Zhang P. Rumen microbes, enzymes, metabolisms, and application in lignocellulosic waste conversion - A comprehensive review. Biotechnol Adv 2024; 71:108308. [PMID: 38211664 DOI: 10.1016/j.biotechadv.2024.108308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 12/14/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024]
Abstract
The rumen of ruminants is a natural anaerobic fermentation system that efficiently degrades lignocellulosic biomass and mainly depends on synergistic interactions between multiple microbes and their secreted enzymes. Ruminal microbes have been employed as biomass waste converters and are receiving increasing attention because of their degradation performance. To explore the application of ruminal microbes and their secreted enzymes in biomass waste, a comprehensive understanding of these processes is required. Based on the degradation capacity and mechanism of ruminal microbes and their secreted lignocellulose enzymes, this review concentrates on elucidating the main enzymatic strategies that ruminal microbes use for lignocellulose degradation, focusing mainly on polysaccharide metabolism-related gene loci and cellulosomes. Hydrolysis, acidification, methanogenesis, interspecific H2 transfer, and urea cycling in ruminal metabolism are also discussed. Finally, we review the research progress on the conversion of biomass waste into biofuels (bioethanol, biohydrogen, and biomethane) and value-added chemicals (organic acids) by ruminal microbes. This review aims to provide new ideas and methods for ruminal microbe and enzyme applications, biomass waste conversion, and global energy shortage alleviation.
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Affiliation(s)
- Jinsong Liang
- School of Energy & Environmental Engineering, Hebei University of Technology, Tianjin 300130, China
| | - Ru Zhang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Jianning Chang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Le Chen
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Mohammad Nabi
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Haibo Zhang
- College of Resources and Environment, Shanxi Agricultural University, Taigu 030801, China
| | - Guangming Zhang
- School of Energy & Environmental Engineering, Hebei University of Technology, Tianjin 300130, China.
| | - Panyue Zhang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China.
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Tamilselvan R, Immanuel Selwynraj A. Enhancing biogas generation from lignocellulosic biomass through biological pretreatment: Exploring the role of ruminant microbes and anaerobic fungi. Anaerobe 2024; 85:102815. [PMID: 38145708 DOI: 10.1016/j.anaerobe.2023.102815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 12/27/2023]
Abstract
Biogas production from Lignocellulosic Biomass (LB) via anaerobic digestion (AD) has gained attention for its potential in self-sustainability. However, the recalcitrance of LB cell walls pose a challenge to its degradability and biogas generation. Therefore, pretreatment of LB is necessary to enhance lignin removal and increase degradability. Among the different approaches, environmentally friendly biological pretreatment ispromising as it avoids the production of inhibitors. The ruminal microbial community, including anaerobic fungi, bacteria, and protozoa, has shown an ability to effectively degrade LB through biomechanical and microbial penetration of refractory cell structures. In this review, we provide an overview of ruminant microbes dominating LB's AD, their degradation mechanism, and the bioaugmentation of the rumen. We also explore the potential cultivation of anaerobic fungi from the rumen, their enzyme potential, and their role in AD. The rumen ecosystem, comprising both bacteria and fungi, plays a crucial role in enhancing AD. This comprehensive review delves into the intricacies of ruminant microorganisms' adhesion to plant cells, elucidates degradation mechanisms, and explores integrated pretreatment approaches for the effective utilization of LB, minimizing the impact of inhibitors. The discussion underscores the considerable potential of ruminant microbes in pretreating LB, paving the way for sustainable biogas production. Optimizing fungal colonization and ligninolytic enzyme production, such as manganese peroxidase and laccase, significantly enhances the efficiency of fungal pretreatment. Integrating anaerobic fungi through bioaugmentation during mainstream processing demonstrably increases methane production. This study opens promising avenues for further research and development of these microorganisms for bioenergy production.
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Affiliation(s)
- R Tamilselvan
- School of Mechanical Engineering, Vellore Institute of Technology, Vellore, 632 014, India
| | - A Immanuel Selwynraj
- School of Mechanical Engineering, Vellore Institute of Technology, Vellore, 632 014, India.
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3
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Heom KA, Wangsanuwat C, Butkovich LV, Tam SC, Rowe AR, O'Malley MA, Dey SS. Targeted rRNA depletion enables efficient mRNA sequencing in diverse bacterial species and complex co-cultures. mSystems 2023; 8:e0028123. [PMID: 37855606 PMCID: PMC10734481 DOI: 10.1128/msystems.00281-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/12/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE Microbes present one of the most diverse sources of biochemistry in nature, and mRNA sequencing provides a comprehensive view of this biological activity by quantitatively measuring microbial transcriptomes. However, efficient mRNA capture for sequencing presents significant challenges in prokaryotes as mRNAs are not poly-adenylated and typically make up less than 5% of total RNA compared with rRNAs that exceed 80%. Recently developed methods for sequencing bacterial mRNA typically rely on depleting rRNA by tiling large probe sets against rRNAs; however, such approaches are expensive, time-consuming, and challenging to scale to varied bacterial species and complex microbial communities. Therefore, we developed EMBR-seq+, a method that requires fewer than 10 short oligonucleotides per rRNA to achieve up to 99% rRNA depletion in diverse bacterial species. Finally, EMBR-seq+ resulted in a deeper view of the transcriptome, enabling systematic quantification of how microbial interactions result in altering the transcriptional state of bacteria within co-cultures.
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Affiliation(s)
- Kellie A. Heom
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, California, USA
| | - Chatarin Wangsanuwat
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, California, USA
| | - Lazarina V. Butkovich
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
| | - Scott C. Tam
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
| | - Annette R. Rowe
- Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Michelle A. O'Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, California, USA
| | - Siddharth S. Dey
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
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4
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Elgart M, Zhang Y, Zhang Y, Yu B, Kim Y, Zee PC, Gellman MD, Boerwinkle E, Daviglus ML, Cai J, Redline S, Burk RD, Kaplan R, Sofer T. Anaerobic pathogens associated with OSA may contribute to pathophysiology via amino-acid depletion. EBioMedicine 2023; 98:104891. [PMID: 38006744 PMCID: PMC10709109 DOI: 10.1016/j.ebiom.2023.104891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 11/27/2023] Open
Abstract
BACKGROUND The human microbiome is linked to multiple metabolic disorders such as obesity and diabetes. Obstructive sleep apnoea (OSA) is a common sleep disorder with several metabolic risk factors. We investigated the associations between the gut microbiome composition and function, and measures of OSA severity in participants from a prospective community-based cohort study: the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). METHODS Bacterial-Wide Association Analysis (BWAS) of gut microbiome measured via metagenomics with OSA measures was performed adjusting for clinical, lifestyle and co-morbidities. This was followed by functional analysis of the OSA-enriched bacteria. We utilized additional metabolomic and transcriptomic associations to suggest possible mechanisms explaining the microbiome effects on OSA. FINDINGS Several uncommon anaerobic human pathogens were associated with OSA severity. These belong to the Lachnospira, Actinomyces, Kingella and Eubacterium genera. Functional analysis revealed enrichment in 49 processes including many anaerobic-related ones. Severe OSA was associated with the depletion of the amino acids glycine and glutamine in the blood, yet neither diet nor gene expression revealed any changes in the production or consumption of these amino acids. INTERPRETATION We show anaerobic bacterial communities to be a novel component of OSA pathophysiology. These are established in the oxygen-poor environments characteristic of OSA. We hypothesize that these bacteria deplete certain amino acids required for normal human homeostasis and muscle tone, contributing to OSA phenotypes. Future work should test this hypothesis as well as consider diagnostics via anaerobic bacteria detection and possible interventions via antibiotics and amino-acid supplementation. FUNDING Described in methods.
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Affiliation(s)
- Michael Elgart
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Ying Zhang
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Yuan Zhang
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Bing Yu
- Human Genetics Centre, The University of Texas Health Science Centre at Houston, Houston, TX, USA; Human Genome Sequencing Centre, Baylor College of Medicine, Houston, TX, USA
| | - Youngmee Kim
- Department of Psychology, University of Miami, Coral Gables, FL, USA
| | - Phyllis C Zee
- Department of Neurology and Sleep Medicine Centre, Northwestern University, Chicago, IL, USA
| | - Marc D Gellman
- Department of Psychology, University of Miami, Coral Gables, FL, USA
| | - Eric Boerwinkle
- Human Genetics Centre, The University of Texas Health Science Centre at Houston, Houston, TX, USA; Human Genome Sequencing Centre, Baylor College of Medicine, Houston, TX, USA
| | - Martha L Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL, USA
| | - Jianwen Cai
- Collaborative Studies Coordinating Centre, University of North Carolina at Chapel Hill, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Robert D Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA; Fred Hutchinson Cancer Research Centre, Division of Public Health Sciences, Seattle, WA, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA.
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5
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Griesemer M, Navid A. Uses of Multi-Objective Flux Analysis for Optimization of Microbial Production of Secondary Metabolites. Microorganisms 2023; 11:2149. [PMID: 37763993 PMCID: PMC10536367 DOI: 10.3390/microorganisms11092149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 09/29/2023] Open
Abstract
Secondary metabolites are not essential for the growth of microorganisms, but they play a critical role in how microbes interact with their surroundings. In addition to this important ecological role, secondary metabolites also have a variety of agricultural, medicinal, and industrial uses, and thus the examination of secondary metabolism of plants and microbes is a growing scientific field. While the chemical production of certain secondary metabolites is possible, industrial-scale microbial production is a green and economically attractive alternative. This is even more true, given the advances in bioengineering that allow us to alter the workings of microbes in order to increase their production of compounds of interest. This type of engineering requires detailed knowledge of the "chassis" organism's metabolism. Since the resources and the catalytic capacity of enzymes in microbes is finite, it is important to examine the tradeoffs between various bioprocesses in an engineered system and alter its working in a manner that minimally perturbs the robustness of the system while allowing for the maximum production of a product of interest. The in silico multi-objective analysis of metabolism using genome-scale models is an ideal method for such examinations.
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Affiliation(s)
| | - Ali Navid
- Lawrence Livermore National Laboratory, Biosciences & Biotechnology Division, Physical & Life Sciences Directorate, Livermore, CA 94550, USA
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6
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Brown JL, Gierke T, Butkovich LV, Swift CL, Singan V, Daum C, Barry K, Grigoriev IV, O’Malley MA. High-quality RNA extraction and the regulation of genes encoding cellulosomes are correlated with growth stage in anaerobic fungi. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1171100. [PMID: 37746117 PMCID: PMC10512310 DOI: 10.3389/ffunb.2023.1171100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/02/2023] [Indexed: 09/26/2023]
Abstract
Anaerobic fungi produce biomass-degrading enzymes and natural products that are important to harness for several biotechnology applications. Although progress has been made in the development of methods for extracting nucleic acids for genomic and transcriptomic sequencing of these fungi, most studies are limited in that they do not sample multiple fungal growth phases in batch culture. In this study, we establish a method to harvest RNA from fungal monocultures and fungal-methanogen co-cultures, and also determine an optimal time frame for high-quality RNA extraction from anaerobic fungi. Based on RNA quality and quantity targets, the optimal time frame in which to harvest anaerobic fungal monocultures and fungal-methanogen co-cultures for RNA extraction was 2-5 days of growth post-inoculation. When grown on cellulose, the fungal strain Anaeromyces robustus cocultivated with the methanogen Methanobacterium bryantii upregulated genes encoding fungal carbohydrate-active enzymes and other cellulosome components relative to fungal monocultures during this time frame, but expression patterns changed at 24-hour intervals throughout the fungal growth phase. These results demonstrate the importance of establishing methods to extract high-quality RNA from anaerobic fungi at multiple time points during batch cultivation.
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Affiliation(s)
- Jennifer L. Brown
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Taylor Gierke
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Lazarina V. Butkovich
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Candice L. Swift
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Christopher Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, United States
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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7
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Dai Q, Ding J, Cui X, Zhu Y, Chen H, Zhu L. Beyond bacteria: Reconstructing microorganism connections and deciphering the predicted mutualisms in mammalian gut metagenomes. Ecol Evol 2023; 13:e9829. [PMID: 36844675 PMCID: PMC9944162 DOI: 10.1002/ece3.9829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/24/2023] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
Numerous gut microbial studies have focused on bacteria. However, archaea, viruses, fungi, protists, and nematodes are also regular residents of the gut ecosystem. Little is known about the composition and potential interactions among these six kingdoms in the same samples. Here, we unraveled the complex connection among them using approximately 123 gut metagenomes from 42 mammalian species (including carnivores, omnivores, and herbivores). We observed high variation in bacterial and fungal families and relatively low variation in archaea, viruses, protists, and nematodes. We found that some fungi in the mammalian intestine might come from environmental sources (e.g., soil and dietary plants), and some might be native to the intestine (e.g., the occurrence of Neocallimastigomycetes). The Methanobacteriaceae and Plasmodiidae families (archaea and protozoa, respectively) were predominant in these metagenomes, whereas Onchocercidae and Trichuridae were the two most common nematodes, and Siphoviridae and Myoviridae the two most common virus families in these mammalian gut metagenomes. Interestingly, most of the pairwise co-occurrence patterns were significantly positive among these six kingdoms, and significantly negative networks mainly occurred between fungi and prokaryotes (both bacteria and archaea). Our study revealed some inconvenient characteristics in the mammalian gut microorganism ecosystem: (1) the community formed by members of the analyzed kingdoms reflects the life history of the host and the potential threat posed by pathogenic protists and nematodes in mammals; and (2) the networks suggest the existence of predicted mutualism among members of these six kingdoms and of the predicted competition, mainly among fungi and other kingdoms.
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Affiliation(s)
- Qinlong Dai
- Sichuan Liziping National Natural ReserveShimianChina
| | | | - Xinyuan Cui
- College of Life ScienceNanjing Normal UniversityNanjingChina
| | - Yudong Zhu
- Sichuan Liziping National Natural ReserveShimianChina
| | - Hua Chen
- Mingke Biotechnology (Hangzhou) Co., Ltd.HangzhouChina
| | - Lifeng Zhu
- College of PharmacyNanjing University of Chinese MedicineNanjingChina
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Vinzelj J, Joshi A, Young D, Begovic L, Peer N, Mosberger L, Luedi KCS, Insam H, Flad V, Nagler M, Podmirseg SM. No time to die: Comparative study on preservation protocols for anaerobic fungi. Front Microbiol 2022; 13:978028. [PMID: 36225373 PMCID: PMC9549207 DOI: 10.3389/fmicb.2022.978028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Anaerobic fungi (AF, phylum Neocallimastigomycota) are best known for their ability to anaerobically degrade recalcitrant lignocellulosic biomass through mechanic and enzymatic means. While their biotechnological potential is well-recognized, applied research on AF is still hampered by the time-consuming and cost-intensive laboratory routines required to isolate, maintain, and preserve AF cultures. Reliable long-term preservation of specific AF strains would aid basic as well as applied research, but commonly used laboratory protocols for AF preservation can show erratic survival rates and usually exhibit only moderate resuscitation success for up to one or two years after preservation. To address both, the variability, and the preservation issues, we have set up a cross-laboratory, year-long study. We tested five different protocols for the preservation of AF. The experiments were performed at three different laboratories (Austria, Germany, Switzerland) with the same three morphologically distinct AF isolates (Anaeromyces mucronatus, Caeocmyces sp., and Neocallimastix cameroonii) living in stable co-culture with their naturally occurring, syntrophic methanogens. We could show that handling greatly contributes to the variability of results, especially in Anaeromyces mucronatus. Cryopreservation of (mature) biomass in liquid nitrogen had the highest overall survival rates (85-100%, depending on the strain and laboratory). Additionally, preservation on agar at 39°C had surprisingly high survival rates for up to 9 months, if pieces of agar containing mature AF thalli were resuscitated. This low-cost, low-effort method could replace consecutive batch cultivation for periods of up to 6 months, while long-term preservation is best done by cryopreservation in liquid nitrogen. Regardless of the method, however, preserving several replicates (>three) of the same strain is highly advisable.
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Affiliation(s)
- Julia Vinzelj
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Akshay Joshi
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
- Institute of Chemistry and Biotechnology, Biocatalysis and Process Technology Unit, Zurich University of Applied Sciences, Wäedenswil, Switzerland
| | - Diana Young
- Micro- and Molecular Biology, Central Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Freising, Germany
| | - Ljubica Begovic
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Nico Peer
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Lona Mosberger
- Institute of Chemistry and Biotechnology, Biocatalysis and Process Technology Unit, Zurich University of Applied Sciences, Wäedenswil, Switzerland
| | - Katharina Cécile Schmid Luedi
- Institute of Chemistry and Biotechnology, Biocatalysis and Process Technology Unit, Zurich University of Applied Sciences, Wäedenswil, Switzerland
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Veronika Flad
- Micro- and Molecular Biology, Central Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Freising, Germany
| | - Magdalena Nagler
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
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Suitability of anaerobic fungi culture supernatant or mixed ruminal fluid as novel silage additives. Appl Microbiol Biotechnol 2022; 106:6819-6832. [PMID: 36100752 PMCID: PMC9529681 DOI: 10.1007/s00253-022-12157-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/12/2022] [Accepted: 08/24/2022] [Indexed: 11/02/2022]
Abstract
Abstract
This study investigated silage quality characteristics and ruminal fiber degradability of grass and straw ensiled with either anaerobic fungi (AF) supernatant with active fungal enzymes or mixed ruminal fluid as novel silage additives. Compared to control silages, AF supernatant improved the quality of grass and straw silages as evidenced by decreased pH, acetic acid concentration, and dry matter losses. Likewise, mixed ruminal fluid enhanced lactic acid fermentation, which further resulted in lower pH of the treated grass silage. The ruminal fiber degradability was determined using in situ incubations and, compared to controls, the cellulose degradability was higher for grass silage with AF supernatant, whereas ruminal degradability of straw silage was reduced by this treatment. In contrast, mixed ruminal fluid did not influence fiber degradability of silages in the rumen. Concluding, both novel additives improved silage quality, whereas only AF supernatant enhanced ruminal fiber degradability of grass silage and therefore may represent an approach for improving forage utilization by ruminants.
Key points
• Enzymes of anaerobic fungi supernatant improve quality of grass and straw silages.
• Mixed ruminal fluid enhances lactic acid fermentation when ensiling grass and straw.
• Enzymes of anaerobic fungi supernatant increase ruminal grass silage degradability.
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10
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Leggieri PA, Valentine MT, O'Malley MA. Biofilm disruption enhances growth rate and carbohydrate-active enzyme production in anaerobic fungi. BIORESOURCE TECHNOLOGY 2022; 358:127361. [PMID: 35609749 DOI: 10.1016/j.biortech.2022.127361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/07/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Anaerobic gut fungi (AGF) are lignocellulose degraders that naturally form biofilms in the rumen of large herbivores and in standard culture techniques. While biofilm formation enhances biomass degradation and carbohydrate-active enzyme (CAZyme) production in some bacteria and aerobic fungi, gene expression and metabolism in AGF biofilms have not been compared to non-biofilm cultures. Here, using the tunable morphology of the non-rhizoidal AGF, Caecomyces churrovis, the impacts of biofilm formation on AGF gene expression, metabolic flux, growth rate, and xylan degradation rate are quantified to inform future industrial scale-up efforts. Contrary to previous findings, C. churrovis upregulated catabolic CAZymes in stirred culture relative to biofilm culture. Using a de novo transcriptome, 197 new transcripts with predicted CAZyme function were identified. Stirred cultures grew and degraded xylan significantly faster than biofilm-forming cultures with negligible differences in primary metabolic flux, offering a way to accelerate AGF biomass valorization without altering the fermentation product profile. The rhizoidal AGF, Neocallimastix lanati, also grew faster with stirring on a solid plant substrate, suggesting that the advantages of stirred C. churrovis cultures may apply broadly to other AGF.
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Affiliation(s)
- Patrick A Leggieri
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.
| | - Megan T Valentine
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106, USA.
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA; Joint BioEnergy Institute (JBEI), Emeryville, CA 94608, USA.
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11
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Kazemi Shariat Panahi H, Dehhaghi M, Guillemin GJ, Gupta VK, Lam SS, Aghbashlo M, Tabatabaei M. A comprehensive review on anaerobic fungi applications in biofuels production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154521. [PMID: 35292323 DOI: 10.1016/j.scitotenv.2022.154521] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Anaerobic fungi (Neocallimastigomycota) are promising lignocellulose-degrading microorganisms that can be exploited by the biofuel industry. While natural production of ethanol by these microorganisms is very low, there is a greater potential for their use in the biogas industry. More specifically, anaerobic fungi can contribute to biogas production by either releasing holocellulose or reducing sugars from lignocelluloses that can be used as a substrate by bacteria and methanogens involved in the anaerobic digestion (AD) process or by metabolizing acetate and formate that can be directly consumed by methanogens. Despite their great potential, the appropriate tools for engineering anaerobic fungi have not been established yet. The first section of this review justifies how the biofuel industry can benefit from using anaerobic fungi and is followed by their taxonomy. In the third section, the possibility of using anaerobic fungi for the consolidated production of bioethanol is briefly discussed. Nevertheless, the main focus of this review is on the upstream and mainstream effects of bioaugmentation with anaerobic fungi on the AD process. The present review also scrutinizes the constraints on the way of efficient engineering of anaerobic rumen fungi. By providing this knowledge, this review aims to help research in this field with identifying the challenges that must be addressed by future experiments to achieve the full potentials of these promising microorganisms. To sum up, the pretreatment of lignocelluloses by anaerobic fungi can prevent carbohydrate loss due to respiration (compared to white-rot fungi). Following fungal mixed acid fermentation, the obtained slurry containing sugars and more susceptible holocellulose can be directly consumed by AD microorganisms (bacteria, methanogens). The bioaugmentation of anaerobic fungi into the AD process can increase methane biosynthesis by >3.3 times. Despite this, for the commercial AD process, novel genetic engineering techniques and kits must be developed to efficiently improve anaerobic fungi viability throughout the AD process.
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Affiliation(s)
- Hamed Kazemi Shariat Panahi
- Henan Province Engineering Research Center for Forest Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou 450002, China; Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, NSW, Australia; Biofuel Research Team (BRTeam), Terengganu, Malaysia
| | - Mona Dehhaghi
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, NSW, Australia; Biofuel Research Team (BRTeam), Terengganu, Malaysia; PANDIS.org, Australia
| | - Gilles J Guillemin
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, NSW, Australia; PANDIS.org, Australia
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK; Centre for Safe and Improved Food, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK
| | - Su Shiung Lam
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia; Henan Province Engineering Research Center for Forest Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou 450002, China.
| | - Mortaza Aghbashlo
- Department of Mechanical Engineering of Agricultural Machinery, Faculty of Agricultural Engineering and Technology, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran; Henan Province Engineering Research Center for Forest Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou 450002, China.
| | - Meisam Tabatabaei
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia; Henan Province Engineering Research Center for Forest Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou 450002, China; Biofuel Research Team (BRTeam), Terengganu, Malaysia.
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12
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Blair EM, Dickson KL, O'Malley MA. Microbial communities and their enzymes facilitate degradation of recalcitrant polymers in anaerobic digestion. Curr Opin Microbiol 2021; 64:100-108. [PMID: 34700124 DOI: 10.1016/j.mib.2021.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 09/21/2021] [Indexed: 11/15/2022]
Abstract
Microbial consortia efficiently degrade complex biopolymers found in the organic fraction of municipal solid waste (OFMSW). Through enzyme production and division of labor during anaerobic digestion, microbial communities break down recalcitrant polymers and make fermentation products, including methane. However, microbial communities remain underutilized for waste degradation as it remains difficult to characterize and predict microbial interactions during waste breakdown, especially as cultivation conditions change drastically throughout anaerobic digestion. This review discusses recent progress and opportunities in cultivating natural and engineered consortia for OFMSW hydrolysis, including how recalcitrant substrates are degraded by enzymes as well as the critical factors that govern microbial interactions and culture stability. Methods to measure substrate degradation are also reviewed, and we demonstrate the need for increased standardization to enable comparisons across different environments.
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Affiliation(s)
- Elaina M Blair
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Katharine L Dickson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA; Joint BioEnergy Institute (JBEI), Emeryville, CA, 94608, USA.
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13
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Leggieri PA, Kerdman-Andrade C, Lankiewicz TS, Valentine MT, O’Malley MA. Non-destructive quantification of anaerobic gut fungi and methanogens in co-culture reveals increased fungal growth rate and changes in metabolic flux relative to mono-culture. Microb Cell Fact 2021; 20:199. [PMID: 34663313 PMCID: PMC8522008 DOI: 10.1186/s12934-021-01684-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/22/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Quantification of individual species in microbial co-cultures and consortia is critical to understanding and designing communities with prescribed functions. However, it is difficult to physically separate species or measure species-specific attributes in most multi-species systems. Anaerobic gut fungi (AGF) (Neocallimastigomycetes) are native to the rumen of large herbivores, where they exist as minority members among a wealth of prokaryotes. AGF have significant biotechnological potential owing to their diverse repertoire of potent lignocellulose-degrading carbohydrate-active enzymes (CAZymes), which indirectly bolsters activity of other rumen microbes through metabolic exchange. While decades of literature suggest that polysaccharide degradation and AGF growth are accelerated in co-culture with prokaryotes, particularly methanogens, methods have not been available to measure concentrations of individual species in co-culture. New methods to disentangle the contributions of AGF and rumen prokaryotes are sorely needed to calculate AGF growth rates and metabolic fluxes to prove this hypothesis and understand its causality for predictable co-culture design. RESULTS We present a simple, microplate-based method to measure AGF and methanogen concentrations in co-culture based on fluorescence and absorbance spectroscopies. Using samples of < 2% of the co-culture volume, we demonstrate significant increases in AGF growth rate and xylan and glucose degradation rates in co-culture with methanogens relative to mono-culture. Further, we calculate significant differences in AGF metabolic fluxes in co-culture relative to mono-culture, namely increased flux through the energy-generating hydrogenosome organelle. While calculated fluxes highlight uncertainties in AGF primary metabolism that preclude definitive explanations for this shift, our method will enable steady-state fluxomic experiments to probe AGF metabolism in greater detail. CONCLUSIONS The method we present to measure AGF and methanogen concentrations enables direct growth measurements and calculation of metabolic fluxes in co-culture. These metrics are critical to develop a quantitative understanding of interwoven rumen metabolism, as well as the impact of co-culture on polysaccharide degradation and metabolite production. The framework presented here can inspire new methods to probe systems beyond AGF and methanogens. Simple modifications to the method will likely extend its utility to co-cultures with more than two organisms or those grown on solid substrates to facilitate the design and deployment of microbial communities for bioproduction and beyond.
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Affiliation(s)
- Patrick A. Leggieri
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Corey Kerdman-Andrade
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Thomas S. Lankiewicz
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106 USA
- Joint BioEnergy Institute (JBEI), Emeryville, CA 94608 USA
| | - Megan T. Valentine
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
- Joint BioEnergy Institute (JBEI), Emeryville, CA 94608 USA
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14
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Abstract
Anaerobic gut fungi (Neocallimastigomycetes) live in the digestive tract of large herbivores, where they are vastly outnumbered by bacteria. It has been suggested that anaerobic fungi challenge growth of bacteria owing to the wealth of biosynthetic genes in fungal genomes, although this relationship has not been experimentally tested. Here, we cocultivated the rumen bacteria Fibrobacter succinogenes strain UWB7 with the anaerobic gut fungi Anaeromyces robustus or Caecomyces churrovis on a range of carbon substrates and quantified the bacterial and fungal transcriptomic response. Synthetic cocultures were established for at least 24 h, as verified by active fungal and bacterial transcription. A. robustus upregulated components of its secondary metabolism in the presence of Fibrobacter succinogenes strain UWB7, including six nonribosomal peptide synthetases, one polyketide synthase-like enzyme, and five polyketide synthesis O-type methyltransferases. Both A. robustus and C. churrovis cocultures upregulated S-adenosyl-l-methionine (SAM)-dependent methyltransferases, histone methyltransferases, and an acetyltransferase. Fungal histone 3 lysine 27 trimethylation marks were more abundant in coculture, and heterochromatin protein-1 was downregulated. Together, these findings suggest that fungal chromatin remodeling occurs when bacteria are present. F. succinogenes strain UWB7 upregulated four genes in coculture encoding drug efflux pumps, which likely protect the cell against toxins. Furthermore, untargeted nonpolar metabolomics data revealed at least one novel fungal metabolite enriched in coculture, which may be a defense compound. Taken together, these data suggest that A. robustus and C. churrovis produce antimicrobials when exposed to rumen bacteria and, more broadly, that anaerobic gut fungi are a source of novel antibiotics.
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15
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Saye LMG, Navaratna TA, Chong JPJ, O’Malley MA, Theodorou MK, Reilly M. The Anaerobic Fungi: Challenges and Opportunities for Industrial Lignocellulosic Biofuel Production. Microorganisms 2021; 9:694. [PMID: 33801700 PMCID: PMC8065543 DOI: 10.3390/microorganisms9040694] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 11/17/2022] Open
Abstract
Lignocellulose is a promising feedstock for biofuel production as a renewable, carbohydrate-rich and globally abundant source of biomass. However, challenges faced include environmental and/or financial costs associated with typical lignocellulose pretreatments needed to overcome the natural recalcitrance of the material before conversion to biofuel. Anaerobic fungi are a group of underexplored microorganisms belonging to the early diverging phylum Neocallimastigomycota and are native to the intricately evolved digestive system of mammalian herbivores. Anaerobic fungi have promising potential for application in biofuel production processes due to the combination of their highly effective ability to hydrolyse lignocellulose and capability to convert this substrate to H2 and ethanol. Furthermore, they can produce volatile fatty acid precursors for subsequent biological conversion to H2 or CH4 by other microorganisms. The complex biological characteristics of their natural habitat are described, and these features are contextualised towards the development of suitable industrial systems for in vitro growth. Moreover, progress towards achieving that goal is reviewed in terms of process and genetic engineering. In addition, emerging opportunities are presented for the use of anaerobic fungi for lignocellulose pretreatment; dark fermentation; bioethanol production; and the potential for integration with methanogenesis, microbial electrolysis cells and photofermentation.
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Affiliation(s)
- Luke M. G. Saye
- Department of Biology, University of York, York YO10 5DD, UK; (L.M.G.S.); (J.P.J.C.)
- Department of Agriculture and the Environment, Harper Adams University, Newport TF10 8NB, UK
| | - Tejas A. Navaratna
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA; (T.A.N.); (M.A.O.)
| | - James P. J. Chong
- Department of Biology, University of York, York YO10 5DD, UK; (L.M.G.S.); (J.P.J.C.)
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA; (T.A.N.); (M.A.O.)
| | - Michael K. Theodorou
- Department of Agriculture and the Environment, Harper Adams University, Newport TF10 8NB, UK
| | - Matthew Reilly
- Department of Biology, University of York, York YO10 5DD, UK; (L.M.G.S.); (J.P.J.C.)
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16
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Hartinger T, Zebeli Q. The Present Role and New Potentials of Anaerobic Fungi in Ruminant Nutrition. J Fungi (Basel) 2021; 7:200. [PMID: 33802104 PMCID: PMC8000393 DOI: 10.3390/jof7030200] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 01/18/2023] Open
Abstract
The ruminal microbiota allows ruminants to utilize fibrous feeds and is in the limelight of ruminant nutrition research for many years. However, the overwhelming majority of investigations have focused on bacteria, whereas anaerobic fungi (AF) have been widely neglected by ruminant nutritionists. Anaerobic fungi are not only crucial fiber degraders but also important nutrient sources for the host. This review summarizes the current findings on AF and, most importantly, discusses their new application potentials in modern ruminant nutrition. Available data suggest AF can be applied as direct-fed microbials to enhance ruminal fiber degradation, which is indeed of interest for high-yielding dairy cows that often show depressed ruminal fibrolysis in response to high-grain feeding. Moreover, these microorganisms have relevance for the nutrient supply and reduction of methane emissions. However, to reach AF-related improvements in ruminal fiber breakdown and animal performance, obstacles in large-scale AF cultivation and applicable administration options need to be overcome. At feedstuff level, silage production may benefit from the application of fungal enzymes that cleave lignocellulosic structures and consequently enable higher energy exploitation from forages in the rumen. Concluding, AF hold several potentials in improving ruminant feeding and future research efforts are called for to harness these potentials.
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Affiliation(s)
- Thomas Hartinger
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, 1210 Vienna, Austria;
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17
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Li Y, Meng Z, Xu Y, Shi Q, Ma Y, Aung M, Cheng Y, Zhu W. Interactions between Anaerobic Fungi and Methanogens in the Rumen and Their Biotechnological Potential in Biogas Production from Lignocellulosic Materials. Microorganisms 2021; 9:190. [PMID: 33477342 PMCID: PMC7830786 DOI: 10.3390/microorganisms9010190] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/29/2022] Open
Abstract
Anaerobic fungi in the digestive tract of herbivores are one of the critical types of fiber-degrading microorganisms present in the rumen. They degrade lignocellulosic materials using unique rhizoid structures and a diverse range of fiber-degrading enzymes, producing metabolic products such as H2/CO2, formate, lactate, acetate, and ethanol. Methanogens in the rumen utilize some of these products (e.g., H2 and formate) to produce methane. An investigation of the interactions between anaerobic fungi and methanogens is helpful as it provides valuable insight into the microbial interactions within the rumen. During the last few decades, research has demonstrated that anaerobic fungi stimulate the growth of methanogens and maintain methanogenic diversity. Meanwhile, methanogens increase the fiber-degrading capability of anaerobic fungi and stimulate metabolic pathways in the fungal hydrogenosome. The ability of co-cultures of anaerobic fungi and methanogens to degrade fiber and produce methane could potentially be a valuable method for the degradation of lignocellulosic materials and methane production.
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Affiliation(s)
- Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Zhenxiang Meng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Yao Xu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Qicheng Shi
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Yuping Ma
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Min Aung
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
- Department of Animal Nutrition, University of Veterinary Science, Nay Pyi Taw 15013, Myanmar
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
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18
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Hauk P, Stephens K, Virgile C, VanArsdale E, Pottash AE, Schardt JS, Jay SM, Sintim HO, Bentley WE. Homologous Quorum Sensing Regulatory Circuit: A Dual-Input Genetic Controller for Modulating Quorum Sensing-Mediated Protein Expression in E. coli. ACS Synth Biol 2020; 9:2692-2702. [PMID: 32822530 DOI: 10.1021/acssynbio.0c00179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We developed a hybrid synthetic circuit that co-opts the genetic regulation of the native bacterial quorum sensing autoinducer-2 and imposes an extra external controller for maintaining tightly controlled gene expression. This dual-input genetic controller was mathematically modeled and, by design, can be operated in three modes: a constitutive mode that enables consistent and high levels of expression; a tightly repressed mode in which there is very little background expression; and an inducible mode in which concentrations of two signals (arabinose and autoinducer-2) determine the net amplification of the gene(s)-of-interest. We demonstrate the utility of the circuit for the controlled expression of human granulocyte macrophage colony stimulating factor in an engineered probiotic E. coli. This dual-input genetic controller is the first homologous AI-2 quorum sensing circuit that has the ability to be operated in three different modes. We believe it has the potential for wide-ranging biotechnological applications due its versatile features.
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Affiliation(s)
- Pricila Hauk
- Institute for Bioscience and Biotechnology Research, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Kristina Stephens
- Institute for Bioscience and Biotechnology Research, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
| | - Chelsea Virgile
- Institute for Bioscience and Biotechnology Research, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Eric VanArsdale
- Institute for Bioscience and Biotechnology Research, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
| | - Alex Eli Pottash
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - John S. Schardt
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Steven M. Jay
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Herman O. Sintim
- Department of Chemistry and Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - William E. Bentley
- Institute for Bioscience and Biotechnology Research, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
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19
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Vinzelj J, Joshi A, Insam H, Podmirseg SM. Employing anaerobic fungi in biogas production: challenges & opportunities. BIORESOURCE TECHNOLOGY 2020; 300:122687. [PMID: 31926794 DOI: 10.1016/j.biortech.2019.122687] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/21/2019] [Accepted: 12/23/2019] [Indexed: 05/24/2023]
Abstract
Anaerobic fungi (AF, phylum Neocallimastigomycota) are best known for their ability to efficiently break down lignocellulosic biomass. Their unique combination of mechanical and enzymatic attacks on recalcitrant plant structures bears great potential for enhancement of the anaerobic digestion (AD) process. Although scientists in this field have long agreed upon the potential of AF for biotechnology, research is only recently gaining traction. This delay was largely due to difficulties in culture-dependent and culture-independent analysis of those high-maintenance organisms with their still unknown complex growth requirements. In this review, we will summarize current research efforts on bioaugmentation with AF and further point out, how the lack of basic knowledge on AF nutritional needs hampers their implementation on an industrial scale. Through this, we hope to further kindle interest into basic research on AF in order to advance their stable integration into biotechnological processes.
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Affiliation(s)
- Julia Vinzelj
- Institute of Microbiology, University of Innsbruck, Technikerstraße 25d, A-6020 Innsbruck, Austria
| | - Akshay Joshi
- ZHAW School of Life Sciences and Facility Management, Einsiedlerstrasse 31, CH-8820 Wädenswil, Switzerland
| | - Heribert Insam
- Institute of Microbiology, University of Innsbruck, Technikerstraße 25d, A-6020 Innsbruck, Austria
| | - Sabine Marie Podmirseg
- Institute of Microbiology, University of Innsbruck, Technikerstraße 25d, A-6020 Innsbruck, Austria
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20
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Lawson CE, Harcombe WR, Hatzenpichler R, Lindemann SR, Löffler FE, O'Malley MA, García Martín H, Pfleger BF, Raskin L, Venturelli OS, Weissbrodt DG, Noguera DR, McMahon KD. Common principles and best practices for engineering microbiomes. Nat Rev Microbiol 2019; 17:725-741. [PMID: 31548653 PMCID: PMC8323346 DOI: 10.1038/s41579-019-0255-9] [Citation(s) in RCA: 231] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2019] [Indexed: 12/16/2022]
Abstract
Despite broad scientific interest in harnessing the power of Earth's microbiomes, knowledge gaps hinder their efficient use for addressing urgent societal and environmental challenges. We argue that structuring research and technology developments around a design-build-test-learn (DBTL) cycle will advance microbiome engineering and spur new discoveries of the basic scientific principles governing microbiome function. In this Review, we present key elements of an iterative DBTL cycle for microbiome engineering, focusing on generalizable approaches, including top-down and bottom-up design processes, synthetic and self-assembled construction methods, and emerging tools to analyse microbiome function. These approaches can be used to harness microbiomes for broad applications related to medicine, agriculture, energy and the environment. We also discuss key challenges and opportunities of each approach and synthesize them into best practice guidelines for engineering microbiomes. We anticipate that adoption of a DBTL framework will rapidly advance microbiome-based biotechnologies aimed at improving human and animal health, agriculture and enabling the bioeconomy.
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Affiliation(s)
- Christopher E Lawson
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA.
| | - William R Harcombe
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | | | - Frank E Löffler
- Center for Environmental Biotechnology, University of Tennessee-Knoxville, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbra, CA, USA
- DOE Joint Bioenergy Institute, Emeryville, CA, USA
| | - Héctor García Martín
- DOE Joint Bioenergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- DOE Agile BioFoundry, Emeryville, CA, USA
- Basque Center for Applied Mathematics, Bilbao, Spain
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Ophelia S Venturelli
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Daniel R Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, Madison, WI, USA
| | - Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
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21
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Lillington SP, Leggieri PA, Heom KA, O'Malley MA. Nature's recyclers: anaerobic microbial communities drive crude biomass deconstruction. Curr Opin Biotechnol 2019; 62:38-47. [PMID: 31593910 DOI: 10.1016/j.copbio.2019.08.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/25/2019] [Accepted: 08/29/2019] [Indexed: 12/13/2022]
Abstract
Microbial communities within anaerobic ecosystems have evolved to degrade and recycle carbon throughout the earth. A number of strains have been isolated from anaerobic microbial communities, which are rich in carbohydrate active enzymes (CAZymes) to liberate fermentable sugars from crude plant biomass (lignocellulose). However, natural anaerobic communities host a wealth of microbial diversity that has yet to be harnessed for biotechnological applications to hydrolyze crude biomass into sugars and value-added products. This review highlights recent advances in 'omics' techniques to sequence anaerobic microbial genomes, decipher microbial membership, and characterize CAZyme diversity in anaerobic microbiomes. With a focus on the herbivore rumen, we further discuss methods to discover new CAZymes, including those found within multi-enzyme fungal cellulosomes. Emerging techniques to characterize the interwoven metabolism and spatial interactions between anaerobes are also reviewed, which will prove critical to developing a predictive understanding of anaerobic communities to guide in microbiome engineering.
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Affiliation(s)
- Stephen P Lillington
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, United States
| | - Patrick A Leggieri
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, United States
| | - Kellie A Heom
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, United States
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, United States.
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22
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Gilmore SP, Lankiewicz TS, Wilken SE, Brown JL, Sexton JA, Henske JK, Theodorou MK, Valentine DL, O’Malley MA. Top-Down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation. ACS Synth Biol 2019; 8:2174-2185. [PMID: 31461261 DOI: 10.1021/acssynbio.9b00271] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Consortium-based approaches are a promising avenue toward efficient bioprocessing. However, many complex microbial interactions dictate community dynamics and stability that must be replicated in synthetic systems. The rumen and/or hindguts of large mammalian herbivores harbor complex communities of biomass-degrading fungi and bacteria, as well as archaea and protozoa that work collectively to degrade lignocellulose, yet the microbial interactions responsible for stability, resilience, and activity of the community remain largely uncharacterized. In this work, we demonstrate a "top-down" enrichment-based methodology for selecting a minimal but effective lignocellulose-degrading community that produces methane-rich fermentation gas (biogas). The resulting enrichment consortium produced 0.75-1.9-fold more fermentation gas at 1.4-2.1 times the rate compared to a monoculture of fungi from the enrichment. Metagenomic sequencing of the top-down enriched consortium revealed genomes encoding for functional compartmentalization of the community, spread across an anaerobic fungus (Piromyces), a bacterium (Sphaerochaeta), and two methanogenic archaea (Methanosphaera and Methanocorpusculum). Guided by the composition of the top-down enrichment, several synthetic cocultures were formed from the "bottom-up" using previously isolated fungi, Neocallimastix californiae and Anaeromyces robustus paired with the methanogen Methanobacterium bryantii. While cross-feeding occurred in synthetic co-cultures, removal of fungal metabolites by methanogens did not increase the rate of gas production or the rate of substrate deconstruction by the synthetic community relative to fungal monocultures. Metabolomic characterization verified that syntrophy was established within synthetic co-cultures, which generated methane at similar concentrations compared to the enriched consortium but lacked the temporal stability (resilience) seen in the native system. Taken together, deciphering the membership and metabolic potential of an enriched gut consortium enables the design of methanogenic synthetic co-cultures. However, differences in the growth rate and stability of enriched versus synthetic consortia underscore the difficulties in mimicking naturally occurring syntrophy in synthetic systems.
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Affiliation(s)
- Sean P. Gilmore
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Thomas S. Lankiewicz
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - St. Elmo Wilken
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Jennifer L. Brown
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Jessica A. Sexton
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - John K. Henske
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michael K. Theodorou
- Harper Adams University, Agriculture Centre for Sustainable Energy Systems, Newport, Shropshire TF10 8NB, United Kingdom
| | - David L. Valentine
- Department of Earth Science and Marine Science Institute, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
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