Symbiotic Fungi: Principles and Practice (Soil Biology)

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10 Assessing the Mycorrhizal Diversity of Soils and Identification of Fungi 173 10.6.1 ‘‘Extraction-Free’’ Preparation of PCR-Ready Material 1. Prepare 2 ml screw-cap microtubes by adding 300 ml PEG200-KOH (adjusted with KOH to pH 13.3–13.5 and autoclaved) and a sterile glass bead of 2–3 mm diameter. 2. Take a loop full of yeast culture or a few mm 3 of fungal fruiting body or a small amount of fungal aerial hyphae from a Petri dish and mix into the PEG200. Freeze if not used right away. 3. Before going to PCR, vortex (the glass bead here supports homogenization) and spin down. The use of sterile sand, a commercial grinding resin, or a microtube pestle to help disrupt the material is optional, e.g., in place of the glass bead. 10.6.2 PEX Extraction For tough fungal herbarium specimens (Krüger 2002) or from mycorrhizal root tips (Martin and Rygiewicz 2005) the xanthogenate (PEX) protocol is a useful and timesaving method. This can be implemented as an alternative to the above PEG200 protocol. Buffers needed: (a) 100 ml TEx buffer stock: 10 mM Tris-HCl (starting from 0.5 ml 2 M Tris-HCl pH 7.4) 1 mM EDTA (starting from 0.2 ml 0.5 M EDTA pH 8.0) 0.5 M CaCl2 (5.5 g) Autoclave (b) 100 ml XT buffer stock: 100 mM Tris-HCl (starting from 5 ml 2 M Tris-HCl pH 7.4) 20 mM EDTA (starting from 4 ml of 0.5 M pH 8.0) 5 ml Tween 20 800 mM sodium acetate (starting from 6.16 g or 16 ml 5 M stock) Autoclave (c) 0.1X TE pH 8.0: =1 mM Tris-HCl, 0.1 mM EDTA, autoclaved. website of the DNA Databank of Japan (DDBJ), allowing query and anchoring sequences to be sent to ClustalW for alignment. Process step f: the program QAlign 2 (Panta Rhei) aligns sequences and can also compute simple phylogenetic trees, here a jackknife resampling, T-Coffee alignment with associated Kimura 2-parameter Neighbour-Joining tree. g: graphical representation of highly similar (top lines) and dissimilar (bottom lines) areas of alignment in POAVIZ (Grasso et al 2003)
174 D. Krüger et al. Fig. 10.7 Workflow of bioinformatic processes in identifying an unknown fungal object (process step query DNA sequence) Part 3. Process step h: visualization of the FASTA formatted alignment as a PDF output from SeaView (Galtier et al 1996). Process step i: using the software Seqverter (GeneStudio, Inc., Suwanee, GA, USA) data can be converted, e.g., from FASTA to the NEXUS
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Soil Biology Volume 18 Series Edito
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Ajit Varma l Amit C. Kharkwal Edito
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Foreword So old, so new... More tha
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Foreword vii Little AE, Robinson CJ
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x Preface work in this challenging
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xii Contents 9 Role of Root Exudate
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Contributors L.K. Abbott School of
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Contributors xvii Falko Feldmann Ju
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Contributors xix K. Nara Asian Natu
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Contributors xxi Marc St-Arnaud Ins
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2 A. Das and A. Varma Fig. 1.1 Type
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4 A. Das and A. Varma the scientifi
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6 A. Das and A. Varma 1.3.2 Symbiot
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8 A. Das and A. Varma all the root
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10 A. Das and A. Varma 1. Such poly
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12 A. Das and A. Varma 1.3.3.9 Nitr
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14 A. Das and A. Varma about 1-2 mm
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16 A. Das and A. Varma fixed nitrog
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18 A. Das and A. Varma Mycorrhizae
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20 A. Das and A. Varma Fig. 1.6 Dia
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22 A. Das and A. Varma a b Root hai
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24 A. Das and A. Varma intracellula
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26 A. Das and A. Varma Becker A, Ni
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28 A. Das and A. Varma Trappe JM, B
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30 A. Jumpponen were once active in
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32 A. Jumpponen GA, USA) to avoid d
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34 A. Jumpponen 2.2.3.6 Cloning, Se
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36 A. Jumpponen Table 2.1 Fungi det
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38 A. Jumpponen of the community st
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40 A. Jumpponen Girvan MS, Bullimor
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42 I.A.F. Djuuna et al. 1991). Crop
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44 I.A.F. Djuuna et al. 3.2.2 Indir
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46 I.A.F. Djuuna et al. Mycorrhiza
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48 I.A.F. Djuuna et al. Boomsma CR,
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50 I.A.F. Djuuna et al. Saito M (19
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52 M. Giovannetti et al. evidenced
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54 M. Giovannetti et al. a c e Ster
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56 M. Giovannetti et al. 4.2.4 Rema
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58 M. Giovannetti et al. a b c Fig.
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60 M. Giovannetti et al. to 4.1 mm
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62 M. Giovannetti et al. The detect
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64 M. Giovannetti et al. Jones MD,
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66 A. Gobert and C. Plassard NO3 fl
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68 A. Gobert and C. Plassard After
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70 A. Gobert and C. Plassard with k
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72 A. Gobert and C. Plassard 10 9 2
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74 A. Gobert and C. Plassard Fig. 5
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76 A. Gobert and C. Plassard connec
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78 A. Gobert and C. Plassard any ti
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80 A. Gobert and C. Plassard Net fl
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82 A. Gobert and C. Plassard a Rati
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84 A. Gobert and C. Plassard - upta
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86 A. Gobert and C. Plassard Table
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88 A. Gobert and C. Plassard Newman
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90 I.M. van Aarle as mycorrhizal hy
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92 I.M. van Aarle a wash buffer. Th
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94 I.M. van Aarle l Usually 20-50 m
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96 I.M. van Aarle Fig. 6.1 Extramat
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98 I.M. van Aarle A disadvantage of
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Chapter 7 In Vitro Compartmented Sy
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7 In Vitro Compartmented Systems to
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13 Isolation, Cultivation and In Pl
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228 K. Vogel-Mikusˇ et al. only be
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230 K. Vogel-Mikusˇ et al. Fig. 14
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232 K. Vogel-Mikusˇ et al. such sp
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234 K. Vogel-Mikusˇ et al. STIM de
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236 K. Vogel-Mikusˇ et al. transfe
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Table 14.1 Element concentrations w
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240 K. Vogel-Mikusˇ et al. Fig. 14
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242 K. Vogel-Mikusˇ et al. Frey B,
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244 E. Dumas-Gaudot et al. TEMED N,
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246 E. Dumas-Gaudot et al. system i
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248 E. Dumas-Gaudot et al. Bromophe
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250 E. Dumas-Gaudot et al. taken to
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252 E. Dumas-Gaudot et al. Note 6:
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254 E. Dumas-Gaudot et al. by Bradf
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256 E. Dumas-Gaudot et al. 3. Take
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258 E. Dumas-Gaudot et al. solubili
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260 E. Dumas-Gaudot et al. Table 15
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262 E. Dumas-Gaudot et al. Table 15
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264 E. Dumas-Gaudot et al. Followin
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266 E. Dumas-Gaudot et al. Once hom
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268 E. Dumas-Gaudot et al. to both
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270 E. Dumas-Gaudot et al. were the
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272 E. Dumas-Gaudot et al. Dumas-Ga
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274 E. Dumas-Gaudot et al. Valot B,
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276 P.A. Olsson Fig. 16.1 Schematic
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278 P.A. Olsson Furthermore, C tran
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280 P.A. Olsson in AM fungi and a h
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282 P.A. Olsson (Graham et al. 1995
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284 P.A. Olsson Nakano A, Takahashi
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286 X.H. He et al. In many cases, N
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288 X.H. He et al. Table 17.1 Exper
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290 X.H. He et al. 17.3.1.1 Comment
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Chapter 18 Analyses of Ecophysiolog
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18 Analyses of Ecophysiological Tra
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308 I. Brito et al. fungi, little i
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310 I. Brito et al. 60% of moisture
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312 I. Brito et al. Thompson 1990;
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314 I. Brito et al. 19.8 Crop Rotat
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316 I. Brito et al. References Abbo
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318 I. Brito et al. Smith SE, Read
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320 F. Feldmann et al. inoculum of
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322 F. Feldmann et al. Table 20.1 B
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324 F. Feldmann et al. transferred
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326 F. Feldmann et al. 20.3.3 The A
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328 F. Feldmann et al. Inoculum is
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330 F. Feldmann et al. Fig. 20.5 Pr
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332 F. Feldmann et al. value for th
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334 F. Feldmann et al. of abiotic a
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336 F. Feldmann et al. Lackie SM, B
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338 M. Vestberg and A.C. Cassells b
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340 M. Vestberg and A.C. Cassells M
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342 M. Vestberg and A.C. Cassells a
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344 M. Vestberg and A.C. Cassells T
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348 M. Vestberg and A.C. Cassells M
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350 M. Vestberg and A.C. Cassells 2
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352 M. Vestberg and A.C. Cassells 2
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354 M. Vestberg and A.C. Cassells C
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356 M. Vestberg and A.C. Cassells G
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358 M. Vestberg and A.C. Cassells P
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360 M. Vestberg and A.C. Cassells V
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362 A. Baldi et al. the capabilitie
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364 A. Baldi et al. 22.2.3 Initiati
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366 A. Baldi et al. 2. Place inocul
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368 A. Baldi et al. 22.5 Analysis 2
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370 A. Baldi et al. 22.5.4 Phenylal
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372 A. Baldi et al. Nicholas JB, Jo
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374 A. Baldi et al. Among these, fu
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376 A. Baldi et al. 3. Place one ex
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378 A. Baldi et al. 23.4 Analysis F
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380 A. Baldi et al. Chattopadhyay S
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382 A. Sirrenberg et al. physical c
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384 A. Sirrenberg et al. Fig. 24.1
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390 A. Sirrenberg et al. in Fig. 24
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392 A. Sirrenberg et al. 24.5.2 Tru
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394 K. Haselwandter and G. Winkelma
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404 E. Mohammadi Goltapeh et al. Fi
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406 E. Mohammadi Goltapeh et al. Th
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408 E. Mohammadi Goltapeh et al. 26
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410 E. Mohammadi Goltapeh et al. co
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412 E. Mohammadi Goltapeh et al. Tw
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414 E. Mohammadi Goltapeh et al. Co
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416 E. Mohammadi Goltapeh et al. qu
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418 E. Mohammadi Goltapeh et al. 26
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420 E. Mohammadi Goltapeh et al. Ch
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Index A A. bisporus var. burnettii,
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Index 425 Dark septate root endophy
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Index 427 Leghemoglobin, 11 Lentinu
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Index 429 Proteomics, 244 Protoplas
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Symbiotic Fungi: Principles and Practice (Soil Biology)

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