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Title: PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities

Abstract

Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored gut and non-gut environments. Additionally many studies are now known to have used primers that provide incomplete coverage of the Neocallimastigomycota. For ecological studies the internal transcribed spacer 1 region (ITS1) has been the taxonomic marker of choice, but due to various limitations the large subunit rRNA (LSU) is now being increasingly used. How the continued expansion of our knowledge regarding anaerobic fungal diversity will impact on our understanding of their biology and ecological role remains unclear; particularly as it is becoming apparent that anaerobic fungi display niche differentiation. As a consequence, there is a need to move beyond themore » broad generalization of anaerobic fungi as fiber-degraders, and explore the fundamental differences that underpin their ability to exist in distinct ecological niches. Application of genomics, transcriptomics, proteomics and metabolomics to their study in pure/mixed cultures and environmental samples will be invaluable in this process. To date the genomes and transcriptomes of several characterized anaerobic fungal isolates have been successfully generated. In contrast, the application of proteomics and metabolomics to anaerobic fungal analysis is still in its infancy. A central problem for all analyses, however, is the limited functional annotation of anaerobic fungal sequence data. There is therefore an urgent need to expand information held within publicly available reference databases. Finally, once this challenge is overcome, along with improved sample collection and extraction, the application of these techniques will be key in furthering our understanding of the ecological role and impact of anaerobic fungi in the wide range of environments they inhabit.« less

Authors:
 [1];  [2];  [3];  [3];  [4];  [5];  [6];  [7];  [8];  [9];  [10];  [10];  [10];  [11];  [1]
  1. Wageningen Univ. & Research, Wageningen (Netherlands). Lab. of Microbiology
  2. Agriculture and Agri-Food Canada, Lethbridge, AB (Canada). Lethbridge Research and Development Centre
  3. Bavarian State Research Center for Agriculture, Freising (Germany). Dept. for Quality Assurance and Analytics
  4. Agharkar Research Inst., Pune (India). Bioenergy Group
  5. Nanjing Agricultural Univ., Nanjing (China). Lab. of Gastrointestinal Microbiology
  6. Korea National Open Univ., Seoul (South Korea). Dept. of Agricultural Science
  7. AgResearch Ltd., Palmerston North (New Zealand). Grasslands Research Centre
  8. Czech Academy of Sciences, Prague (Czechia). Inst. of Animal Physiology and Genetics
  9. Guru Angad Dev Veterinary and Animal Sciences Univ., Ludhiana (India). College of Dairy Science and Technology; CAR-National Dairy Research Inst., Karnal (India). Dairy Microbiology Division
  10. Univ. of California, Santa Barbara, CA (United States). Dept. of Chemical Engineering
  11. Aberystwyth Univ., Aberystwyth (United Kingdom). Inst. of Biological Environmental and Rural Sciences
Publication Date:
Research Org.:
Univ. of California, Santa Barbara, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); European Union (EU); National Science Foundation (NSF)
OSTI Identifier:
1424614
Grant/Contract Number:
SC0010352; AC02-05CH11231; AC05-76RL01830
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 8; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; anerobic fungi; Neocallimastigomycota; rumen; phylogeny; genomics; (meta) transcriptomics; proteomics; metabolomics

Citation Formats

Edwards, Joan E., Forster, Robert J., Callaghan, Tony M., Dollhofer, Veronika, Dagar, Sumit S., Cheng, Yanfen, Chang, Jongsoo, Kittelmann, Sandra, Fliegerova, Katerina, Puniya, Anil K., Henske, John K., Gilmore, Sean P., O'Malley, Michelle A., Griffith, Gareth W., and Smidt, Hauke. PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities. United States: N. p., 2017. Web. doi:10.3389/fmicb.2017.01657.
Edwards, Joan E., Forster, Robert J., Callaghan, Tony M., Dollhofer, Veronika, Dagar, Sumit S., Cheng, Yanfen, Chang, Jongsoo, Kittelmann, Sandra, Fliegerova, Katerina, Puniya, Anil K., Henske, John K., Gilmore, Sean P., O'Malley, Michelle A., Griffith, Gareth W., & Smidt, Hauke. PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities. United States. doi:10.3389/fmicb.2017.01657.
Edwards, Joan E., Forster, Robert J., Callaghan, Tony M., Dollhofer, Veronika, Dagar, Sumit S., Cheng, Yanfen, Chang, Jongsoo, Kittelmann, Sandra, Fliegerova, Katerina, Puniya, Anil K., Henske, John K., Gilmore, Sean P., O'Malley, Michelle A., Griffith, Gareth W., and Smidt, Hauke. Mon . "PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities". United States. doi:10.3389/fmicb.2017.01657. https://www.osti.gov/servlets/purl/1424614.
@article{osti_1424614,
title = {PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities},
author = {Edwards, Joan E. and Forster, Robert J. and Callaghan, Tony M. and Dollhofer, Veronika and Dagar, Sumit S. and Cheng, Yanfen and Chang, Jongsoo and Kittelmann, Sandra and Fliegerova, Katerina and Puniya, Anil K. and Henske, John K. and Gilmore, Sean P. and O'Malley, Michelle A. and Griffith, Gareth W. and Smidt, Hauke},
abstractNote = {Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored gut and non-gut environments. Additionally many studies are now known to have used primers that provide incomplete coverage of the Neocallimastigomycota. For ecological studies the internal transcribed spacer 1 region (ITS1) has been the taxonomic marker of choice, but due to various limitations the large subunit rRNA (LSU) is now being increasingly used. How the continued expansion of our knowledge regarding anaerobic fungal diversity will impact on our understanding of their biology and ecological role remains unclear; particularly as it is becoming apparent that anaerobic fungi display niche differentiation. As a consequence, there is a need to move beyond the broad generalization of anaerobic fungi as fiber-degraders, and explore the fundamental differences that underpin their ability to exist in distinct ecological niches. Application of genomics, transcriptomics, proteomics and metabolomics to their study in pure/mixed cultures and environmental samples will be invaluable in this process. To date the genomes and transcriptomes of several characterized anaerobic fungal isolates have been successfully generated. In contrast, the application of proteomics and metabolomics to anaerobic fungal analysis is still in its infancy. A central problem for all analyses, however, is the limited functional annotation of anaerobic fungal sequence data. There is therefore an urgent need to expand information held within publicly available reference databases. Finally, once this challenge is overcome, along with improved sample collection and extraction, the application of these techniques will be key in furthering our understanding of the ecological role and impact of anaerobic fungi in the wide range of environments they inhabit.},
doi = {10.3389/fmicb.2017.01657},
journal = {Frontiers in Microbiology},
number = ,
volume = 8,
place = {United States},
year = {Mon Sep 25 00:00:00 EDT 2017},
month = {Mon Sep 25 00:00:00 EDT 2017}
}

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