Agricultural field

From MicrobeWiki, the student-edited microbiology resource
Jump to: navigation, search
This student page has not been curated.
The figure is demonstrated the agricultural field environment.


“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.” [7]

An agricultural field can be defined as a field that is used for growing crops or other high-value plant species. This land is highly managed and often provisioned with artificial nutrients (i.e. fertilized). Normally, only a single plant species is grown in an agricultural field at any particular time, and additional management activities are practiced to suppress the growth of weeds and pests.

Physical environment


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]

Soil pH is an important chemical property that affects the availability of nutrients in the soil as well as the structure and activity of the soil microbial community. These soil microorganisms have important functions that not only build soil structure, but also cycle organic matters and nitrogen compounds.

Most soil microorganisms and plants prefer a neutral pH of 6 to 7 because most soil nutrient compounds are available in this pH range. In deep layer of soil, anaerobic microorganisms produce organic acid by anaerobic respiration and fermentation. Furthermore, aerobic also generate proton ions with sulfur and ammonia oxidizing, and alter the soil pH. [15]

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 fields, the addition of nitrogen fertilizers or organic nutrient sources such as compost and manure an add lots of nitric acid and sulfuric acid. These strong acids increase the soil acidity and reduce the pH of the soil. Lime may be used as a management practice to control pH. It not only increases the availability of nutrients from soil, but it 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 pathways 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 polysaccharides, glomalin and hyphae. Soil microbes also can bind soil particles to contribute to the formation of soil structure. Furthermore, the products of soil microorganisms, organic matters, are central factors for soil aggregation [15].

In agricultural fields, soil structure is disturbed by tillage, liming, crop rotation, and other human activities. Thus, while the role of microorganisms in soil structure stabilization is important, there are many disturbances to the soil in agricultural land, and this reduces the influence of microbes in the process of soil aggregation in all but the deeper soil layers.

Factors affecting microbial communities in agricultural fields

Crop rotation

Crop rotation is a method that utilizes different type of crops in the same field in different time periods. It is one of the oldest agricultural methods, and it is beneficial for pest and pathogen control. Rotation also can help increase biodiversity and soil nutrients by using dissimilar crops with differing essential nutrient demands.


Nitrogen (N) and Phosphorus (P) are the essential elements for all organisms. Crop fertilization is an important factor of the soil nutrient pools [14]. The availability of nutrients have also been reported to influence soil microbial growth and activity [2],[4]. Recent studies have indicated that high concentrations of NH4+ can inhibit NO3- uptake by fungi [18],Additionally, high soil phosphorus concentrations have been reported to impact the diversity of soil bacteria, and saprophytic and arbuscular mycorrhizal (AM) fungi. Soil fertility has also been shown to affect microbial activities [6],[19].


“Tillage is a mechanical stirring of soil surface to provide a suitable environment for seed germination and root growth” [15]. Tillage overturns the soil and affect soil microbial communities in several aspects, including N transformation rates and the build-up of soil organic matter (SOM) [8]; [16].

Microbial processes

Nitrogen cycle

Schematic of the flow of nitrogen through the environment. The important microbial functions indicated in the cycle.:From:[2]

Nitrogen is present in various chemical forms, including dinitrogen gas, organic nitrogen, and inorganic ammonium and nitrate ions. The microbial consortia involved in nitrogen cycling play an important role in transforming N between these various forms. Important bacterial N-cycling functions include nitrogen fixation, ammonification, nitrification, and denitrification. Except for denitrification, most of these processes can increase nitrogen level in the soil and produce nitrogen that is available to plants [15].

In the nitrogen cycle, there are several enzymes involved in maintaining 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

In modern agricultural field, artificial inorganic nitrogen sources take place the nitrogen from mineralization by soil microorganisms. Furthermore, high concentration of inorganic nitrogen compounds could inhibit the nitrogen fixing process by soil microbes. However, artificial nitrogen fixing need lots of energy for progressing. In order to reduce energy wasting and sustainable using natural resources, the organic farmer become a trend in the field of agriculture. The nitrogen sources of agricultural field are the important issues. 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 organic farming system. Some of them are symbiotic with plants infection of their root systems. Rhizobium is an important genus of nitrogen fixing bacteria, which infects the roots of the bean family (Fabaceae or Leguminosae).


Ammonification occurs in the soil with aerobic environment, and microorganisms are involved in the decay of dead organic matter. The end product of ammonification is ammonium. Otherwise, in anaerobic conditions, different microbial decay reactions will occur, and these produce nitrogen compounds known as amines. The bacteria that produce ammonia from organic compounds include Bacillus, Clostridium, Proteus, Pseudomonas, and Streptomyces). They are called ammonifying bacteria


Nitrification is the process of producing nitrate through the oxidation of the reduced nitrogen compounds. Most nitrification is performed by autotrophic microorganisms, and it consists of two principal reaction steps. The first step of nitrification is ammonia oxidation, which is the conversion of ammonium to nitrite by ammonia oxidizing bacteria. The second step is nitrite oxidation, which transforms nitrite to nitrate.[15] These micorogranisms include Nitrobacter, Nitrococcus, Nitrosococcus, and Nitrosomonas, Alcaligenes, Asprgillus and some actinomycetes Several heterotrophic microorganisms also have ability to oxidize either ammonium or organic nitrogen to nitrite or nitrate. These bacteria which include (Nitrobacter, Nitrococcus, Nitrosococcus, and Nitrosomonas) are called nitrifying bacteria.


Some microbes can utilize nitrate as an electron acceptor for the metabolism of organic substances. The end products of the process are free nitrous oxide and nitrogen gases that are released into the atmosphere. The bacteria belonging to this group include Alcaligenes, Bacillus, Paracoccus, Pseudomonas, and they are called denitrifying bacteria.

Carbon cycle

The carbon cycle is one of the most important cycles on earth. There are two major biological fluxes of carbon dioxide in nature: photosynthesis and respiration. Photosynthesis can reduce and transfer carbon compounds form inorganic form to organic form. In respiration process, carbon dioxide is the end product in aerobic respiration and some of anaerobic respiration processes (Methanogenesis).

In agricultural fields, soil microbes are not directly linked with photosynthetic fixation. However, they are correlated with metabolic processes such as ammonification, nitrification, denitrification and decomposition.

Decomposition is one part of carbon cycle, and soil microbes play an important role in this process [15].

Soil microorganisms decompose leaf litter and crop residues and transform soil organic matter (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.

In agricultural fields, tillage increases aeration in the soil and help plant residues break down faster. This factor not only accelerates growth rates of soil microorganisms, but also increases the decomposition processes of the associated with soil microbial community.

Key Microorganisms


Legumes were recognized and used on agricultural very early in the history of agriculture, and their symbiotic root-nodule bacteria of the genus Rhizobium was identified to have the ability of nitrogen fixation in 1888. [15]

Another Alphaproteobacteria, Agrobacterium tumefaciens, is a very important bacterium for agriculture.Agrobacterium tumefaciens is a plant pathogen that has the ability to transfer DNA between itself and plants. It is used in agricultural biotechnology for the generation of genetically modified organisms (GMO) to create higher yield and stress tolerant crops species.


Betaproteobacteria is an important soil bacterial group that functions in ammonia oxidation. Ammonia oxidation is a vital process that can transform organic nitrogen into inorganic forms that are easy for plants to acquire from the soil, and this leads to increased crop yield.


There are several papers reporting that Bacteroidetes have high abundances in agricultural fields; however, the functions of Bacteroidetes are not very clear. Flavobacterium sp is one of Bacteroidetes bacteria that are reported to have denitrification genes [13]), and this might reveal the ecological niche of Bacteroidetes.


Actinobacteria are a group of Gram-positive bacteria with high G+C ratio [17]. They play an important role in decomposition of organic matter such as cellulose and chitin. This means that Actinobacteria take part in the global carbon cycle. Furthermore, Actinobacteria are well-known bacteria group for produce antibiotics that are important in the medical field.

Example of organisms within the group

Diverse microorganisms inhabit an agricultural field, including Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Firmicutes and Fungi.

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


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

Nitrosomonas is a genus of chemoautotrophic bacteria that acquire energy from the ammonia oxidation process in aerobic environments. The artificial fertilizers such as urea and anhydrous ammonia are used very often in the modern agricultural field. Ammonification can oxidize ammonia to nitrite, and it is very an important process for crops which uptake different forms of N sources.

Current Research

Soil microbial communities are important and are directly involved in the functions of soil. Before high throughput DNA fingerprinting identification, it was very difficult to identify the soil microbial diversity. In a previous study, Dr. Bornman and Dr. Triplett investigated soil microbial community in the Amazonia forest and pasture soil.[1]

The results indicated that microbial communities are significantly different in these two soils, and this might be related to the pH and other factors such as high soil nutrients due to deforestation [10]. In a recent study, pyrosequencing, a high throughput DNA sequencing technology, was used to identify soil microbial diversity in forest and agricultural soils [11]. The results demonstrated that the richness of soil microbes is immense and the most abundant bacterial groups in three agricultural soils were Bacteroidetes, Betaproteobacteria and Alphaproteobacteria. Some bacteria in these three classes are linked with Nitrogen cycle.

Current research is not only focused on the soil microbial diversity. Soil organic matter (SOM) is also an important factor for crop yield and soil structure in agricultural fields. The Ultuna Long-Term Soil Organic Matter Experiment is located at Ultuna, Uppsala and was established in 1956 to study the effects of fertilizing and other factors in the agricultural systems. In 2005, Dr. Enwall’s group published a paper report about relationship between soil nutrient content and different kinds of organic and inorganic fertilizers. The report showed that the addition of fertilizers can affect the microbial activity and the composition of the denitrifying communities. Different molecular fingerprinting technologies such as ribosomal intergenic spacer analysis (RISA), denaturing gradient gel electrophoresis (DGGE) and restriction fragment length polymorphism (RFLP) were used in this article for identifying the denitrifying bacterial communities. The results showed that it is not only the well-known bacterial class Alphaproteobacteria that is involved in the denitrifying process, but some actinomycetes belonging to Actinobacteria also take part in this process in agricultural fields [5].

Land usage is another disturbance that can influence soil microbial community and functions. In 2009, Dr. Jesus’s group reported the relationship between land usage use systems and bacterial community composition [3]. The results showed that the bacterial community structure is correlated with the soil attributes, and the bacterial communities are very different between crops and the forest soil.


[1]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.

[2]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.

[3]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.

[4]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.</ref>

[5]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.

[6]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.

[7]Hirst, K. K. Agricultural Field Systems. from</

[8]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.



[11]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.

[12]Soil pH Modification. from

[13]Spanning, R., Delgado, M., & Richardson, D. (2005). The Nitrogen Cycle: Denitrification and its Relationship to N2 Fixation (pp. 277-342).

[14]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.

[15]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.

[16]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.

[17]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.

[18]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.

[19]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]

Edited by student of Angela Kent at the University of Illinois at Urbana-Champaign.