4. Alcance de los Estudios Efectuados
4.1. Objetivos del Contrato de Consultoría
Table S7.1. Bacterial and fungal strains used in this study. All strains were previously isolated from the rhizosphere of Carex arenaria or Ammophila arenaria growing on sandy dune soils at different places of the Netherlands.
Bacterial & fungal strains
(Accesion number) Origin Phylum/ Division (Family)
Burkholderia sp. AD024
(PRJNA320371) Dune grassland near Ouddorp, Zeeland (De Ridder-Duine et al. 2005) Beta-Proteobacteria (Burkholderiaceae)
Collimonas pratensis Ter91
(CP013234) Inner coastal dune soil in Terschelling (De Boer et al. 2004) Beta-Proteobacteria (Oxalobacteraceae)
Dyella sp. AD056
(KJ685269) Drift sand near Loon op Zand, Brabant (De Ridder-Duine et al. 2005) Gamma-Proteobacteria (Xanthomonadaceae)
Janthinobacterium sp. AD080
(KJ685292) Coastal outer dunes of Midsland, Terschelling (De Ridder-Duine et al. 2005) Beta-Proteobacteria (Oxalobacteraceae)
Paenibacillus sp. AD087
(LXQN00000000) Pine plantation near Loon op Zand, Brabant (De Ridder-Duine et al. 2005) Firmicutes (Paenibacillaceae)
Pseudomonas sp. AD021
(DQ778036) Coastal inner dunes of Midsland, Terschelling (De Ridder-Duine et al. 2005) Gamma-Proteobacteria (Pseudomonadaceae)
Fusarium culmorum PV Dutch Coastal foredunes
Table S7.2. Pure volatile compounds used in the volatile diffusion assay. Compounds were detected for roots of Carex arenaria (Carex) in absence or presence of the fungus Fusarium culmorum (Carex + FC) as well as F. culmorum (FC) in soil.
Compound CAS number RI‡ Exact mass
(Da)§ Compound class Treatment α-Pinene* 80-56-8 937±3 136 Terpene FC Amylene hydrate (2-Methyl-2-butanol)* 75-85-4 628±4 88 Alcohol FC Benzil
(Diphenyl-ethanedione)* 134-81-6 1766±2 210 Aromatic ketone Carex/ Carex + FC
Benzofuran
(Coumarone)* 271-89-6 1004±4 118 Aromatic ether Carex + FC
Benzonitrile* 100-47-0 985±4 103 Aromatic compound Carex/ Carex + FC
Benzothiazole* 95-16-9 1229±8 135 Sulfur compound FC
Camphene* 79-92-5 952±2 136 Terpene FC
Dimethyl disulfide* 624-92-0 746±6 94 Sulfur compound Carex/ Carex + FC
γ-Nonalactone
(Dihydro-5-pentyl- 2(3H)-Furanone)* 104-61-0 1363±5 156 Ester Carex/ Carex + FC
Nonanoic acid* 112-05-0 1273±7 158 Carbonic acid Carex/ Carex + FC
3-Octanone* 106-68-3 986±3 128 Ketone FC
Phenol† 108-95-2 980±4 94 Aromatic compound Carex/ Carex + FC
Propanal
(Propionaldehyd)* 123-38-6 461±18 58 Aldehyde FC
* Purchased from Sigma-Aldrich Chemie N.V. (Zwijndrecht, The Netherlands). † Purchased from VWR International (Radnor, USA).
‡ Obtained from NIST 2014 V2.20 spectral library.
Figure S7.1. Set-up of the belowground olfactometer system to test the bacterial attraction by Carex arenaria root volatiles or volatiles emitted by the fungus Fusarium culmorum PV in soil. The system was covered with aluminium foil (A) to protect the soil from light above. For treatments with C. arenaria in the central vessel, four replicates were set up and three replicates were set up for the other treatments (B).
GC-MS analysis of VOCs
VOCs were desorbed from the traps or PDMS tubes (see below) by using an automated thermodesorption unit (model UnityTD-100, Markes International Ltd., UK) at 250°C for 12 min (He flow 50 ml/min). The desorbed VOCs were subsequently collected on a cold trap at -10°C and introduced into the GC-QTOF (model Agilent 7890B GC and the Agilent 7200AB QTOF, USA) by heating the cold trap for 10 min to 280°C. A split ratio was set to 1:10 and 1:2 to analyze VOCs produced by Carex or F. culmorum in soil and diffused pure volatile compounds, respectively. The column used was a 30 × 0.25 mm ID DB-5MS with as film thickness of 0.25 μm (Agilent 122-5532, USA). The temperature program was as follows: 2 min at 39°C, 3.5°C/min to 95°C, 4°C/min to 165°C and finally 15°C/min to 280°C that was hold for 15 min. VOCs were detected by the MS operating at 70 eV in EI mode. Mass spectra were acquired in full scan mode (30–400 AMU, 4 spectras/sec). Collected GC/MS data was converted to mzData files using the Chemstation B.06.00 (Agilent Technologies, Santa Clara, USA) and further processed (peak picking, baseline correction and peak alignment) in an untargeted manner with MetAlign (Lommen & Kools 2012) and MSClust (Tikunov et al. 2012). Detected compounds were identified by using NIST-MS Search by comparing the spectra, accurate mass, linear retention indices and spectra match factor with NIST 2014 V2.20 (National Institute of Standards and Technology, USA, http://www.nist.gov), Wiley 9th edition, and in-house spectral libraries. The linear retention indices of VOCs were calculated according to the method of Strehmel et al. (2008). Chromatograms obtained for the mix of introduced pure VOCs in soil (see below) were analyzed with Chemstation B.06.00 and AMDIS 2.72 (National Institute of Standards and Technology, Gaithersburg, USA).
DNA extraction and qPCR
DNA extraction was performed with DNeasy PowerSoil Kit (Qiagen Benelux B.V., Venlo, The Netherlands) with modification from the manufacturer’s protocol. About 0.3-0.35 g soil was weighted in PowerBead Tubes and mixed by vortexing with 100 µl low molecular weight salmon sperm DNA (10 mg ml-1, pH 8, Sigma-Aldrich Chemie N.V., Zwijndrecht, The Netherlands) as well as 60 µl solution C1 provided by the kit. The tubes were incubated for 30 min at 60°C and vortexed in a Vortex Adapter for 15 min at maximum speed. The solutions was spin down at 10,000 g for 1 min and the supernatant was mixed in a fresh collection tube with solution C2 and C3 followed by an incubation for 5 min on ice. The following steps were performed according to the protocol. The DNA was quantified by NanoDrop and stored at -20°C until use.
All quantitative PCR (qPCR) of the 16S rRNA genes of five of the six bacterial strains was performed according to Schulz-Bohm et al. (2015). The 20 μl reaction mixture to amplify
16S rRNA genes of C. pratensis Ter91 consisted of 1-fold SensiFAST™ SYBR® No-ROX Kit (GC biotech B.V., Alphen aan den Rijn, The Netherlands), BSA (0.5 μg μl-1), 375 nM forward and reverse primers (Eddy3for and Eddy3rev; Höppener-Ogawa et al. 2007), and 5 μl of DNA (2-6 ng μl-1). No template controls consisting of DNase- and RNase-free water were included in every qPCR run. The thermal cycling program was as followed: 5 min initial denaturation at 95°C , ensued by 40 cycles of denaturation for 30 s at 95°C, annealing for 20 s at 62°C, elongation for 20 s at 72°C, and fluorescence signal detection for 15 s at 77°C. Immediately after the 40th PCR cycle, a melting curve analyses from 62°C to 95°C with increments of 1.0°C was followed.
Direct interaction assay
A fungal plug (1 cm diameter) with Fusarium culmorum PV (Table S7.1) pre-grown on 0.5 PDA (Schmidt et al. 2016) was transferred to the top of a petri-dish which was filled with 20 ml 0.1 TSA (Tyc et al. 2014) and incubated for 24 h at 25°C. Bacterial suspensions (108 CFU ml- 1) of Burkholderia sp. AD024, Collimonas pratensis Ter91, Dyella sp. AD056,
Janthinobacterium sp. AD080, Paenibacillus sp. AD087, and Pseudomonas sp. AD021 (Table
S7.1) were prepared as described before (main text). 50 µl of bacterial suspension per strain and, in case of the control, 50 µl of sterile P-buffer (10mM KH2PO4, pH 6.5) was spread in the middle of the agar plate. Petri-dishes were closed with parafilm and incubated for 5 days at 25°C. Pictures of the agar plate were taken with a Panasonic DMC-FZ200 digital camera.