Taxon-specific oligonucleotide primers for detection of Glomus etunicatum

The 5.8S subunit and flanking internal transcribed spacer (ITS) regions in nuclear ribosomal DNA (rDNA) from spores of Glomus etunicatum MD107, MD127, TN101, and FL329 were amplified by polymerase chain reaction (PCR) using ITS1Kpn and ITS4Pst as primers. The amplification products (597, 599, 598, and 613 bp, respectively) were cloned and sequenced. The similarity among ITS region sequences from MD107, MD127, and TN101 was 99%, whereas the sequence similarity between the ITS regions of these three DNAs and that from FL329 was 91%. The 5.8S rDNA sequences of all four G. etunicatum isolates were identical. In contrast, major dissimilarities in the corresponding rDNA sequence regions of other glomalean taxa were observed. Oligonucleotide sequences unique to G. etunicatum were tested for their specificity in PCR amplification of genomic DNA from spores of 55 isolates comprising 29 glomalean fungi: 18 isolates of G. etunicatum, five G. intraradices, three G. claroideum, 16 other Glomus isolates, and 11 other glomalean taxa from each of four other genera. The G. etunicatum isolates were from a broad range of geographic regions and soils. The oligonucleotide pair GETU1:GETU2 primed specific amplification of an oligonucleotide sequence (approximately 400 bp) present in all G. etunicatum. This primer pair did not prime PCR when template consisted of DNA from any of the other glomalean fungi or any of the non-mycorrhizal controls, including roots of corn (Zea mays). In addition, the pair successfully detected G. etunicatum in nested PCR using a primary PCR product amplified from highly diluted extracts of colonized corn roots using modified ITS1:ITS4 primers. In the phylogenetic analysis of Glomus 5.8S and ITS2 rDNA region sequences, which included 500 bootstrap data sets, confidence in the G. etunicatum branch was very strong (90%) and clearly independent of G. claroideum and G. intraradices, to which it is very closely related. Accepted: 15 October 2000     

Influence of soil impoverishment on the interaction between Glomus mosseae and saprobe fungi

 The effect of the saprobe fungi Wardomyces inflatus (Marchal) Hennebert, Paecilomyces farinosus (Holm & Gray) A. H. S. Brown & G. Sm., Gliocladium roseum Bain., Trichoderma pseudokoningii Rifai and T. harzianum Rifai, isolated from sporocarps of Glomus mosseae, on arbuscular mycorrhizal (AM) colonisation and plant dry matter of soybean was studied in 2/3 and 1/5 diluted soils in a greenhouse trial. Soil dilution to 1/5 had no effect on shoot dry matter of soybean but decreased AM colonisation and root dry weight of plants. CFU of saprobe fungi, except T. harzianum, were higher in 1/5 than in 2/3 diluted soils. W. inflatus and Gliocladium roseum decreased the shoot dry weight of soybean plant when inoculated together with Glomus mosseae. The saprobe fungi P. farinosus and T. pseudokoningii increased the shoot dry weights of plants grown in 1/5 diluted soil. The shoot dry weight and AM colonisation in 1/5 diluted soil were also increased when T. harzianum was inoculated together with Glomus mosseae. Thus, saprobe fungi increased AM colonisation of soybean plants by indigenous endophytes. The AM colonisation of plants at both soil dilutions was increased by Glomus mosseae. The highest level of AM colonisation was observed when P. farinosus and T. pseudokoningii were inoculated together Glomus mosseae. The dilution of soils influenced the interaction between inoculated microorganisms and their effect on plant growth. Accepted: 7 June 1999     

The effect of culture conditions on the mycelial growth and luminescence of naturally bioluminescent fungi

A unique oligonucleotide pair, GOCC56:GOCC427, was designed that correctly primed specific amplification of a approximately 370-bp sequence spanning the ITS and 5.8S rDNA regions of Glomus occultum and Glomus brasilianum. In addition, this primer pair successfully detected G. occultum and G. brasilianum DNA in nested PCR using a primary PCR product amplified from highly diluted extracts of colonized corn (Zea mays) roots using modified ITS1:ITS4 primers. A second primer pair, GBRAS86:GBRAS388, primed specific amplification of a approximately 200-bp sequence spanning the ITS and 5.8S rDNA regions present only in G. brasilianum and Glomus strain GR582. Combined use of both primer pairs provides the means to detect and differentiate two ancient endomycorrhizal species, G. occultum and G. brasilianum, undetectable by standard root staining procedures. Sequence analysis showed that the purported G. occultum strain GR582 is likely a strain of G. brasilianum.     

Morpho-Typing and Molecular Diversity of Arbuscular Mycorrhizal Fungi in Sub-Tropical Soils of Coimbatore Region, Tamil Nadu, India

The diversity potential of arbuscular mycorrhizal fungi (AMF) in three different tropical soils of southern part of India was assessed by traditional morpho-typing of AMF-spores and by culture-independent nested-PCR of internal transcribed spacer region of ribosomal genes. The population diversity of AMF in soil was strongly correlated with available P₂O₅ in soil. Among the three different soils, black-cotton soil had more diversified AMF species than alluvial and red sandy soils. Pooled data of morpho-typing and sequence-driven analysis revealed that Glomus, Gigaspora, Scutellospora and Acaulospora are the AMF genera present in these soils. The diversity of AMF in soil differs with the mycorrhiza colonizing the plant roots.     

Production and specificity of polyclonal antibodies against soluble proteins from the arbuscular mycorrhizal fungus Glomus intraradices

Rabbit polyclonal antibodies were produced against a soluble protein fraction from a vesicle and spore mixture of the arbuscular mycorrhizal fungus (AMF) Glomus intraradices. The protocol for isolation of vesicles and spores from plant roots was optimized to minimize debris contamination. Protein extract purification and preparation for immunization was adapted to increase protein content and immunogenicity. Active antisera were produced starting from the second boost immunization. Antibodies obtained were specific for surface antigens of AMF and revealed different patterns of soluble protein antigens in G. intraradices, G. constrictum and an unidentified Glomus species. Accepted: 6 December 2000     

A procedure for the establishment of Glomus mosseae in dual culture with Ri T-DNA-transformed carrot roots

 A stepwise procedure was investigated to determine the optimal conditions for the establishment of Glomus mosseae (Nicol. & Gerd.) Gerdemann & Trappe in dual in vitro culture with Ri T-DNA-transformed roots of Daucus carota L. Glomus mosseae spores germinated best in 10 mm Tris or MES-buffered medium at pH values just above neutral. Growth of hyphae from germinated spores was much greater in the presence of Tris than MES, eg. 8 mm versus 4 mm per spore for Tris and MES, respectively, at pH 7.2. Roots exhibited a broad pH optimum for growth of 6.0–7.0 in both MES and Tris, but did not grow well above pH 7.5. In addition, purified gelling agent, gellan gum, was utilized to lower the P concentration of media. With these factors combined, mycorrhizas were successfully established in 14% of dual cultures. Accepted: 5 March 1997     

Comparison of two test systems for measuring plant phosphorus uptake via arbuscular mycorrhizal fungi

 Plant phosphorus uptake via external hyphae of arbuscular mycorrhizal fungi has been measured using compartmented systems where a hyphal compartment is separated from a rooting compartment by a fine mesh. By labelling the soil within the hyphal compartment with a radioactive phosphorus (P) isotope, hyphal uptake of P into the plant can be traced. The objective of this growth chamber study was to test two hyphal compartments of different design with respect to their suitabilities for measurement of hyphal P uptake. One hyphal compartment was simply a nylon mesh bag filled with ³²P-labelled soil. The labelled soil in the other hyphal compartment was completely surrounded by an 8–10 mm layer of unlabelled soil that served as a buffer zone. Mycorrhizal and non-mycorrhizal subterranean clover plants were grown in pots with a centrally positioned hyphal compartment. Uptake of radioactive P by non-mycorrhizal control plants was 25% of that by mycorrhizal plants with the mesh bag but only 3% when including the buffer zone. Based on this good control of non-mycorrhizal P uptake from within the hyphal compartment and its greater ease of handling once produced, we judged the hyphal compartment including a buffer zone to be superior to the mesh bag. Accepted: 15 September 1998     

Molecular characterization of Pisolithus spp. isolates by rDNA PCR-RFLP

 Variation within ribosomal DNA (rDNA) genes of 19 isolates of Pisolithus from different geographic origins and hosts was examined by polymerase chain reaction (PCR) coupled with restriction fragment length polymorphism (RFLP) analysis. The primers utilized amplify rDNA regions in a wide range of fungi. One amplified region includes the internal transcribed spacer (ITS), which has a low degree of conservation. The ITS amplification products (640–750 bp) were digested with a variety of restriction endonucleases. Cluster analysis based on the restriction fragments grouped the isolates into three distinct groups: group I contained isolates collected in the northern hemisphere, except Pt 1, group II contained those collected in Brazil and group III contained isolate Pt 1. Additional analysis of other rDNA regions, IGS, 17 S and 25 S rDNA, resulted in similar groups. The data suggest that the taxonomy and systematics of this ectomycorrhizal fungus should be revised. Accepted: 16 September 1998     

Surface-sterilization of Glomus mosseae sporocarps for studying endomycorrhization in vitro

 The effects of sterilization time, sterilizing agents (ethanol, Chloramine T, calcium hypochlorite) and antibiotics (streptomycin and gentamycin) on Glomus mosseae (BEG 12) sporocarp germination and contamination were evaluated. Incubation for 10 s in 96 % ethanol, followed by 10 min in a solution of 2% Chloramine T, 0.02% streptomycin, 0.01% gentamycin and Tween 20, and then 6 min in 6% calcium hypochlorite greatly reduced fungal and bacterial contamination from sporocarps and caused little change in germination rate in water agar medium. Accepted: 4 March 1999     

Sequencing of the internal transcribed spacer region ITS1 as a molecular tool detecting variation in the Stylosanthes guianensis species complex

 The internal transcribed spacer (ITS) regions 1 and 2 of the ribosomal DNA from Stylosanthes guianensis CIAT 1283 and cv ‘Schofield’ were amplified by polymerase chain reaction using conserved ITS primers from the 18S, 5.8S and 26S ribosomal genes flanking those regions. The entire region of 683 bp long was cloned, and seven clones were sequenced. Comparison of the ITS spacer regions with published DNA sequences of other plant species revealed limited homology only; this was in contrast to their comparison with the 5.8S rDNA sequences. The ITS1 region of 45 S. guianensis accessions was amplified by PCR and sequenced on both strands using the conserved primers ITS2-ITS5. These sequences, ranging from 201 to 204 bp, were aligned to each other to assess intra-specific polymorphism. Within the S. guianensis (Aubl.) Sw. species complex, 11 DNA sequence types could be distinguished based on an insertion/deletion (indel) event and 15 single base-pair substitutions. In 1 of the S. guianensis types, two kinds of ITS1 sequence were observed in each individual, reminiscent of an incomplete homogenization of the repeat structure in this type. Polymorphisms in the sequence of the ITS1 region were used to define molecular markers for S. guianensis on the basis of PCR-restriction fragment length polymorphism and selective PCR. Received: 24 June 1997 / Accepted: 31 October 1997     

Determination of the nitrogen source for arbuscular mycorrhizal fungi by 15N application to soil and plants

The source of nitrogen in the spores of arbuscular mycorrhizal (AM) fungi was quantified by a ¹⁵N-labeling technique. N was applied as coated urea to the soil and in solution to plant shoots. Soil-applied fertilizer had a significant effect on spore % ¹⁵N (P<0.01), with a 24–75% contribution to spore N. Fertilizer applied to either alfalfa shoots or bahia grass shoots had little effect on spore % ¹⁵N, accounting for 0–14% or 1–9% of spore N, respectively. These results indicate that AM fungi obtain spore N mostly from the soil. The small amount of spore N originating from shoot-applied N may have been obtained via root exudation. Accepted: 6 November 2000     

The response of Glomus fistulosum–maize mycorrhiza to treatments with culture fractions from Pseudomonas putida

 This study examined which culture fraction of the plant-growth-promoting bacterium Pseudomonas putida (Trevisan) Migula has an effect on growth and mycorrhiza formation of maize (Zea mays L.). Shoot dry weight and total leaf area of plants did not increase after inoculation with Glomus fistulosum but were significantly higher than the controls when the plants were dualinoculated with G. fistulosum and living cells of P. putida. Mycorrhizal infection of the roots was significantly higher when plants were inoculated with G. fistulosum together with living cells of P. putida or with G. fistulosum and dialysed cell extracts of P. putida than with G. fistulosum alone. Development of arbuscular mycorrhizal (AM) extraradical hyphae and the proportion of extraradical hyphae showing NADH diaphorase activity were significantly enhanced by inoculation of plants with living cells of P. putida or dialysed cell extracts of P. putida. No stimulation of extraradical hyphae proliferation from in vitro incubated mycorrhizal root segments was observed after application of culture fractions of P. putida. However, the percentage contamination of the root segments by extraneous filamentous fungi significantly decreased in the presence of livingcells of P. putida. Accepted: 12 January 1996     

The fungicides Terrazole and Terraclor and the nematicide Fenamiphos have little effect on root colonisation by Glomus mosseae and growth of cotton seedlings

 The effect of three pesticides on the initiation and early development of arbuscular mycorrhiza in cotton was examined in experiments under controlled conditions. The fungicides Terrazole and Terraclor initially inhibited mycorrhizal infection of roots of cotton. The inhibition disappeared after 4 weeks, and neither fungicide had a lasting effect. The nematicide Fenamiphos slightly increased shoot dry weight at 6–10 weeks from planting and had no effect on mycorrhizal infection. We conclude that these pesticides have no sustained, detrimental effect on mycorrhizal infection or growth of cotton seedlings when applied at recommended rates. Accepted: 30 May 1997     

Effects of Glomus intraradices on the reproduction of the burrowing nematode (Radopholus similis) in dixenic culture

The effects of Glomus intraradices on the reproduction of the burrowing nematode Radopholus similis were studied under dixenic culture conditions. The life cycles of both the arbuscular mycorrhizal fungus (AMF) and the nematode were completed in presence of each other and a transformed carrot root as host. The AMF suppressed the R. similis population by almost 50% and thus increased protection of the root against the nematode. This reduction was significant for both females and males within roots. There was no correlation between nematode population density and either AMF internal root colonization, external hyphal development or spore production. These results demonstrate that the dixenic system, although artificial, is a valuable tool for studying AMF–nematode interactions, complementing the classical experimental approaches. Accepted: 6 February 2001     

Detection of the 3-phosphoglycerate kinase protein of Glomus mosseae

 The Glomus mosseae 3-phosphoglycerate kinase (PGK) gene encodes a polypeptide of 416 amino acids. A synthetic peptide was designed to the C-terminus of the polypeptide for the production of a polyclonal antibody. The antibody was tested against the synthetic peptide in an immuno-dot blot and was then used to investigate the asymbiotic and symbiotic accumulation of the PGK protein. Western blot analysis revealed that a polypeptide of approximately 45 kDa accumulated in G. mosseae-colonised tomato roots; this is similar to the theoretical molecular weight of 44.764 kDa. The protein was not detected in non-mycorrhizal roots. Quantitative immuno-dot blotting revealed that the polypeptide accumulated in germinating spores and hyphae of G. mosseae and also in tomato roots colonised by G. mosseae. The amount detected in the mycorrhizal root system was significantly higher than that found in germinating sporocarps. The variation in the levels of glycolytic activity in the symbiotic and asymbiotic developmental stages of G. mosseae is discussed. Accepted: 20 April 2000     

Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies

The internal transcribed spacer regions (ITS1 and ITS2) of the tandemly repeated nuclear ribosomal DNA clusters are frequently used as markers for fine scale analyses in diverse animals. In certain taxa, ITS is nearly exclusively used for population level or inter-specific studies, despite the frequent presence of divergent paralogs within individual genomes that can be phylogenetically misleading. For the first time we survey diverse marine sponges to determine the extent and phylogenetic implications of intragenomic polymorphisms (IGPs) exhibited at their ITS loci. We discover that the extent of IGP varies greatly between taxa (with most taxa exhibiting very few) and cannot be predicted by taxonomy. Furthermore, we demonstrate that ITS can be phylogenetically informative between species when moderate levels of IGPs are detected, but that ITS paralogy can interfere with population level studies. We caution against the routine use of ITS in phylogenetic studies of sponges without (1) screening for IGPs in specimens from every population sampled; (2) including all divergent paralogs in phylogenetic analyses; (3) testing ITS data using other single-copy, unlinked loci (such as nuclear introns).     

Phylogenetic relationships of coffee-tree species (Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA

 Phylogenetic relationships of Coffea species were estimated from the sequences of the internal transcribed spacer (ITS 2) region of nuclear ribosomal DNA. The ITS 2 region of 37 accessions belonging to 26 Coffea taxa and to three Psilanthus species was directly sequenced from polymerase chain reaction (PCR)-amplified DNA fragments. The level of variation was high enough to make the ITS 2 a useful tool for phylogenetic reconstruction. However, an unusual level of intraspecific variation was observed leading to some difficulty in interpreting rDNA sequence divergences. Sequences were analysed using Wagner parsimony as well as the neighbour-joining distance method. Coffea taxa were divided into several major groups which present a strong geographical correspondence (i.e. Madagascar, East Africa, Central Africa and West Africa). This organisation is well supported by cytogenetic evidence. On the other hand, the results were in contradiction with the present classification of coffee-tree taxa into two genera, namely Coffea and Psilanthus. Furthermore, additivity of parental rDNA types was not observed in the allotetraploid species C. arabica. Received: 25 July 1996 / Accepted: 18 October 1996     

Effect of host shoot clipping on carbon and nitrogen sources for arbuscular mycorrhizal fungi

The effect of clipping of the host-plant shoot on the sources of carbon and nitrogen for the arbuscular mycorrhizal (AM) fungus Gigaspora margarita was determined by measuring ¹³C in spores and hyphae in cocultures of C₃ and C₄ plants and by differential ¹⁵N labeling. C₃ and C₄ plants, which have different δ¹³C values, were grown in the same container separated by a series of hyphal compartments. The C₃ and C₄ plants were applied with ¹⁴N- and ¹⁵N-urea, respectively. After clipping of the C₃ shoots, spore δ ¹³C gradually approached that of the C₄ roots. Hyphal δ ¹³C paralleled that of spores. Spore % ¹⁵N was similar to that of mineral N in the C₄ plant compartment. Thus C in G. margarita coming from the clipped plants decreased with time. This demonstrates that C in AM fungi comes from living plants, whilst the N in spores comes mostly from the soil. Accepted: 28 November 2000     

Identification to the species level of the plant pathogens Phytophthora and Pythium by using unique sequences of the ITS1 region of ribosomal DNA as capture probes for PCR ELISA

The ribosomal internal transcribed spacer 1 region was sequenced for 10 species of Pythium and eight species of Phytophthora. Alignment of the sequences revealed considerable sequence microheterogeneity, which was utilized to prepare a capture probe of unique sequence for each species. The capture probes were tested by PCR ELISA, combining the sensitivity and specificity of the polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA). The probes were entirely species specific, enabling the detection and identification of the amplified DNA of species from individual cultures or from mixed samples of the DNAs of two different species. This approach to species identification, which provides a molecular technology to process large numbers of samples and still identify the fungi with a high level of confidence, may greatly reduce the resources and the time of highly trained specialists currently needed to identify these important species of plant pathogenic fungi.