A combined morphological and molecular approach to characterize isolates of arbuscular mycorrhizal fungi in Gigaspora (Glomales)

Size matters: three methods for estimating nuclear size in mycorrhizal roots of Medicago truncatula by image analysis

BACKGROUND

The intracellular accommodation of arbuscular mycorrhizal (AM) fungi involves a profound molecular reprogramming of the host cell architecture and metabolism, based on the activation of a symbiotic signaling pathway. In analogy with other plant biotrophs, AM fungi are reported to trigger cell cycle reactivation in their host tissues, possibly in support of the enhanced metabolic demand required for the symbiosis.

RESULTS

We here compare the efficiency of three Fiji/ImageJ image analysis plugins in localizing and quantifying the increase in nuclear size - a hallmark of recursive events of endoreduplication - in M. truncatula roots colonized by the AM fungus Gigaspora margarita. All three approaches proved to be versatile and upgradeable, allowing the investigation of nuclear changes in a complex tissue; 3D Object Counter provided more detailed information than both TrackMate and Round Surface Detector plugins. On this base we challenged 3D Object Counter with two case studies: verifying the lack of endoreduplication-triggering responses in Medicago truncatula mutants with a known non-symbiotic phenotype; and analysing the correlation in space and time between the induction of cortical cell division and endoreduplication upon AM colonization. Both case studies revealed important biological aspects. Mutant phenotype analyses have demonstrated that the knock-out mutation of different key genes in the symbiotic signaling pathway block AM-associated endoreduplication. Furthermore, our data show that cell divisions occur during initial stages of root colonization and are followed by recursive activation of the endocycle in preparation for arbuscule accommodation.

CONCLUSIONS

In conclusion, our results indicate 3D Object Counter as the best performing Fiji/ImageJ image analysis script in plant root thick sections and its application highlighted endoreduplication as a major feature of the AM pre-penetration response in root cortical cells.

Arbuscular mycorrhizal fungi, Bacillus cereus, and Candida parapsilosis from a multicontaminated soil alleviate metal toxicity in plants

We investigated if the limited development of Trifolium repens growing in a heavy metal (HM) multicontaminated soil was increased by selected native microorganisms, bacteria (Bacillus cereus (Bc)), yeast (Candida parapsilosis (Cp)), or arbuscular mycorrhizal fungi (AMF), used either as single or dual inoculants. These microbial inoculants were assayed to ascertain whether the selection of HM-tolerant microorganisms can benefit plant growth and nutrient uptake and depress HM acquisition. The inoculated microorganisms, particularly in dual associations, increased plant biomass by 148% (Bc), 162%, (Cp), and 204% (AMF), concomitantly producing the highest symbiotic (AMF colonisation and nodulation) rates. The lack of AMF colonisation and nodulation in plants growing in this natural, polluted soil was compensated by adapted microbial inoculants. The metal bioaccumulation abilities of the inoculated microorganisms and particularly the microbial effect on decreasing metal concentrations in shoot biomass seem to be involved in such effects. Regarding microbial HM tolerance, the activities of antioxidant enzymes known to play an important role in cell protection by alleviating cellular oxidative damage, such as superoxide dismutase, catalase, glutathione reductase, and ascorbate peroxidase, were here considered as an index of microbial metal tolerance. Enzymatic mechanisms slightly changed in the HM-adapted B. cereus or C. parapsilosis in the presence of metals. Antioxidants seem to be directly involved in the adaptative microbial response and survival in HM-polluted sites. Microbial inoculations showed a bioremediation potential and helped plants to develop in the multicontaminated soil. Thus, they could be used as a biotechnological tool to improve plant development in HM-contaminated environments.

Phylogenetic analysis of the Glomeromycota by partial beta-tubulin gene sequences

The 3' end of the beta-tubulin gene was amplified from 50 isolates of 45 species in Glomeromycota. The analyses included a representative selection of all families except Pacisporaceae and Geosiphonaceae. Phylogenetic analyses excluded three intron regions at the same relative positions in all species due to sequence and length polymorphisms. The beta-tubulin gene phylogeny was similar to the 18S rRNA gene phylogeny at the family and species level, but it was not concordant at the order level. Species in Gigasporaceae and Glomeraceae grouped together but without statistical support. Paralogous sequences in Glomus species likely contributed to phylogenetic ambiguity. Trees generated using different fungal phyla as out-groups yielded a concordant topology. Family relationships within the Glomeromycota did not change regardless if the third codon position was included or excluded from the analysis. Multiple clones from three isolates of Scutellospora heterogama yielded divergent sequences. However, phylogenetic patterns suggested that only a single copy of the beta-tubulin gene was present, with variation attributed to intraspecific sequence divergence.

Phylogenetic analysis of Glomeromycota by partial LSU rDNA sequences

We analyzed the large subunit ribosomal RNA (rRNA) gene [LSU ribosomal DNA (rDNA)] as a phylogenetic marker for arbuscular mycorrhizal (AM) fungal taxonomy. Partial LSU rDNA sequences were obtained from ten AM fungal isolates, comprising seven species, with two new primers designed for Glomeromycota LSU rDNA. The sequences, together with 58 sequences available from the databases, represented 31 AM fungal species. Neighbor joining and parsimony analyses were performed with the aim of evaluating the potential of the LSU rDNA for phylogenetic resolution. The resulting trees indicated that Archaeosporaceae are a basal group in Glomeromycota, Acaulosporaceae and Gigasporaceae belong to the same clade, while Glomeraceae are polyphyletic. The results support data obtained with the small subunit (SSU) rRNA gene, demonstrating that the LSU rRNA gene is a useful molecular marker for clarifying taxonomic and phylogenetic relationships in Glomeromycota.

Intraspecific genetic variation in arbuscular mycorrhizal fungi and its consequences for molecular biology, ecology, and development of inoculum

It has been known for some time that different arbuscular mycorrhizal fungal (AMF) taxa confer differences in plant growth. Although genetic variation within AMF species has been given less attention, it could potentially be an ecologically important source of variation. Ongoing studies on variability in AMF genes within Glomus intraradices indicate that at least for some genes, such as the BiP gene, sequence variability can be high, even in coding regions. This suggests that genetic variation within an AMF may not be selectively neutral. This clearly needs to be investigated in more detail for other coding regions of AMF genomes. Similarly, studies on AMF population genetics indicate high genetic variation in AMF populations, and a considerable amount of variation seen in phenotypes in the population can be attributed to genetic differences among the fungi. The existence of high within-species genetic variation could have important consequences for how investigations on AMF gene expression and function are conducted. Furthermore, studies of within-species genetic variability and how it affects variation in plant growth will help to identify at what level of precision ecological studies should be conducted to identify AMF in plant roots in the field. A population genetic approach to studying AMF genetic variability can also be useful for inoculum development. By knowing the amount of genetic variability in an AMF population, the maximum and minimum numbers of spores that will contain a given amount of genetic diversity can be estimated. This could be particularly useful for developing inoculum with high adaptability to different environments.Key words: arbuscular mycorrhizas, symbiosis, genomics, genetic diversity, population genetics, evolutionary ecology.

Vertical transmission of endobacteria in the arbuscular mycorrhizal fungus Gigaspora margarita through generation of vegetative spores

Arbuscular mycorrhizal (AM) fungi living in symbiotic association with the roots of vascular plants have also been shown to host endocellular rod-shaped bacteria. Based on their ribosomal sequences, these endobacteria have recently been identified as a new taxon, Candidatus Glomeribacter gigasporarum. In order to investigate the cytoplasmic stability of the endobacteria in their fungal host and their transmission during AM fungal reproduction (asexual), a system based on transformed carrot roots and single-spore inocula of Gigaspora margarita was used. Under these in vitro sterile conditions, with no risk of horizontal contamination, the propagation of endobacteria could be monitored, and it was shown, by using primers designed for both 16S and 23S ribosomal DNAs, to occur through several vegetative spore generations (SG0 to SG4). A method of confocal microscopy for quantifying the density of endobacteria in spore cytoplasm was designed and applied; endobacteria were consistently found in all of the spore generations, although their number rapidly decreased from SG0 to SG4. The study demonstrates that a vertical transmission of endobacteria takes place through the fungal vegetative generations (sporulation) of an AM fungus, indicating that active bacterial proliferation occurs in the coenocytic mycelium of the fungus, and suggests that these bacteria are obligate endocellular components of their AM fungal host.

PCR-denaturing gradient gel electrophoresis profiling of inter- and intraspecies 18S rRNA gene sequence heterogeneity is an accurate and sensitive method to assess species diversity of arbuscular mycorrhizal fungi of the genus Gigaspora

Despite the importance of arbuscular mycorrhizal fungi in the majority of terrestrial ecosystems, their ecology, genetics, and evolution are poorly understood, partly due to difficulties associated with detecting and identifying species. We explored the inter- and intraspecies variations of the 18S rRNA genes of the genus Gigaspora to assess the use of this marker for the discrimination of Gigaspora isolates and of Gigasporaceae populations from environmental samples. Screening of 48 Gigaspora isolates by PCR-denaturing gradient gel electrophoresis (DGGE) revealed that the V3-V4 region of the 18S rRNA gene contained insufficient variation to discriminate between different Gigaspora species. In contrast, the patterns of 18S ribosomal DNA (rDNA) heterogeneity within the V9 region of this marker could be used for reliable identification of all recognized species within this genus. PCR-DGGE patterns provided insight into some putative misidentifications and could be used to differentiate geographic isolates of G. albida, G. gigantea, and G. margarita but not G. rosea. Two major clusters were apparent based upon PCR-DGGE ribotype patterns, one containing G. albida, G. candida, G. ramisporophora, and G. rosea and the other containing G. decipiens and G. margarita. Dissection of the DGGE patterns by cloning, DGGE screening, and sequencing confirmed these groupings and revealed that some ribotypes were shared across species boundaries. Of the 48 isolates examined, only two displayed any spore-to-spore variation, and these exceptions may be indicative of coisolation of more than one species or subspecies within these cultures. Two Brazilian agricultural soils were also analyzed with a Gigasporaceae-specific nested PCR approach, revealing a dominance of G. margarita within this family.