Tomato (Solanum lycopersicum L.) is one of the most important vegetables globally and is cultivated in temperate to tropical regions. Recent world production of fresh tomato fruits was 165 million tons with a value of about 60 billion US dollars in 2013  .
Tomato fruits contain protein, fat, carbohydrate, minerals (such as calcium, phosphorus, and iron), carotene, thiamine, nicotinic acid, riboflavin, and ascorbic acid  . Tomato is also an important source for vitamins A and C, carotenoids, and lycopene  . Lycopene helps to reduce cancer risks  and protects the skin from ultraviolet radiation  . Carotenoids are useful against breast cancer and prostate cancer  . Tomato is ranked among the top five vegetables in terms of antioxidant activity  .
Tomatoes are cultivated mainly by conventional methods using chemical fertilizers and agrochemicals. A recent report showed that only 1% of agricultural fields in the world are cultivated under organic farming systems  . Although the yield is relatively stable in conventional farming systems, excessive use of chemical fertilizers and agrochemicals can cause severe environmental, socio-economic, and human health problems. As a result, consumer awareness towards organic foods has been increasing recently.
Organic cultivation methods cause relatively lower environmental damage if compared with conventional farming and the organic crop product is considered tasty and healthy  . Studies on tomato have also shown that antioxidants, flavonoids, sugar, and vitamin C are generally higher in organically grown fruits than conventionally grown fruits    . However, the yield is more unstable and/or lower in organic farming systems than conventional systems     . Therefore, an alternative organic agricultural system is required to ensure high yield and quality of agricultural products. In addition, the cultivation method must be efficient, reliable, reproducible, and simple.
Soil microorganisms play several beneficial roles such as decomposing organic materials, releasing nutrients to plants, and bioremediation of pesticide polluted soils    . Therefore, soil microorganisms are considered key players in maintaining soil fertility. A large and active microorganism community is needed for efficient nutrient cycling and steady supply of nutrients to the plants. Improving soil environment by controlling the organic matter level and nutrient ratio in the soil is important for soil microorganisms   .
In our previous study, we developed a soil fertility index, SOFIX, for the evaluation of soil fertility  . Analysis of the SOFIX data from several agricultural fields clearly showed that the number and activities of microorganisms can be significantly enhanced by controlling total carbon (TC) and total nitrogen (TN) contents, and carbon-to-nitrogen ratios (C/N ratios) at ≥25,000 mg/kg, ≥2500 mg/kg, and 10 - 25, respectively. However, the relationship between microbial activities and plant growth remains unknown. The objective of this study was to determine suitable soil conditions for improving the yield and quality of tomato under an organic farming system by enhancing the number and activities of soil microorganisms.
2. Materials and Methods
2.1. The Study Site
This study was carried out in agricultural fields located in Moriyama, Shiga prefecture, Japan (35˚5'33.85''N, 135˚58'28.57''E). The experiments were performed in three consecutive years from 2013 to 2015 to confirm the reproducibility under seasonal fluctuation. Moriyama has a humid temperate climate, where July is the warmest month and January is the coolest. Weather data of the nearest meteorological station (Hikone, Shiga, Japan) from the experimental field during the tomato growth period is shown in Figure 1. The initial physico-chemical properties of soil in the experimental field are shown in Table 1.
2.2. Cultivation of Tomato in the Fields under Chemical and Organic Farming Systems
In our previous study, we found that microorganisms and nutrient cycling activities in the soil are highly enhanced at TC ≥ 25,000 mg/kg and C/N ratios from 10 to 25 in soil  . In this study, the soil conditions suitable for enhancing the activity of microorganisms were examined for tomato cultivation. Seven organic and two chemical experimental conditions were prepared by using 3 field compartments in 2013 to 2015 (Table 2). Organic experimental fields were prepared with TC from 27,500 to 58,000 mg/kg, TN from 1000 to 4300 mg/kg, and C/N ratio from 13 to 30 (Fields A and B in 2013, Fields C and D in 2014, and Fields G, H, and I in 2015). To provide different TC, TN, and C/N ratio in the organic fields, cow manure, chicken manure, and soybean meal were used. The nutrient contents in the organic fertilizers are shown in Table 3.
In 2013 and 2014, a control experiment was simultaneously carried out using the chemical fertilization plan recommended for tomato by Shiga prefecture, Japan (200:180:250 kg N:P2O5:K2O per ha) (Field E in 2013 and Field F in 2014). A half dose of N and full doses of P and K were applied on the day of transplanting and the remaining half dose of N was top dressed after one month. Following chemical fertilizers were used: ammonium sulfate (21% N), single super phosphate (17.5% P2O5), and potassium sulfate (50% K2O). The differences in TC, TN, and C/N ratio between the two chemical fields was due to the seasonal effect.
Each field was 24 m2 (6 m × 4 m) and had 6 plant rows with 60 plants (10 plants per row). Fields were 1 m apart to prevent interaction between the treatments. One-month old seedlings of tomato (cv. Momotaro) were transplanted in May. The seedlings were purchased from TAKII & Co. Ltd., Kyoto, Japan. No pesticides were used in both chemical and organic fields. Black plastic mulch was used to control weeds and conserve the soil moisture.
2.3. Harvesting and Yield Measurement
Tomatoes were harvested once the fruits turned light red. In all years, harvesting began at the end of June and lasted until the beginning of August. The fresh
Figure 3. Microbiological properties of soil in three experimental fields of 2015. Bacterial biomass (×108 cells/g) (a), N circulation activity (point) (b), and P circulation activity (point) (c) of Fields G, H, and I are shown. Bars filled with solid gray ( ) and with horizontal lines ( ) indicate the values at one week and one month after organic fertilizer application, respectively. Values with same letter in an observation period (lowercase for one week and uppercase for one month) do not significantly differ (p < 0.05, Tukey’s test). Asterisk (*) indicates significant difference between two observation periods in the same field (p < 0.05, t-test).
Recent reports show that only 1% of agricultural fields in the world are cultivated under an organic farming system  . This is typically because the yields under organic farming are unstable or because a successful organic cultivation requires several years of experience     . In the current study, we investigated the suitable soil conditions for tomato cultivation under an organic farming system.
Soil microorganisms play several beneficial roles in cultivated land such as decomposition of organic materials, nitrification, and P mineralization. Therefore, microorganisms are important parameters for soil fertility. In our previous study, we showed that TC, TN, and C/N ratio are closely related to the bacterial biomass and nutrient cycling activities in soil   Enhancement of microorganisms and their activities are more important under organic systems than under conventional systems, because microorganisms help to supply nutrients to plants by decomposing the added organic materials. Properly controlled TC, TN
Table 6. Relationship between soil properties and tomato yield in the experimental fields of 2015. Soil properties analyzed after one week of organic fertilizer application are shown.
Means followed by same letter do not significantly differ (p < 0.05, Tukey’s test). Value in parenthesis followed by ± is standard deviation (n = 3).
and C/N ratios result in a high level bacterial biomass and enhanced N and P circulation activities.
Generally, the yields under organic systems are either unstable or lower compared to those in the conventional systems     . Nitrogen availability is the most important in limiting yield of tomato under organic farming systems  . A previous study demonstrated that high level of tomato yields under organic farming systems than that under conventional systems was associated to the high nitrogen mineralization rate and higher microbial diversity in soils under organic systems  . In this study, we found that properly controlled TC, TN, and C/N ratio and high levels of N circulation activity and P circulation activity resulted into higher tomato yield in the organic fields compared to the chemically fertilized fields. Therefore, enhancement of the number and activities of microorganisms by maintenance of the soil condition (especially TC, TN, and C/N ratio) seem necessary for achieving high yield of tomato from organic farming systems.
Organic crop products are typically considered to be of high quality   . In general, quality and quantity are oppositely related in crop products obtained under conventional farming systems  . In this study, lycopene, glutamic acid, and acid contents in tomato fruit seemed to be enhanced in the high-yielding organic fields. Lycopene is a major antioxidant component  , and glutamic acid, sugar, and acidity are the major taste indicators in tomato  . Enhancement of sugar and organic acid contents in organically produced tomatoes have also been reported previously  . Therefore, appropriate soil conditions in organic systems not only enhance the yield of tomato but also can improve the quality.
A suitable organic soil condition of tomato would be also effective for other vegetable fruits. In this point, the amount of TN and the balance of C/N in soil are most important, because higher C/N ratio inhibits reproduction and enhances vegetative growth (Table 4). However, crop production could be increased only after the organic soil enhances activities of microorganisms maintaining appropriate nutrients for plants.
In this experiment, a suitable soil condition for increasing the yield of tomatoes in an organic farming system was determined as TC of 30,000 - 36,000 mg/kg, TN of 1600 - 1900 mg/kg, and a C/N ratio of 18 - 21. The quality of tomato also seems to be changed by soil environmental condition.
We would like to acknowledge the support provided by Dr. Chikayoshi Kitamura (Kinki Agri-Hightech, Kyoto, Japan), Mr. Hitoshi Kawabata (JA Ominchi, Moriyama, Shiga, Japan), and Mr. Kiyokazu Morita (Yasu, Shiga, Japan) during the field experiment. The authors also acknowledge the CCP program.
Conflict of Interest
The authors declare no conflicts of interest in this paper.
 Food and Agricultural Organization of the United Nations (2014) FAOSTAT: Crop Data, 2014.
 Sánchez-Moreno, C., Plaza, L., de Ancos, B. and Cano, M.P. (2006) Nutritional Characterisation of Commercial Traditional Pasteurised Tomato Juices: Carotenoids, Vitamin C and Radical-Scavenging Capacity. Food Chemistry, 98, 749-756.
 Giovannucci, E., Ascherio, A., Rimm, E.B., Stampfer, M.J., Colditz, G.A. and Willett, W.C. (1995) Intake of Carotenoids and Retino in Relation to Risk of Prostate Cancer. Journal of the National Cancer Institute, 87, 1767-1776.
 Easdown, W. and Kalb, T. (2004) Antioxidant Capacities and Daily Antioxidant Intake from Vegetables Consumed in Taiwan. AVRDC Progress Report, Asian Vegetable Research and Development Center, Shanhua.
 FiBL and IFOAM (2017) The World of Organic Agriculture Statistics and Emerging Trends, 2017. Research Institute of Organic Agriculture FiBL and IFOAM-Organics International.
 Woese, K., Lange, D., Boess, C. and Bogl, K.W. (1997) A Comparison of Organically and Conventionally Grown Foods—Results of a Review of the Relevant Literature. Journal of the Science of Food and Agriculture, 74, 281-293.
 Chassy, A.W., Bui, L., Renaud, E.N., Van Horn, M. and Mitchell, A.E. (2006) Three-Year Comparison of the Content of Antioxidant Microconstituents and Several Quality Characteristics in Organic and Conventionally Managed Tomatoes and Bell Peppers. Journal of Agricultural and Food Chemistry, 54, 8244-8252.
 Mitchell, A.E., Hong, Y.J., Koh, E., Barrett, D.M., Bryant, D.E., Denison, R.F. and Kaffka, S. (2007) Ten-Year Comparison of the Influence of Organic and Conventional Crop Management Practices on the Content of Flavonoids in Tomatoes. Journal of Agricultural and Food Chemistry, 55, 6154-6159.
 Vallverdú-Queralt, A., Jáuregui, O., Medina-Remón, A. and Lamuela-Raventos, R.M. (2012) Evaluation of a Method to Characterize the Phenolic Profile of Organic and Conventional Tomatoes. Journal of Agricultural and Food Chemistry, 60, 3373-3380.
 Mäder, P., Fliessbach, A., Dubois, D., Gunst, L., Fried, P. and Niggli, U. (2002) Soil Fertility and Biodiversity in Organic Farming. Science, 296, 1694-1697.
 Singh, J.S., Pandey, V.C. and Singh, D.P. (2011) Efficient Soil Microorganisms: A New Dimension for Sustainable Agriculture and Environmental Development. Agriculture, Ecosystems and Environment, 140, 339-353.
 Chen, M., Xu, P., Zeng, G., Yang, C., Huang, D. and Zhang, J. (2015) Bioremediation of Soils Contaminated with Polycyclic Aromatic Hydrocarbons, Petroleum, Pesticides, Chlorophenols and Heavy Metals by Composting: Applications, Microbes and Future Research Needs. Biotechnology Advances, 33, 745-755.
 Adhikari, D., Perwira, I.Y., Araki, K.S. and Kubo, M. (2016) Stimulation of Soil Microorganisms in Pesticide-Contaminated Soil Using Organic Materials. AIMS Bioengineering, 3, 379-388.
 Adhikari, D., Kai, T., Mukai, M., Araki, K.S. and Kubo, M. (2014) A New Proposal for a Soil Fertility Index (SOFIX) for Organic Agriculture and Development of a SOFIX Database for Agricultural Fields. Current Topics in Biotechnology, 8, 81-91.
 Aoshima, H., Kimura, A., Shibutani, A., Okada, C., Matsumiya, Y. and Kubo, M. (2006) Evaluation of Soil Bacterial Biomass Using Environmental DNA Extracted by Slow-Stirring Method. Applied Microbiology and Biotechnology, 71, 875-880.
 Horii, S., Matsuno, T., Tagomori, J., Mukai, M., Adhikari, D. and Kobo, M. (2013) Isolation and Identification of Phytate-Degrading Bacteria and Their Contribution to Phytate Mineralization in Soil. The Journal of General and Applied Microbiology, 59, 353-360.
 Fish, W.W., Perkins-Veazie, P. and Collins, J.K. (2002) A Quantitative Assay for Lycopene That Utilizes Reduced Volumes of Organic Solvents. Journal of Food Composition and Analysis, 15, 309-317.
 Takehana, H., Shibuya, T., Nakagawa, H. and Ogura, N. (1977) Purification and Some Properties of Endo-Polygalacturonase from Tomato Pericarp. Technical Bulletin of Faculty of Horticulture No. 25, Chiba University, Chiba. (In Japanese)
 Tucker, G.A., Robertson, N.G. and Grierson, D. (1981) The Conversion of Tomato-Fruit Polygalacturonase Isoenzyme 2 into Isoenzyme 1 in Vitro. European Journal of Biochemistry, 115, 87-90.
 Bradley, D.B. (1960) The Separation of Organic and Inorganic Acid Anions in Filtered Tomato Puree by Partition Chromatography. Journal of Agricultural and Food Chemistry, 8, 232-234.
 Garner, D., Crisosto, C.H., Wiley, P. and Crisosto, G.M. (2003) Measurement of pH and Titratable Acidity.
 Araki, K.S., Perwira, I.Y., Adhikari, D. and Kubo, M. (2016) Comparison of Soil Properties between Upland and Paddy Fields Based on the Soil Fertility Index (SOFIX). Current Trends in Microbiology, 10, 85-94.
 Clark, M.S., Horwath, W.R., Shennan, C., Scow, K.M., Lantni, W.T. and Ferris, H. (1999) Nitrogen, Weeds and Water as Yield-Limiting Factors in Conventional, Low-Input, and Organic Tomato Systems. Agriculture, Ecosystems and Environment, 73, 257-270.
 Drinkwater, L.E., Letourneau, D.K., Workneh, F.A.C.H., Van Bruggen, A.H.C. and Shennan, C. (1995) Fundamental Differences between Conventional and Organic Tomato Agroecosystems in California. Ecological Applications, 5, 1098-1112.
 Worthington, V. (2001) Nutritional Quality of Organic versus Conventional Fruits, Vegetables, and Grains. Journal of Alternative and Complementary Medicine, 7, 161-173.
 Caliman, F.R.B., da Silva, D.J.H., Stringheta, P.C., Fontes, P.C.R., Moreira, G.R. and Mattedi, A.P. (2008) Relation between Plant Yield and Fruit Quality Characteristics of Tomato. Bioscience Journal, 24, 46-52.
 Oruna-Concha, M.J., Methven, L., Blumenthal, H., Young, C. and Mottram, D.S. (2007) Differences in Glutamic Acid and 5’-Ribonucleotide Contents between Flesh and Pulp of Tomatoes and the Relationship with Umami Taste. Journal of Agricultural and Food Chemistry, 55, 5776-5780.
 Xu, H.L., Wang, R. and Mridha, M.A.U. (2001) Effects of Organic Fertilizers and a Microbial Inoculant on Leaf Photosynthesis and Fruit Yield and Quality of Tomato Plants. Journal of Crop Production, 3, 173-182.