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
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
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
Mycorrhiza influences plant diversity and productivity (van der Heijden et al. 2008 Ecol. Lett. 11: 296) 5
Mycorrhiza could explain 0-57% of variatnce in plant community structure (Klironomos et al. 2011 New Phytol. 189: 366) 6
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It is Pulsatilla important patens to & Pulsatilla know pratensis which AMF are where 2.5 2.0 P. patens P. pratensis c d biomass 1.5 1.0 0.5 0.0 b ab a M+ soil1 M+ soil 2 M- a Moora et al. 2004, Functional Ecology 18:554-562 8
SEQUENCE BASED IDENTIFICATION OF AMF 9
Use of nuclear ribosomal markers in AMF diversity surveys Öpik et al., 2014. Botany 92: 135-147 10
Morphological vs sequence-based species diversity? Number of MOTUs c. 2 times that of morphospecies? Öpik et al., 2014. Botany 92: 135-147 11
FM875888 Ipsilantis 2009 Greece Vicia faba 100 94 94 AF074357 Helgason 1998 Glo1 UK Pisum sativum AJ306438 Schuessler 2001 Glomus mosseae Australia isolate W3528 AY129632 Husband 2002 Glo1B Panama Faramea occidentalis VT 67 FJ194506 Schreiner 2009 ORVINGlo2 USA Vitis vinifera 100 AJ418861 Opik 2003 MO-G5 Estonia Pulsatilla patens AF074365 Helgason 1998 Glo2 UK Glechoma hederacea VT 129 100 97 AM849279 Opik 2008 MO-G5 Estonia Galeobdolon luteum AJ854089 Helgason 2007 Glo18 UK Ajuga reptans 88 AY129576 Husband 2002 Glo17 Panama Tetragastris panamensis 64 AJ563866 Wirsel 2004 OTU8 Germany Phragmites australis EU417640 Merckx 2008 Cameroon Sciaphila ledermannii VT 166 0.01 63 AJ418860 Opik 2003 MO-G4 Estonia Pulsatilla patens AY512376 Scheublin 2004 Glo53 Netherlands Plantago lanceolata 12
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
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: http://maarjam.botany.ut.ee Sequence/ecological data download available in sign-in environment Öpik et al., 2010. New Phytologist 188: 223-241 Öpik et al., 2014. Botany 92: 135-147 14
Why SSU: where is sequence variation located? Glomeromycota: SSU rrna gene Lee et al., 2008, FEMS Microbiol. Ecol. 65:339-349 15
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: 135-147: Diversispora sp., one culture Thiéry et al., in prep. 16
DIVERSITY PATTERNS OF AMF 17
Cluster analysis: AM fungal community composition differs among major habitat types Öpik et al., 2006, J Ecol 94:778-790 18
State of the art 2010: DNA-based AMF richness pattern b Residuals -3.87 - -0.39-0.38 - -0.03-0.02-0.14 0.15-0.31 0.32-1.57 Distribution of standardised residual VT richness (effect of sample size removed) Öpik et al., 2010. New Phytologist 188: 223-241. 19
Virtual taxa 57% 17% of records 41% 65% 20
AM fungal community composition differs among continents and major habitat types Kivlin et al., 2011. Soil Biol. Biochem. 43: 2294-2303. 21
Uniform global sampling: better picture? Öpik et al., 2013. Mycorrhiza 23: 411-430 22
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: 421-430 23
AMF VT richness appears similar in continents and climatic zones (excpt. boreal, polar?) Öpik et al., 2013. Mycorrhiza 23: 411-430 24
AMF community composition differs among climatic zones and continents 454-sequenced samples Cloned-Sanger sequenced samples Öpik et al., 2013. Mycorrhiza 23: 411-430 25
Forest specialist plant species Generalist plant species Öpik et al., 2009, New Phytologist 184:424-437 26
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
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 184:424-437 28
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 130:259-265 29
Root-colonising vs soil-dwelling AMF richness VT Sequences Saks et al., 2014, Botany 92: 277-285 30
and phylogenetic diversity Calamagrostis arundinacea Convallaria majalis Hepatica nobilis Mercurialis perennis Pulmonaria obscura Rubus saxatilis soil Saks et al., 2014, Botany 92: 277-285 31
MORPHOLOGICAL VS. DNA-BASED DIVERSITY 32
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
New higher level clades within Glomeromycota? New family? New family? Öpik et al., 2013, Mycorrhiza 34
Schüssler & Walker 2010 Oehl et al. 2011 & following? Öpik et al., 2010, New Phytol. 188: 223-241 Redecker et al., 2013, Mycorrhiza 21: 515-531 35
Schüssler & Walker 2010 Oehl et al. 2011 & following 36
Oehl et al. 2011 & following Schüssler & Walker 2010 How to delimit morphologically recognised genera on the background of environmental sequences? Glomus (s.l.), Glomeraceae Claroideoglomus, Claroideoglomeraceae
Kõljalg et al., 2013, Mol. Ecol. 22: 5271-5277 38
Do we ever see the fungus? Paraglomus majewskii case: 1. 2011: Paraglomus Pa1 detected in Spain, in roots of Pistacia lentiscus and Rhamnus lycioides (Alguacil et al. 2011, Soil Biol Biochem 43:167-173) 2. 2012: Pa1 sequences added to MaarjAM, new VT erected: Paraglomus VT335 3. 2012: Paraglomus majewskii described based on collections from Turkey and elsewhere (Blaszkowski et al. 2012, Mycologia 104: 148-156) 39
Paraglomus majewskii / Paraglomus VT335 Blaszkowski et al. 2012, Mycologia 104: 148-156. 40
CONCLUSIONS & WHERE NEXT? 41
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
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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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