Exploring slime mould diversity in high-altitude forests and grasslands by environmental RNA analysis

FEMS Microbiology Ecology

Volumn 84, Issue 1, 2013, Pages 98-109

  Kamono, Akiko ^a   Meyer, Marianne ^b   Cavalier Smith, Thomas ^c   Fukui, Manabu ^a   Fiore Donno, Anna Maria ^c,d  

^a HOKKAIDO UNIVERSITY   (Japan)

^b Le Bayet ^*  (France)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d UNIVERSITY OF COLOGNE   (Germany)

Author keywords

Environmental RNA sampling; Myxogastria; Myxomycetes; Protists; Soil biodiversity; Soil microbiology

Indexed keywords

PROTOZOAL RNA;

ALTITUDE; BIODIVERSITY; BIOME; COMMUNITY COMPOSITION; FOREST ECOSYSTEM; GRASSLAND; RNA; SLIME MOULD; TERRESTRIAL ECOSYSTEM;

ALTITUDE; ARTICLE; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; ECOSYSTEM; FRANCE; GENETICS; ISOLATION AND PURIFICATION; JAPAN; MYXOGASTRIA; SOIL; TREE; UNITED KINGDOM;

ALTITUDE; BIODIVERSITY; ECOSYSTEM; FRANCE; JAPAN; MYXOMYCETES; RNA, PROTOZOAN; SCOTLAND; SOIL; TREES;

FRANCE; JAPAN; SCOTLAND; UNITED KINGDOM;

AMOEBOZOA; MYXOGASTRIA; PROTISTA;

EID: 84874718993     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/1574-6941.12042     Document Type: Article

References (50)

1. Bailly J, Fraissinet-Tachet L, Verner M-C, Debaud J-C, Lemaire M, Wésolowski-Louvel M & Marmeisse R (2007) Soil eukaryotic functional diversity, a metatranscriptomic approach. ISME J 1: 632-642.
2. Brown M, Philip G, Bunge J, Smith M, Bissett A, Lauro F, Fuhrman J & Donachie S (2009) Microbial community structure in the North Pacific ocean. ISME J 3: 1374-1386.
3. Buée M, Reich M, Murat C, Morin E, Nilsson R, Uroz S & Martin F (2009) 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol 184: 449-456.
4. Caron DA (2009) New accomplishments and approaches for assessing protistan diversity and ecology in natural ecosystems. Bioscience 59: 287-299.
5. Caron DA & Countway PD (2009) Hypotheses on the role of the protistan rare biosphere in a changing world. Aquat Microb Ecol 57: 227-238.
6. Caron DA, Countway PD, Savai P, Gast RJ, Schnetzer A, Moorthi SD, Dennett MR, Moran DM & Jones AC (2009) Defining DNA-based operational taxonomic units for microbial-eukaryote ecology. Appl Environ Microbiol 75: 5797-5808.
7. Cavalier-Smith T (2012) Early evolution of eukaryote feeding modes, cell structural diversity, and classification of the protozoan phyla Loukozoa, Sulcozoa, and Choanozoa. Eur J Protistol. In press. doi: http://dx.doi.org/10.1016/j.ejop.2012.06.001.
8. Chao A, Chazdon RL, Colwell RK & Shen T-J (2006) Abundance-based similarity indices and their estimation when there are unseen species in samples. Biometrics 62: 361-371.
9. Countway PD, Gast RJ, Dennett MR, Savai P, Rose JM & Caron DA (2007) Distinct protistan assemblages characterize the euphotic zone and deep sea (2500 m) of the western North Atlantic (Sargasso Sea and Gulf Stream). Env Microbiol 9: 1219-1232.
10. Damon C, Lehembre F, Oger-Desfeux C, Luis P, Ranger J, Fraissinet-Tachet L & Marmeisse R (2012) Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils. PLoS ONE 7: e28967.
11. Dyková I, Lom J, Dvořáková H, Pecková H & Fiala I (2007) Didymium-like myxogastrids (class Mycetozoa) as endocommensals of sea urchins (Sphaerechinus granularis). Folia Parasitol 54: 1-12.
12. Feest A (1987) The quantitative ecology of soil Mycetozoa. Progr Protistol 2: 331-361.
13. Feest A & Madelin MF (1985) A method for the enumeration of myxomycetes in soils and its application to a wide range of soils. FEMS Microbiol Ecol 31: 103-109.
14. Finlay BJ (2002) Global dispersal of free-living microbial eukaryote species. Science 296: 1061-1063.
15. Fiore-Donno AM, Meyer M, Baldauf SL & Pawlowski J (2008) Evolution of dark-spored Myxomycetes (slime-molds): molecules versus morphology. Mo. Phyl Evol 46: 878-889.
16. Fiore-Donno AM, Kamono A, Chao EE, Fukui M & Cavalier-Smith T (2010) Invalidation of Hyperamoeba by transferring its species to other genera of Myxogastria J. Euk Microbiol 57: 189-196.
17. Fiore-Donno AM, Novozhilov Y, Meyer M & Schnittler M (2011) Genetic structure of two protist species (Myxogastria, Amoebozoa) suggests asexual reproduction in sexual amoebae. PLoS ONE 6: e22872.
18. Fiore-Donno AM, Kamono A, Meyer M, Schnittler M, Fukui M & Cavalier-Smith T (2012) 18S rDNA phylogeny of Lamproderma and allied genera (Stemonitales, Myxomycetes, Amoebozoa). PLoS ONE 7: e35359.
19. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95-98.
20. Jobb G (2008) TREEFINDER version of October 2008. Munich, Germany.
21. Kamono A & Fukui M (2006) Rapid PCR-based method for detection and differentiation of Didymiaceae and Physaraceae (Myxomycetes) in environmental samples. J Microbiol Methods 67: 496-506.
22. Kamono A, Kojima H, Matsumoto J, Kawamura K & Fukui M (2009a) Airborne myxomycete spores: detection using molecular techniques. Naturwissenschaften 96: 147-151.
23. Kamono A, Matsumoto J, Kojima H & Fukui M (2009b) Characterization of myxomycete communities in soil by reverse transcription polymerase chain reaction (RT-PCR)-based method. Soil Biol Biochem 41: 1324-1330.
24. Lado C (2001) Nomenmyx. A nomenclatural taxabase of Myxomycetes. Cuad Trab Flora Micol Iber 16: 1-221.
25. 2 affects soil microbial diversity associated with trembling aspen. Env Microbiol 10: 926-941.
26. Lipson DA & Schmidt SK (2004) Seasonal changes in an alpine soil bacterial community in the Colorado Rocky Mountains. Appl Environ Microbiol 70: 2867-2879.
27. Madelin MF (1990) Methods for studying the ecology and population dynamics of soil myxomycetes. Methods Microbiol 22: 405-416.
28. Mao CX & Colwell RK (2005) Estimation of species richness: mixture models, the role of rare species, and inferential challenges. Ecology 86: 1143-1153.
29. Meylan C (1931) Les espèces nivales du genre Lamproderma. Bull Soc Vaud Sci Nat 57: 359-373.
30. Moon-van der Staay SY, Tzeneva VA, van der Staay GW, de Vos WM, Smidt H & Hackstein JH (2006) Eukaryotic diversity in historical soil samples. FEMS Microbiol Ecol 57: 420-428.
31. Mora C, Tittensor DP, Adl SM, Simpson AGB & Worm B (2011) How many species are there on earth and in the ocean? PLoS Biol 9: e1001127.
32. Nebel M, Pfabel C, Stock A, Dunthorn M & Stoeck T (2010) Delimiting operational taxonomic units for assessing ciliate environmental diversity using small-subunit rRNA gene sequences. Environ Microbiol Rep 3: 154-158.
33. Nikolaev SI, Berney C, Petrov NB, Mylnikov AP, Fahrni JF & Pawlowski J (2006) Phylogenetic position of Multicilia marina and the evolution of Amoebozoa. Int J Syst Evol Microbiol 56: 1449-1458.
34. Pawlowski J, Christen R, Lecroq B, Bachar D, Shahbazkia HR, Amaral Zettler LA & Guillou L (2011) Eukaryotic richness in the abyss: insights from pyrotag sequencing. PLoS ONE 6: e18169.
35. Posada D (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25: 1253-1256.
36. Poulain M, Meyer M & Bozonnet J (2011) Les Myxomycètes. Fédération Mycologique et Botanique Dauphiné-Savoie, Sevrier, France.
37. R Development Core Team (2011) R: A language and evironments for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
38. Ronikier A & Ronikier M (2009) How 'alpine' are nivicolous myxomycetes? A worldwide assessment of altitudinal distribution. Mycologia 101: 1-16.
39. Ronquist F & Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
40. Sauvadet A-L, Gobet A & Guillou L (2010) Comparative analysis between protist communities from the deep-sea pelagic ecosystem and specific deep hydrothermal habitats. Environ Microbiol 12: 2946-2964.
41. Scheckenbach F, Hausmann K, Wylezich C, Weitere M & Arndt H (2010) Large-scale patterns in biodiversity of microbial eukaryotes from the abyssal sea floor. P Natl Acad Sci USA 107: 115-120.
42. Stephenson SL, Schnittler M & Novozhilov Y (2008) Myxomycete diversity and distribution from the fossil record to the present. Biodiv Conserv 17: 285-301.
43. Stephenson SL, Fiore-Donno AM & Schnittler M (2011) Myxomycetes in soil. Soil Biol Biochem 43: 2237-2242.
44. Stoeck T & Epstein SS (2009) Crystal ball - protists and the rare biosphere. Environ Microbiol Rep 1: 20-22.
45. Suutari M, Majaneva M, Fewer DP, Voirin B, Aiello A, Friedl T, Chiarello AG & Blomster J (2010) Molecular evidence for a diverse green algal community growing in the hair of sloths and a specific association with Trichophilus welckeri (Chlorophyta, Ulvophyceae). BMC Evol Biol 10: 1471-2148.
46. Urich T, Lanzén A, Qi J, Huson DH, Schleper C & Schuster SC (2008) Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE 3: e2527.
47. Walochnik J, Michel R & Aspock H (2004) A molecular biological approach to the phylogenetic position of the genus Hyperamoeba. J Eukaryot Microbiol 51: 433-440.
48. Wikmark OG, Haugen P, Haugli K & Johansen S (2007) Obligatory group I introns with unusual features at positions 1949 and 2449 in nuclear LSU rDNA of Didymiaceae myxomycetes. Mol Phyl Evol 43: 596-604.
49. Willerslev E, Hansen AJ, Christensen B & Steffensen JP (1999) Diversity of Holocene life forms in fossil glacier ice. P Natl Acad Sci USA 96: 8017-8021.
50. Win Ko Ko T, Stephenson SL, Jeewon R & Hyde KD (2009) Molecular diversity of myxomycetes associated with decaying wood and forest floor leaf litter. Mycologia 101: 592-598.