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Applied and Environmental Microbiology, November 2005, p. 6673-6679, Vol. 71, No. 11
0099-2240/05/$08.00+0 doi:10.1128/AEM.71.11.6673-6679.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Laboratory of Microbiology, University of Neuchâtel, Neuchâtel, Switzerland,1 Institute of Botany, University of Basel, Basel, Switzerland,2 Institute of Geology, University of Neuchâtel, Neuchâtel, Switzerland3
Received 6 December 2004/ Accepted 23 June 2005
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An optimal colonization of plant roots, particularly in disturbed habitats such as agricultural fields, depends not only on the presence of extraradical hyphae or mycorrhizal root debris but, mainly, on the survival and well-timed germination of AMF spores in the soil. This process can be altered by various abiotic and biotic factors, in particular by the association with soil microorganisms (38). Indeed, some bacterial populations, called mycorrhiza helper bacteria, have beneficial effects on AMF growth not only by improving mycorrhizal root colonization and stimulating extraradical hyphal growth but also by facilitating AMF spore germination (11, 12). The latter effect has been shown for Actinomycetes (2, 7, 22), Pseudomonas and Corynebacterium (21), and Bacillus (38) spp.
Bacteria associated with AMF spores colonize mainly the outer wall layer and rarely penetrate into the inner layers (5, 9, 19, 36). Nevertheless, some bacteria have been found in the cytoplasm of AMF spores (4, 18). The role of AMF spore-associated bacteria is not clear. They could stimulate spore germination by eroding spore walls (9, 19), by producing stimulatory compounds such as CO2 and other volatiles (7), or by influencing AMF phosphorus acquisition (30).
Root exudation could enhance spore germination by stimulating the growth of bacteria beneficial for AMF (21). However, since the quantity and composition of exudates differ from one plant to another (17), different bacterial populations could be stimulated, depending on their preference for distinct plant exudates.
In most of the previous studies on spore-associated microorganisms, the bacteria were isolated upon culturing. However, bacteria not cultivable on ordinary media could represent a significant part of the bacterial community associated with AMF spores. Indeed, only a small fraction (1 to 10%) of the total bacterial community is cultivable (1). Direct molecular approaches that avoid a cultivation step give a broader picture of bacterial communities. PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analysis of the 16S rRNA gene permits fingerprinting of the dominant bacteria of a given sample (10, 23). The detection of populations representing as little as 0.1 to 1% of the total target organisms is feasible. In the present study, the bacterial community associated with spores of Glomus geosporum BEG 18 and G. constrictum BEG 19 was assessed with PCR-DGGE analysis. In order to find out whether specific root exudates or, rather, the fungal species determine the bacterial community structure, spores of the two Glomus species were harvested from both pot cultures with Plantago lanceolata (Plantaginaceae) and pot cultures with Hieracium pilosella (Asteraceae) as host plants.
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Experimental setup.
Twelve 1-liter plastic pots were filled with sterile substrate composed of TerraGreen, quartz sand, and loess (5:4:1) and moistened with water. In each pot, a small hole was drilled, in which a teaspoon of mycorrhizal inoculum was placed. On top of the inoculum, a few seeds of Hieracium pilosella or Plantago lanceolata were sown and covered with sterile quartz sand. The Tropf-Blumat watering system was installed, and the cultures were grown in a greenhouse in spring and summer under ambient conditions. The following four combinations of symbionts were cultivated in triplicates: H. pilosella with either G. geosporum or G. constrictum and P. lanceolata with either G. geosporum or G. constrictum.
Sampling.
Six 15-ml soil cores were sampled from each pot after 170 days of growth in the case of H. pilosella and 247 days of growth in the case of P. lanceolata in order to obtain a sufficient amount of spores. The soil cores were wet sieved through 250- and 63-µm meshes. The suspension of residue gained from the 63-µm mesh sieve was centrifuged at 900 x g for 2 min in a sterile density gradient with a 70% (wt/vol) sucrose layer at the bottom. The spores were collected from the gradient interphase, placed in glass plates, and rinsed three times with sterile milli Q water. For the DNA extraction, 200 spores per pot were individually recovered under a stereomicroscope with a micropipette. For scanning electron microscopy (SEM) analysis, the sampling procedure from the G. geosporum/P. lanceolata replicates was repeated to recover more than 100 spores.
DGGE analysis.
DNA extraction for the DGGE analysis was performed with 200 spores per pot, using the FastDNA spin kit for soil (Bio101, Vista, Calif.) according to the manufacturer's protocol and a bead beater (Fast-Prep model FP 120; Bio101). A double-step PCR was used to amplify the V3 region, a fragment of about 200 bp of the bacterial 16S rRNA gene, as described by Weisskopf et al. (37). A composite mix of bacterial 16S rRNA gene fragments from Pseudomonas fluorescens ATCC 27663, Acidovorax facilis DSM 550, Bacillus subtilis ATCC 14893, Sinorhizobium meliloti DSM 1981, and Aquaspirillum dispar ATCC 27650 was added on each side of the DGGE gel as a reference DGGE pattern. DGGE was performed using an 8% (wt/vol) acrylamide-bisacrylamide gel (37.5:1; Qbiogene, Illkirch, France) with a 30 to 60% linear urea-formamide (Fluka, Buchs, Switzerland; Qbiogene) denaturing gradient (100% denaturant corresponds to 40% formamide plus 7 M urea). Five hundred nanograms of the PCR product was electrophoresed in 1x Tris-acetate-EDTA buffer (Qbiogene) at 60°C with a constant voltage of 150 V for 5.5 h using the Bio-Rad D-Code electrophoresis system (Bio-Rad Inc., Richmond, Calif.). The gels were stained in the dark for 20 min in 0.01% Sybr Green I (Molecular Probes, Leiden, The Netherlands) in 1x Tris-acetate-EDTA solution. The gels were photographed with the Multi-Analyst package (Bio-Rad Inc.). The DGGE fingerprints were normalized according to the reference patterns and were compared using the GelCompar software (Applied Maths, Kortrijk, Belgium). DGGE banding patterns were then converted into a numerical matrix used in the statistical analysis. Each band was considered a single bacterial population, and the band intensity was representative of the relative abundance of the population (10). The bands whose average relative contributions were below 1% were discarded.
Band sequencing.
The DGGE profiles were more similar among H. pilosella pot replicates. Therefore, 10 DGGE bands in the profile of one replicate of H. pilosella/G. geosporum and 10 more bands in the profile of one replicate of H. pilosella/G. constrictum were cut out for sequencing. DNA was recovered and purified as follows. The selected bands were cut out and placed in a 1.5-ml Eppendorf tube containing 100 µl 10 mM Tris-HCl, pH 7.5, and incubated at 4°C for 3 days. The supernatant was then recovered in a new Eppendorf tube. One volume of iced isopropanol (20°C) and 1/10 volume of 3 M sodium acetate were added, and this mixture was incubated at 20°C for 1 day. After centrifugation at 13,000 rpm at 4°C for 30 min, the supernatant was discarded. The pellet containing the DNA was washed with 1 volume of 100% ethanol and then centrifuged at 13,000 rpm for 30 min. The supernatant was completely removed, and the pellet was air dried for 15 min. The DNA was resuspended in 50 µl 10 mM Tris-HCl, pH 7.5. The V3 region of the DNA was then reamplified according to the PCR protocol described above. Again, the amplified products were loaded on a DGGE gel to improve DNA yield and check band purity. If the band on this second gel matched the previously selected one, it was cut out, purified, and reamplified the same way. The amplified products were then purified with the NUCLEOTRAP-CR kit (Macherey-Nagel, Düren Germany) according to the manufacturer's protocol. The DNA fragments were ligated using the pGEM-T vector system (Promega), following the protocol of the manufacturer. Transformation was performed by electroporation using the Bio-Rad Gene Pulser XCell and PC module into E. coli XLI-Blue. The transformed bacterial cells were then plated onto Luria-Bertani (LB) agar containing ampicillin (150 µg/ml), X-Gal (5-bromo-4-chloro-3-indolyl-ß-D-galactopyranoside) (0.1 mM) and IPTG (isopropyl-ß-D-thiogalactopyranoside) (0.2 mM). Plasmids were recovered from white colonies by using the NucleoSpin plasmid kit (Macherey-Nagel) according to the manufacturer's protocol. The resulting DNA fragments were sequenced by Macrogen Corp., South Korea. Three clones per band were sequenced, and only the bands having similar sequences in two out of these three clones are presented in Results. The 16S rRNA gene sequences were aligned using the ClustalX software (34), and the phylogenetic trees were constructed using the neighbor-joining method (31) with the Njplot software (ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot) (25). The topology of the distance tree was tested by resampling data with 100 bootstraps (8) to provide confidence estimates for tree topologies.
SEM analysis.
The spores were fixed using 1% OsO4 and air dried. After being coated with gold, the samples were examined with a Phillips XL 30 scanning electron microscope with an acceleration voltage of 10 kV.
Statistical analysis.
To analyze the relationships between the DGGE patterns of the different samples, correspondence analysis (CA) was used. This ordination method is adapted to analyze presence/absence or abundance data tables and is well suited for populations with unimodal distributions along environmental gradients (10). To perform the CA, a data matrix was composed of rows of objects representing the culture condition replicate and columns of species representing a DGGE band position along the vertical gel gradient. The relative abundance of a species in a sample corresponded to the DGGE band's relative intensity with regard to the sum of all band intensities in a pattern. The CA was then applied on the basis of numerical data matrices converted using the program Progiciel R (16). From the association matrix obtained, the characteristic values associated with the characteristic vectors were calculated using a multidimensional dispersion cloud of the data with the Canoco 4.0 software (Microcomputer Power, Ithaca, N.Y.). Variation partitioning analysis (6) enables display of the variability of patterns constrained by the factors of interest. Therefore, this analysis was used to display the contributions of an AMF species or plant species to the bacterial community profiles. The significance of the results was tested with the Monte Carlo permutation test. Variation partitioning analysis was performed with the software R (26).
Nucleotide sequence accession numbers.
The DGGE band sequences were submitted to the EMBL nucleotide sequence database and assigned accession no. AJ864379 to AJ864393.
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FIG. 1. DGGE gels of the 16S rRNA gene V3 region for bacterial communities associated with the spores of G. geosporum and G. constrictum. Ref, reference pattern composed of five known bacterial sequences. The amplified product of each of the three replicates per culture condition was loaded on the gel. Bands cut and sequenced are indicated with arrows and labeled 1 to 15.
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FIG. 2. Ordination plot generated by correspondence analysis, representing the relationships between AMF spore-associated bacterial communities defined by the DGGE patterns. Three replicates per culture condition were integrated. Circles, G. geosporum; triangles, G. constrictum; open symbols, P. lanceolata; gray symbols, H. pilosella. Values on the axes indicate the percentage of the total variation explained by the axes. CA1, correspondence analysis axis 1; CA2, correspondence analysis axis 2.
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FIG. 3. Distribution of the bands composing the DGGE profiles among the different culture conditions. The bands are named after their vertical position along the DGGE gel. The relative intensity as a mean value of the intensities of the bands obtained for the corresponding culture conditions is indicated in parentheses. Bands excised, cloned, and sequenced are underlined, and their assigned number is given.
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FIG. 4. Affiliation of the sequences retrieved from the DGGE bands with existing 16S rRNA gene sequences, using neighbor-joining trees. Bootstrap values of below 50 are not indicated. The sequences from the database are indicated in italic with their accession numbers. The sequenced bands are shown in boldface. A, Fibrobacteres-Acidobacteria group; B, Cytophaga-Flexibacter-Bacteroides group; C, Betaproteobacteria; D, Deltaproteobacteria; E, Gammaproteobacteria.
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FIG. 5. SEM images of the surface of G. geosporum spores. (A) Young, light yellow-brown spore with its sloughed and eroded outer hyaline layer covering the whole surface; (B) older, medium-brown spore with a residual outer hyaline layer; (C) old, dark orange-brown spore that has lost almost all its outer hyaline layer; (D) outer hyaline layer starting to "peel off" and being replaced by mucilaginous products (arrow); (E) mucilaginous outer hyaline layer; (F) bacterial cells of various shapes adhering to the surface of the laminated layer, with holes possibly corresponding to lysis zones in the spore wall; (G) filamentous bacterial cells adhering to the laminated layer covered with mucilaginous products; (H) coccus-shaped bacteria in division state on the spore surface; (I) chain of coccus-shaped bacteria covered with mucilaginous products. Bars (in micrometers): A and B, 50; C, 100; D, E, F, and G, 10; H and I, 1.
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Roughly one-third of the DGGE bands, among which were some exhibiting the highest relative intensities, were found in the profiles of cultures from all conditions. As a whole, these bands represented more than 50% of the relative intensity of the entire profiles. They comprised sequences affiliated mainly with genera with hydrolytic representatives (Cellvibrio, Chondromyces, Flexibacter, Lysobacter, and Pseudomonas). These biopolymer-degrading bacteria are possibly feeding on the outer hyaline spore layer that is present in both species and consists mainly of chitin, a straight-chain polymer of N-acetylglucosamine (32). Filippi et al. (9) actually demonstrated that many bacteria were attached to the hyaline wall layer of Glomus mosseae spores and that up to 107 CFU/g chitinolytic microorganisms were present on the sporocarp surface. Moreover, Maia and Kimbrough (19) observed bacteria colonizing the walls of a Glomus sp., which they apparently degraded until some remnants were left over. Finally, Walley and Germida (36) observed that the presence and activity of bacteria were generally limited to the outer spore wall surface. In our study, evidence of a bacterial saprophytic activity was suggested by SEM observations of G. geosporum spores, showing that the spore's outer hyaline layer was strongly eroded and that the spore surface was covered with mucilaginous products. Moreover, the outer hyaline layer of the light-colored, juvenile spores showed an early stage of degradation, whereas in the more mature, darker spores this layer was in most cases completely degraded. We also observed that many bacterial cells were either adhering to the laminated layer or embedded in the sloughing hyaline layer. Using transmission electron microscopy, Filippi et al. (9) found bacterial forms in holes within the outer layer of the Glomus mosseae spores and suggested that the holes were formed by the bacterial lytic activity. We also observed many holes on the spore, but as only the surface is seen by SEM, we were not able to confirm the presence of bacteria in these holes.
The most dominant bacterial population we identified was constituted by the genus Flexibacter. This genus is well known for its ability to degrade biomacromolecules in various habitats (27). Some Flexibacter species can form long threads of up to 50 µm long (27). In our study, SEM observations revealed that many long filaments were present on the spore surface. However, these filaments could also be actinobacteria. Actinobacteria were often found to be associated with AMF spores. For example, Mugnier and Mosse (22) reported that G. mosseae spores germinated in vitro only in the presence of microorganisms, including Streptomyces orientalis. Ames and coworkers (2) found that out of 190 spores examined, 100 were colonized by one or more chitin-decomposing microorganisms; 82% were colonized by actinomycetes, 17% by bacteria, and 1% by fungi. Carpenter-Boggs et al. (7) demonstrated a positive correlation between higher germination rate and the amount of production of geosmin, CO2, and 2-methylisoborneol by the actinomycetes. In our study, none of the DGGE bands sequenced were affiliated with actinobacteria. As not all the discrete bands of the DGGE profiles were sequenced, we may have missed this group of microorganisms. However, the studies mentioned above were performed with isolation-cultivation techniques. It is probable that the more abundant spore-associated bacteria might have been neglected, as only 1 to 10% of the total bacterial community is cultivable (1). Moreover, Walley and Germida (36) observed many dwarf cells (<0.3 µm in diameter) embedded within the spore walls, which could represent bacteria in a viable but not cultivable state (20).
Several bands sequenced were affiliated with genera capable of cellulolytic activity. The presence of cellulolytic bacteria on the spore surface indicates that microorganisms attached to the spores may also degrade plant material around them (e.g., cellulose from sloughed off cortical root cells). Gryndler et al. (13) have reported that an amendment of cellulose, if incubated in the soil for a long time, increased the number of bacteria and saprophytic fungi in the soil and also stimulated AMF growth. They suggested that this AMF stimulation could result from an AMF uptake of nutrients released from the decomposing saprophytic microflora. Root exudates also provide the microorganisms with readily assimilable organic substrates (17) and thus stimulate the growth of the biopolymer-degrading populations that would in turn accelerate the decay of the outer spore walls. Indeed, the outer hyaline layers, which are generally the first component of the spore wall synthesized in juvenile spores, are rarely present on mature spores in the soil (14). The presence of active biopolymer-degrading bacterial populations on the spore surface could support also spore germination by releasing nutrients or degrading toxic compounds that inhibit germination. Thus, the process of maturation and eventual germination of AMF spores might benefit from the activity of the surface microorganisms degrading the outer hyaline layer.
This study was supported by the Swiss Agency for Development and Cooperation (SDC) in the framework of the Indo-Swiss Collaboration in Biotechnology (ISCB) program and the National Centre of Competence in Research (NCCR) in Plant Survival, University of Neuchâtel.
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