Agricultural field

The figure is demonstrated the agricultural field environment.

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

Nutrient availability and microbial activity as affected by soil pH; the wider the band, the greater the availability or activity. (Adapted from Truog, USDA Yearbook of Agriculture 1943-1047):From:[1]

“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) It is important for providing flow pathway for water and nutrients. Aggregation of soil particles determinants the soil structure and microorganisms play important role for soil aggregation. Microorganisms can promote aggregation by extracellular poly saccharides, glomalin and hyphae, otherwise, soil microbes also can bind soil particles to create soil formation. Furthermore, the products of soil microorganisms, organic matters, are central factors for soil aggregation. (D. M. Sylvia, J. J. Fuhrmann, P. G. Hartel, & D. A. Zuberer, 2005)

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, 2005). 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

Figure of the flow of nitrogen through the environment. The important of functions of microorganisms are marked in the cycle.:From:[2]

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, 2005).

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., 2005).

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.

Key Microorganisms

Alphaproteobacteria

Legumes was recognized and used on agricultural very early in the history of agriculture. The root-nodule bacterium Rhizobium was identified to hace the ability of nitrogen fixation in 1888 (Sylvia, et al., 2005).

Another Alphaproteobacteria, Agrobacterium tumefaciens, is a very important bacterium for agriculture. Agrobacterium tumefaciens is the plant pathogen which has the ability to transfer DNA between itself and plants. It is used on genetically modified organism (GMO) to create higher yield and stress tolerant crops species.

Betaproteobacteria

Betaproteobacteria is an important soil bacterial group which has function of ammonia oxidation. Ammonia oxidation is an vital process that can transfer the Nitrogen forms and let plants easy to uptake nitrogen from soil and to increase the crop yield.

Bacteroidetes

There are serveral papers reported that Bacteroidetes had high abundances in the agricultural field, however, the functions of Bacteroidetes are not very clear. Flavobacterium sp is one of Bacteroidetes baceria which had report having denitrification genes (Spanning, Delgado, & Richardson, 2005) and might reveal the ecological niche of Bacteroidetes.

Acidobacteria

Actinobacteria are a group of Gram-positive bacteria with high G+C ratio (Ventura et al., 2007). They play an important role in decomposition of organic matters which contain cellulose and chitin. It also means that Actinobacteria takes part in the global carbon cycle. Furthermore, Actinobacteria are well-known bacteria group for produce antibiotics and it is also important for medical field.

Example of organisms within the group

Agrobacterium tumefaciens Agrobacterium tumefaciens is a plant pathogen which has ability to transfer DNA between itself to plants. Agrobacterium is a good biotechnological tools and is used to make theses GMO foods in USA .

Soybean

Cotton Corn

Sugar Beet

Alfalfa

WheatRapeseed Oil (Canola)

Creeping bentgrass (for animal feed)

Rice (Golden Rice)

Nitrosomonas

Nitrosomonas. Image from The Microbe Zoo (by Yuichi Suwa).

Nitrosomonas is a genus of chemoautotrophic bacteria which can uptake the energy from the ammonia oxidation process in aerobic environment. The artificial fertilizers which include Urea and anhydrous ammonia are used very often in the modern agricultural field. Ammonification can oxidize ammonia to nitrite and transfer to different form of N sources and it is very an important process for crops which uptake different forms of N sources.

Nitrosomonas europeae

Nitrosomonas eutrophus

Nitrosomonas halophila

Nitrosomonas communis

Nitrosomonas nitropha

Nitrosomonas oligotropha

Nitrosomonas ureae

Nitrosomonas aestuarii

Nitrosomonas marina

(Sylvia, et al., 2005)

Current Research

Soil microbial community is important and directly relates with the functions of soil. Before high throughput DNA fingerprinting identification technology publishing, it is nearly impossible to identify the soil microbial diversity. The disturbances of soil can affect the soil community structure. Dr. Bornman and Dr. Triplett investigated soil microbial community in the Amazonia forest and pasture soil.(Borneman & Triplett, 1997) The results indicated that microbial communities are significant differences and it might link to the pH and other factors of soil nutrients increasing by deforestation (Piccolo, Neill, & Cerri, 1994).

In recent study, pyrosequencing technique, a high throughput DNA sequencing technology, was used to identify microbial diversity in the forest and agricultural soils (Roesch et al., 2007) The results demonstrated the richness of soil microbes are immense and the most abundant bacteria groups in three agricultural soils were Bacteroidetes, Betaproteobacteria and Alphaproteobacteria. Some bacteria which are contained in these three classes are linked with Nitrogen cycle. Furthermore, this report also demonstrated the diversity and the detecting technology of the soil microbial diversity and functions.

Ultuna Long-Term Soil Organic Matter Experiment, is located at Ultuna which was established in 1956 Uppsala to study the effects of fertilizing and other factors in the agricultural system. In 2005, Dr. Enwall’s group published a paper report about the effects of different organic and inorganic fertilizers and the soil bacterial community composition. The report showed that the addition fertilizers can affect the microbial activity and the composition of the denitrifying communities. They used different molecular tools that included ribosomal intergenic spacer region analysis (RISA), denaturing gradient gel electrophoresis (DGGE) and restriction fragment length polymorphism (RFLP) to identified the denitrifying bacterial communities and displayed that it is not only the well-known bacterial class Alphaproteobacteria involving denitrifying process, some actinomycetes which belong to Actinobacteria also take part in this process, too (Enwall, Philippot, & Hallin, 2005).

In 2009, Dr. Jesus’s group reported the relationship between land usage use systems and bacterial community composition (da C Jesus, Marsh, Tiedje, & de S Moreira, 2009). The results showed the bacterial community structure is correlated with the soil attributes and the bacterial communities are very different between crops and the forest soil.

References

Borneman, J., & Triplett, E. W. (1997). Molecular microbial diversity in soils from eastern Amazonia: Evidence for unusual microorganisms and microbial population shifts associated with deforestation. Applied and Environmental Microbiology, 63(7), 2647-2653.

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 C Jesus, E., Marsh, T. L., Tiedje, J. M., & de S Moreira, F. M. (2009). Changes in land use alter the structure of bacterial communities in Western Amazon soils. The ISME Journal.

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.

Enwall, K., Philippot, L., & Hallin, S. (2005). Activity and composition of the denitrifying bacterial community respond differently to long-term fertilization. [Article]. Applied and Environmental Microbiology, 71(12), 8335-8343.

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

Piccolo, M. C., Neill, C., & Cerri, C. C. (1994). NATURAL-ABUNDANCE OF N-15 IN SOILS ALONG FOREST-TO-PASTURE CHRONOSEQUENCES IN THE WESTERN BRAZILIAN AMAZON BASIN. Oecologia, 99(1-2), 112-117.

Roesch, L. F. W., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., et al. (2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal, 1(4), 283–290-283–290.

Soil pH Modification. from http://www.extension.org/pages/Soil_pH_Modification Spanning, R., Delgado, M., & Richardson, D. (2005). The Nitrogen Cycle: Denitrification and its Relationship to N2 Fixation (pp. 277-342).

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, D. A. (2005). 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.

Ventura, M., Canchaya, C., Tauch, A., Chandra, G., Fitzgerald, G. F., Chater, K. F., et al. (2007). Genomics of Actinobacteria: Tracing the Evolutionary History of an Ancient Phylum. [10.1128/MMBR.00005-07]. Microbiology and Molecular Biology Reviews, 71(3), 495-548.

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.

External links

Soil pH: [3]

Tillage: [4]