Arbuscular mycorrhiza

network of arbuscular mycorrhizal fungi (AMF) extends beyond the depletion zone (grey), accessing a greater area of soil for phosphate uptake. A mycorrhizal-phosphate depletion zone will also eventually form around AM hyphae (purple). Other nutrients that have enhanced assimilation in AM-roots include nitrogen (ammonium) and zinc. Benefits from colonization include tolerances to many abiotic and biotic stresses through induction of systemic acquired resistance. Paleobiology Both paleobiological and molecular evidence indicate that AM is an ancient symbiosis that originated at least 460 million years ago. AM symbiosis is ubiquitous among land plants, which suggests that mycorrhizas were present in the early ancestors of extant land plants. This positive association with plants may have facilitated the development of land plants. The fossilized plants containing mycorrhizal fungi were preserved in silica. The Early Devonian saw the development of terrestrial flora. Plants of the Rhynie chert from the Lower Devonian (400 m.yrs ago) were found to contain structures resembling vesicles and spores of present Glomus species. Colonized fossil roots have been observed in Aglaophyton major and Rhynia, which are ancient plants possessing characteristics of vascular plants and bryophytes with primitive protostelic rhizomes. However, it can be argued that the efficacy of signaling processes is likely to have evolved since the Miocene, and this can not be detected in the fossil record. A finetuning of the signaling processes would improve coordination and nutrient exchange between symbionts while increasing the fitness of both the fungi and the plant symbionts. The nature of the relationship between plants and the ancestors of arbuscular mycorrhizal fungi is contentious. Two hypotheses are: • Mycorrhizal symbiosis evolved from a parasitic interaction that developed into a mutually beneficial relationship. • Mycorrhizal fungi developed from saprobic fungi that became endosymbiotic. These structures were reported in both sporophytes and gametophytes of the early land plants. These three genes could be sequenced from all major clades of modern land plants, including liverworts, the most basal group, and phylogeny of the three genes proved to agree with then current land plant phylogenies. This implies that mycorrhizal genes must have been present in the common ancestor of land plants, and that they must have been vertically inherited since plants colonized land. This finding of a genetic fossil inside AM fungi raises the possibility of an intimate relationship between AM fungi and cyanobacterial ancestors. A similar Geosiphon–Nostoc symbiosis was previously reported. Circadian clock evolution in AM fungi Surprisingly, despite their long evolution as an underground partner of plant roots, whose environment is far from light or temperature fluctuation, AMF still have a conserved circadian clock whose fungal circadian oscillator (frq) is activated by the blue light, similar to the model circadian fungus Neurospora crassa. The proven conservation of a circadian clock and output genes in R. irregulare opens the door to the study of circadian clocks in the fungal partner of AM symbiosis. The same research characterized the AMF frq gene, which is the first frq gene identified outgroup of Dikarya, and suggests the frq gene evolution in the fungal kingdom is much older than previously thought. == Physiology ==

Presymbiosis The development of the AM fungi prior to root colonization, known as presymbiosis, consists of three stages: spore germination, hyphal growth, host recognition and appressorium formation. Spore germination '' live spore. Nuclei were visualized as large green spots with SytoGreen fluorescent dye, while mitochondria were stained with MitoTracker and are shown as small red spots. The movie was acquired at 1 frame every 5 min for a total of 90 min and displayed at a rate of 5 frames/sec. Spores of the AM fungi are thick-walled multi-nucleate resting structures. Hyphal growth The growth of AM hyphae through the soil is controlled by host root exudates known as strigolactones, and the soil phosphorus concentration. The branching of AM fungal hyphae grown in phosphorus media of 1 mM is significantly reduced, but the length of the germ tube and total hyphal growth were not affected. A concentration of 10 mM phosphorus inhibited both hyphal growth and branching. This phosphorus concentration occurs in natural soil conditions and could thus contribute to reduced mycorrhizal colonization. Molecular techniques have been used to understand the signaling pathways between arbuscular mycorrhizae and plant roots. In 2003 it was shown how the AM undergoes physiological changes in the presence of exudates from potential host plant roots, to colonize it. Host plant root exudates trigger and turn on AM fungal genes required for the respiration of spore carbon compounds. In experiments, transcription rate of 10 genes increased half-hour after exposure and at an even greater rate after 1 hour. after 4 hours exposure AM respond with morphological growth. Genes isolated from that time are involved in mitochondrial activity and enzyme production. The fungal respiration rate, measured by O2 consumption rate, increased by 30% 3 hours after exposure to root exudates, indicating that host plant root exudates stimulate AMF spore mitochondrial activity. It may be part of a fungal regulatory mechanism that conserves spore energy for efficient growth and the hyphal branching upon receiving signals from a potential host plant. Appressorium When arbuscular mycorrhizal fungal hyphae encounter the root of a host plant, an appressorium or 'infection structure' forms on the root epidermis. From this structure hyphae can penetrate into the host's parenchyma cortex. AM need no chemical signals from the plant to form the appressoria. AM fungi could form appressoria on the cell walls of "ghost" cells in which the protoplast had been removed to eliminate signaling between the fungi and the plant host. However, the hyphae did not further penetrate the cells and grow in toward the root cortex, which indicates that signaling between symbionts is required for further growth once appressoria are formed. The choice between Paris type and Arum type is primarily determined by the host plant family, although some families or species are capable of either type. The host plant exerts a control over the intercellular hyphal proliferation and arbuscule formation. There is a decondensation of the plant's chromatin, which indicates increased transcription of the plant's DNA in arbuscule-containing cells. AMF hyphae are also finer than roots and can enter into pores of the soil that are inaccessible to roots. The fourth type of AMF hyphae grows from the roots and colonizes other host plant roots. The four types of hyphae are morphologically distinct. AM fungi take up the products of the plant host's photosynthesis as hexoses. Carbon transfer from plant to fungi may occur through the arbuscules or intraradical hyphae. Secondary synthesis from the hexoses by AM occurs in the intraradical mycelium. Inside the mycelium, hexose is converted to trehalose and glycogen. Trehalose and glycogen are carbon storage forms that can be rapidly synthesized and degraded and may buffer the intracellular sugar concentrations. Likewise, phosphorus uptake and transfer is lowered when the photosynthate supplied to the fungi is decreased. Species of AMF differ in their abilities to supply the plant with phosphorus. In some cases, arbuscular mycorrhizae are poor symbionts, providing little phosphorus while taking relatively high amounts of carbon. Meiosis and recombination AM fungi have been regarded as asexual because they lack observable sexual structures. However, homologs of 51 genes that function in meiosis, including seven meiosis-specific genes were found to be conserved in the genomes of several AMF species, suggesting that these supposedly ancient asexual fungi may be capable of undergoing conventional meiosis. Furthermore, in Rhizophagus irregularis genetic exchange involving reciprocal recombination was found to occur in dikaryons between haploid genomes. ==Mechanism of colonization==

Recent research has shown that AM fungi release a diffusional factor, known as the myc factor, which activates the nodulation factor's inducible gene MtEnod11. This is the same gene involved in establishing symbiosis with the nitrogen fixing, rhizobial bacteria (Kosuta et al. 2003). The factor was first identified by Fabienne Maillet and coworkers in a groundbreaking work published in Nature, where they have extracted three hundred litre mycorrhized carrot roots and exudates from 40 million germinating spores of Rhizophagus irregularis and purified the active fraction. They demonstrated this active principle is lipo-chito-oligosaccharide in nature. Recognition of Myc factors triggers the common symbiotic signaling pathway (CSSP) that eventually leads to plant's accommodation programme to provide hostage to the arbuscular mycorrhizae. File:MycRi-IV (C16-0,S).svg|thumb|alt=chemical structure of a LipoChitoOligosaccharide molecule| The chemical structure of MycRi-IV (C16:0,S), a Myc factor of Rhizophagus irregularis as indicated in 'Maillet, F et al.' (2011) "Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza." Nature 469:58–63. The common symbiosis signaling pathway (CSSP) is a Signaling cascade in plants that seen to be activated in both NOD-factor perception (for nodule forming Rhizobia), as well as found in MYC-factor perception that are released from Arbuscular mycorrhizal fungi. The pathway is distinguished from the pathogen recognition pathways, but may have some common receptors involved in both pathogen recognition as well as CSSP. A recent work by Kevin Cope and colleagues shown that possibly other type of mycorrhizae may involve the CSSP components such as Myc-factor recognition. The AMF colonization requires the following chain of events that can be roughly divided into following steps - :1.The Pre-Contact Signaling, :2. The CSSP :::2.A. Perception :::2.B. Transmission :::2.C. Transcription :3. The Accommodation program ==Ecology==

Biogeography Arbuscular mycorrhizal fungi are most frequent in plants growing on mineral soils, and are of extreme importance for plants growing in nutrient-deficient substrates such as in volcanic soil and sand dune environments. The populations of AM fungi is greatest in plant communities with high diversity such as tropical rainforests and temperate grasslands where they have many potential host plants and can take advantage of their ability to colonize a broad host range. There is a lower incidence of mycorrhizal colonization in very arid or nutrient-rich soils. Mycorrhizas have been observed in aquatic habitats; however, waterlogged soils have been shown to decrease colonization in some species. and have been surveyed on all continents except Antarctica. environmental factors such as climate, soil nutrients and plant community. While evidence from 2000 suggests that AM fungi are not specialists on their host species, studies as of 2002 have indicated that at least some fungi taxa are host specialists. The ecology of Mucoromycotinian fungi, which form "fine root endophyte" arbuscular mycorrhizas is largely unknown. Response to plant communities The specificity, host range, and degree of colonization of mycorrhizal fungi are difficult to analyze in the field due to the complexity of interactions between the fungi within a root and within the system. There is no clear evidence to suggest that arbuscular mycorrhizal fungi exhibit specificity for colonization of potential AM host plant species as do fungal pathogens for their host plants. with obligate mycorrhizal plants occupying warmer, drier habitats while facultative mycorrhizal plants occupy larger ranges of habitats. The ability of the same AM fungi to colonize many species of plants has ecological implications. Plants of different species can be linked underground to a common mycelial network. and in return AM fungi can acquire up to 80% of plant phosphorus and nitrogen. plant productivity and herbivory. Arbuscular mycorrhizal fungi can be influenced by small scale interactions with the local plant community. For example, the plant neighborhood around a focal plant can alter AM fungal communities as can the order of plant establishment within sites. AM fungi and plant invasion During invasions of plant species, the AM fungal community and biomass can be drastically altered. In the majority of cases AM fungal biomass and diversity decrease with invasions. However, some mycotrophic plant species may actually increase AM fungal diversity during invasion. The mycorrhizal status of invasive plant species often varies between regions. For example, in the United Kingdom and central Europe recently invasive plants are more frequently obligately mycorrhizal than expected, while invasive plants in California were found to be less frequently mycorrhizal than expected. Interactions between AM fungi and other plant symbionts All symbionts within a plant host interact, often in unpredictable ways. A 2010 meta-analysis indicated that plants colonized by both AM fungi and vertically transmitted endophytes often are larger than plants independently colonized by these symbionts. However, this relationship is context-dependent as AM fungi can interact synergistically with fungal endophytes inhabiting the leaves of their host plant, or antagonistically. Similar ranges of interactions can occur between AM fungi and ectomycorrhizal fungi and dark septate endophytes. Response to environmental gradients Arbuscular mycorrhizal fungi vary across many environmental gradients. Their tolerance to freezing and drying is known to shift between AM fungal taxa. AM fungi become less prevalent and diverse at higher soil nutrient and moisture concentrations, presumably because both plants allocate less carbon to AM fungi and AM fungi reallocate their resources to intraradical hyphae in these environmental conditions. Over the long term, these environmental conditions can even create local adaptation between plant hosts, AM fungi and the local soil nutrient concentrations. AM composition often becomes less diverse on mountain tops than at lower elevations, which is driven by the composition of plant species. AM fungi have been shown to improve plant tolerance to abiotic environmental factors such as salinity. They alleviate salt stress and benefit plant growth and productivity. Rhizosphere ecology The rhizosphere is the soil zone in the immediate vicinity of a root system. Arbuscular mycorrhizal symbiosis affects the community and diversity of other organisms in the soil. This can be directly seen by the release of exudates, or indirectly by a change in the plant species and plant exudates type and amount. Mycorrhizae diversity has been shown to increase plant species diversity as the potential number of associations increases. Dominant arbuscular mycorrhizal fungi can prevent the invasion of non-mycorrhizal plants on land where they have established symbiosis and promote their mycorrhizal host. When rhizobium bacteria are present in the soil, mycorrhizal colonization is increased due to an increase in the concentration of chemical signals involved in the establishment of symbiosis (Xie et al. 2003). Molecules similar to Nod factors were isolated from AM fungi and were shown to induce MtEnod11, lateral root formation and enhance mycorrhization. Effective mycorrhizal colonization can also increase the nodulations and symbiotic nitrogen fixation in mycorrhizal legumes. Bacterial species differ in their abilities to compete for carbon compound root exudates. A change in the amount or composition of root exudates and fungal exudates due to the existing AM mycorrhizal colonization determines the diversity and abundance of the bacterial community in the rhizosphere. In recent meta-analyses, AM fungi were found to increase plant biomass under drought conditions and decrease plant biomass under simulated nitrogen deposition studies. Arbuscular mycorrhizal fungi themselves have been shown to increase their biomass in response to elevated atmospheric . Plants lacking arbuscular mycorrhizae Members of the mustard family (Brassicaceae), such as cabbage, cauliflower, canola, and crambe, do not establish arbuscular mycorrhizal fungi on their roots. ==Molecular genetic analyses of arbuscular mycorrhizal fungi==

In the past ten years there have been spectacular advances in molecular genetic technologies and tools. These advances allow microbial and mycorrhizal ecologists to ask new and exciting questions about the ecological and evolutionary roles of arbuscular mycorrhizal (AM) fungi as individuals, in communities and ecosystems. Genetic analyses of AM fungi have been used to explore the genetic structure of single spores using multilocus genotyping, AM fungal diversity and adaptation across multiple grassland communities, all the way up to a global investigation of AM fungal diversity, which greatly increased the described molecular diversity within the phylum Glomeromycota. All the recent advances in molecular genetics clearly permit the analysis of microbial communities at much finer and functional scales and potentially with more confidence than previous methods. The classical AM fungal identification method of spore extraction from soil and further spore morphological analysis is fraught with complicating issues due to the various strategies and forms of AM fungi, e.g., lack of sporulation in certain species, seasonality, high unculturability, possible misidentification (human error), and new evidence of multi-nucleate spores and high genetic variation within clonal AM species. Because of these various problems, in the past researchers likely misrepresented the true composition of AM fungal communities present at any one point in time or place. Additionally, by following the traditional extraction, culture and microscopic identification methods, there is no way to determine active/functioning AM fungal populations, which are likely the most important when attempting to relate plant-AM symbiotic interactions and mechanisms to ecological or ecosystem function. This is especially true in the case of root colonization analyses, which can determine percentage of roots colonized by AM fungi. The major problem with this analysis is in field soils, which contain multiple species of AM fungi in association with a target plant at the same time (see Ecology of AM). The identification of the associated fungal symbionts is impossible without the use of molecular methods. Though genetic analysis of AM fungal communities has advanced a great deal in the past decade, the methodology is not yet completely refined. Below is an overview of the methods used in molecular genetic analyses of AM fungi, along with applications to research, future directions and some of their problems. Overview of methods DNA/RNA Genetic analyses of AM fungi from soil and root samples range in their applicability to answer ecological or phylogenetic questions. DNA analyses utilize various nuclear markers to describe AM fungi and represent different regions of the nuclear ribosomal operon (18S rRNA) found in all eukaryotic organisms. The DNA analysis of AM fungi using these markers began in the early 1990s and are continuing to be developed today. The small subunit (SSU) rRNA gene, the internal transcribed spacer (ITS) gene, and the large subunit (LSU) rRNA gene are currently the most common DNA markers used. The SSU region has been used most frequently in ecological studies, while the ITS and LSU regions have been predominantly used in taxonomic constructions of the phylum Glomeromycota. qPCR and qRT-PCR Real-time PCR or quantitative PCR (qPCR), is becoming a well-established method to quickly amplify and simultaneously quantify targeted AM fungal DNA from biological samples (plant roots or soils). Fairly recent developments in qPCR markers allow researchers to explore the relative abundance of AM fungal species within roots in greenhouse experiments as well as in the field to identify local AM fungal communities. qPCR markers for arbuscular mycorrhizal fungi will consist of AM specific primers and fluorescently labeled hydrolysis probes. These AM specific primers (discussed above) can be chosen by the researcher and this decision is typically guided by the question at hand, resources available, and willingness to troubleshoot in the lab. Microarray DNA microarray analysis is currently being used in AM fungal research to simultaneously measure the expression of many genes from target species or experimental samples. The most common tool or method is to use functional gene array (FGA) technology, a specialized microarray that contains probes for genes that are functionally important in microbial processes such as carbon, nitrogen or phosphorus cycling. FGAs have the ability to simultaneously examine many functional genes. This technique is typically used for general analysis of functional microbial genes, but when complemented with genetic sequencing, inferences can be made about the connection between fungal community composition and microbial functionality. ====PLFA/==== Specific organismal chemical signatures can be used to detect biomass of more cryptic organisms, such as AM fungi or soil bacteria. Lipids, more specifically phospholipids and neutral lipids, contain fatty acids connected to a glycerol backbone. The fatty acid composition of organisms varies, and the proportions of specific fatty acids can be organism specific. For example, in AM fungi the proportion of the fatty acids, 16:1ω5 and 18:1ω7, in the phospholipid portion account for approximately 58% of total fatty acid composition. The fatty acid, 16:1ω5 is the most commonly used acid to characterize AM fungi in soils and can be used as a strong indicator of mycelial biomass in soil sample. More work must be done to identify the efficacy of this method in field soils with many genera and species of AM fungi to discern the methods ability to discriminate between many varying fatty acid compositions. Future research directions with AM fungi One prospect for future analysis of AM fungi is the use of stable isotope probes. Stable isotope probing (SIP) is a technique that can be used to determine the active metabolic function of individual taxa within a complex system of microbes. This level of specificity, linking microbial function and phylogenetics, has not been achieved previously in microbial ecology. This method can also be used independently of classical culture methods in microbial ecology, allowing for in situ analysis of functional microbes. Application of sequencing of single nucleus from spores of AM fungi has also been developed recently and also circumvents the need of culture methods. Stable Isotope Probing (SIP) SIP, more explicitly DNA/RNA-based SIP, uses stable-isotope enriched substrates, such as 13C, 15N, or H218O, and then analyzes the 'labeled' markers using species specific DNA or RNA markers. The analysis of labeled DNA is performed by separating unlabeled and labeled DNA on a cesium chloride gradient formed in an ultra centrifuge. Because all microbial organisms are capable of importing water into their cells, the use of H218O stable isotope probing is a very exciting new method that can shed light on questions microbial ecologists and biologists have struggled with answering for years, in particular, what are the active microbial organisms in my system? The H218O, or heavy water method will target all organisms that are actively growing, and induce little influence on growth itself. This would be especially true with most greenhouse experiments with arbuscular mycorrhizas because plants must be watered anyway, and water does not directly select for organisms with specific metabolic pathways, sRNAs processing mechanism is thus, important for understanding AM symbiosis. It seems that AM fungi have their unique features to have bacterial type core enzyme as well as the large number of Argonaute proteins in their sRNA processing system (or RNAi system). sRNA and sRNA processing mechanism research is also exciting topic to understand AM fungi symbiosis. ==Phytoremediation==

Disturbance of native plant communities in desertification-threatened areas is often followed by degradation of physical and biological soil properties, soil structure, nutrient availability, and organic matter. When restoring disturbed land, it is essential to replace not only the above ground vegetation but also biological and physical soil properties. A relatively new approach to restoring land is to inoculate soil with AM fungi when reintroducing vegetation in ecological restoration projects (phytoremediation). It has enabled host plants to establish themselves on degraded soil and improve soil quality and health. Soils' quality parameters were significantly improved long-term when a mixture of indigenous arbuscular mycorrhizal fungi species was introduced compared to noninoculated soil and soil inoculated with a single exotic species of AM fungi. and soil nitrogen content, higher soil organic matter content, and soil aggregation, attributed to higher legume nodulation in the presence of AM fungi, better water infiltration, and soil aeration due to soil aggregation. ==Agriculture==

Many modern agronomic practices are disruptive to mycorrhizal symbiosis. There is great potential for low-input agriculture to manage the system in a way that promotes mycorrhizal symbiosis. Conventional agriculture practices, such as tillage, heavy fertilizers and fungicides, poor crop rotations, and selection for plants that survive these conditions, hinder the ability of plants to form symbiosis with arbuscular mycorrhizal fungi. Most agricultural crops can perform better and are more productive when well-colonized by AM fungi. AM symbiosis increases the phosphorus and micronutrient uptake and growth of their plant host (George et al. 1992). Management of AM fungi is especially important for organic and low-input agriculture systems where soil phosphorus is, in general, low, although all agroecosystems can benefit by promoting arbuscular mycorrhizae establishment. Some crops that are poor at seeking out nutrients in the soil are very dependent on AM fungi for phosphorus uptake. For example, flax, which has poor chemotaxic ability, is highly dependent on AM-mediated phosphorus uptake at low and intermediate soil phosphorus concentrations (Thingstrup et al. 1998). Proper management of AMF in the agroecosystems can improve the quality of the soil and the productivity of the land. Agricultural practices such as reduced tillage, low phosphorus fertilizer usage, and perennialized cropping systems promote functional mycorrhizal symbiosis. Tillage Tillage reduces the inoculation potential of the soil and the efficacy of mycorrhizaes by disrupting the extraradical hyphal network (Miller et al. 1995, McGonigle & Miller 1999, Mozafar et al. 2000). By breaking apart the soil macro structure, the hyphal network is rendered non-infective (Miller et al. 1995, McGonigle & Miller 1999). The disruption of the hyphal network decreases the absorptive abilities of the mycorrhizae because the surface area spanned by the hyphae is greatly reduced. This, in turn, lowers the phosphorus input to the plants that are connected to the hyphal network (Figure 3, McGonigle & Miller 1999). In reduced-tillage system, heavy phosphorus fertilizer input may not be required as compared to heavy-tillage systems. This is due to the increase in mycorrhizal network, which allows mycorrhizae to provide the plant with sufficient phosphorus (Miller et al. 1995). Phosphorus fertilizer The benefits of AMF are greatest in systems where inputs are low. Heavy usage of phosphorus fertilizer can inhibit mycorrhizal colonization and growth. As the soil's phosphorus levels available to the plants increases, the amount of phosphorus also increases in the plant's tissues, and carbon drain on the plant by the AM fungi symbiosis become non-beneficial to the plant (Grant 2005). A decrease in mycorrhizal colonization due to high soil-phosphorus levels can lead to plant deficiencies in other micronutrients that have mycorrhizal-mediated uptake such as copper (Timmer & Leyden 1980). Perennialized cropping systems Cover crops are grown in the fall, winter, and spring, covering the soil during periods when it would commonly be left without a cover of growing plants. Mycorrhizal cover crops can be used to improve the mycorrhizal inoculum potential and hyphal network (Kabir and Koide 2000, Boswell et al.1998, Sorensen et al. 2005). Since AM fungi are biotrophic, they are dependent on plants for the growth of their hyphal networks. Growing a cover crop extends the time for AM growth into the autumn, winter, and spring. Promotion of hyphal growth creates a more extensive hyphal network. The mycorrhizal colonization increase found in cover crops systems may be largely attributed to an increase in the extraradical hyphal network that can colonize the roots of the new crop (Boswell et al. 1998). The extraradical mycelia are able to survive the winter, providing rapid spring colonization and early season symbiosis (McGonigle and Miller 1999). This early symbiosis allows plants to tap into the well-established hyphal network and be supplied with adequate phosphorus nutrition during early growth, which greatly improves the crop yield. Soil quality Restoration of native AM fungi increases the success of ecological restoration projects and the rapidity of soil recovery. and grasslands treated with fungicide. == See also ==