Plant root symbiotic arbuscular mycorrhizal fungi: patterns of diversity from global to local scales

Transcription

1 Plant root symbiotic arbuscular mycorrhizal fungi: patterns of diversity from global to local scales Maarja Öpik Department of Botany, University of Tartu, Estonia April 2014

2 Arbuscular mycorrhizal (AM) fungi Ph. Glomeromycota, c. 240 spp. Obligate symbionts with most terrestrial plants Fossils from Ordovician, possibly aided colonisation of land by plants Functions: Plant mineral nutrition (P, N) Alleviation of abiotic, biotic stress (drought, heavy metals, pathogens) Improvement of soil structure 2

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4 Carbon sink: Up to 20% of plant s photosynthate can be spent on AM fungi Nutrient uptake: Up to 100% of P taken up by a plant can go via mycorrhizal pathway 4

5 Mycorrhiza influences plant diversity and productivity (van der Heijden et al Ecol. Lett. 11: 296) 5

6 Mycorrhiza could explain 0-57% of variatnce in plant community structure (Klironomos et al New Phytol. 189: 366) 6

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8 It is Pulsatilla important patens to & Pulsatilla know pratensis which AMF are where P. patens P. pratensis c d biomass b ab a M+ soil1 M+ soil 2 M- a Moora et al. 2004, Functional Ecology 18:

9 SEQUENCE BASED IDENTIFICATION OF AMF 9

10 Use of nuclear ribosomal markers in AMF diversity surveys Öpik et al., Botany 92:

11 Morphological vs sequence-based species diversity? Number of MOTUs c. 2 times that of morphospecies? Öpik et al., Botany 92:

12 FM Ipsilantis 2009 Greece Vicia faba AF Helgason 1998 Glo1 UK Pisum sativum AJ Schuessler 2001 Glomus mosseae Australia isolate W3528 AY Husband 2002 Glo1B Panama Faramea occidentalis VT 67 FJ Schreiner 2009 ORVINGlo2 USA Vitis vinifera 100 AJ Opik 2003 MO-G5 Estonia Pulsatilla patens AF Helgason 1998 Glo2 UK Glechoma hederacea VT AM Opik 2008 MO-G5 Estonia Galeobdolon luteum AJ Helgason 2007 Glo18 UK Ajuga reptans 88 AY Husband 2002 Glo17 Panama Tetragastris panamensis 64 AJ Wirsel 2004 OTU8 Germany Phragmites australis EU Merckx 2008 Cameroon Sciaphila ledermannii VT AJ Opik 2003 MO-G4 Estonia Pulsatilla patens AY Scheublin 2004 Glo53 Netherlands Plantago lanceolata 12

13 Virtual Taxon (VT) = phylogenetic clade of DNA sequences at about species level ( 97% similarity) Uniform delimitation principles across Glomeromycota phylogeny Based on SSU rrna gene Analogous terms: phylogroup, sequence type, (M)OTU 13

14 DNA sequences of Glomeromycota from published papers Ecological and taxonomic papers serve as source of data Representatives of OTUs included from each paper New phylogeny performed over all accessions: virtual taxa (VT) delineated VT = phylogenetic clade of DNA sequences at about species level ( 97% similarity) Open access: Sequence/ecological data download available in sign-in environment Öpik et al., New Phytologist 188: Öpik et al., Botany 92:

15 Why SSU: where is sequence variation located? Glomeromycota: SSU rrna gene Lee et al., 2008, FEMS Microbiol. Ecol. 65:

16 Lee et al., 2008: all Glomeromycota sequenced at the time Interspecific variation of central fragment of SSU is comparable to ITS and LSU in the case of AMF Thiéry et al., 2012, Symbiosis 58: : Diversispora sp., one culture Thiéry et al., in prep. 16

17 DIVERSITY PATTERNS OF AMF 17

18 Cluster analysis: AM fungal community composition differs among major habitat types Öpik et al., 2006, J Ecol 94:

19 State of the art 2010: DNA-based AMF richness pattern b Residuals Distribution of standardised residual VT richness (effect of sample size removed) Öpik et al., New Phytologist 188:

20 Virtual taxa 57% 17% of records 41% 65% 20

21 AM fungal community composition differs among continents and major habitat types Kivlin et al., Soil Biol. Biochem. 43:

22 Uniform global sampling: better picture? Öpik et al., Mycorrhiza 23:

23 Global root sampling: 2 nearby replicate sites per biome, typical vegetation of the region à 4 common plant species à 10 individuals Öpik et al., 2013, Mycorrhiza 23:

24 AMF VT richness appears similar in continents and climatic zones (excpt. boreal, polar?) Öpik et al., Mycorrhiza 23:

25 AMF community composition differs among climatic zones and continents 454-sequenced samples Cloned-Sanger sequenced samples Öpik et al., Mycorrhiza 23:

26 Forest specialist plant species Generalist plant species Öpik et al., 2009, New Phytologist 184:

27 Host group specificity of AMF in a 10 x 10 m plot Number of AMF VT in Forest plant species: 46 Generalist plant species: 25 Mean number of AMF per host (P < 0.003): Forest plant species: 28.8 (± 7.6) Generalist plant species: 13.0 (± 3.0) 27

28 There is ecological group level specificity among AMF and host plants Fungi found in forest and generalist plant roots - what is known about them globally: Forest plants hosted more fungi known only from forests than expected at random Generalist plants hosted less fungi known only from forests, and more fungi found in several habitat types (P < 0.05, log-linear analysis) Öpik et al., 2009, New Phytologist 184:

29 Soil spores vs DNA sequences in roots: aspects of same thing or not? Scutellospora Acaulospora Glomus Spore-based: - Acaulospora - Scutellospora Sequence-based: - Acaulospora - Scutellospora - Glomus Acer forest Quercus forest Clapp et al., 1995, New Phytologist 130:

30 Root-colonising vs soil-dwelling AMF richness VT Sequences Saks et al., 2014, Botany 92:

31 and phylogenetic diversity Calamagrostis arundinacea Convallaria majalis Hepatica nobilis Mercurialis perennis Pulmonaria obscura Rubus saxatilis soil Saks et al., 2014, Botany 92:

32 MORPHOLOGICAL VS. DNA-BASED DIVERSITY 32

33 Major proportion of AMF diversity not yet described by morphospecies sequencing Why: 1. Do not sporulate, thus species never described? 2. Have not been brought into culture? 3. Culture has not been sequenced? 4. New species / clades? Öpik et al., 2010, New Phytol. Öpik et al., 2013, Mycorrhiza 33

34 New higher level clades within Glomeromycota? New family? New family? Öpik et al., 2013, Mycorrhiza 34

35 Schüssler & Walker 2010 Oehl et al & following? Öpik et al., 2010, New Phytol. 188: Redecker et al., 2013, Mycorrhiza 21:

36 Schüssler & Walker 2010 Oehl et al & following 36

37 Oehl et al & following Schüssler & Walker 2010 How to delimit morphologically recognised genera on the background of environmental sequences? Glomus (s.l.), Glomeraceae Claroideoglomus, Claroideoglomeraceae

38 Kõljalg et al., 2013, Mol. Ecol. 22:

39 Do we ever see the fungus? Paraglomus majewskii case: : Paraglomus Pa1 detected in Spain, in roots of Pistacia lentiscus and Rhamnus lycioides (Alguacil et al. 2011, Soil Biol Biochem 43: ) : Pa1 sequences added to MaarjAM, new VT erected: Paraglomus VT : Paraglomus majewskii described based on collections from Turkey and elsewhere (Blaszkowski et al. 2012, Mycologia 104: ) 39

40 Paraglomus majewskii / Paraglomus VT335 Blaszkowski et al. 2012, Mycologia 104:

41 CONCLUSIONS & WHERE NEXT? 41

42 Conclusions There are many more Glomeromycota out there than morphospecies number suggests DNA based detection and identification provides data that can be easily compared, (re-)analysed and reidentified VT nomenclature implemented in MaarjAM database is open and ready-to-use system for AMF ecologists AMF have diversity patterns at different spatial scales and these are important 42

43 Where next? Ways to close the gap between morphological & molecular views? Ignore morphotaxonomy? All-inclusive DNA-based taxonomy covering both DNA-only and culture-originating species / taxa? More sequencing of (well and not so well identified) cultures? More culturing (and sequencing of cultures) from more habitats, hosts, with various conditions?? 43

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45 Plant Ecology Team, University of Tartu: Prof. Martin Zobel Drs. Mari Moora, Maarja Öpik Dr. John Davison, MSc Martti Vasar Drs. Teele Jairus, Ülle Saks PhD students: Maret Gerz, Lena Neuenkamp, Jaak-Albert Metsoja MSc students: Siim-Kaarel Sepp, Kertu Kais 45