Một cuộc kiểm kê phát sinh loài về sự đa dạng toàn cầu của nấm kị khí trong ruột và một khung phân loại mới

Springer Science and Business Media LLC - Tập 89 - Trang 253-266 - 2018
Shyam Sundar Paul1,2, Dengpan Bu3,4,5, Jianchu Xu3,6, Kevin D. Hyde7, Zhongtang Yu1,3
1Department of Animal Sciences, The Ohio State University, Columbus, USA
2ICAR-Central Institute for Research on Buffaloes, Hisar, India
3State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
4CAAS-ICRAF Joint Lab on Agroforestry and Sustainable Animal Husbandry, World Agroforestry Centre East and Central Asia, Beijing, China
5Hunan Co-Innovation Center of Animal Production Safety, CICAPS, Changsha, China
6Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
7Center of Excellence in Fungal Diversity, Mae Fah Luang University, Chiang Rai, Thailand

Tóm tắt

Nấm kị khí bắt buộc thuộc ngành Neocallimastigomycota đóng vai trò quan trọng trong việc tiêu hóa thức ăn xơ tại ruột của động vật ăn cỏ, nhưng vẫn còn rất ít thông tin về sự đa dạng toàn cầu của chúng. Trong nghiên cứu này, sự đa dạng tập thể của nấm kị khí trong ruột đã được khảo sát bằng cách sử dụng tất cả các trình tự không gian phiên mã nội bộ 1 (ITS1) đã được chỉnh sửa của nấm kị khí trong ruột có sẵn trong GenBank. Có tổng cộng 262.770 trình tự ITS1 nấm đã được kiểm tra chất lượng tải về từ GenBank đã được phân loại thành 274 đơn vị phân loại hoạt động (OTUs) ở mức độ gần tương đương loài. Trong số các OTUs gần tương đương loài này, 119 được đại diện bởi ít nhất năm trình tự ITS1, trong đó có 38 OTUs chứa các loài đã biết và 81 OTUs không chứa loài nào đã biết. Dựa trên phân tích hiếm gặp, các trình tự ITS1 hiện có đại diện cho gần như tất cả các loài chính của nấm kị khí trong ruột, nhưng cần nhiều nỗ lực giải trình tự hơn nữa để đánh giá sự phong phú thực tế của các OTUs nhỏ hơn. Một tập hợp dữ liệu của các trình tự tham chiếu ITS1 (được gọi là AF-RefSeq) và một khung phân loại toàn diện cũng được trình bày, và chúng được cho là thích hợp cho việc phân loại các trình tự ITS1 trong GenBank. Kết quả của nghiên cứu hiện tại có thể giúp hướng dẫn các nghiên cứu trong tương lai liên quan đến phân loại và phân tích phát sinh loài của các trình tự ITS1 của nấm kị khí cũng như việc phân lập và định danh các nấm kị khí mới.

Từ khóa

#nấm kị khí #Neocallimastigomycota #sự đa dạng toàn cầu #phân tích phát sinh loài #phân loại

Tài liệu tham khảo

Akin DE, Gordon GL, Hogan JP (1983) Rumen bacterial and fungal degradation of Digitaria pentzii grown with or without sulfer. Appl Environ Microbiol 46:738–748 Akin DE (1994) Ultrastructure of plant cell walls degraded by anaerobic fungi. In: Mountfort D, Orpin CG (eds) Anaerobic Fungi: Biology, Ecology and Function. Marcel Dekker, New York, pp 169–190 Ariyawansa HA, Hyde KD, Jayasiri SC et al (2015) Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa. Fungal Divers 75:27–274. https://doi.org/10.1007/s13225-015-0346-5 Barr DJS, Kudo H, Jakober KD, Cheng KJ (1989a) Morphology and development of rumen fungi: Neocallimastix sp., Piromyces communis, and Orpinomyces bovis gen. nov., sp. nov. Can J Bot 67:2815–2824 Barr DJS, Kudo H, Jakober KD, Chong KJ (1989b) Morphology and development of rumen fungi: Neocallimastix sp., Piromyces communis and Orpinomyces bovis. Can J Bot 67:2815–2819 Berger SA, Stamatakis A (2011) Aligning short reads to reference alignments and trees. Bioinformatics 27:2068–2075. https://doi.org/10.1093/bioinformatics/btr320 Breton A, Bernalier A, Bonnemoy F (1989) Morphology and metabolic characterization of a new species of strictly anaerobic rumen fungus: Neocallimastix joyonii. FEMS Microbiol Lett 58:309–314 Breton A, Bernalier M, Dusser G, Fonty B, Martinie Gaillard, Guillot J (1990) Anaeromyces mucronatus nov. gen., nov. sp.: a new strictly anaerobic rumen fungus with polycentric thallus. FEMS Microbiol Lett 70:177–182 Brookman JL, Mennim G, Trinci APJ, Theodorou MK, Tuckwell DS (2000) Identification and characterization of anaerobic gut fungi using molecular methodologies based on ribosomal ITS1 and 18S rRNA. Microbiology 146:393–403 Cai Y, Sun Y (2011) ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time. Nucleic Acids Res 39:e95 Calderon-Cortes JF, Elliott R, Ford CW (1989) Influence of rumen fungi on the nutrition of sheep fed forage diets. In: Nolan JV, Leng RA, Demeyer DI (eds) The Roles of Protozoa and Fungi in Ruminant Digestion. Penumbul Books, Armidale, Australia, pp 181–187 Callaghan TM, Podmirseg SM, Hohlweck D, Edwards JE, Puniya AK, Dagar SS, Griffith GW (2015) Buwchfawromyces eastonii gen. nov., sp. nov.: a new anaerobic fungus (Neocallimastigomycota) isolated from buffalo feces. MycoKeys 9:11–28. https://doi.org/10.3897/mycokeys.9.9032 Chen YC, Tsai SD, Cheng HL, Chien CY, Hu CY, Cheng TY (2007) Caecomyces sympodialis sp. nov., a new rumen fungus isolated from Bos indicus. Mycologia 99:125–130 Dagar SS, Kumar S, Griffith GW, Joan E, Edwards JE, Callaghan TM, Singh R, Nagpal AK, Puniya AK (2015) A new anaerobic fungus (Oontomyces anksri gen. nov., sp. nov.) from the digestive tract of the Indian camel (Camelus dromedarius). Fungal Biol 119:731–737 Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772 Doré J, Stahl DA (1991) Phylogeny of anaerobic rumen Chytridiomycetes inferred from small subunit ribosomal RNA sequence comparisons. Can J Bot 69:1964–1971 Elliott R, Ash AJ, Calderon-Cortes Norton BW, Bauchop T (1987) The influence of anaerobic fungi on rumen volatile fatty acid concentrations in vivo. J Agric Sci 109:13–17 Fliegerova K, Hodrova B, Voigt K (2004) Classical and molecular approaches as a powerful tool for the characterization of rumen polycentric fungi. Folia Microbiol 49:157–164 Gold JJ, Heath IB, Bauchop T (1988) Ultrastructural description of a new chytrid genus of caecum anaerobe, Caecomyces equi gen. nov. sp. nov. assigned to the Neocallimastcaceae. Biosystems 21:403–415 Gordon GLR, Phillips MW (1998) The role of anaerobic gut fungi in ruminants. Nutr Res Rev 11:133–168 Grenet E, Breton A, Barry P, Fonty G (1989) Rumen anaerobic fungi and plant substrate colonization as affected by diet composition. Anim Feed Sci Technol 26:55–70 Griffith GW, Baker S, Fliegerova K, Liggenstoffer A, Giezen M, Voigt K, Beakes G (2010) Anaerobic fungi: Neocallimastigomycota. IMA Fungus 1:181–185 Gruninger RJ, Puniya AK, Callghan TM et al (2014) Anaerobic fungi (phylum Neocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential. FEMS Microbiol Ecol 90:1–17 Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321 Hanafy RA, Elshahed MS, Liggenstoffer AS, Griffith GW, Youssef NH (2017) Pecoramyces ruminantium, gen. nov., sp. nov., an anaerobic gut fungus from the feces of cattle and sheep. Mycologia 109:231–243 Heath IB, Kaminasky J, Bauchop T (1986) Basal body loss during fungal zoospore encystment: evidence against centriole autonomy. J Cell Sci 83:135–140 Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PE et al (2007) A higher-level phylogenetic classification of the fungi. Mycol Res 111:509–547 Ho YW, Barr DJS (1995) Classification of anaerobic gut fungi from herbivores with emphasis on rumen fungi from Malaysia. Mycologia 87:655–677 Ho YW, Bauchop T (1990) Ruminomyces elegans gen. eet sp. nov. A polycentric anaerobic rumen fungus from cattle. Mycotoxon 38:397–405 Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31:3429–3431 Hughes JB, Bohannan BJM (2004) Application of ecological diversity statistics in microbial ecology. Mol Microb Ecol Manual 7(01):1321–1344 Huse SM, Welch DM, Morrison HG, Sogin ML (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 12:1889–1898 Ishaq SL, AlZahal O, And Walker, McBride B (2017) An investigation into rumen fungal and protozoal diversity in three rumen fractions, during high-fiber or grain-induced subacute ruminal acidosis conditions, with or without active dry yeast supplementation. Front Microbiol 8:1943 Kim M, Morrison M, Yu ZT (2011) Status of microbial diversity census of ruminal microbiomes. FEMS Microbiol Ecol 76:49–63 Kittelmann S, Naylor GE, Koolaard JP, Janssen PH (2012) A proposed taxonomy of anaerobic fungi (Class Neocallimastigomycetes) suitable for large scale sequence based community structure analysis. PLoS ONE 7:e36866. https://doi.org/10.1371/journal.pone.0036866 Koetschan C, Kittelmann S, Lu J, Al-Halbouni D, Jarvis GN et al (2014) Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota). PLoS ONE 9:e91928. https://doi.org/10.1371/journal.pone.0091928 Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874 Larsson A (2014) AliView: a fast and lightweight alignment viewer and editor for large data sets. Bioinformatics 30:3276–3278 Larue R, Yu Z, Parisi VA, Egan AR, Morrison M (2005) Novel microbial diversity adherent to plant biomass in the herbivore gastrointestinal tract, as revealed by ribosomal intergenic spacer analysis and rrs gene sequencing. Environ Microbiol 7:530–543 Letunic I, Bork P (2016) Interactive tree of life (iTOL) v3: an online tool for display and annotation of phylogenetic and other trees. Nucleic Acids Res 44 (Web Server issue):W242–W245 Li J, Heath IB, Bauchop T (1990) Piromyces mae and Piromyces dumbonica, two new species of uniflagellate anaerobic chytridomycete fungi from hindgut of the horse and elephant. Can J Bot 68:1021–1033 Liggenstoffer AS, Youssef NH, Couger MB, Elshahed MS (2010) Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores. ISME J 4:1225–1235 Ljungdahl LG (2008) The cellulase/hemicellulase system of the anaerobic fungus Orpinomyces PC-2 and aspects of its use. Ann NY Acad Sci 1125:308–321 Matsen FA, Kodner RB, Armburst EV (2010) PPLACER: linear time maximum - likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11:538 Min B, Solaiman SG, Shange R, Eun J (2014) Gastrointestinal bacterial and methanogenic archaea diversity dynamics associated with condensed tannin containing pine bark diet in goats using 16S rDNA amplicon pyrosequencing. Int J Microbiol. https://doi.org/10.1155/2014/141909 Monard C, Gantner S, Stenlid J (2013) Utilizing ITS1 and ITS2 to study environmental fungal diversity using pyrosequencing. FEMS Microbiol Ecol 84:165–175 Nguyen LT, Schmidt HA, Haeseler A, Minh BQ (2014) A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol Biol Evol 32:268–274 Nguyen N, Warnow T, Pop M, White B (2016) A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity. Biofilms Microbiomes 2:16004. https://doi.org/10.1038/npjbiofilms.2016.4 Nicholson MJ, McSweeney CS, Mackie RI, Brookman JL, Theodorou MK (2010) Diversity of anaerobic gut fungal populations analyzed using ribosomal ITS1 sequences in faeces of wild and domesticated herbivores. Anaerobe 16:66–73 Orpin CG (1975) Studies on the rumen flagellate Neocallimastix frontalis. J Gen Microbiol 91:249–262 Orpin CG (1976) Studies on the rumen flagellate Sphaeromonas communis. J Gen Microbiol 94:270–280 Orpin CG (1977) The rumen flagellate Piromonas communis: its life history and invasion of plant material in the rumen. J Gen Microbiol 99:107–117 Orpin CG, Munn EA (1986) Neocallimastix patriciarum sp. nov., a new member of the Neocallimasticaceae inhabiting the rumen of sheep. Trans Br Mycol Soc 86:178–181 Ozkose E, Thomas BJ, Davies DR, Griffith GW, Theodorou MK (2001) Cyllamyces aberensis gen.nov. sp.nov., a new anaerobic gut fungus with branched sporangiophores isolated from cattle. Can J Bot 79:666–673 Paul SS, Kamra DN, Sastry VRB, Sahu NP, Agarwal N (2004) Effect of administration of an anaerobic gut fungus isolated from wild blue bull (Boselaphus tragocamelus) to buffaloes (Bubalus bubalis) on in vivo ruminal fermentation and digestion of nutrients. Anim Feed Sci Technol 115:143–157 Paul SS, Deb SM, Punia BS, Singh D, Kumar R (2010) Fibrolytic potential of anaerobic fungi (Piromyces sp.) isolated from wild cattle and wild blue bull in pure culture and effect of their addition on in vitro fermentation of wheat straw and methane emission by rumen fluid of buffaloes. J Sci Food Agric 90:1218–1226 Phillips MW, Gordon GLR (1988) Sugar and polysaccharide fermentation by anaerobic fungi from Australia, Britain and New Zealand. Biosystems 21:377–383 Price MN, Dehal PS, Arkin AP (2010) FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5:e9490 Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542 Schloss PD, Handelsman J (2006) Toward a census of bacteria in soil. PLoS Comput Biol 2:e92. https://doi.org/10.1371/journal.pcbi.0020092 Schloss PD, Westcott SL, Thomas R et al (2009) Introducing Mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541 Seibel PN, Müller T, Dandekar T, Schultz J, Wolf M (2006) 4SALE—a tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics 7:498 Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O’Dwyer JP, Green JL, Eisen JA, Pollard KS (2011) PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Comput Biol 7:e1001061 Tang J, Iliev ID, Brown J, Underhill DM, Funari VA (2015) Mycobiome: approaches to analysis of intestinal fungi. J Immunol Methods 421:112–121 Tuckwell DS, Nicholson MJ, McSweeney CS, Theodorou MK, Brookman JL (2005) The rapid assignment of ruminal fungi to presumptive genera using ITS1 and ITS2 RNA secondary structures to produce group-specific fingerprints. Microbiology 151:1557–1567 Vargas-Gastelum L, Romero-Olivares Al, Escalante AE, Rocha-Olivares A, Brizuela C, Riquelme M (2015). Impact of seasonal changes on fungal diversity of a semi-arid ecosystem revealed by 454 pyrosequencing. FEMS Microbiol Ecol 91(5). https://doi.org/10.1093/femsec/fiv044. Epub 2015 Apr 14 Webb J, Theodorou MK (1991) Neocallimastix hurleyensis sp. nov., an anaerobic fungus from the ovine rumen. Can J Bot 69:1220–1224 Wei S, Morrison M, Yu Z (2013) Bacterial census of poultry intestinal microbiome. Poult Sci 92:671–683 Zhang B, Wang L, Liu L (2014) Bacterial community structure and its regulating factors in the intertidal sediment along the Liadong Bay of Bohai Sea, China. Microbiol Res 169:585–592