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Wei Y, Yang H, Wang Z, Zhao J, Qi H, Wang C, Zhang J, Yang T. Roughage biodegradation by natural co-cultures of rumen fungi and methanogens from Qinghai yaks. AMB Express 2022; 12:123. [PMID: 36121525 PMCID: PMC9485394 DOI: 10.1186/s13568-022-01462-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 09/10/2022] [Indexed: 11/10/2022] Open
Abstract
Anaerobic fungus–methanogen co-cultures from rumen liquids and faeces can degrade lignocellulose efficiently. In this study, 31 fungus–methanogen co-cultures were first obtained from the rumen of yaks grazing in Qinghai Province, China, using the Hungate roll-tube technique. The fungi were identified according to morphological characteristics and internal transcribed spacer (ITS) sequences. The methanogens associated with each fungus were identified by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rRNA gene sequencing. They were five co-culture types: Neocallimastix frontalis + Methanobrevibacter ruminantium, Neocallimastix frontalis + Methanobrevibacter gottschalkii, Orpinomyces joyonii + Methanobrevibacter ruminantium, Caecomyces communis + Methanobrevibacter ruminantium, and Caecomyces communis + Methanobrevibacter millerae. Among the 31 co-cultures, during the 5-day incubation, the N. frontalis + M. gottschalkii co-culture YakQH5 degraded 59.0%–68.1% of the dry matter (DM) and 49.5%–59.7% of the neutral detergent fiber (NDF) of wheat straw, corn stalk, rice straw, oat straw and sorghum straw to produce CH4 (3.0–4.6 mmol/g DM) and acetate (7.3–8.6 mmol/g DM) as end-products. Ferulic acid (FA) released at 4.8 mg/g DM on corn stalk and p-coumaric acid (PCA) released at 11.7 mg/g DM on sorghum straw showed the highest values, with the following peak values of enzyme activities: xylanase at 12,910 mU/mL on wheat straw, ferulic acid esterase (FAE) at 10.5 mU/mL on corn stalk, and p-coumaric acid esterase (CAE) at 20.5 mU/mL on sorghum straw. The N. frontalis + M. gottschalkii co-culture YakQH5 from Qinghai yaks represents a new efficient combination for lignocellulose biodegradation, performing better than previously reported fungus–methanogen co-cultures from the digestive tract of ruminants.
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Affiliation(s)
- Yaqin Wei
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China. .,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China.
| | - Hui Yang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Zhiye Wang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Jiang Zhao
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Hongshan Qi
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Chuan Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730000, People's Republic of China
| | - Jingrong Zhang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Tao Yang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
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YÜCEL H, EKİNCİ K. Carbohydrate active enzyme system in rumen fungi: a review. INTERNATIONAL JOURNAL OF SECONDARY METABOLITE 2022. [DOI: 10.21448/ijsm.1075030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Hydrolysis and dehydration reactions of carbohydrates, which are used as energy raw materials by all living things in nature, are controlled by Carbohydrate Active Enzyme (CAZy) systems. These enzymes are also used in different industrial areas today. There are different types of microorganisms that have the CAZy system and are used in the industrial sector. Apart from current organisms, there are also rumen fungi within the group of candidate microorganisms with the CAZy system. It has been reported that xylanase (EC3.2.1.8 and EC3.2.1.37) enzyme, a member of the glycoside hydrolase enzyme family obtained from Trichoderma sp. and used especially in areas such as bread, paper, and feed industry, is more synthesized in rumen fungi such as Orpinomyces sp. and Neocallimastix sp. Therefore, this study reviews Neocallimastixsp., Orpinomyces sp., Caecomyces sp., Piromyces sp., and Anaeromyces sp., registered in the CAZy and Mycocosm database for rumen fungi to have both CAZy enzyme activity and to be an alternative microorganism in the industry. Furthermore the CAZy enzyme activities of the strains are investigated. The review shows thatNeocallimax sp. and Orpinomyces sp. areconsidered as candidate microorganisms.
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Affiliation(s)
- Halit YÜCEL
- KAHRAMANMARAŞ SÜTÇÜ İMAM ÜNİVERSİTESİ, ZİRAAT FAKÜLTESİ
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Chang J, Park H. Nucleotide and protein researches on anaerobic fungi during four decades. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2020; 62:121-140. [PMID: 32292921 PMCID: PMC7142291 DOI: 10.5187/jast.2020.62.2.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/07/2020] [Accepted: 03/07/2020] [Indexed: 01/26/2023]
Abstract
Anaerobic fungi habitat in the gastrointestinal tract of foregut fermenters or
hindgut fermenters and degrade fibrous plant biomass through the hydrolysis
reactions with a wide variety of cellulolytic enzymes and physical penetration
through fiber matrix with their rhizoids. To date, seventeen genera have been
described in family Neocallimasticaceae, class
Neocallimastigomycetes, phylum
Neocallimastigomycota and one genus has been described in
phylum Neocallimastigomycota. In National Center for
Biotechnology Information (NCBI) database (DB), 23,830 nucleotide sequences and
59,512 protein sequences have been deposited and most of them were originated
from Piromyces, Neocallimastix and
Anaeromyces. Most of protein sequences (44,025) were
acquired with PacBio next generation sequencing system. The whole genome
sequences of Anaeromyces robustus, Neocallimastix
californiae, Pecoramyces ruminantium,
Piromyces finnis and Piromyces sp. E2 are
available in Joint Genome Institute (JGI) database. According to the results of
protein prediction, average Isoelectric points (pIs) were ranged from 5.88
(Anaeromyces) to 6.57 (Piromyces) and
average molecular weights were ranged from 38.7 kDa
(Orpinomyces) to 56.6 kDa (Piromyces). In
Carbohydrate-Active enZYmes (CAZY) database, glycoside hydrolases (36),
carbohydrate binding module (11), carbohydrate esterases (8),
glycosyltransferase (5) and polysaccharide lyases (3) from anaerobic fungi were
registered. During four decades, 1,031 research articles about anaerobic fungi
were published and 444 and 719 articles were available in PubMed (PM) and PubMed
Central (PMC) DB.
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Affiliation(s)
- Jongsoo Chang
- Department of Agricultural Sciences, Korea National Open University, Seoul 03087, Korea
| | - Hyunjin Park
- Department of Agricultural Sciences, Korea National Open University, Seoul 03087, Korea
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Calkins SS, Elledge NC, Mueller KE, Marek SM, Couger MB, Elshahed MS, Youssef NH. Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. PeerJ 2018; 6:e4276. [PMID: 29404209 PMCID: PMC5796279 DOI: 10.7717/peerj.4276] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/29/2017] [Indexed: 12/25/2022] Open
Abstract
Members of the anaerobic gut fungi (AGF) reside in rumen, hindgut, and feces of ruminant and non-ruminant herbivorous mammals and reptilian herbivores. No protocols for gene insertion, deletion, silencing, or mutation are currently available for the AGF, rendering gene-targeted molecular biological manipulations unfeasible. Here, we developed and optimized an RNA interference (RNAi)-based protocol for targeted gene silencing in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. Analysis of the C1A genome identified genes encoding enzymes required for RNA silencing in fungi (Dicer, Argonaute, Neurospora crassa QDE-3 homolog DNA helicase, Argonaute-interacting protein, and Neurospora crassa QIP homolog exonuclease); and the competency of C1A germinating spores for RNA uptake was confirmed using fluorescently labeled small interfering RNAs (siRNA). Addition of chemically-synthesized siRNAs targeting D-lactate dehydrogenase (ldhD) gene to C1A germinating spores resulted in marked target gene silencing; as evident by significantly lower ldhD transcriptional levels, a marked reduction in the D-LDH specific enzymatic activity in intracellular protein extracts, and a reduction in D-lactate levels accumulating in the culture supernatant. Comparative transcriptomic analysis of untreated versus siRNA-treated cultures identified a few off-target siRNA-mediated gene silencing effects. As well, significant differential up-regulation of the gene encoding NAD-dependent 2-hydroxyacid dehydrogenase (Pfam00389) in siRNA-treated C1A cultures was observed, which could possibly compensate for loss of D-LDH as an electron sink mechanism in C1A. The results demonstrate the feasibility of RNAi in anaerobic fungi, and opens the door for gene silencing-based studies in this fungal clade.
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Affiliation(s)
- Shelby S Calkins
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Nicole C Elledge
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,Current affiliation: University of Texas A&M Corpus Christi, Department of Life Sciences, Marine Biology Program, USA
| | - Katherine E Mueller
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Stephen M Marek
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA
| | - M B Couger
- High Performance Computing Center, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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