IJERD – International Journal of Environmental and Rural Development (2022) 13-1

Research article
erdInteractions among Soil Physical, Chemical and Biological
Properties under Different Farming Systems
MARISOL TERASHIMA
Graduate School of Agriculture, Tokyo University of Agriculture, Japan
Email: chamiter@hotmail.com

MACHITO MIHARA*
Faculty of Regional Environment Science, Tokyo University of Agriculture, Japan
Email: m-mihara@nodai.ac.jp
Received 14 December 2020

Accepted 9 July 2021(*Corresponding Author)

Abstract The definition of soil quality has always been changing over time within the soil
science community. At first, the study focused more on chemical and physical properties
and less importance on a sustainable environment. Therefore, the definition of soil quality
has changed in the last decade. The importance of biodiversity that exists both on thesurface and within the soil began to be understood. These organisms have essentialfunctions such as nutrient cycling, provision of plant nutrients, and modification of physicalsoil structure, water regimes, and suppression of undesirable organisms on cropland. It has
defined soil quality as the function it has within the environment, sustaining productivity,
maintaining environmental quality, and promoting health in plants and animals. However,
the interaction between some microorganisms is still unknown, or how it could affect thedifferent parameters in the biodiversity of an agro ecosystem. Furthermore, it is unknown
what parameters are important in determining soil quality. Therefore, this study analyzed
the biological, physical, and chemical properties of the soil of two farms whose practices isdifferent. Water retention capacity, aggregate distribution, organic matter, total nitrogen,NO3, NH4, and biomass of microorganisms were measured. Soils were air dried and sieved
to 2mm. They were analyzed after drying in an oven at 105° C for 24 h. The biomass of
microorganisms was measured by the direct extraction method. The results indicated that
there was a significant difference between the microorganisms but could not be found withphysical and chemical properties. This result could indicate the importance of biologicalproperties over other parameters to discuss soil quality. In addition, the differences
observed could be explained by the different practices carried out on each farm.
Keywords soil quality, soil health, biomass of microorganisms, aggregates, total nitrogen

INTRODUCTION
Soil health is associated with soil biological parameters, such as biodiversity and its stability in theenvironment. When there are outbreaks of plant diseases, they are indicators of ecosysteminstability and poor health. Thus, healthy soil has the ability of the biological community tosuppress plant pathogens, the population of plant pathogens in the soil, and control the incidence
and severity of diseases (Bruggen van and Grunwald, 1996). Accordingly, Cruz (2004) defines soil
quality as dynamic, changing over time within the soil science community. At first, it was focusedmore on fertility, the yield of crops, and less importance on a sustainable environment. In otherwords, science has defined soil quality in chemical and physical parameters, such as the quantity orconcentration of nutrients, organic matter, and water retention.
In the last few decades significant efforts have been made to increase agricultural productivity
through increased fertilization and pesticide application, improved irrigation, soil management
regimes and crops, and massive land conversions (Tilman et al., 2002). There is increasing concern,
however, that agricultural intensification is placing tremendous pressure on the soil’s capacity toⒸ ISERD

1

IJERD – International Journal of Environmental and Rural Development (2022) 13-1

maintain its other functions leading to largescale ecosystem degradation and loss of productivity inthe long term (Tilman et al., 2001; Foley et al., 2005; Vitousek et al., 2009). Since microorganisms
are involved in many soil processes, they may also give an integrated measure of soil health, an
aspect that cannot be obtained with physical/chemical measures alone (Nielsen et al., 2002;
Kibblewhite et al., 2008; Mueller et al., 2010; Sharma et al., 2011).
There have been a few reports that have indicated that organic farming practices have positiveeffects on soil microbial populations, processes and activities (Clark et al., 1998; Doran et al.,
1996; Drinkwater et al., 1995). Applications of insecticides may promote changes in population
biodiversity and dynamics by inhibiting or killing components of the soil microbial community.
Fungicide application can cause significant changes to the relative sizes of the bacterial and fungal
communities in soil (Sall et al., 2006; Sigler and Turco, 2002). Although most of the research has
shown increased microbial diversity in soils from organic farming systems compared toconventional farming systems, some studies have found different results. Shannon et al. (2002)
studied microbial communities in soils managed under organic and conventional regimes, andfound conflicting evidence that the size, composition and activity of the soil microbial biomass
were attributed to management practice. They found that differences in microbial communities insoils under different management practices were subtle rather than dramatic (Liu et al., 2007).
Therefore this study focus on analyzing some physical, chemical, and biological (themicroorganism communities) properties as indicator of soil quality / soil health of two agro
ecosystem which have different practices. In addition, the discussion about what parameters could
be important to determine soil health.
MATERIAL AND METHODS
Soils from 2 farms in Kanto Area, Japan, with a history of natural and conventional crop
production were sampled. These were sampled at a depth of the upper 5 cm of the soil. Soils were
air dried and sieved to 2mm. The dry weight of the soil was determined after drying in an oven at
105°C for 24 h.
The biomass of microorganism was measure by direct extraction method. Ten subsamples of
5.00 g of each soil were weighed separately into 50 ml centrifuge tubes and 20 ml of 0.5 M K2SO4
was added to each. To three subsamples, 0.5 ml of ethanol-free chloroform was added. Both thechloroform-exposed and the non-fumigated samples were capped and shaken simultaneously for 1
h. After shaking, the suspensions could settle for 10 min and the supernatants were filtered throughWhatman No. 42 filter. For the sub-samples with chloroform, only the top 15 ml of the supernatant
was filtered to reduce the amount chloroform in the filtrate. Filtrates from soils with and withoutchloroform were immediately bubbled with air for 30 min to remove any residual chloroform.
Blanks were treated in the same manner. Dissolved organic carbon in all filtrates was determined
after dichromate digestion by titrating with 0.033 M acidified ferrous ammonium sulphate(Anderson, et al. 1993). Chloroform labile C was calculated as the difference between the C
extracted from the chloroform fumigated and the non-fumigated sample. All results are expressedon an oven-dry basis. No conversion factor (kEC) was used to convert chloroform labile C tomicrobial biomass C because the range of kEC values (0.41 - 0.58) is used in the literature and it
has not been tested which is best suited for the soils used here (Setia et al., 2012).
In addition, number of culturable bacteria and fungus were quantified. The plate countmethodology by plating is a widely used methodology (Hoben and So-masegaran, 1982), which
consists of making 1:10 serial dilutions and spreading 100 µl of each dilution on a plate; plates are
incubated until colonies are countable.
The chemical and physical properties were measured as aggregate size, water retention
capacity, organic matter, total nitrogen, total phosphorus, nitrates, and ammonia. Soil samples
analyzed the aggregate's stability and distribution to observe the resistance in the water. Stability is
influenced by the physical and chemical properties of soils. In addition, the soil samples were
evaluated for their relationship with the organic matter.

Ⓒ ISERD

2

IJERD – International Journal of Environmental and Rural Development (2022) 13-1

For NO3 it was measured by nitration of salicylic acid (Cataldo et al., 1975) and for NH4 withindophenol blue method described by Searle (1984). Statistical analysis with ANOVA was done forall the treatments.
RESULTS AND DISCUSSION
Soil Physical and Chemical Properties

Aggregate %In Fig. 1 it shows us the distribution of soil aggregates. Soil aggregates play an essential role in theformation of soil structure and soil health. In agriculture, the stability of the aggregates is important
for the functioning of the agroecosystem. The pore spaces influence the storage of air and waterand the gas exchange. They create a habitat for soil microorganisms and allow the development andpenetration of plant roots. They also help in nutrient cycling and transportation.
It indicates that there are bigger aggregates in the conventional than in the natural one.
Although, no significant difference was found between the different agroecosystems. Thus, both
the Conventional and Natural ones mostly had aggregates greater than 0.5 mm.

Fig. 1 Aggregates (%) in both agroecosystems
Table 1 Soil organic matter (SOM) and water holding capacity in both agroecosystem
Agroecosystem

SOM (%)

Water holding capacity (%)

Conventional

11.82

76.67

Natural

6.18

61.5

No significance difference

The amount of organic matter in the soil depends on many factors, such as its rate of chemicaland biological oxidation, the rate of decomposition of organic matter already existing in the soil,
soil texture, aeration, humidity and climatic factors. Crop management practices can also influence
this parameter, since, for example, the use of mineral fertilizers accelerates the decomposition of
the organic matter in the soil. The water holding capacity depends on its texture, its structure, andthe depth of the roots. That is why the results relate to the fact that there is more organic matter,larger aggregates, and better retention in the conventional agroecosystem (Table 1).
These results may be related to conventional agricultural management. They use synthetic
fertilizers, fungicides, and pesticides, but they also make crop rotations and incorporate animal
manure as an organic amendment. On the other hand, in Natural Farm for many years, noamendments have been incorporated, only making crop rotations.
Table 2, total nitrogen analysis measures N in all organic and inorganic forms. Nitrate
nitrogen (NO3-N) is important because it is the primary form of nitrogen available to trees and,
therefore, an indicator of nitrogen soil fertility. However, soil concentrations of NO 3-N depend
upon the biological activity and may fluctuate with changes in soil temperature, soil moisture, andⒸ ISERD

3

IJERD – International Journal of Environmental and Rural Development (2022) 13-1

other conditions. Nitrate is also easily leached with rainfall or irrigation. Most ammonia is
produced by bacteria in water and soil as a product of plant and animal waste decomposition. It isfound in relatively low nontoxic concentrations in soil and provides a source of nitrogen for plants.
Ammonium rarely accumulates in soil because bacteria will rapidly convert the ammonium that is
not taken up by plant roots into nitrates (nitrification).
Table 2 Chemicals properties in both agro ecosystem
Agroecosystem

TN (mg/kg)

TP (mg/kg)

NO3 (mg/kg)

NH3 (mg/kg)

Conventional

2343.33

267.140.15

6.86

Natural1563.33

370.000.13

5.57

No significance difference

Even the results are no significance difference, indicate that there was a higher level ofnitrogen in the Conventional Farm than in the Natural ones, but, in the total phosphorus, the casewas the opposite. P deficiency being common in weathered and tropical soils throughout the world,by rising costs of P fertilizer, and because efficiency of P use by plants from soil and fertilizer
sources is often poor despite containing a relatively large amount of total P that is sparingly
available to plants. Soil P exists predominantly in inorganic fractions that adsorb to mineral soil
surfaces or appear as poorly available precipitates and in organic forms that adsorb, incorporate
into biomass, or associate with soil organic matter (Richardson and Simpson, 2011). Although nosignificant difference was found, the value of TP in the Natural Farm is higher, which can indicate
related to the microbial biomass. Thus, it can also be related to the organic content, which was
higher in Conventional Farm. Other parameters need to be analyzed to be able to discuss themfurther.
Soil Biological Properties
Soil microorganisms affect attributes like aggregate formation and water movement. In addition to
fertility, soil microorganisms also play essential roles in the nutrient cycles that are fundamentally
important to life on the planet. The microorganisms that live in the soil and interact with the othercomponents, varies greatly depending upon conditions and it is highly complex and dynamic. The
most numerous microbes in soil are the bacteria, followed in decreasing numerical order by theactinomycetes, the fungi, soil algae and soil protozoa. Soil microorganisms are both components
and producers of soil organic carbon, a substance that locks carbon into the soil for long periods.
Abundant soil organic carbon improves soil fertility and water-retaining capacity.
Table 3 indicates that in the number of colonies formed in both fungi and bacteria there weremore in the Natural agroecosystem. In addition, soil microbial biomass also it was found more in
Natural agroecosystem than Conventional agroecosystem. Although with these results its richness
and abundance of species cannot be determined, it could be thought that microorganisms are
essential to maintain a healthy soil. This is because in the Natural Farm, for more than 20 years notype of amendments has been incorporated. It is that its maintenance of functioning in the soil
depends 100 percent on the internal activity that exists between microorganisms, plants andorganisms that live in the environment and soil. They could not be correlated with the chemical andphysical properties, but this can be thought to be related to the management that the Conventional
agroecosystem had. The Conventional agroecosystem, add manure, synthetic fertilization,
pesticides and fungicides. Pesticides and fungicides are known to affect the microbial population
rapidly, which may be the reason why there is less in the results obtained. In addition, anotherpractice that they carry out is weeding. In Natural Farm, they only weed in the first growth stage ofthe crop. On the other hand, in the Conventional Farm, they try to keep the soil without weeds. This
practice could be affecting microorganisms. According to Massenssini et al. (2014), the soil
microbial community structure might change depending on the crop species. Studies have shownthat the relationships of weeds and crops with the soil microbiota may be different. Weeds seem toⒸ ISERD

4

IJERD – International Journal of Environmental and Rural Development (2022) 13-1

show higher dependence on interactions with soil microorganisms. The structure of the soil
microbial community is responsive to competition between plants. In general, the competition
promotes changes in the soil microbial community structure, making it different from that foundwhen plants are grown in monoculture. Furthermore, weeds tend to have positive feedback
interactions with soil microorganisms, while crops may present neutral or negative feedback
interactions.
Table 3 Biological properties in both agro ecosystem
Agroecosystem

Number of colony forming units/g dry soil
Total culturable fungi
Total culturable bacteria

Total microbial
biomass (μg/g)

Conventional

6.92 x 101a3.15 x 103A

0.16α

Natural1.71 x 103b1.10 x 104B

0.22β

a, A, α significance difference p> 0.05

CONCLUSION
The difference between both farms is by using fertilizers and pesticides. The Natural Farm is not
adding any amendments for 20 years. Furthermore, Conventional Farm use more manure thanchemical fertilizers. Pesticides affect the survival of soil microorganisms more severely than otherpractices carried out by the farm. The diversity of plant roots helps to maintain soil microorganism
diversity and abundance.
Interdisciplinary soil research is necessary to better understand the biological properties of soil.
To maintain the sustainability of the production it is necessary to maintain the population of soil
microorganisms. Further research is needed to understand the correlation with chemical andphysical properties. As well as to begin to understand the function that each group of bacteria andfungi has, its relationship with other living organism in the soil.
The production system influences the diversity of arthropods and microorganisms in an
agricultural ecosystem. Therefore, if a system cannot conserve or increase agricultural landbiodiversity, it will be more unstable and poor health of the soil ecosystem.
ACKNOWLEDGEMENTS
I would like to express my gratitude to Nakamura farm as well as the people of the NPO Tagayasu,
who gave me the opportunity to take the samples from their farms.
REFERENCES
Anderson, J.M. and Ingram, J.S.I. 1993. Tropical soil biology and fertility. A Handbook of Methods (2nded.), CAB International, Wallingford, UK.
Bruggen, A.H.C. van and Grünwald, J.N. 1997. Tests for risk assessment of root infection by plant pathogens.
Methods for Assessing Soil Quality, 49, Soil Science Society of America, Madison, 293-310.
Cataldo, D.A., Haroon, M., Schrader, L.E. and Youngs, V.L. 1975. Rapid colorimetric determination of
nitrate in plant tissue by nitration of salicylic acid. Communications in Soil Science and Plant Analysis, 6,71-80.
Clark, M.S., Horwath, W.R., Sherman, C. and Scow, K.M. 1998. Changes in soil chemical properties
resulting from organic and low-input farming practices. Agronomy Journal, 90, 662-671.
Cruz, B.A., Barra, E.J, Castillo, F.R. del and Gutiérrez, C. 2004. La calidad del suelo y sus indicadores.
Ecosistemas, 13 (2), 90-97.
Doran, J.W., Sarrantonio, M. and Liebig, M.A. 1996. Soil health and sustainability. Advances in Agronomy,
56, 1-54.

Ⓒ ISERD

5

IJERD – International Journal of Environmental and Rural Development (2022) 13-1

Drinkwater, L.E., Letourneau, D.K., Workneh, F., Bruggen, A.H.C. van and Shennan, C. 1995. Fundamental
differences betwee conventional and organic tomato agroecosystems in California. EcologicalApplications, 5 (4), 1098-1112.
Foley, A.J., Defries, R., Asner, P.G., Barford, C., Bonan, G., Carpenter, R.S., Chapin, S.F., Coe, T.M., Daily,
C.G., Gibbs, K.H., Helkowski, H.J., Holloway, T., Howard, A.E., Kucharik, J.C., Monfreda, C., Patz,
A.J., Prentice, C.I., Ramankutty, N. and Snyder, K.P. 2005. Global consequences of land use. Science,
309, 570-574, Retrieved from DOI https://doi.org/10.1126/science.1111772
Hoben, J.H. and Somasegaran, P. 1982. Comparison of the pour, spread, and drop plate methods forenumeration of Rhizobium spp. in inoculants made from presterilized peat. Applied and Environmental
Microbiology, 44 (5), 1246-1247.
Kibblewhite, M.G., Jones, R.J.A., Montanarella, L., Baritz, R., Huber, S., Arrouays, D., Micheli, E. andStephens, M. (Eds.) 2008. Environmental assessment of soil for monitoring. Volume VI, Soil Monitoring
System for Europe, Luxembourg, JRC Scientific and Technical Reports, European Communities, 72.
Liu, B., Tu, C., Hu, S., Gumpe rtz, M. and Ristaino, J.B. 2007. Effect of organic, sustainable andconventional management strategies in grower fields on soil physical, chemical and biological factors
and the incidence of Southern blight. Applied Soil Ecology, 202-214.
Massenssini, M.A., Bonduki, H.V., Melo, C., Tótola, M., Ferreira, A.F. and Costa, D.M. 2014. Soil
microorganism and their role in the interactions between weeds and crops. Planta Daninha, 32 (4), 873884.
Mueller, L., Schindler, U., Mirschel, W., Shepherd, G.T., Ball, C.B., Helming, K., Rogasik, J., Eulenstein, F.
and Wiggering, H. 2010. Assessing the productivity function of soils, A review. Agronomy for
Sustainable Development, 30, 601-614, Retrieved from DOI https://doi.org/10.1051/agro/2009057
Nielsen, N.M. and Winding, A. 2002. Microorganisms as indicators of soil health. NERI Technical Report,
388, National Environmental Research Institute, 82.
Richardson, E.A. and Simpson, J.R. 2011. Soil microorganisms mediating phosphorus availability update on
microbial phosphorus. Plant Physiology, 156 (3), 989-996.
Sall, S., Masse, D., Ndour, Y. and Chotte, J. 2006. Does cropping modify the decomposition function and thediversity of the soil microbial community of tropical fallow soil? Applied Soil Ecology, 31 (3), 211-219.
Schlesinger, H.W. and Bernhardt, S.E. 2012. Biogeochemstry an analysis of global change (3rd ed.).
Academic Press, New York.
Searle, L.P. 1984. The berthelot or indophenol reaction and its use in the analytical chemistry of nitrogen, A
review. Analyst, 109, 549.
Setia, R., Verma, L.S. and Marschner, P. 2012. Measuring microbial biomass carbon by direct extraction,
Comparison with chloroform fumigation-extraction. European Journal of Soil Biology, 53, 103-106.
Shannon, D., Sen, A.M. and Johnson, D.B. 2006. A comparative study of the microbiology of soils managed
under organic and conventional regimes. Soil Use Management, 18, 274-283.
Sharma, K.S., Ramesh, A., Sharma, P.M., Joshi, P.O., Govaerts, B., Steenwerth, L.K. and Karlen, L.D. 2011.
Microbial community structure and diversity as indicators for evaluating soil quality. Biofuels,
Agroforestry and Conservation Agriculture, Springer, Dordrecht, 317-358.
Sigler, V.W. and Turco, F.R. 2002. The impact of chlorothalonil application on soil bacterial and fungal
populations as assessed by denaturing gradient gel electrophoresis. Applied Soil Ecology, 21, 107-118.
Tilman, D., Cassman, G.K., Matson, A.P., Naylor, R. and Polasky, S. 2002. Agricultural sustainability andintensive production practices. Nature 418, 671-677, Retrieved from DOI https://doi.org/10.1038/nature
01014
Tilman, D., Fargione, J., Wolff, B., D'antonio, C., Dobson, A., Howarth, R., Schindler, D., Schlesinger, H.W.,
Simberloff, D. and Swackhamer, D. 2001. Forecasting agriculturally driven global environmental change.
Science, 292, 281-284, Retrieved from DOI https://doi.org/10.1126/science.1057544
Trivedi, P., Delgado-Baquerizo, M., Anderson, C.I. and Singh, K.B. 2016. Response of soil properties andmicrobial communities to agriculture: Implications for primary productivity and soil health indicators.
Frontiers in Plant Science, Retrieved from DOI https://doi.org/10.3389/fpls.2016.00990
Vitousek, M.P., Naylor, R., Crews, T., David, B.M., Drinkwater, E.L., Holland, E., Johnes, J.P.,
Katzenberger, J., Martinelli, A.L., Matson, A.P., Nziguheba, G., Oojima, D., Palm, A.C., Robertson, P.G.,
Sanchez, A.P., Townsend, R.A. and Zhang, S.F. 2009. Nutrient imbalances in agricultural development.
Science 324, 1519-1520, Retrieved from DOI https://doi.org/10.1126/science.1170261Ⓒ ISERD

6