Phosphate transporter genes as reliable gene markers for the identification and discrimination of arbuscular mycorrhizal fungi in the genus glomus

Beneficial Effects of the Five Isolates of Funneliformis mosseae on the Tomato Plants Were Not Related to Their Evolutionary Distances of SSU rDNA or PT1 Sequences in the Nutrition Solution Production

The symbiosis and beneficial effects of arbuscular mycorrhizal fungi (AM fungi) on plants have been widely reported; however, the effects might be unascertained in tomato industry production with coconut coir due to the nutrition solution supply, or alternatively with isolate-specific. Five isolates of AM fungi were collected from soils of differing geographical origins, identified as Funneliformis mosseae and evidenced closing evolutionary distances with the covering of the small subunit (SSU) rDNA regions and Pi transporter gene (PT1) sequences. The effects of these isolates on the colonization rates, plant growth, yield, and nutrition uptake were analyzed in tomato nutrition solution production with growing seasons of spring-summer and autumn-winter. Our result indicated that with isolate-specific effects, irrespective of geographical or the SSU rDNA and PT1 sequences evolution distance, two isolates (A2 and NYN1) had the most yield benefits for plants of both growing seasons, one (E2) had weaker effects and the remaining two (A2 and T6) had varied seasonal-specific effects. Inoculation with effective isolates induced significant increases of 29.0-38.0% (isolate X5, T6) and 34.6-36.5% (isolate NYN1, T6) in the plant tissues respective nitrogen and phosphorus content; the plant biomass increased by 18.4-25.4% (isolate T6, NYN1), and yields increased by 8.8-12.0% (isolate NYN1, A2) compared with uninoculated plants. The maximum root biomass increased by 28.3% (isolate T6) and 55.1% (isolate E2) in the autumn-winter and spring-summer growing seasons, respectively. This strong effect on root biomass was even more significant in an industry culture with a small volume of substrate per plant. Our results reveal the potential benefits of using selected effective isolates as a renewable resource that can overcome the suppressing effects of sufficient nutrient availability on colonization rates, while increasing the yields of industrially produced tomatoes in nutrition solution with coconut coir.

Host identity influences nuclear dynamics in arbuscular mycorrhizal fungi

The arbuscular mycorrhizal fungi (AMF) are involved in one of the most ecologically important symbioses on the planet, occurring within the roots of most land plants.¹ Knowledge of even basic elements of AM fungal biology is still poor, with the discovery that AMF may in fact have a sexual life cycle being only very recently reported.^2-5 AMF produce asexual spores that contain up to several thousand individual haploid nuclei⁶ of either largely uniform genotypes (AMF homokaryons) or nuclei originating from two parental genotypes^2-5 (AMF dikaryons or heterokaryons). In contrast to the sexual dikaryons in the phyla Ascomycota and Basidiomycota,^7,8 in which pairs of nuclei coexist in single hyphal compartments, AMF dikaryons carry several thousand nuclei in a coenocytic mycelium. Here, we set out to better understand the dynamics of this unique multinucleate condition by combining molecular analyses with advanced microscopy and modeling. Herein, we report that select AMF dikaryotic strains carry the distinct nucleotypes in equal proportions to one another, whereas others show an unequal distribution of parental nucleotypes. In both cases, the relative proportions within a given strain are inherently stable. Simulation models suggest that AMF dikaryons may be maintained through nuclear cooperation dynamics. Remarkably, we report that these nuclear ratios shift dramatically in response to plant host identity, revealing a previously unknown layer of genetic complexity and dynamism within the intimate interactions that occur between the partners of a prominent terrestrial symbiosis.

Diversity of a phosphate transporter gene among species and isolates of arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi (AMF) are a key group of beneficial obligate biotrophs, establishing a mutualistic symbiosis with the roots of most land plants. The molecular markers generally used for their characterization are mainly based on informative regions of nuclear rDNA (SSU-ITS-LSU), although protein-encoding genes have also been proposed. Within functional genes, those encoding for phosphate transporters (PT) are particularly important in AMF, given their primary ability to take up Pi from soil, and to differentially affect plant phosphate nutrition. In this work, we investigated the genetic diversity of PT1 gene sequences and sequences of the taxonomically relevant SSU-ITS-LSU region in two isolates of the species Funneliformis coronatus, three isolates of the species Funneliformis mosseae and two species of the genus Rhizoglomus, originated from geographically distant areas and cultured in vivo. Our results showed that partial PT1 sequences not only successfully differentiated AMF genera and species like ribosomal gene sequences but also highlighted intraspecific diversity among F. mosseae and F. coronatus isolates. The study of functional genes related to the uptake of key mineral nutrients for the assessment of AMF diversity represents a key step in the selection of efficient isolates to be used as inocula in sustainable agriculture.

A population genomics approach shows widespread geographical distribution of cryptic genomic forms of the symbiotic fungus Rhizophagus irregularis

Arbuscular mycorrhizal fungi (AMF; phylum Gomeromycota) associate with plants forming one of the most successful microbe-plant associations. The fungi promote plant diversity and have a potentially important role in global agriculture. Plant growth depends on both inter- and intra-specific variation in AMF. It was recently reported that an unusually large number of AMF taxa have an intercontinental distribution, suggesting long-distance gene flow for many AMF species, facilitated by either long-distance natural dispersal mechanisms or human-assisted dispersal. However, the intercontinental distribution of AMF species has been questioned because the use of very low-resolution markers may be unsuitable to detect genetic differences among geographically separated AMF, as seen with some other fungi. This has been untestable because of the lack of population genomic data, with high resolution, for any AMF taxa. Here we use phylogenetics and population genomics to test for intra-specific variation in Rhizophagus irregularis, an AMF species for which genome sequence information already exists. We used ddRAD sequencing to obtain thousands of markers distributed across the genomes of 81 R. irregularis isolates and related species. Based on 6 888 variable positions, we observed significant genetic divergence into four main genetic groups within R. irregularis, highlighting that previous studies have not captured underlying genetic variation. Despite considerable genetic divergence, surprisingly, the variation could not be explained by geographical origin, thus also supporting the hypothesis for at least one AMF species of widely dispersed AMF genotypes at an intercontinental scale. Such information is crucial for understanding AMF ecology, and how these fungi can be used in an environmentally safe way in distant locations.

Molecular cloning and functional analysis of two phosphate transporter genes from Rhizopogon luteolus and Leucocortinarius bulbiger, two ectomycorrhizal fungi of Pinus tabulaeformis

Inorganic phosphorus (Pi) is essential for plant growth, and phosphate (P) deficiency is a primary limiting factor in Pinus tabulaeformis development in northern China. P acquisition in mycorrhizal plants is highly dependent on the activities of phosphate transporters of their root-associated fungi. In the current study, two phosphate transporter genes, RlPT and LbPT, were isolated from Rhizopogon luteolus and Leucocortinarius bulbiger, respectively, two ectomycorrhizal fungi forming symbiotic interactions with the P. tabulaeformis. Phylogenetic analysis suggested that the sequence of the phosphate transporter of L. bulbiger is most closely related to a phosphate transporter of Hebeloma cylindrosporum, whereas the phosphate transporter of R. luteolus is most closely related to that of Piloderma croceum. The subcellular localization indicated that RlPT and LbPT were expressed in the plasma membrane. The complementation assay in yeast indicated that both RlPT and LbPT partially compensated for the absence of phosphate transporter activity in the MB192 yeast strain, with a K m value of 57.90 μmol/L Pi for RlPT and 35.87 μmol/L Pi for LbPT. qPCR analysis revealed that RlPT and LbPT were significantly up-regulated at lower P availability, which may enhance P uptake and transport under Pi starvation. Our results suggest that RlPT and LbPT presumably play a key role in Pi acquisition by P. tabulaeformis via ectomycorrhizal fungi.

Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi

Sexual reproduction is ubiquitous among eukaryotes, and fully asexual lineages are extremely rare. Prominent among ancient asexual lineages are the arbuscular mycorrhizal fungi (AMF), a group of plant symbionts with a multinucleate cytoplasm. Genomic divergence among co-existing nuclei was proposed to drive the evolutionary success of AMF in the absence of sex(1), but this hypothesis has been contradicted by recent genome analyses that failed to find significant genetic diversity within an AMF isolate(2,3). Here, we set out to resolve issues surrounding the genome organization and sexual potential of AMF by exploring the genomes of five isolates of Rhizophagus irregularis, a model AMF. We find that genetic diversity in this species varies among isolates and is structured in a homo-dikaryon-like manner usually linked with the existence of a sexual life cycle. We also identify a putative AMF mating-type locus, containing two genes with structural and evolutionary similarities with the mating-type locus of some Dikarya. Our analyses suggest that this locus may be multi-allelic and that AMF could be heterothallic and bipolar. These findings reconcile opposing views on the genome organization of these ubiquitous plant symbionts and open avenues for strain improvement and environmental application of these organisms.

Relationship between genetic variability in Rhizophagus irregularis and tolerance to saline conditions

Reclamation of saline soils produced by extraction of bitumen from oil sands is challenging. The main objective of this study was to select a salt-tolerant arbuscular mycorrhizal (AM) fungal isolate that could, in the future, be used to pre-inoculate plants used in reclamation of saline substrates produced by oil sand industry. To achieve this, the effects of NaCl, Na(2)SO(4), and saline release water from composite tailings (CT) on hyphal growth of two AM fungal isolates from non-saline (Rhizophagus irregularis DAOM 181602, Rhizophagus sp. DAOM 227023) and three isolates of R. irregularis isolated from saline or sodic soils (DAOM 234181, DAOM241558, and DAOM241559) were tested in vitro. Pre-symbiotic hyphal growth of the five isolates, in absence of a host plant, decreased with increasing salt stress and no spores germinated in CT. The symbiotic extraradical phase of the four isolates of R. irregularis developed well in saline media compared to the Rhizophagus sp. Nevertheless, fungal development of the four R. irregularis isolates differed in saline media indicating phenotypic variations between isolates.