Agricultural field
Introduction
“An agricultural "field system" generally refers to innovative elements of prehistoric and historic agricultural programs. Agriculture is a variably complicated process, and improvements and innovations in the part of a field system used in some civilizations such as the Maya and Tiwanaku are centered on improving access to water, elimination of weeds, facilitating growth and even some temperature control.” (Hirst)
Physical environment
pH
“Vegetables grown on mineral soils have a target pH of 6.1 to 6.5. On muck soils the target pH is 5.1 to 5.5.”("pH - SOIL DIAGNOSTICS,") The best pH condition for most plants in mineral soils is between 6.0 and 7.0. pH between 5.5 and 6.5 are the best condition for turfgrasses. Furthermore, some evergreen trees and shrubs grow better in pH 5.0 to 6.0. There are some acid-loving plants which contains blueberries, azaleas, and rhododendrons needing acid environment between pH 4.5 to 5.2. ("Soil pH Modification,") Soil pH is an important chemical property which affects the availability of nutrients in the soil and structure and activity of soil microbial community. These soil microorganisms have important functions that not only build soil structure, but also cycle organic matters and nitrogen compounds. The low pH condition will suppress the availability of phosphorus which is the important nutrient to the plants in the soil. Besides, aluminum ions will become more available and might have negative effects for the plants to reducing crop yields. In agricultural field, nitrogen fertilizers, organic nutrient sources which contain compost and manure bring lots of nitric acid and sulfuric acid. These strong acids are increase in soil acidity and reducing pH of the soil. Lime is used to control pH. It not only increases the availability of nutrients from soil, but also provides extra calcium and magnesium for plants and soil microorganisms.
Soil structure
“Soil structure is defined as the arrangement of particles and associated pores in soils across the size range from nanometres to centimetres.” (Oades, 1993)
Factors of microbial community in agricultural field
Crop rotation
Crop rotation is a method which grows different type of crops in the same field in different time periods. It is one of the oldest cultural methods and the benefits contain pests and pathogens control. Furthermore, based on the diverse essential nutrients of dissimilar crops, crop rotation can avoid over exhaustion of soil nutrients the purpose of crop rotation is to avoid. Because of plant-microbes interaction, rotation can help increase and keep biodiversity; furthermore, it also can increase nutrients to the soil. For example, Legumes have nodules on their roots which contain nitrogen-fixing bacteria. These bacterial consortia can convert nitrogen in the air to ammonia.
Fertilization
Nitrogen (N) and Phosphorus (P) are the essential elements for lives. Crop fertilization is a important factor of the soil nutrient pools composition changes (Stevenson & Cole, 1999). The availability of nutrients also have reported that can influence soil microbial growth and activity (Broeckling, Broz, Bergelson, Manter, & Vivanco, 2008; da Silva & Nahas, 2002). Recently studies indicated that high concentration of NH4+ can inhibit NO3- uptake by fungi (Wang et al., 2007), otherwise, high soil phosphorus concentration also have reported to impact the soil bacteria, fungi, and arbuscular mycorrhizal (AM) fungi diversity. Furthermore, Soil fertility also has been proved to affect the microbial community compositions from different aspects which included the diversity, and activates (Fox & MacDonald, 2003; Wei et al., 2008).
Tillage
“Tillage is a mechanical stirring of soil surface to provide a suitable environment for seed germination and root growth” (D. M. Sylvia, J. J. Fuhrmann, P. G. Hartel, & B. D. A. Zuberer, 2005a). Tillage overturns the soil and affect soil microbial community in several aspects which contain the Nitrogen transformation rates and the soil organic matter (SOM) increasing (Muruganandam, Israel, & Robarge, 2010; van Groenigen et al., 2010). These effects are not only promoting the soil carbon storage without change the soil microbial community structures, but also activation the microbes and increase the microbial biomass.
Microbial processes
Nitrogen cycle
Nitrogen is presented in various chemical forms which contain dinitrogen gas, organic nitrogen, ammonium and nitrate ions. The microbial consortia which involved in nitrogen cycle are playing important role. These bacteria have some functions that contain nitrogen fixing, ammonification, nitrification and denitrification. Excepting denitrification process, all processes of nitrogen cycle can increase nitrogen level in the soil and provide to plants as nitrogen sources. (D. M. Sylvia, J. J. Fuhrmann, P. G. Hartel, & D. A. Zuberer, 2005b) In the nitrogen cycle, there are several enzymes involve to increasing the nitrogen pool in the soil which contain nitrogenase for nitrogen fixation; Gln Synthetase (GS), Glu 2-oxoglutarate (GOGAT) and Glu Dehydrogenase (GDH) for ammonification; ammonia monooxygenase and nitrite oxidoreductase for nitrification; and nitrate reductase, nitrite reductase and other enzymes for denitrification. The anaerobic process of denitrification removes the oxygen from nitrate and nitrite and also releases nitrogen gas from soil into the air. This can process remove the nitrogen from soil and also degrade soil fertility.
Nitrogen fixing bacteria
Bacteria are the only organisms capable of taking nitrogen in the air and combining it with hydrogen to make ammonia. Nitrogen fixing bacteria are important in global nitrogen cycle and some of them are symbiotic with plants by infection their roots system. Most of nitrogen fixing bacteria belongs to the genus Rhizobium, which infects the roots of the bean family (Fabaceae or Leguminosae).
Ammonification
Ammonification occurs under oxidizing conditions that microorganisms are involved in the decay of dead organic matter. In the soil where oxygen is not present, a condition referred to as anaerobic, different microbial decay reactions occur, and these produce nitrogen compounds known as amines. The bacteria that produce ammonia from organic compounds Bacillus, Clostridium, Proteus, Pseudomonas, and Streptomyces) are called ammonifying bacteria
Nitrification
Some microbes can utilize nitrates to replace oxygen as electron acceptors and metabolize organic substances. This process reduces nitrates to nitrites and the nitrites is the end product for these bacteria. These bacteria which include (Nitrobacter, Nitrococcus, Nitrosococcus, and Nitrosomonas) are called nitrifying bacteria.
Denitrification
Some microbes can utilize nitrites as electron acceptors and metabolize organic substances. The end products of the process are free nitrous oxide and nitrogen gases which will release into the atmosphere. The bacteria belonging to this group which contains Alcaligenes, Bacillus, Paracoccus, Pseudomonas are called denitrifying bacteria.
Carbon cycle
The carbon cycle is on of the most important cycle of the earth. The main purpose of carbon cycle is transform inorganic carbon (carbon dioxide) to organic carbon sources for life on earth. There are two major biological fluxes of carbon dioxide in nature which are photosynthetic fixation and respiration. Soil microbes play an important role in decomposition process which means using residue component as energy and cell structure sources. Decomposition is one part of carbon cycle and is progressed by microorganisms (Sylvia, et al., 2005b). Soil microorganisms decompose the litters and transform as Soil organic matters (SOM). SOM also can be used as carbon source for soil microbes and the end product of decomposition is carbon dioxide which is released back into the atmosphere.
References
Broeckling, C. D., Broz, A. K., Bergelson, J., Manter, D. K., & Vivanco, J. M. (2008). Root exudates regulate soil fungal community composition and diversty. Applied and Environmental Microbiology, 74(3), 738-744.
da Silva, P., & Nahas, E. (2002). Bacterial diversity in soil in response to different plants, phosphate fertilizers and liming. Brazilian Journal of Microbiology, 33(4), 304-310.
Fox, C. A., & MacDonald, K. B. (2003). Challenges related to soil biodiversity research in agroecosystems - Issues within the context of scale of observation. Canadian Journal of Soil Science, 83(3), 231-244.
Hirst, K. K. Agricultural Field Systems. from http://archaeology.about.com/bio/K-Kris-Hirst-3021.htm
Muruganandam, S., Israel, D. W., & Robarge, W. P. (2010). Nitrogen Transformations and Microbial Communities in Soil Aggregates from Three Tillage Systems. [Article]. Soil Science Society of America Journal, 74(1), 120-129.
Oades, J. M. (1993). THE ROLE OF BIOLOGY IN THE FORMATION, STABILIZATION AND DEGRADATION OF SOIL STRUCTURE. Geoderma, 56(1-4), 377-400.
pH - SOIL DIAGNOSTICS. from http://www.omafra.gov.on.ca/IPM/english/soil-diagnostics/ph.html
Soil pH Modification. from http://www.extension.org/pages/Soil_pH_Modification
Stevenson, F. J., & Cole, M. A. (1999). Cycles of soil: carbon, nitrogen, phosphorus, sulfur, micronutrients. Cycles of soil: carbon, nitrogen, phosphorus, sulfur, micronutrients., 427 pp.
Sylvia, D. M., Fuhrmann, J. J., Hartel, P. G., & Zuberer, B. D. A. (2005a). Principles and applications of soil microbiology (2nd Edition ed.). Upper Saddle River, N.J.: Pearson Prentice Hall.
Sylvia, D. M., Fuhrmann, J. J., Hartel, P. G., & Zuberer, D. A. (2005b). Principles and applications of soil microbiology (2nd ed.). Upper Saddle River, N.J.: Pearson Prentice Hall.
van Groenigen, K.-J., Bloem, J., Baath, E., Boeckx, P., Rousk, J., Bode, S., et al. (2010). Abundance, production and stabilization of microbial biomass under conventional and reduced tillage. [Article]. Soil Biology & Biochemistry, 42(1), 48-55.
Wang, Y., Li, W., Siddiqi, Y., Kinghorn, J. R., Unkles, S. E., & Glass, A. D. M. (2007). Evidence for post-translational regulation of NrtA, the Aspergillus nidulans high-affinity nitrate transporter. New Phytologist, 175(4), 699-706.
Wei, D., Yang, Q., Zhang, J. Z., Wang, S., Chen, X. L., Zhang, X. L., et al. (2008). Bacterial community structure and diversity in a black soil as affected by long-term fertilization. Pedosphere, 18(5), 582-592.
