User:Smckitrick/sandbox

This is to be a continuation on the existing orchid mycorrhiza Wikipedia article https://en.wikipedia.org/wiki/Orchid_mycorrhiza

Orchid Mycorrhiza Nutrient Transport
Orchids mycorrhiza (OM) are found in approximately 10% of the botanical diversity of earth and have unique and specialized mycorrhizal nutrient transfer interactions which define the fitness and diversity of the orchid family. Orchid mycorrhizal associations involve a plethora of distinctive nutrient transport systems, structures and phenomenon which have only been observed in the orchidaceae family. These interactions are formed between basidiomycete fungi and all orchidaceae species. The basidiomycete fungi most commonly found associated with orchids, rhizoctonia, are known for their saprophytic abilities making this fungi orchid association anomalous, allowing both the plant and fungi to access a source of carbon within the mycorrhizal association not available in arbuscular mycorrhiza. The way and degree to which different orchid species exploit these interactions varies. . Orchid mycorrhizal interactions can range from wholly parasitic on the fungal partner, to a mutualistic interaction involving bidirectional nutrient transfer between the plant and mycorrhizal fungus. Orchid plants have an obligatory parasitic life stage at germination where all of their nutrients must be supplied by a fungus. Post germination, the orchid mycorrhizal interactions will become specialized to utilize the carbon and nutrients available in the environment surrounding the interaction. These associations are often thought to be dictated by the plant. It has been indicated in past studies that orchid plant individuals which inhabit dense highly shaded forests may depend significantly more on their fungal partner for carbon, varying within and between species, demonstrating the variable and reactive nature of these interaction. .

Nutrient transfer interfaces and mechanisms
At infection of an orchid by a mycorrhizal fungus both partners are altered considerably to allow for nutrient transfer and symbiosis.Nutrient transfer mechanisms and the symbiotic mycorrhizal peloton organs start to appear only shortly after infection around 20-36 hours after initial contact. There is significant genetic upregulation and downregulation of a multitude of different genes to facilitate the creation of the symbiotic organ, and the pathways with which nutrients travel. As the fungus enters the parenchyma cells of the orchid the plasma membrane invaginates to facilitate fungal infection and growth. This newly invaginated plasma membrane surrounds the growing pelotons and creates a huge surface area from which nutrients can be exchanged. The pelotons of orchid mycorrhiza are intensely coiled dense fungal hyphae that are often more extensive in comparison to endomycorrhizal structures of arbuscular mycorrhiza. The surrounding plant membrane essentially becomes rough endoplasmic reticulum with high amounts of ribosomes and a plethora of transporter proteins, and aquaporins. Additionally there is evidence from electron microscopy that indicates the occurrence of exocytosis from the plant membrane. This highly convoluted and transporter rich membrane expertly performs the duties of nutrient exchange between the plant and fungus and allows for molecular manipulation by ribosomes and excreted enzymes within the interfacial apoplast. Pelotons are not permanent structures and are readily degraded and digested within 30 to 40 hours of their formation in orchid mycorrhiza. This happens in all endomycorrhizal associations but orchid plants readily digest fungal pelotons sooner after formation and more often than is seen in arbuscular mycorrhizal interactions. It is proposed that the occurrence of this more extreme digestive pattern may have something to do with necrotorphic nutrient transfer which is the absorption of nutrients form dead cells. .The key nutrients involved in the majority of the transfer between fungi and orchid plants are carbon, nitrogen and phosphorus.

Orchid mycorrhizal interactions are unique in the flow of nutrients. Typically in arbuscular mycorrhizal interactions the plants will unidirectionally supply the fungi with carbon in exchange for phosphorus or nitrogen or both depending on the environment, but orchid mycorrhizal nutrient transfer is less specific (but no less regulated) and there is often bidirectional flow of carbon between the fungus and plant, as well as flow of nitrogen and phosphorus from the fungus to plant. In around 400 species of plants there is no flow of carbon from plant and all of the nutrients of the plant are supplied by the fungus. That being said the net carbon gain by the plant in these interactions is positive in majority of the observed interactions.

Phosphorus Transport
Phosphorus is a crucial nutrient needed by all plants and often phosphorus deficiency in soil will dictate the formation of a symbiotic relationship. Phosphorus is obtained by the mycorrhizal fungus from the surrounding soil in three different forms; organic phosphorus, phosphate, and inorganic phosphorus compounds. Often times these compounds are strongly bound to cations and need to be protonated and, or catabolized to become bioavailable. Mycorrhizal fungi are extremely efficient at doing this due to their extensive soil surface area as well as high enzymatic diversity. Once freed from the soil the phosphorus compounds, primarily inorganic phosphate, are transferred through two proposed pathways. The first involves the active transport of inorganic phosphorus, primarily as phosphate through Pi(inorganic phosphorus) transporters out of the fungus into the interfacial apoplast, where it is protonated due to the acidic nature of the interfacial apoplast to form dihydrogen phosphate and then subsequently transferred through active Pi transporters into the plant cell. The second method relies on passive efflux of Pi from the fungus and active uptake by the plant, as in the prior pathway. It is observed that free living fungi ordinarily have very slight losses of Pi, thought to be due to the re-absorptive nature of the fungal hyphae, but it is proposed that during symbiosis the reabsorption of Pi is reduced thus increasing the net efflux out of the fungi. Both pathways depend on relatively high concentrations of Pi in the fungal cells and low Pi concentrations inside the plant cell for efficient transport, although the second method is far more dependent on this condition. Additionally these methods are not mutually exclusive and may occur in the same individuals, but more research is required to uncover the complexities of the interaction. To facilitate phosphorus exchange an array of genes are upregulated; Pi transporter genes such as MtPT4 and StPT3 are up regulated in orchids plants along with H+ ATPase transporters. Fungal partners upregulated Pi transporter genes as well as alkaline phosphatase encoding genes (Perotto). The upregulation of phosphatase genes is significant in that it indicates that a significant portion of the phosphorus obtained by the fungi in some environments may be from organic molecule catabolism. It is important to note that once a mycorrhizal symbiosis is established the only phosphorus obtained by the plant comes through the fungal tissue. Additionally the large scale assisted transport of phosphorus from fungi to plant only occurs when the fungal pelotons are alive, once these structures start to degrade significant flow of phosphorus ceases. This classifies this pathway as biotrophic, meaning transfer of nutrients between two or more organisms that are both alive.

Nitrogen Transport
Nitrogen transport is an equally important and influential process that often occurs through mycorrhizal associations. Nitrogen is significantly easier to obtain than phosphorus and far more abundant, but mycorrhizal interactions still provide a significant benefit in the allocation of nitrogen. Bioavailable nitrogen as nitrate and ammonium are absorbed from the soil media into the extraradical mycelium of the mycorrhizal fungi and assimilated into amino acids. In some cases amino acids and other nitrogenous organic compounds may be present in the surrounding soil. If so organic nitrogen uptake also takes place through amino acid permeases and peptide transporters. Once incorporated into the fungi as amino acids, there are a few different proposed mechanisms with which the nitrogen is transferred to the host plant. These pathways of nitrogen transfer are thought to be exclusively biotrophic, a significant amount of nitrogen may also be transferred necrotorphically but through a significantly different process. . In the first pathway the amino acids are transferred to the extraradical mycelium where the amino acids are broken down by the catabolic stage of the urea cycle. The primary amino acid synthesized and intra-fungally transferred is arginine, which is catabolized into ammonium.The ammonium is then shunted into the interfacial space between the peloton and the surrounding plant membrane,and transported into the plant cell via ammonium transporters and incorporated into the plant .To accommodate the transport of nitrogen via this pathway, primarily as ammonium, an array of ammonium transporter genes are up regulated in the plant partners, and additionally the mycorrhizal fungal partners often upregulate a group of protease genes as well as external amino acid permeases, nitrate transporters and ammonium transporters. As proposed by Cameron 2006 and Fochi 2016, nitrogen may also be transferred as amino acids such as arginine, glycine and glutamine into the cell via a select few specialized amino acid transporters. As discussed in Fochi 2016, when in symbiotic relationship with orchid plants the mycorrhizal fungus T. calospora upregulates the expression of SvAAP1 and SvAAP2, these genes encode amino acid permeases, supporting the hypothesis that amino acids are an important molecule involved in nitrogen transport. .    It is important to note that amino acids contain a significant amount of carbon as well and the transport of carbon may be the primary driving cause of the observed upregulation of the amino acid transporter genes, none the less nitrogen can still be transported to the plant via this pathway. The transport of inorganic nitrogen in the form of ammonium and the transport of organic nitrogen as amino acids most likely will occur simultaneously in the same species and or organism, depending on the abundance of different nitrogenous species in the soil, Fochi 2016 along with Dearnaley 2007 suggest that amino acids may in fact be the primary nitrogen compound transferred to orchids, evidence for this coming from isotopic ratios of enriched C13 and N15 within plants associated with mycorrhizal fungi, but more research is needed to fully understand this transport relationship.

Carbon Transport
Apart from the unique peloton structures which transfer nitrogen and phosphorus from mycorrhizal fungi to orchid plants the transfer of these nutrients, as discussed, above is almost identical to that observed in arbuscular mycorrhiza and ericoid mycorrhiza, but when it comes to arguably the most fundamental element involved in mycorrhizal transport carbon, orchid mycorrhiza show a distinct divergence form the traditional paradigm of unidirectional nutrient transfer in mycorrhizal associations. Orchid mycorrhizal interactions encompass a large variety of symbiotic scenarios, ranging from fully mycoheterotrophic plants or in other words parasitic on their fungal inhabitant such as Monotropa uniflora which lacks chlorophyll, to interactions that take on a similar nature to those found in arbuscular mycorrhiza, where in bidirectional nutrient transport takes place such as in green leaved Goodyera repens. For the documented interactions in orchid mycorrhiza it has been observed that even in photosynthetically capable species carbon will readily flow from fungi to the plant. This may or may not occur simultaneously with the transfer of carbon from plant to fungi. The evolutionary reasoning for this phenomenon is yet to be deduced. Due to this orchid mycorrhiza in general are considered at least partially mycoheterotrophic interactions. In the mycoheterotrophic orchid mycorrhiza carbon is taken up, by the fungi, as an array of peptide and carbohydrate species often the products of saprophytic reactions taking place in the soil. These reactions are often instigated and progressed by the activity of the mycorrhizal fungus, being part of the basidiomycete phyla, orchid associated fungi have an extensive metabolic arsenal with which to pull from, and are readily able to digest cellulose and lignin to obtain the carbon. Genes encoding proteases, cellulose and lignin digestive enzymes, as well as oligopeptide and carbohydrate transporters are upregulated in the mycelial soil webs to facilitate increased carbon uptake. Further more the fungi which mycoheterotrophically interact with orchid plants are often also found in mycorrhizal association with beech trees, and translocation of photosynthate from tree to fungus and then to orchid has been proposed, but a thorough study is still lacking. Once acquired by the fungus the carbon is either converted into sugars, trehalose being extremely common for most mycorrhizal fungus, amino acids, or simply assimilated into the fungal organism. The transfer of carbon from fungi to plant happens in one of two forms either as carbohydrates primarily trehalose, but glucose and sucrose may also be involved, or as an amino acids primarily as arginine but glycine and glutamine can also be transferred. These molecules are transported, via specialized amino acid permeases and carbohydrate transporters embedded in the fungal peloton membrane, into the interficial space where they are absorbed into the plant through similar analogous transporters in the plant endoplasmic reticulum membrane which surrounds the peloton. Genes which encode for such transporters experience significant upregulation in both plant and fungi, similar to the upregulation seen in nitrogen and phosphorus compound transporter genes during symbiosis. This active transport of carbon from fungi to plant is an exclusively biotorphic reaction but it is thought that a significant amount of carbon may also be transferred to the plant when the fungal pelotons degrade and are digested.

Mycophagy (Necrotrophy)
The transfer of nitrogen and carbon as discussed above readily occurs through live pelotons, but it has been observed by Kuga 2014 and Rasumussen 2009 that large amount of carbon and nitrogen may also be taken up by the plant during the senescence and digestion of fungal pelotons. This process is called Mycophagy. Lysis of pelotons begins between 30 and 40 hours after contact and initial peloton formation within the majority of observed orchid plants. As mentioned above as pelotons are formed they are covered by a plant derived membrane, which eventually takes on the properties of endoplasmic reticulum surrounded by Golgi apparatuses. The presence of these organelles is indicative of their purpose, which is thought to be the excretion of digestive enzymes into the interficial space between the peloton and the plant membrane to digest the fungal cells. Once the fate of the peloton is decided, and degradation and digestion are to occur, a secondary membrane forms around the fungal peloton which is essentially a large vacuole which will allow the isolated degradation of the peloton. Additionally peroxisomes accumulate within the digestive plant cells and undergo exosytosis into the newly formed vacuole, this process concentrates a plethora of enzymes such as uricases, chitinases, peptidases, oxidases and catalses within the vacuole facilitating the breakdown of the peloton. Once degraded the fungal remnants are absorbed into the plant, transferring the nutrients and energy to the plant host. Stable isotope imaging reveals that C13 and N15 applied to mycorrhizal hyphea webs was found to be readily transferred to the plant via fungal pelotons, leading to a disproportionate amount of these isotopes within the peloton containing plant cells and the peloton itself, but in senescencing pelotons the concentrations of these C13 and N15 containing compound was found to be even more pronounced, and significantly higher than in live pelotons. This indicates that as plant pelotons start to senescence they are loaded with carbon and nitrogen nutritive compounds, hypothetically to be transferred to the plant during lysis. Morphological changes in the hyphea further support this proposition, in that the last morphological change in the peloton before is collapses is a swelling, perhaps due to the increased nutritive compound load. Once digestion is complete reinfection of the digestive cell will occur shortly after and a new peloton will form, and eventually will be degraded. Reinfection and digestion are a continuum and will cyclically occur throughout the entire life span of the cooperation. Rasmussen 2009 differentiates two types of plant host cells which are involved in nutrient transfer, so called 'digestion cells' and so called 'host cells', 'digestive cells' apparently engage in dense hyphal peloton formation followed by a rapid digestion and subsequent reinfection, where as 'host cells' contain live hyphae pelotons, which will not be digested, or at least not as readily. Rasmussen 2002 discusses an additional mode of nutrient transfer called pytophagy involving lysis of fungal cells but instead of lysing the entire fungal hyphae only the growing end is degraded releasing the contents of the fungal cytoplasm into the interfacial space between the plant and fungi membranes, where the plant can uptake the necessary compounds. There is little information on this mode of nutrient transfer and it is still speculative, and more research is needed.

Micro-nutrient transfer
Micro-nutreint transfer is thought, for the most part, to occur by passive transport across cellular membranes, both during absorption, from soil by fungi, and transfer from fungi to host plants. This is not always the case though and although research on the topic is limited, there is evidence of active transport and allocation of micro-nutrients in certain conditions. The upregulation of cation transporters is observed in orchid D. officinale symbioses, suggesting fungi may assisted in the transfer of nutrients from fungi to plant,. Cations, especially iron, are often bound tightly to organic and clay substrates keeping them out of reach of plants, fungi and bacteria, but compounds such as spiderophores are often secreted into the soil by fungi and bacteria to aid in the acquisition of these cations. A spiderophore is a small molecule which has extremely high affinity for Fe3+ and is commonly found being utilized by many bacteria and fungal species. These compounds are released into the soil surrounding the hyphal web and strip iron from mineral compounds in the soil, the spiderophore can then be reabsorbed into the fungal hyphae where the iron can be dissociated from the spiderohore and used. Haselwandter investigates the presence of spiderophores in orchid associated mycorrhizal fungi within the genusRhizoctonia which utilize the spiderophore, basidiochrome as the major iron-chelating compound. Other vital nutrients may be transferred between mycorrhizal fungi and orchid plants via specialized methods, such as chelating molecules, but more research on this subject is needed.