The dawn of symbiosis between plants and fungi

The colonization of land by plants relied on fundamental biological innovations, among which was symbiosis with fungi to enhance nutrient uptake. Here we present evidence that several species representing the earliest groups of land plants are symbiotic with fungi of the Mucoromycotina. This finding brings up the possibility that terrestrialization was facilitated by these fungi rather than, as conventionally proposed, by members of the Glomeromycota. Since the 1970s it has been assumed, largely from the observation that vascular plant fossils of the early Devonian (400 Ma) show arbuscule-like structures, that fungi of the Glomeromycota were the earliest to form mycorrhizas, and evolutionary trees have, until now, placed Glomeromycota as the oldest known lineage of endomycorrhizal fungi. Our observation that Endogone-like fungi are widely associated with the earliest branching land plants, and give way to glomeromycotan fungi in later lineages, raises the new hypothesis that members of the Mucoromycotina rather than the Glomeromycota enabled the establishment and growth of early land colonists.     

Pteridophyte fungal associations: Current knowledge and future perspectives

Current understanding of the nature and function of fungal associations in pteridophytes is surprisingly patchy given their key evolutionary position, current research foci on other early-branching plant clades, and major efforts at unravelling mycorrhizal evolution and the mechanisms underlying this key interaction between plants and fungi. Here we provide a critical review of current knowledge of fungal associations across pteridophytes and consider future directions making recommendations along the way. From a comprehensive survey of the literature, a confused picture emerges: suggestions that members of the Lycopsida harbour Basidiomycota fungi contrast sharply with extensive cytological and recent molecular evidence pointing to exclusively Glomeromycota and/or Mucoromycotina associations in this group. Similarly, reports of dark septate, assumingly ascomycetous, hyphae in a range of pteridophytes, advocating a mutualistic relationship, are not backed by functional evidence and the fact that the fungus invariably occupies dead host tissue points to saprotrophy and not mutualism. The best conclusion that can be reached based on current evidence is that the fungal symbionts of pteridophytes belong to the two fungal lineages Mucoromycotina and Glomeromycota. Do symbiotic fungi and host pteridophytes engage in mutually beneficial partnerships? To date, only two pioneering studies have addressed this key question demonstrating reciprocal exchange of nutrients between the sporophytes of Ophioglossum vulgatum and Osmunda regalis and their fungal symbionts. There is a pressing need for more functional investigations also extending to the gametophyte generation and coupled with in vitro isolation and resynthesis studies to unravel the effect of the fungi on their host.     

Proximal and distal mechanisms through which arbuscular mycorrhizal associations alter terrestrial denitrification

Plant and Soil - The vast majority of terrestrial plants, including most crops, associate with fungi of the phylum Glomeromycota to form symbiotic associations, known as arbuscular mycorrhizas....     

Guilds of mycorrhizal fungi and their relation to trees,ericads, orchids and liverworts in a neotropical mountain rain forest

Mycorrhizas of vascular plants and mycorrhiza-like associations of liverworts and hornworts are integral parts of terrestrial ecosystems, but have rarely been studied in tropical mountain rain forests. The tropical mountain rain forest area of the Reserva Biológica San Francisco in South Ecuador situated on the eastern slope of the Cordillera El Consuelo is exceptionally rich in tree species, ericads and orchids, but also in liverworts. Previous light and electron microscopical studies revealed that tree roots are well colonized by structurally diverse Glomeromycota, and that epiphytic, pleurothallid orchids form mycorrhizas with members of the Tulasnellales and the Sebacinales (Basidiomycota). Sebacinales also occurred in mycorrhizas of hemiepiphytic ericads and Tulasnellales were found in liverworts belonging to the Aneuraceae. On the basis of these findings, we hypothesized that symbiotic fungi with a broad host range created shared guilds or even fungal networks between different plant species and plant families. To test this hypothesis, molecular phylogenetic studies of the fungi associated with roots and thalli were carried out using sequences of the nuclear rDNA coding for the small subunit rRNA (nucSSU) of Glomeromycota and the large subunit rRNA (nucLSU) of Basidiomycota. Sequence analyses showed that Sebacinales and Tulasnellales were only shared within but not between ericads and orchids or between liverworts and orchids, respectively. Regarding arbuscular-mycorrhiza-forming trees, however, 18 out of 33 Glomus sequence types were shared by two to four tree species belonging to distinct families. Nearly all investigated trees shared one sequence type with another tree individual. Host range and potential shared guilds appeared to be restricted to the plant family level for Basidiomycota, but were covering diverse plant families in case of Glomeromycota. Given that the sequence types as defined here correspond to fungal species, our findings indicate potential fungal networks between trees.     

Molecular evolution patterns reveal life history features of mycoplasma‐related endobacteria associated with arbuscular mycorrhizal fungi

The mycoplasma‐related endobacteria (MRE), representing a recently discovered lineage of Mollicutes, are widely distributed across arbuscular mycorrhizal fungi (AMF, Glomeromycota). AMF colonize roots of most terrestrial plants and improve plant mineral nutrient uptake in return for plant‐assimilated carbon. The role of MRE in the biology of their fungal hosts is unknown. To start characterizing this association, we assessed partitioning of MRE genetic diversity within AMF individuals and across the AMF phylogeographic range. We further used molecular evolution patterns to make inferences about MRE codivergence with AMF, their lifestyle and antiquity of the Glomeromycota–MRE association. While we did not detect differentiation between MRE derived from different continents, high levels of diversity were apparent in MRE populations within AMF host individuals. MRE exhibited significant codiversification with AMF over ecological time and the absence of codivergence over evolutionary time. Moreover, genetic recombination was evident in MRE. These patterns indicate that, while MRE transmission is predominantly vertical, their complex intrahost populations are likely generated by horizontal transmission and recombination. Based on predictions of evolutionary theory, we interpreted these observations as a suggestion that MRE may be antagonists of AMF. Finally, we detected a marginally significant signature of codivergence of MRE with Glomeromycota and the Endogone lineage of Mucoromycotina, implying that the symbiosis between MRE and fungi may predate the divergence between these two groups of fungi.     

Programming good relations--development of the arbuscular mycorrhizal symbiosis

The majority of plants live in symbiotic associations with fungi or bacteria that improve their nutrition. Critical steps in a symbiosis are mutual recognition and subsequently the establishment of an intimate association, which involves the penetration of plant tissues and, in many cases, the invasion of individual host cells by the microbial symbiont. Recent advances revealed that in the arbuscular mycorrhizal symbiosis with soil fungi of the order Glomeromycota, plant-derived signals attract fungal hyphae and stimulate their growth. Upon physical attachment of the fungal symbiont to the root surface, an active plant developmental program prepares the epidermal cells for penetration by the fungus. Thus, plants actively help symbiotic fungi to colonize their roots rather than just tolerating them.     

Sphaerocreas pubescens is a member of the Mucoromycotina closely related to fungi associated with liverworts and hornworts

The phylogenetic position of Sphaerocreas pubescens was investigated. Three isolates and ten sporocarps sampled in Japan were analyzed phylogenetically using 18S rRNA gene sequences. The results indicated that S. pubescens is a member of Mucoromycotina. It formed an independent clade separated from the other known orders of this subphylum and it is closely related to the uncultured and unidentified Mucoromycotinan fungi recently reported as environmental DNAs in liverworts and hornworts.     

Successful joint ventures of plants: arbuscular mycorrhiza and beyond

Among the oldest symbiotic associations of plants are arbuscular mycorrhiza (AM) with fungi of the phylum Glomeromycota. Although many of the symbiotic signaling components have been identified on the side of the plant, AM fungi have long evaded genetic analysis owing to their strict biotrophy and their exceptional genetics. Recently, the identification of the fungal symbiosis signal (Myc factor) and of a corresponding Myc factor receptor, and new insights into AM fungal genetics, have opened new avenues to address early communication and functional aspects of AM symbiosis. These advances will pave the way for breeding programs towards adapted AM fungi for crop production, and will shed light on the ecology and evolution of this remarkably successful symbiosis.     

Combined inoculation with Glomus intraradices and Rhizobium tropici CIAT899 increases phosphorus use efficiency for symbiotic nitrogen fixation in common bean (Phaseolus vulgaris L.)

This study compared the response of common bean (Phaseolus vulgaris L.) to arbuscular mycorrhizal fungi (AMF) and rhizobia strain inoculation. Two common bean genotypes i.e. CocoT and Flamingo varying in their effectiveness for nitrogen fixation were inoculated with Glomus intraradices and Rhizobium tropici CIAT899, and grown for 50 days in soil–sand substrate in glasshouse conditions. Inoculation of common bean plants with the AM fungi resulted in a significant increase in nodulation compared to plants without inoculation. The combined inoculation of AM fungi and rhizobia significantly increased various plant growth parameters compared to simple inoculated plants. In addition, the combined inoculation of AM fungi and rhizobia resulted in significantly higher nitrogen and phosphorus accumulation in the shoots of common bean plants and improved phosphorus use efficiency compared with their controls, which were not dually inoculated. It is concluded that inoculation with rhizobia and arbuscular mycorrhizal fungi could improve the efficiency in phosphorus use for symbiotic nitrogen fixation especially under phosphorus deficiency.     

Dating in the dark: how roots respond to fungal signals to establish arbuscular mycorrhizal symbiosis

The arbuscular mycorrhizal symbiosis that involves most plants and Glomeromycota fungi is the result of a complex exchange of molecular information, which commences before the partners are in physical contact. On the one hand, plants release soluble factors, including strigolactones that activate both the metabolism and branching of the fungal partners. On the other hand, fungi use compounds that trigger the signaling transduction pathways that are required for the symbiotic modus of plant cells. Here we describe some of the recent discoveries regarding the fungal molecules involved in rhizospheric conversation, and the way in which they are perceived by their hosts. We conclude that similar signaling molecules may have different meanings, depending on the context. However, at the end, specificity must be maintained to ensure appropriate partners enter symbiosis.     

Arbuscular Mycorrhiza: Studies on the Geosiphon Symbiosis Lead to the Characterization of the First Glomeromycotan Sugar Transporter

The intimate arbuscular mycorrhiza (AM) association between roots and obligate symbiotic Glomeromycota (‘AM fungi’) ‘feeds’ about 80% of land plants. AM forming fungi supply land plants with inorganic nutrients and have an enormous impact on terrestrial ecosystems. In return, AM fungi obtain up to 20% of the plant-fixed CO₂, putatively as monosaccharides. In a recent work we have reported the characterization of the first glomeromycotan monosaccharide transporter, GpMST1, and its gene sequence. We discuss that AM fungi might take up sugars deriving from plant cell-wall material. The GpMST1 sequence delivers valuable data for the isolation of orthologues from other AM fungi and may eventually lead to the understanding of C-flows in the AM.Key Words: arbuscular mycorrhiza, Geosiphon symbiosis, monosaccharide transporter, hexosesThe arbuscular mycorrhiza (AM) as an outstanding terrestrial plant symbiosis directly and indirectly is a driver of most terrestrial ecosystems. It is formed by ∼80% of land plants and by obligate symbiotic fungi of the phylum Glomeromycota.¹ The glomeromycotan fungi usually are called ‘arbuscular mycorrhizal (AM) fungi’, or ‘AMF’, and obviously play an enormous ecological (and economical) role. Most land plants and glomeromycotan fungi are ‘joint systems’, forming the intimate AM.² By this fact, statements like that of the BEG (European Bank of Glomeromycota) committee (1993): “The study of plants without their mycorrhizas is the study of artefacts; the majority of plants, strictly speaking, do not have roots—they have mycorrhizas” were provoked. AM fungi supply the vast majority of land plants with inorganic nutrients, mainly phosphorous, but also nitrogen, trace elements, and water. In return, they obtain up to >20% of the photosynthetically fixed CO₂ as carbohydrates from the plants.³ It was calculated that, each year, 5 billion tons of carbon are transferred from plants to fungi (and therefore partly get deposited in the soil) via the AM symbiosis. AM fungi therefore represent a large sink for atmospheric CO₂ on our planet and play a role in C-deposition in the soil.     

Surprising spectra of root-associated fungi in submerged aquatic plants

Similarly to plants from terrestrial ecosystems, aquatic species harbour wide spectra of root-associated fungi (RAF). However, comparably less is known about fungal diversity in submerged roots. We assessed the incidence and diversity of RAF in submerged aquatic plants using microscopy, culture-dependent and culture-independent techniques. We studied RAF of five submerged isoetid species collected in four oligotrophic freshwater lakes in Norway. Levels of dark septate endophytes (DSE) colonization differed among the lakes and were positively related to the organic matter content and negatively related to pH. In total, we identified 41 fungal OTUs using culture-dependent and culture-independent techniques, belonging to Mucoromycotina, Chytridiomycota, Glomeromycota, Ascomycota as well as Basidiomycota. Sequences corresponding to aquatic hyphomycetes (e.g. Nectria lugdunensis, Tetracladium furcatum and Varicosporium elodeae) were obtained. Eight arbuscular mycorrhizal taxa belonging to the orders Archaeosporales, Diversisporales and Glomerales were also detected. However, the vast majority of the fungal species detected (e.g. Ceratobasidium sp., Cryptosporiopsis rhizophila, Leptodontidium orchidicola, and Tuber sp.) have previously been known only from roots of terrestrial plants. The abundance and phylogenetic distribution of mycorrhizal as well as nonmycorrhizal fungi in the roots of submerged plants have reshaped our views on the fungal diversity in aquatic environment.     

Experimental evidence of bark beetle adaptation to a fungal symbiont

The importance of symbiotic microbes to insects cannot be overstated; however, we have a poor understanding of the evolutionary processes that shape most insect–microbe interactions. Many bark beetle (Coleoptera: Curculionidae, Scolytinae) species are involved in what have been described as obligate mutualisms with symbiotic fungi. Beetles benefit through supplementing their nutrient‐poor diet with fungi and the fungi benefit through gaining transportation to resources. However, only a few beetle–fungal symbioses have been experimentally manipulated to test whether the relationship is obligate. Furthermore, none have tested for adaptation of beetles to their specific symbionts, one of the requirements for coevolution. We experimentally manipulated the western pine beetle–fungus symbiosis to determine whether the beetle is obligately dependent upon fungi and to test for fine‐scale adaptation of the beetle to one of its symbiotic fungi, Entomocorticium sp. B. We reared beetles from a single population with either a natal isolate of E. sp. B (isolated from the same population from which the beetles originated), a non‐natal isolate (a genetically divergent isolate from a geographically distant beetle population), or with no fungi. We found that fungi were crucial for the successful development of western pine beetles. We also found no significant difference in the effects of the natal and non‐natal isolate on beetle fitness parameters. However, brood adult beetles failed to incorporate the non‐natal fungus into their fungal transport structure (mycangium) indicating adaption by the beetle to particular genotypes of symbiotic fungi. Our results suggest that beetle–fungus mutualisms and symbiont fidelity may be maintained via an undescribed recognition mechanism of the beetles for particular symbionts that may promote particular associations through time.     

Arbuscular mycorrhiza: the mother of plant root endosymbioses

Arbuscular mycorrhiza (AM), a symbiosis between plants and members of an ancient phylum of fungi, the Glomeromycota, improves the supply of water and nutrients, such as phosphate and nitrogen, to the host plant. In return, up to 20% of plant-fixed carbon is transferred to the fungus. Nutrient transport occurs through symbiotic structures inside plant root cells known as arbuscules. AM development is accompanied by an exchange of signalling molecules between the symbionts. A novel class of plant hormones known as strigolactones are exuded by the plant roots. On the one hand, strigolactones stimulate fungal metabolism and branching. On the other hand, they also trigger seed germination of parasitic plants. Fungi release signalling molecules, in the form of 'Myc factors' that trigger symbiotic root responses. Plant genes required for AM development have been characterized. During evolution, the genetic programme for AM has been recruited for other plant root symbioses: functional adaptation of a plant receptor kinase that is essential for AM symbiosis paved the way for nitrogen-fixing bacteria to form intracellular symbioses with plant cells.     

Cyanobacteria-bryophyte symbioses

Cyanobacteria are a large group of photosynthetic prokaryotesof enormous environmental importance, being responsible fora large proportion of global CO₂ and N₂ fixation. They formsymbiotic associations with a wide range of eukaryotic hostsincluding plants, fungi, sponges, and protists. The cyanobacterialsymbionts are often filamentous and fix N₂ in specialized cellsknown as heterocysts, enabling them to provide the host withfixed nitrogen and, in the case of non-photosynthetic hosts,with fixed carbon. The best studied cyanobacterial symbiosesare those with plants, in which the cyanobacteria can infectthe roots, stems, leaves, and, in the case of the liverwortsand hornworts, the subject of this review, the thallus. Thesymbionts are usually Nostoc spp. that gain entry to the hostby means of specialized motile filaments known as hormogonia.The host plant releases chemical signals that stimulate hormogoniaformation and, by chemoattraction, guide the hormogonia to thepoint of entry into the plant tissue. Inside the symbiotic cavity,host signals inhibit further hormogonia formation and stimulateheterocyst development and dinitrogen fixation. The cyanobiontsundergo morphological and physiological changes, including reducedgrowth rate and CO₂ fixation, and enhanced N₂ fixation, andrelease to the plant much of the dinitrogen fixed. This shortreview summarizes knowledge of the cyanobacterial symbioseswith liverworts and hornworts, with particular emphasis on theimportance of pili and gliding motility for the symbiotic competenceof hormogonia. Key words: Bryophyte, cyanobacteria, gliding motility, pili, symbiosis Received 1 August 2007; Revised 23 December 2007 Accepted 7 January 2008     

Genetic processes in arbuscular mycorrhizal fungi

Arbuscular mycorrhizal (AM) fungi (Glomeromycota) colonize roots of the majority of land plants and facilitate their mineral nutrient uptake. Consequently, AM fungi play an important role in terrestrial ecosystems and are becoming a component of sustainable land management practices. The absence of sexual reproductive structures in modern Glomeromycota combined with their long evolutionary history suggest that these fungi may represent an ancient asexual lineage of great potential interest to evolutionary biology. However, many aspects of basic AM fungal biology, including genome structure, within-individual genetic variation, and reproductive mode are poorly understood. These knowledge gaps hinder research on the mechanisms of AM fungal interactions with individual plants and plant communities, and utilization of AM fungi in agricultural practices. I present here the current state of research on the reproduction in AM fungi and indicate what new findings can be expected in the future.     

Mycoheterotrophic interactions are not limited to a narrow phylogenetic range of arbuscular mycorrhizal fungi

The majority of achlorophyllous mycoheterotrophic plant species associate with arbuscular mycorrhizal fungi (AMF). Previous studies have shown that some species are highly specialized towards narrow lineages of AMF and have suggested that only particular lineages of these fungi are targeted by mycoheterotrophic plants. To test this hypothesis, we analyzed all available partial SSU sequences of AMF associated with mycoheterotrophic plants including data from 13 additional specimens from French Guiana, Gabon and Australia. Sequences were assigned to 'virtual taxa' (VT) according to the MaarjAM database. We found that 20% of all known Glomeromycota VT are involved in mycoheterotrophic interactions and the majority of associations involve Glomeraceae (Glomus Group A) fungi. While some mycoheterotrophic plant species have been found growing with only a single VT, many species are able to associate with a wide range of AMF. We calculated significant phylogenetic clustering of Glomeromycota VT involved in mycoheterotrophic interactions, suggesting that associations between mycoheterotrophic plants and AMF are influenced by the phylogenetic relationships of the fungi. Our results demonstrate that many lineages of AMF are prone to exploitation by mycoheterotrophic plants. However, mycoheterotrophs from different plant lineages and different geographical regions tend to be dependent on lineages of AMF that are phylogenetically related.     

Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus

Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.     

Multiple exocytotic markers accumulate at the sites of perifungal membrane biogenesis in arbuscular mycorrhizas

Arbuscular mycorrhizas (AMs) are symbiotic interactions established within the roots of most plants by soil fungi belonging to the Glomeromycota. The extensive accommodation of the fungus in the root tissues largely takes place intracellularly, within a specialized interface compartment surrounded by the so-called perifungal membrane, an extension of the host plasmalemma. By combining live confocal imaging of green fluorescent protein (GFP)-tagged proteins and transmission electron microscopy (TEM), we have investigated the mechanisms leading to the biogenesis of this membrane. Our results show that pre-penetration responses and symbiotic interface construction are associated with extensive membrane dynamics. They involve the main components of the exocytotic machinery, with a major participation of the Golgi apparatus, as revealed by both TEM and in vivo GFP imaging. The labeling of known exocytosis markers, such as v-SNARE proteins of the VAMP72 family and the EXO84b subunit of the exocyst complex, allowed live imaging of the cell components involved in perifungal membrane construction, clarifying how this takes place ahead of the growing intracellular hypha. Lastly, our novel data are used to illustrate a model of membrane dynamics within the pre-penetration apparatus during AM fungal penetration.