Transcriptomic Characterization of Caecomyces Churrovis: a Novel, Non‑Rhizoid‑Forming Lignocellulolytic Anaerobic Fungus John K

Total Page:16

File Type:pdf, Size:1020Kb

Transcriptomic Characterization of Caecomyces Churrovis: a Novel, Non‑Rhizoid‑Forming Lignocellulolytic Anaerobic Fungus John K Henske et al. Biotechnol Biofuels (2017) 10:305 https://doi.org/10.1186/s13068-017-0997-4 Biotechnology for Biofuels RESEARCH Open Access Transcriptomic characterization of Caecomyces churrovis: a novel, non‑rhizoid‑forming lignocellulolytic anaerobic fungus John K. Henske1, Sean P. Gilmore1, Doriv Knop1, Francis J. Cunningham1, Jessica A. Sexton1, Chuck R. Smallwood2, Vaithiyalingam Shutthanandan2, James E. Evans2, Michael K. Theodorou3 and Michelle A. O’Malley1* Abstract Anaerobic gut fungi are the primary colonizers of plant material in the rumen microbiome, but are poorly studied due to a lack of characterized isolates. While most genera of gut fungi form extensive rhizoidal networks, which likely participate in mechanical disruption of plant cell walls, fungi within the Caecomyces genus do not possess these rhizoids. Here, we describe a novel fungal isolate, Caecomyces churrovis, which forms spherical sporangia with a limited rhizoidal network yet secretes a diverse set of carbohydrate active enzymes (CAZymes) for plant cell wall hydrolysis. Despite lacking an extensive rhizoidal system, C. churrovis is capable of growth on fbrous substrates like switchgrass, reed canary grass, and corn stover, although faster growth is observed on soluble sugars. Gut fungi have been shown to use enzyme complexes (fungal cellulosomes) in which CAZymes bind to non-catalytic scafoldins to improve bio- mass degradation efciency. However, transcriptomic analysis and enzyme activity assays reveal that C. churrovis relies more on free enzymes compared to other gut fungal isolates. Only 15% of CAZyme transcripts contain non-catalytic dockerin domains in C. churrovis, compared to 30% in rhizoid-forming fungi. Furthermore, C. churrovis is enriched in GH43 enzymes that provide complementary hemicellulose degrading activities, suggesting that a wider variety of these activities are required to degrade plant biomass in the absence of an extensive fungal rhizoid network. Overall, molecular characterization of a non-rhizoid-forming anaerobic fungus flls a gap in understanding the roles of CAZyme abundance and associated degradation mechanisms during lignocellulose breakdown within the rumen microbiome. Keywords: Anaerobic fungi, Neocallimastigomycota, Cellulase, Enzyme, Cellulosome Background application in the production of lignocellulose-derived Anaerobic gut fungi are robust degraders of plant bio- chemical products [6]. Most known genera (Anaeromy- mass in the guts of ruminants and other large monogas- ces, Buwchfawromyces, Neocallimastix, Oontomyces, tric herbivorous mammals [1]. Tey have also been Orpinomyces, Pecoramyces, Piromyces) of gut fungi have identifed using microscopy and molecular methodolo- an extensive network of penetrating rhizoids (tapering gies in the digestive tract of herbivorous reptiles [2]. Due mycelia) that aid, alongside enzymatic activity, in biomass to the large amount of biomass-degrading enzymes that colonization and deconstruction [7–11]. However, two these organisms secrete [3–5], they have potential for known genera within the clade of anaerobic fungi (Cae- comyces, Cyllamyces) do not produce rhizoidal networks, *Correspondence: [email protected] but form a limited system simply capable of attaching to 1 Department of Chemical Engineering, University of California, Santa plant biomass [7, 12]. However, like their rhizoidal coun- Barbara, CA 93106, USA Full list of author information is available at the end of the article terparts, non-rhizoid producing gut fungi are profcient © The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Henske et al. Biotechnol Biofuels (2017) 10:305 Page 2 of 12 degraders of crude plant biomass. Tis raises the possi- Microscopic analysis suggested that C. churrovis is a bility that there are diferences between the diversity of monocentric fungus, and confrmed that it does not pos- enzymes employed by rhizoid-forming vs. non-rhizoid- sess an extensive rhizoidal network to penetrate biomass. forming fungi, and/or the mechanisms they use for enzy- Rather, C. churrovis forms a large, spherical sporangium matic degradation of lignocellulose. with holdfast structures to attach it to plant biomass While there is a general lack of genomic information and other solid substrates (Fig. 1). Although there is not for the Neocallimastigomycota, recently fve complete an extensive rhizoidal network that aids in biomass dis- genomes and transcriptomes have been published for ruption, these fungi still localize to, and colonize, the rhizoid-forming anaerobic fungi—two representatives cellulose-rich surface of plant biomass. Figure 1 shows from the Piromyces genus, one each from Anaeromy- sections of plant material almost entirely covered in C. ces and Neocallimastix [13], and one from Orpinomyces churrovis sporangia. Sporangia are present within a range [14] (recently reclassifed as Pecoramyces [10]). Interest- of sizes, some near 20 µm in diameter, while others are ingly, this wealth of sequencing data has revealed that greater than 50 µm in diameter. Furthermore, Fig. 1B anaerobic fungi can draw from two modes of biomass- highlights the lytic life cycle of gut fungi, as a fraction degradation via the secretion of freely difusive enzymes of colonized mature zoosporangia rupture and collapse as well as via fungal cellulosomes (complexes of enzymes over time, releasing the cellular contents and motile zoo- tethered together for synergistic action) [13]. However, spores. Tese zoospores likely chemotax towards a car- at the present time, no high-resolution transcriptomic or bon source (e.g., biomass) and initiate the formation of genomic information has been reported for non-rhizoid- new monocentric sporangia. forming isolates. Tis precludes insight into the enzy- While morphological characterization indicates that matic machinery of non-rhizoid-forming fungi, or the the isolated fungal strain is likely a member of the Cae- mode of biomass degradation that they favor. comyces genus, anaerobic fungi are often pleomorphic Here, we describe a novel species of non-rhizoid- and require phylogenetic analysis of conserved genomic forming fungi belonging to the Caecomyces genus iso- sequences to confrm classifcation. Te internal tran- lated from the fecal pellets of a Navajo Churro sheep scribed spacer (ITS) regions are commonly used to deter- collected in 2015. While other Caecomyces isolates mine the genera of newly isolated fungi [18–21]. Te ITS1 have been described using morphological and phyloge- and ITS2 regions for C. churrovis (GenBank #MF460993) netic analyses [15, 16], including some analysis of the were amplifed and sequenced using PCR primers JB206 cellulolytic enzyme activity [17], extensive genomic or and JB205 [20], and subjected to phylogenetic analysis. transcriptomic sequencing has not been completed. By Given the abundance of ITS1 sequences deposited in assembling the frst sequenced transcriptome for an GenBank, we relied primarily on comparative alignment anaerobic gut fungus within the Caecomyces genus, C. with this region for preliminary identifcation and classi- churrovis, our analysis enabled us to identify the range of fcation. While other neighboring DNA sequences, such CAZymes available to a non-rhizoidal genus and test the as the ITS2 [20] and large subunit (28S) [22], have been null hypothesis that additional degradation mechanisms, used for phylogenetic analysis, restricting our analysis mechanical or enzymatic, are not required for dissolu- to ITS1 enabled comparison with the maximum num- tion of plant biomass. Tis isolated fungal strain was ber of GenBank submissions. From this analysis (Fig. 2), assessed for its ability to grow on a range of substrates, the isolated strain C. churrovis clearly clusters with other and demonstrated a greater preference for soluble sub- Caecomyces fungi. Subsequently, additional phylogenetic strates compared to other rhizoid-forming strains that analysis was completed using only sequences from fungi have been analyzed to date [5]. Transcriptome assem- within the Caecomyces genus to ensure that this isolated bly and analysis identifed a broad range of CAZymes strain was signifcantly divergent from previously char- within the genome, including a relative abundance of acterized strains to constitute its classifcation as a novel carbohydrate esterase and hemicellulase (GH 11/12, 43) species. Generation of the phylogenetic tree isolated C. transcripts. Comparison to other sequenced gut fungal churrovis from other Caecomyces strains with a bootstrap isolates also revealed a greater reliance on free enzymes value of 98, indicating that this node occurred in 98% of rather than enzymes bound in fungal cellulosome trees generated during the bootstrap analysis (Additional complexes. fle 1: Figure S1). Tus, the ITS1 region of C. churrovis was signifcantly diferent compared to other Caecomyces Results and discussion strains with ITS1 sequences available on GenBank, sug- Isolation and molecular classifcation of C.
Recommended publications
  • A Parts List for Fungal Cellulosomes Revealed by Comparative Genomics Charles H
    LETTERS PUBLISHED: 30 MAY 2017 | VOLUME: 2 | ARTICLE NUMBER: 17087 A parts list for fungal cellulosomes revealed by comparative genomics Charles H. Haitjema1, Sean P. Gilmore1,JohnK.Henske1, Kevin V. Solomon1†, Randall de Groot1, Alan Kuo2, Stephen J. Mondo2, Asaf A. Salamov2, Kurt LaButti2, Zhiying Zhao2, Jennifer Chiniquy2, Kerrie Barry2, Heather M. Brewer3,SamuelO.Purvine3,AaronT.Wright4, Matthieu Hainaut5,6, Brigitte Boxma7,TheovanAlen7†, Johannes H. P. Hackstein7, Bernard Henrissat5,6,8, Scott E. Baker3, Igor V. Grigoriev2,9 and Michelle A. O’Malley1* Cellulosomes are large, multiprotein complexes that tether enzyme transcripts yet found in nature7. The vast majority of plant biomass-degrading enzymes together for improved these enzymes carry non-catalytic dockerin domains (NCDDs), hydrolysis1. These complexes were first described in anaerobic which mediate assembly into large multiprotein complexes, or bacteria, where species-specific dockerin domains mediate the cellulosomes7. Cellulosomes were first described in anaerobic assembly of enzymes onto cohesin motifs interspersed within bacteria, and the modular interaction scheme native to these protein scaffolds1. The versatile protein assembly mechanism complexes has rapidly been exploited for biomass conversion and conferred by the bacterial cohesin–dockerin interaction is now enzyme tethering applications8–10. However, since the first report a standard design principle for synthetic biology2,3.For of cellulosome-like structures in anaerobic fungi more than decades, analogous structures have been reported in anaerobic twenty years ago11, the identification of dockerin-binding cohesins, fungi, which are known to assemble by sequence-divergent or scaffoldins that mediate assembly, has yet to be accomplished non-catalytic dockerin domains (NCDDs)4. However, the due to a lack of genomic data, functional proteomics and components, modular assembly mechanism and functional characterized strains.
    [Show full text]
  • Hydrolysis of Untreated Lignocellulosic Feedstock Is Independent of S-Lignin
    Hooker et al. Biotechnol Biofuels (2018) 11:293 https://doi.org/10.1186/s13068-018-1292-8 Biotechnology for Biofuels RESEARCH Open Access Hydrolysis of untreated lignocellulosic feedstock is independent of S‑lignin composition in newly classifed anaerobic fungal isolate, Piromyces sp. UH3‑1 Casey A. Hooker1,2, Ethan T. Hillman1,3, Jonathan C. Overton1,2, Adrian Ortiz‑Velez1, Makayla Schacht4, Abigail Hunnicutt1, Nathan S. Mosier1,2 and Kevin V. Solomon1,2,3* Abstract Background: Plant biomass is an abundant but underused feedstock for bioenergy production due to its complex and variable composition, which resists breakdown into fermentable sugars. These feedstocks, however, are routinely degraded by many uncommercialized microbes such as anaerobic gut fungi. These gut fungi express a broad range of carbohydrate active enzymes and are native to the digestive tracts of ruminants and hindgut fermenters. In this study, we examine gut fungal performance on these substrates as a function of composition, and the ability of this isolate to degrade inhibitory high syringyl lignin-containing forestry residues. Results: We isolated a novel fungal specimen from a donkey in Independence, Indiana, United States. Phylogenetic analysis of the Internal Transcribed Spacer 1 sequence classifed the isolate as a member of the genus Piromyces within the phylum Neocallimastigomycota (Piromyces sp. UH3-1, strain UH3-1). The isolate penetrates the substrate with an extensive rhizomycelial network and secretes many cellulose-binding enzymes, which are active on various components of lignocellulose. These activities enable the fungus to hydrolyze at least 58% of the glucan and 28% of the available xylan in untreated corn stover within 168 h and support growth on crude agricultural residues, food waste, and energy crops.
    [Show full text]
  • The Cellulosome Paradigm in an Extreme Alkaline Environment Paripok Phitsuwan, Sarah Moraïs, Bareket Dassa, Bernard Henrissat, Edward Bayer
    The Cellulosome Paradigm in An Extreme Alkaline Environment Paripok Phitsuwan, Sarah Moraïs, Bareket Dassa, Bernard Henrissat, Edward Bayer To cite this version: Paripok Phitsuwan, Sarah Moraïs, Bareket Dassa, Bernard Henrissat, Edward Bayer. The Cellulo- some Paradigm in An Extreme Alkaline Environment. Microorganisms, MDPI, 2019, 7 (9), pp.347. 10.3390/microorganisms7090347. hal-02612575 HAL Id: hal-02612575 https://hal-amu.archives-ouvertes.fr/hal-02612575 Submitted on 19 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License microorganisms Article The Cellulosome Paradigm in An Extreme Alkaline Environment 1, 1,2 1 3,4 Paripok Phitsuwan y, Sarah Moraïs , Bareket Dassa , Bernard Henrissat and Edward A. Bayer 1,* 1 Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel 2 Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8499000, Israel 3 Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille University and CNRS, 13288 Marseille, France 4 USC1408, INRA, Architecture et Fonction des Macromolécules Biologiques, 13288 Marseille, France * Correspondence: [email protected] Present address: Division of Biochemical Technology, School of Bioresources and Technology, y King Mongkut’s University of Technology Thonburi, Bangkuntien, Bangkok 10150, Thailand.
    [Show full text]
  • Sequence Based Prediction of Novel Domains in the Cellulosome of Ruminiclostridium Thermocellum
    bioRxiv preprint doi: https://doi.org/10.1101/066357; this version posted July 27, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Sequence based prediction of novel domains in the cellulosome of Ruminiclostridium thermocellum Zarrin Basharat, Azra Yasmin* Microbiology & Biotechnology Research Lab, Department of Environmental Sciences, Fatima Jinnah Women University, 46000, Pakistan *Corresponding author Email:[email protected] Abstract Ruminiclostridium thermocellum strain ATCC 27405 is valuable with reference to the next generation biofuel production being a degrader of crystalline cellulose. The completion of its genome sequence has revealed that this organism carries 3,376 genes with more than hundred genes encoding for enzymes involved in cellulysis. Novel protein domain discovery in the cellulose degrading enzyme complex of this strain has been attempted to understand this organism at molecular level. Streamlined automated methods were employed to generate possibly unreported or new domains. A set of 12 novel Pfam-B domains was developed after detailed analysis. This finding will enhance our understanding of this bacterium and its molecular processes involved in the degradation of cellulose. This approach of in silico analysis prior to experimentation facilitates in lab study. Previously uncorrelated data has been utilized for rapid generation of new biological information in this study. Keywords: Domain prediction, in silico, R. thermocellum, cellulosome. Note: This research was conducted in 2014 for Clostridium thermocellum ATCC 27405. The bacterium was later reannotated as Ruminiclostridium thermocellum.
    [Show full text]
  • Non-Cellulosomal Cohesin- and Dockerin-Like Modules in the Three Domains of Life Ayelet Peera, Steven P
    1 Non-cellulosomal Cohesin- and Dockerin-like Modules in the Three Domains of Life Ayelet Peera, Steven P. Smithb, Edward A. Bayerc,*, Raphael Lameda and Ilya Borovoka aDepartment of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978 Israel bDepartment of Biochemistry, Queen’s University Kingston Ontario Canada K7L 3N6 cDepartment of Biological Sciences, Weizmann Institute of Science, Rehovot 76100 Israel *Corresponding author: Edward A. Bayer Tel: (+972) -8-934-2373 Fax: (+972)-8-946-8256 Email: [email protected] Supplementary Table S1. Compendium of cohesins and dockerins in the three domains of life. In order to discover new putative cohesin/dockerin-containing proteins, we used sequences of all the classical cohesin and dockerin modules from C. thermocellum, C. cellulovorans, C. cellulolyticum, B. cellulosolvens and Acetivibrio cellulolyticus as well as cohesins and dockerins recently discovered in rumen bacteria, Ruminococcus albus and R. flavefaciens as BlastP queries for the main NCBI Blast server against all non- redundant protein sequences deposited in GenBank/EMBL/DDBJ databases. We also performed extensive searches using the TblastN algorithm through all publicly available microbial genome databases including those attached to the NCBI BLAST server for bacterial genomes (http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi?), as well as several additional microbial genome databases – Microbial Genomics at the DOE Joint Genome Institute (http://genome.jgi-psf.org/mic_home.html), the Rumenomics database at TIGR/JCVI (http://tigrblast.tigr.org/rumenomics/index.cgi) and Bacterial Genomes at the Sanger Centre (http://www.sanger.ac.uk/Projects/Microbes/). Once a putative cohesin or dockerin-encoding gene product was identified, gene-walking techniques were employed to analyze and locate possible cellulosome-like gene clusters.
    [Show full text]
  • S41467-021-25308-W.Pdf
    ARTICLE https://doi.org/10.1038/s41467-021-25308-w OPEN Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota ✉ ✉ Luis Javier Galindo 1 , Purificación López-García 1, Guifré Torruella1, Sergey Karpov2,3 & David Moreira 1 Compared to multicellular fungi and unicellular yeasts, unicellular fungi with free-living fla- gellated stages (zoospores) remain poorly known and their phylogenetic position is often 1234567890():,; unresolved. Recently, rRNA gene phylogenetic analyses of two atypical parasitic fungi with amoeboid zoospores and long kinetosomes, the sanchytrids Amoeboradix gromovi and San- chytrium tribonematis, showed that they formed a monophyletic group without close affinity with known fungal clades. Here, we sequence single-cell genomes for both species to assess their phylogenetic position and evolution. Phylogenomic analyses using different protein datasets and a comprehensive taxon sampling result in an almost fully-resolved fungal tree, with Chytridiomycota as sister to all other fungi, and sanchytrids forming a well-supported, fast-evolving clade sister to Blastocladiomycota. Comparative genomic analyses across fungi and their allies (Holomycota) reveal an atypically reduced metabolic repertoire for sanchy- trids. We infer three main independent flagellum losses from the distribution of over 60 flagellum-specific proteins across Holomycota. Based on sanchytrids’ phylogenetic position and unique traits, we propose the designation of a novel phylum, Sanchytriomycota. In addition, our results indicate that most of the hyphal morphogenesis gene repertoire of multicellular fungi had already evolved in early holomycotan lineages. 1 Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France. 2 Zoological Institute, Russian Academy of Sciences, St. ✉ Petersburg, Russia. 3 St.
    [Show full text]
  • University of Groningen Multiple Origins of Hydrogenosomes
    University of Groningen Multiple origins of hydrogenosomes Voncken, F; Boxma, B; Tjaden, J; Akhmanova, A; Huynen, M; Tielens, AGM; Haferkamp, [No Value]; Neuhaus, HE; Vogels, G; Veenhuis, M Published in: Molecular Microbiology DOI: 10.1046/j.1365-2958.2002.02959.x IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2002 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Voncken, F., Boxma, B., Tjaden, J., Akhmanova, A., Huynen, M., Tielens, AGM., Haferkamp, N. V., Neuhaus, HE., Vogels, G., Veenhuis, M., Hackstein, JHP., Tielens, A. G. M., Haferkamp, I., & Hackstein, J. H. P. (2002). Multiple origins of hydrogenosomes: functional and phylogenetic evidence from the ADP/ATP carrier of the anaerobic chytrid Neocallimastix sp. Molecular Microbiology, 44(6), 1441-1454. https://doi.org/10.1046/j.1365-2958.2002.02959.x Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum.
    [Show full text]
  • UC Santa Barbara Dissertation Template
    UNIVERSITY OF CALIFORNIA Santa Barbara Deciphering the Functions of Natural Products from Anaerobic Fungi for Applications in Biotechnology A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Chemical Engineering by Candice Lee Swift Committee in charge: Professor Michelle A. O’Malley, Chair Professor Siddharth Dey Professor Song-I-Han Professor David Low December 2020 The dissertation of Candice Lee Swift is approved. ____________________________________________ Siddharth Dey ____________________________________________ Song-I Han ____________________________________________ David Low ____________________________________________ Michelle A. O’Malley, Committee Chair December 2020 ACKNOWLEDGEMENTS I would like to thank my advisor, Michelle O’Malley, for the opportunity to work in her lab and achieve the work described in this dissertation. I would also like to thank all O’Malley lab members, both past and present. I am extremely grateful for the training I received from others in the lab and for the foundation that previous lab members laid in isolating anaerobic fungi and sequencing their genomes and transcriptomes. I also want to thank Nikola Malinov, the diligent undergraduate researcher whose help in lab was invaluable to me and who contributed to the experiments in Chapter five. I would also like to thank our collaborators at the Joint Genome Institute, the Environmental Molecular Sciences Laboratory, and both the Keller lab at the University of Wisconsin-Madison as well as the Solomon lab at Purdue for their experimental contributions and insight. Dr. Jennifer Smith at the Biological Nanostructures Laboratory at UCSB was particularly helpful to me during the library preparation steps of Chapter five. I am grateful to professors Jennifer Reed, Nicholas Abbott, and Betty Chewning for writing letters of recommendation for me when I applied to graduate school after working for five years in industry.
    [Show full text]
  • MICRO-ORGANISMS and RUMINANT DIGESTION: STATE of KNOWLEDGE, TRENDS and FUTURE PROSPECTS Chris Mcsweeney1 and Rod Mackie2
    BACKGROUND STUDY PAPER NO. 61 September 2012 E Organización Food and Organisation des Продовольственная и cельскохозяйственная de las Agriculture Nations Unies Naciones Unidas Organization pour организация para la of the l'alimentation Объединенных Alimentación y la United Nations et l'agriculture Наций Agricultura COMMISSION ON GENETIC RESOURCES FOR FOOD AND AGRICULTURE MICRO-ORGANISMS AND RUMINANT DIGESTION: STATE OF KNOWLEDGE, TRENDS AND FUTURE PROSPECTS Chris McSweeney1 and Rod Mackie2 The content of this document is entirely the responsibility of the authors, and does not necessarily represent the views of the FAO or its Members. 1 Commonwealth Scientific and Industrial Research Organisation, Livestock Industries, 306 Carmody Road, St Lucia Qld 4067, Australia. 2 University of Illinois, Urbana, Illinois, United States of America. This document is printed in limited numbers to minimize the environmental impact of FAO's processes and contribute to climate neutrality. Delegates and observers are kindly requested to bring their copies to meetings and to avoid asking for additional copies. Most FAO meeting documents are available on the Internet at www.fao.org ME992 BACKGROUND STUDY PAPER NO.61 2 Table of Contents Pages I EXECUTIVE SUMMARY .............................................................................................. 5 II INTRODUCTION ............................................................................................................ 7 Scope of the Study ...........................................................................................................
    [Show full text]
  • Effects of Piromyces Sp. CN6 CGMCC 14449 on Fermentation Quality
    Wang et al. AMB Expr (2019) 9:121 https://doi.org/10.1186/s13568-019-0846-x ORIGINAL ARTICLE Open Access Efects of Piromyces sp. CN6 CGMCC 14449 on fermentation quality, nutrient composition and the in vitro degradation rate of whole crop maize silage Dangdang Wang1, Congcong Zhao1, Shimin Liu2, Tao Zhang1, Junhu Yao1 and Yangchun Cao1* Abstract This study investigated the efects of the rumen fungus Piromyces sp. CN6 CGMCC 14449 as a silage additive on the fermentation quality, nutrient composition and in vitro digestibility of whole crop maize silage. Whole crop maize served as the silage material and was vacuum packed in polyethylene bags. Three ensiling treatments were applied: a control (CK), addition of a fungus (FU) at 105 thallus-forming units per gram, and addition of compound enzyme (EN) at 0.033 mg/g (containing cellulase and xylanase at activities of 90 flter paper units and 6000 IU per gram, respec- tively). Compared with the CK, the FU and EN treatments decreased the pH after 30 days fermentation (P <0.05). Both FU and EN treatments increased the lactate, crude protein, and water-soluble carbohydrate contents (P <0.05), whereas reduced the acetate, ADF and NDF contents as well as the ammonia nitrogen to total nitrogen ratio in silage after 30 days of ensilaging (P <0.05), compared with those for the CK, while no changes were found in the dry matter and dry matter recovery (P > 0.05). The fungal inoculant increased the in vitro digestibility of dry matter, NDF and ADF in silage after 30 days fermentation (P <0.05).
    [Show full text]
  • A R T IC L E Anaerobic Fungi: Neocallimastigomycota
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE IMA FuNgus · voluMe 1 · No 2: 181–185provided by PubMed Central Anaerobic fungi: Neocallimastigomycota ARTICLE Gareth W Griffith1, Scott Baker2, Kate Fliegerova3, Audra Liggenstoffer4, Mark van der Giezen5, Kerstin Voigt6 and Gordon Beakes7 1IBERS, Aberystwyth University, Aberystwyth SY23 3DD, Wales; corresponding author e-mail: [email protected] 2Chemical and Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MSIN P8-60 Richland, WA 99352 USA 3Institute of Animal Physiology and Genetics, Academy of Sciences of Czech Republic, Videnska 1083, Prague 4 - Krc, 142 20 Czech Republic 4Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA 5Centre for Eukaryotic Evolutionary Microbiology, Biosciences, College of Life & Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK 6Friedrich Schiller University Jena, Institute of Microbiology, Department of Microbiology and Molecular Biology, Jena Microbial Research Collection, Neugasse 25, 07743 Jena, Germany 7School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK Abstract: This contribution is based on the six oral presentations given at the Special Interest Group Key words: session on anaerobic fungi held during IMC9. These fungi, recently elevated to the status of a separate chytrid phylum (Neocallimastigomycota), distinct from the chytrid
    [Show full text]
  • Cytosolic Enzymes with a Mitochondrial Ancestry from the Anaerobic Chytrid Piromyces Sp
    Molecular Microbiology (1998) 30(5), 1017–1027 Cytosolic enzymes with a mitochondrial ancestry from the anaerobic chytrid Piromyces sp. E2 Anna Akhmanova,†‡* Frank G. J. Voncken,‡ Harry zoospore stages and a vegetative phase in which a com- Harhangi, Ken M. Hosea, Godfried D. Vogels and plex rhizomycelial system is formed. The hyphae of the Johannes H. P. Hackstein rhizomycelial system attach to plant-derived particles of Department of Microbiology and Evolutionary Biology, the digesta, and the intestinal chytrids contribute signifi- Faculty of Science, University of Nijmegen, Toernooiveld, cantly to the digestion of plant polymers by the production NL-6525 ED Nijmegen, The Netherlands. and excretion of a broad spectrum of (cellulolytic and other) enzymes (Teunissen et al., 1991; Orpin, 1994). Summary These highly specialized anaerobic chytrids evolved from mitochondria-bearing aerobic ancestors, as phylo- The anaerobic chytrid Piromyces sp. E2 lacks mito- genetic analysis of their rRNA genes has shown unequivo- chondria, but contains hydrogen-producing organ- cally that yeasts and fungi belong to a ‘crown group’ of elles, the hydrogenosomes. We are interested in how eukaryotic microorganisms that includes the aerobic and the adaptation to anaerobiosis influenced enzyme com- anaerobic chytrids (Sogin, 1991; Knoll, 1992). DNA sequ- partmentalization in this organism. Random sequenc- ence analysis reveals a clustering of both aerobic and ing of a cDNA library from Piromyces sp. E2 resulted anaerobic chytrids (Dore and Stahl, 1991; Bowman et in the isolation of cDNAs encoding malate dehydro- al., 1992; Li and Heath, 1992). Also, an analysis of bio- genase, aconitase and acetohydroxyacid reductoiso- chemical (Ragan and Chapman, 1978) and morphological merase.
    [Show full text]