From BIOL 2P96 Jan 2013 Group 09
Ecological contributions of fungi (biochemistry).
Fungus is a group of unicellular, multicellular, or syncytial spore-producing organisms feeding on organic matter, including moulds, yeast, mushrooms, and toadstools. Fungi are widely known for their culinary uses, however fungi have a significant ecological impact that can both benefit and harm the worlds ecology. Ecological studies have found that in healthy forest soils, 90% of the total living organisms consist of fungi. The remaining 10% are made up of organisms such as nematodes, algae, rotifiers, protozoa, springtails, mites and worms . In addition, fungi are used in the agriculture, medicine, research, and biotechnology sectors.
Some common examples of the impact of fungi include:
- The antibiotic Penicillin was first discovered in 1928 by Alexander Fleming from cultures of bacteria that had had their growth inhibited by Penicillium
- The use of endogenous fungal products in the manufacturing and production of herbicides
Fungi may contribute substantially to soil microbial biomass as well as to the genetic diversity among soil microorganisms.  Fungi can utilize carbohydrates like L-arabinose, D-xylose and cellobiose aerobically and some soil yeasts have also been found to assimilate intermediates of lignin degradation.  It has also been shown that fungi can enhance plant growth as well. They do this by expanding the plant's roots and thus making it easier for both the plant and fungi to get nutrients. 
Fungi are found everywhere in the natural environment and they play fundamental roles in the ecosystem. Several biochemical processes controlled by fungi are thus; decomposition of dead biomass, the recycling of nutrient, plant nutrition and release of gases to the atmosphere. Fungi can respond to processes altered by global change such as soil temperature and moisture, availability of nutrient and atmosphere component.
Decomposition is a vital ecological process driven by fungi. Without decomposition, the world would be filled with piles of dead biomass or dead organic matter. For decomposition to fully take effect, fungi secretes chemical that digests dead organic matter, following the initial decomposition process by detritus. Fungi are saprophytes. Saprophytes together with detritus are essential in the recycling and fragmentation processes of decomposition. 
- Contribution of fungi to leaf litter decomposition
Contribution of fungi in the decomposition of leaf litter results in the generation of inorganic compounds, fine-particulate organic matter and decomposer biomass. Contribution of stream detrivores, fungi, and bacteria to leaf breakdown based on biomass estimates. In ecosystem, decomposition of leaf litters in stream or rivers depends on the activity of invertebrates and microorganism. Fungi and some bacterial mediates the conversion of leaf litters to microbial biomass, the prevalence of fungi in microbial decomposer assemblages has been found in aquatic environment. Not only do fungi contribute to decomposition of leaf litter, they increase the food value of leaves in the aquatic environment. Hyphomycetes fungi which are mostly aquatic have been recognized as playing a major task in microbial decomposition of leaf litter in stream or rivers. Contribution of fungi and bacteria to leaf litter decomposition in a polluted river. Extracellular enzymes are released to degrade the leaf constituent such as cellulose, hemicelluloses and pectin, thereby making the leaf material more suitable food source for invertebrates in aquatic environment.
- Contribution of fungi to the decomposition of soil organic matter/plant residue
Fungi breaks down organic matter and these are returned to the soil where they are absorbed by plants and other organisms. Fungi decompose various organic matters such as cellulose, hemicellulose, lignin, starch, pectin, chitin, protein and nucleic acids.  The large quantity of fungi in the soil and the rate with which organic matter is broken down depends on many factors like nutrient availability, oxygen, pH, temperature and moisture. Major studies show that temperature and moisture influence the decomposition of organic matter, in that, warmer temperatures and high moisture level results in higher decomposition rate. Extremely high or low temperature can decrease the activity of fungal and other microorganisms. Low oxygen can hinder the activity on fungi in decomposing organic matter, in that, when water is excess, anaerobic condition occurs eliminating the aerobic condition for the advantage of fungi. Climate, leaf litter chemistry and leaf litter decomposition in terrestrial ecosystems: a triangular relationship. Under anaerobic condition fungi are most suppressed. Soil pH affects the activity of fungi; there are more fungi in neutral soil pH than in acidic soil. Hence, the rate of decomposition is higher in neutral soil.
Plant gains nutrient from the partially digested organic matter left in the soil called humus. With the help of fungi, humus is made availability to plant for use and for development. In addition, fungi help plant absorb water and minerals from soil. The fungus mostly involved in plant nutrition is Mycorrhizas (ectomychorrhiza and arbuscular). Mycorrhizal fungi increase the capability of nutrient absorption of host plant. These fungi colonize plant root by penetrating the root and thereby, increasing the plant feeding range and as well allowing neighboring trees to interconnect for proper nutrient distribution. When mycorrhizal fungi penetrates plant root, they increase the surface area of the root for the better opportunity to access soil resources. 
In addition to the well recognize role fungi play in plant nutrition, mycorrhizas fungi can influence the process of soil aggregation. Many factors contribute to soil aggregation; however, mycorrhizas are recognized to play an essential part. The amount of aggregation in the soil relates to the length of fungal hyphae in the soil, which are long, threadlike. With their hyphae, fungi form aggregates in the soil by entangling the soil particles and forming cross-links between soil particles. Mycorrhizal Fungi can influence different processes affecting soil aggregate/structure mediated by root such as root entanglement and physical force, soil water regime alteration, rhizodeposition and root decomposition.
Fungi releases CO2 to the atmosphere following the decomposition of soil organic matter. The release of CO2 is very effective on global carbon balance as soil contain the largest carbon pool in the ecosystem. When there is a high soil temperature, fungi and other microorganism decomposed soil organic matter at a faster rate, thereby releasing more carbon into the atmosphere. CO2 have a vast positive feedback on soil by further increasing plant productivity and nutrients.
Fungi are essential to the health and success of most ecosystems both aquatic and terrestrial. They are present almost everywhere in the ecosystem and have a great impact in the stability of ecosystem. Decomposition of organic matter, plant nutrition, soil aggregation, recycling of nutrient, and the release of carbon into the atmosphere are processes influenced by fungi. So far, the positive impact of fungi has being discussed in different aspects. Little is known that, some fungi have a negative effect on the ecosystem by causing infection and destruction in several part of the ecosystem.
 Species Types
Many fungal species contribute ecologically, although the most common relationship between a fungi and plants can be seen as Mycorrhiza. A mycorrhiza is a symbiotic relationship in which a fungus can associate with the roots of a vascular plant. In a mycorrhizal association, the fungus has the ability to colonize the host plant's roots. This process generally occurs intracellularly as in arbuscular mycorrhizal fungi (AMF or AM), but may also occur extracellularly as in ectomycorrhizal fungi. The relationship between these fungi and their plant host's is extremely important in maintaining soil growth and soil chemistry. The two morphological types of Arbuscular mycorrhiza, the Arum and Paris, have been found in ~80% of all major plant lineages.
Many Fungi Decomposers use their physical form and enzyme capabilities and metabolism to help decay dead animals and plant remains in the soil. some famous fungi decomposers are :
- Zygomycetes: The only saprotrophic zygomyces are found in the mucorales. Most of these mucorals are specialized to breaking down starch, fats and proteins. Extracellular enzymes such as lipases and proteases are produced during decomposition. The mucorales' ability to decompose depends on the proper substrate in their immediate environment. 
- Basidiomycetes: The saprotophic species of basidiomycetes are the parts adapted morphologically and biochemically to live on cellulose and lignocellulose. basidiomycetes are types of fungi that are able to degrade lignin, and with the help of ants and beetles these fungi are able to remove woody remains from the ecosystem. 
 Lichens & Pedogenesis
Lichens are organisms made up of both fungi and a photosynthetic partner in which they form a symbiotic relationship. This has actually become one of the most successful ways of nutrient uptake for a fungi. It is because of lichens you have healthy forests and plants all over the planet and importantly creates a habitable soil for photosynthetic organisms to thrive in. Soil formation or Pedogenesis is one of the most important impacts that fungi have contributed for organisms in many environments.  Most lichens are usually grown under rocks and slabs where they act as grazers and degrade the rock into soil. Vasily Dokuchaev has created this equation that involved consequences of climate and biological process involving organisms and minerals. 
Soil = f(C, PM, O) x time
where C = climate
PM = parent material
O = biological processes
The main fungal component of lichens that starts this process is the excretion of extracellular organic acids, specifically oxalic acid. This process also known as mineral etching results in disordered structures of silicate all under cool conditions.
 Signal Transduction Pathways
Signal transduction is the result of a biochemical event which transmits a signal from the fungal cell’s exterior, through the cell membrane via membrane proteins, into the cytoplasm. This system is called a pathway. The signal transduction pathways of fungi rely on three components: receptors to interpret the changes in the environment, intermediate proteins to relay information from the cell’s exterior to the interior, and messengers which devise a plan and react to the external change. Many pathways in fungi regulate cell processes such as growth, differentiation and proliferation. These pathways also link fungal development to product biosynthesis, such as antibiotics.
Two of the most important pathways in fungi are:
1) MAP Kinase Pathway (mitogen-activated protein): This pathway is involved in many aspects of fungal growth and cell proliferation, particularly haploid mating and diploid growth. The main components of this pathway respond to temperature, external osmoregularity changes, nutrition availability and mating pheromones.The result of this pathway is spore formation, mating, filamentation, pheromone response and cell wall synthesis. This pathway works parallel to the cAMP/PKA pathway to regulate pseudohyphal growth.
2) cAMP/ PKA Pathway (cyclic adenosine monophosphate/protein kinase A): This pathway promotes cell growth along with metabolism, stress resistance and adherence. cAMP helps to regulate pseudohyphal growth, filamentation and differentiation. It is activated by a lack of nutrients as well as other environmental factors. In pathogens, a switch from budding to filamentous growth results in the cause of diseases.
These two pathways result in a ‘signal cascade’ which helps to regulate cell function and growth. Both of these pathways require various kinases and transcription factors, some of which can be seen in the image below.
 Fungal Decomposition/ Recycling
Decomposition is a general term used to describe the interrelated processes by which organic matter is broken down to CO2 and humus with a simultaneous release of nutrients.
Some types of fungi in the soil act as decomposes, plants use nitrogen as a building block of tissues of its leaves, woods and even fruits. If no decomposition occurs than all this nitrogen will be remain inside the dead leaves and stems; making the nitrogen amount available to make new tissues very little therefore the growth of plant will start decreasing causing ecological catastrophy since plants are the basic supplies for all human needs. also all these non-decomposed leaves and woods will cover the surface of the ground.(REFRENCE IS :Dickinson, C. H. and G. J. F. Pugh. 1974. Biology of plant litter decomposition. 2 volumes. Academical Press, New York.). The rate of decomposition is the main factor that effects the speed at which fungi break down the dead matters which can be measured as (Mt) = M0 e-kt 
- M is the mass of litter at a certain time;
- M0 is the initial mass of litter;
- e is the base of the natural logarithm;
- k is the decomposition constant; and
- t is the amount of time passed since the initial measurement
Leaf decomposition is commonly observed throughout many ecosystems, of which fungi can be classified the secondary contributor next to detritivorous invertebrates (shredders). Experimental results show that samples of alder (Alnus glutinosa) and willow (Salix fragilis) leaves placed in a stream during peak leaf fall, and retrieved periodically to determine leaf mass remaining and the biomass of leaf-associated organisms indicated that shredders accounted for approximately 51% of leaf mass loss, while fungi contributed approximately 18%, and bacteria approximately 7%. 
- The decomposition by fungi and bacteria is also dependent on:*
- chemical composition of organic matter
when the temperature is to high or too low for fungal and bacterial growth the rate of decomposition stars decreasing, also if the leafes carry small amount of nitrogen the rate of decomposition starts becoming low as well since the fungi doesn't have enough nitrogen to use it to build proteins that help in its growth . Another very imoportant factor that will slow down the decomposition rate is low level of oxygen, since fungal growth requires oxygen. 
 Nutrient Uptake
One ecologically important task arbuscular mycorrhizal fungi do is increase the uptake of phosphorus. Phosphorus is a important macronutrient used in all organisms in structures such as nucleic acids, enzymes, coenzymes and phospholipids, as well as being used in cell functions such as the regulation of enzymes, metabolic intermediate activation, the metabolism of energy, and signal transduction cascades. The fungi have access to different sources of soluble phosphate than the plant roots which allows the plant to get phosphate after it has taken up all the phosphate it can after the root level phosphate has been exhausted. In grain, this is most effective when the plant is at maturity. The increased phosphate uptake has been shown to increase crop yield.
Phosphate is selectively taken up by the fungi cells using specialized membrane proteins called phosphate transporters and proton-ATPases. This process requires energy as it is working against a large concentration and electrochemical gradient. The phosphate taken up can then be bartered with the plant in exchange for photosynthetic sugars. Arbuscules, a type of differentiated hyphae, develop within the cortical cells of the plant root. The plant is able to transport the phosphate across a symbiotic membrane between the arbuscules and the cortical cells. This membrane is also known as the periarbuscular membrane.
 Biochemical By-Products
The arbuscular mycorrhizal fungi(AM) discussed above have many biochemical by-products observed through soil and root analysis of host plants/organisms. Glomalin is a common glycoprotein produced on the hyphae and spores of AM fungi, which has been shown to carry specific Glomalin-related soil proteins or GRSPs. These GRSPs are very common to organic soil matter and have been proven to aid in carbon sequestration, which is the process where carbon dioxide (CO2) or other forms of carbon are stored for long-term periods. This process of storing carbon species for long periods of time has been shown to slow the release of atmospheric and marine greenhouse gases produced naturally. This process of carbon sequestration carried out by the AM fungi, more specifically the GRSPs have been theorized to have a primary productivity relationship with its ecosystem and has also been shown to aid directly in the ecosystems ability to remain healthy and produce viable soil.
 Notes and References
- ↑ Fungus (2013) Oxford University Press http://oxforddictionaries.com/definition/english/fungus
- ↑ Grey P (2004) The impact of Fungi in the Environment and the Importance of Conservation Warringal Conservation Society http://home.vicnet.net.au/~warringa/meetings_maj04.htm
- ↑ May, G. S., & Adams, T. H. (1997). The importance of fungi to man. Genome research, 7(11), 1041-1044.
- ↑ Ligon, B. L. (2004, January). Penicillin: its discovery and early development. In Seminars in pediatric infectious diseases (Vol. 15, No. 1, pp. 52-57). WB Saunders.
- ↑ Mougin, C., Laugero, C., Asther, M., Dubroca, J., Frasse, P., & Asther, M. (1994). Biotransformation of the herbicide atrazine by the white rot fungus Phanerochaete chrysosporium. Applied and environmental microbiology, 60(2), 705-708.
- ↑ 6.0 6.1 6.2 Botha, A. (2011). The importance and ecology of yeasts in soil. Soil Biology and Biochemistry, 43(1), 1-8.
- ↑ http://science.jrank.org/pages/1967/Decomposition.html
- ↑ leaflitterclimate.blogspot.com
- ↑ 9.0 9.1 Hieber, M., & Gessner, M. O. (2002). Contribution of stream detrivores, fungi, and bacteria to leaf breakdown based on biomass estimates.
- ↑ 10.0 10.1 10.2 10.3 Pascoal, C., & Cássio, F. (2004). Contribution of fungi and bacteria to leaf litter decomposition in a polluted river. Applied and Environmental Microbiology, 70(9), 5266-5273
- ↑ trunktravel.mongabay.com
- ↑ 12.0 12.1 12.2 12.3 Aerts, R. (1997). Climate, leaf litter chemistry and leaf litter decomposition in terrestrial ecosystems: a triangular relationship. Oikos, 439-449.
- ↑ Van Breemen, N., Finlay, R., Lundström, U., Jongmans, A. G., Giesler, R., & Olsson, M. (2000). Mycorrhizal weathering: A true case of mineral plant nutrition?. Biogeochemistry, 49(1), 53-67.
- ↑ 14.0 14.1 Rillig, M. C., & Mummey, D. L. (2006). Mycorrhizas and soil structure. New Phytologist, 171(1), 41-53.
- ↑ 15.0 15.1 Zhang H. X., Wang X. K., Feng Z. W., Pang J. Z., Lu F., Ouyang Z. Y., 2011. Soil temperature and moisture sensitivities of soil CO2 efflux before and after tillage in a wheat field of Loess Plateau, China. Journal of Environmental Sciences, 23(1): 79–86.
- ↑ Habte, M. "Mycorrhizal Fungi and Plant Nutrition." Journal of Plant Nutrition 18.10 (1995): 2191-198.
- ↑ 17.0 17.1 17.2 Vladimir, K., & Marcel, B. (2005). Symbiotic phosphate transport in arbuscular mycorrhizas. Trends In Plant Science, 1022-29. doi:10.1016/j.tplants.2004.12.003
- ↑ 18.0 18.1 Beever, Ross E., and others. ‘The hidden kingdoms: fungi, lichens and some bacteria.’ In Waitakere Ranges, edited by Bruce Harvey and Trixie Harvey, 102–113. Waitakere City: Waitakere Ranges Protection Society, 2006.
- ↑ http://www.pnas.org/content/96/7/3404/F5.expansion.html
- ↑ 20.0 20.1 Oksanen I., I (2006). "Ecological and biotechnological aspects of lichens". Applied Microbiology and Biotechnology
- ↑ Odling-Smee F. J., Laland K. N. & Feldman M. W. (2003). "Niche Construction: The Neglected Process in Evolution
- ↑ M. J. Wilson, Department of Mineral Soils, The Macaulay Institute for Soil Research
- ↑ http://www.bio.miami.edu/dana/226/226F09_13.html
- ↑ 24.0 24.1 24.2 )Fernandes L, et al (2005). Cell signaling pathways in Paracoccidioides brasiliensis inferred from comparison with other fungi. Genetics and Research, May 5 2005, Pages 216-231. Accessed from http://www.funpecrp.com.br/gmr/year2005/vol2-4/Pb02_full_text.htm
- ↑ 25.0 25.1 Calvo, Ana M., et al (2002). Relationship between Secondary Metabolism and Fungal development. Microbiology and Molecular Biology Review, Volume 66, Issue 3, Spetember 2002, Pages 447-459. doi: 10.1128/MMBR.66.3.447-459.2002 Accessed from http://mmbr.asm.org/content/66/3/447.full#sec-25
- ↑ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99013/
- ↑ 27.0 27.1 27.2 Lengeler, Klaus B., et al (2000). Signal Transduction Cascades Regulating Fungal Development and Virulence. Microbiology and Molecular Biology Review, Volume 64, Issue 4, December 2000, Pages 746-785. Accessed from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99013/
- ↑ Dahlgren R and Turner M (2002). Decomposition. University of California http://lawr.ucdavis.edu/classes/ssc219/biogeo/decomp.htm
- ↑ Rate of Decomposition (2009) http://nre509.wikidot.com/lecture-5:decomposition-constant
- ↑ Mason, C. F. 1976. Decomposition. Edward Arnold Publ. Ltd, Southampton.
- ↑ Li, H., Smith, S. E., Holloway, R. E., & Smith, F. (2006). Arbuscular Mycorrhizal Fungi Contribute to Phosphorus Uptake by Wheat Grown in a Phosphorus-Fixing Soil Even in the Absence of Positive Growth Responses. New Phytologist, (3), 536. doi:10.2307/4131237
- ↑ Harrison, M. J., Dewbre, G. R., & Liu, J. (2002). A Phosphate Transporter from Medicago truncatula Involved in the Acquisition of Phosphate Released by Arbuscular Mycorrhizal Fungi. The Plant Cell October 2002 vol. 14 no. 10 2413-2429 doi: http://dx.doi.org/10.1105/tpc.004861
- ↑ Purin, Sonia; Rillig, Matthias C. (20 June 2007). "The arbuscular mycorrhizal fungal protein glomalin: Limitations, progress, and a new hypothesis for its function". Pedobiologia 51 (2): 123–130.