Research Proposal
By
Rahayu Widyastuti
Bogor, Indonesia
Supervisors
Prof. Paul L.G. Vlek
Prof. Matthias Schaefer
Dr. Christopher Martius

I.
Introduction 1
Background 1
Objectives 2
Hypothesis 2
II.
Methodology 3
1. The screening of soil fauna in different ecosystems of the region 3
b. Study of organic matter decomposition 5
c. Study of nitrogen turn-over 5
III.
Time table 6
2. Study of the important soil fauna in rainfed paddy field ecosystem 3
a. Study of the two important macrofauna dynamics 4
Preparation
Experiment
6
7
IV.
References
Appendix
8
1

I. INTRODUCTION
Background
Production of staple food crops, such as rice and maize, to compensate the growth of the population has become a major challenge for many developing countries, like in
Indonesia. To cope with the encountered problems, either crop production or management of land has to be improved. Management of land by introducing of organic inputs, such as pruning and crop residues, and utilization of new agricultural resources has to be considered.
Productive irrigated areas in Indonesia are estimated to decrease by 30,000 -
40,000 ha annually due to industrial development and settlement. Consequently, it becomes necessary to utilize other agricultural resources to increase crop production.
Rainfed lowland rice ecosystems have great potential to be used in more productive way
(Syamsiah et al . 1994). Despite the increase in area planted of rainfed lowland rice, the yields remain low due to the low soil fertility and the lack of infrastructure and water resources. Improvement of rainfed lowland management is therefore needed in order to increase yields.
Rainfed paddy field ecosystem is found widespread in Indonesia and it cover about 2.6 million ha, distributed in Central Java, East Java, South Sulawesi, Southeast
Sulawesi, Nusatenggara, and Maluku Archipelago (Syamsiah et al . 1994). This system is not irrigated and therefore depends on rainfall. The water is impounded by bunds and water-depth may exceed 50 cm. No additional water is supplemented. Rainfed paddy field system is characterized by lack of water control, with floods and drought being potential problems. This system consisted of three different planting seasons per year, i.e. rice planting in the beginning of rainy season, upland crop planting in the end of rainy season and after the harvest of crop the field is left fallow during the dry season.
Therefore, the rainfed paddy field system undergoes two different systems, i.e. flooded and dry system. Consequently, the population and diversity of soil fauna, organic matter, and nitrogen turn-over are different in those systems.
Little is known about the influence of the dynamics of soil fauna on organic matter decomposition in rainfed paddy field system. Therefore, the study of environmental changes is important to optimalize organic matter decomposition and nitrogen turn-over of the system. According to Watanabe and Roger (1985) the major component of soil fauna in flooded water is dominated by zooplankton and aquatic invertebrates, including Tubificidae (Oligochaetes). Tubificidae are key component of the soil fauna in wetland ricefields. Their major role regarding soil fertility is the translocation of components of photosynthetic aquatic biomass from the surface to the deeper soil layer. The breakdown products of photosynthetic biomass contribute to the replenishment of soil microbial biomass and the provision of nutrients to the rice plant
(Lavelle et al . 1997).
In upland subsystem (terrestrial phase), the soil fauna is more diverse, e.g. group of earthworms, termites, millipedes, collembola, acari, etc. (Tian 1992; Bardgentt and
Cook 1998). Earthworms and termites, however, are the dominance organisms among the soil fauna that have function as litter decomposers in the terrestrial ecosystems
(Lavelle et al . 1997).
1

Termites are found in open savannas, tropical and subtropical area with arid to semi arid soils (Eggleton 1996). In Amazonian forest, floodplain-inhabiting termites play important role on wood decay and its decay is enhanced by intermittent aquatic and terrestrial environment in varzea floodplain forest (Martius 1997). The species richness and abundance of soil invertebrate communities was severely affected due to land management practices, such as ploughing and harrrowing the soil in the agricultural system during crop rotation (Lavelle et al . 1997), ploughing back of the organic matter, such as crop residue, however, encouraged the increase of earthworm species (Bhadauria et al. 1997).
The abundance and diversity of soil fauna in upland subsystem may support organic matter decomposition, intensively. The upland subsystem is therefore expected to be capable of influencing the productivity of entire rainfed paddy field ecosystem.
Objectives
The study will cover the screening of soil fauna in different ecosystems as natural ecosystems of region in which is intended to obtain a spectrum of the soil fauna and assess the potential group diversity in natural ecosystems as a standard against which to compare the agricultural site. The two important soil fauna groups will then be studied indepth in rainfed paddy field ecosystem.
The specific objectives of this research are summarized as follows:
1. To study the diversity and density of two important soil fauna in the three phases of a rainfed paddy field ecosystem: fallow, paddy field and upland crop subsystem.
2. To study the role of the two important soil fauna on organic matter decomposition and nitrogen turn-over in the subsystem as above.
3. To study the role of crops (legumes and cassava) planted in the bunds, on the diversity and density of two important soil fauna in the fields (fallow-paddy fieldupland crop subsystems) as well as in their bunds.
4. To study the influence of different bund distancing on the population of the two important fauna in the fields.
Hypothesis
1. The diversity and density of soil fauna varies in subsystems of fallow-paddy field- upland crop.
2. The diversity and density of soil fauna in crop-planted bunds is higher than that in the bunds without plant.
3. The increase of soil fauna population in the terrestrial phase (upland crop subsystem) after the periods of flooded is faster in plots with crop-planted bunds than that in plots with no planted bunds.
4. The increase of soil fauna population in the terrestrial phase after the periods of flooded is faster in plots with short bund distance (3 m) than that in plots with long bund distance (6 m).
5. The organic matter decomposition and nitrogen turn-over predominantly happen in the terrestrial phase of the rice paddy field ecosystem.
2

II. METHODOLOGY
The study area will be located in the district of Lamongan in East Java, Indonesia.
Different natural ecosystems are found in this area, namely dipterocarp (teak or Tektona grandis ) forest, bamboo forest, home garden and rainfed paddy field. The study will cover two steps, i.e. first, the screening of soil fauna in different ecosystems of the region, and second, the further study of the two important macrofauna groups of the screening in rainfed paddy field ecosystem.
1. The screening of soil fauna in different ecosystems of the region
The assessment of soil fauna in the different ecosystems of the study area is aimed to obtain a general idea of soil fauna in the natural ecosystems. The soil fauna will be collected by using a soil corer of 21 cm diameter from 10 to 20 randomized points of the ecosystems of teak forest, bamboo forest, home garden and rainfed paddy field, respectively. Population of soil fauna in each ecosystem are then extracted in Berlese apparatus (heat extraction) (Beck et al.
1998). Chemical extraction and hand sorting methods will be used for larger animals, especially earthworms. Depending on water content of the soil, an enclosed sampling area (0.5 m
2
) will be poured by 5-10 L of a 0.2-
0.4 % formalin solution in repeated intervals of 10 min. The sampling will be finished at least 30 min. after the application (Meyer 1996). The big earthworms that expelled from the soil will be collected by hand and small ones by using a forceps. The collected earthworms will be fixed immediately in 70% ethanol using the labeled plastic-container
(Meller and Römbke unpublished).
The two dominant soil fauna groups of those ecosystems will be studied further in rainfed paddy field ecosystem. Earthworms and termites are expected to be the most abundant groups in the screening. According to Schulte 1996, in dipterocarps forest ecosystems in Malaysia, the higher termite family ( Termitidae ) can form more than 70% of the total litter invertebrate biomass and occur at densities of up to 4.000 individuals or
10 g m
-2
. In rain forests of Amazonia, termites and earthworms are the two decomposer groups that have the highest biomass (Martius unpubl. result).
2. Study of the important soil fauna in rainfed paddy field ecosystem
The research will be carried out in the rainfed paddy field ecosystem. The most typical cropping patterns in relation to the monthly distribution of rainfall in this area are rice planted in flooded fields at the beginning of rainy season, upland crop (maize, soybean, cassava, etc.) on the dry fields at the end of rainy season, and a fallow during the subsequent dry season. In a normal year, a wet season runs from October or
November and continues into April, whereas the dry season covers the period of May to
August or September.
The research will be conducted starting in the fallow subsystem during dry season, followed by the next planting season or paddy field subsystem in the rainy season, and the last phase is upland crop (maize) planted at the end of rainy season.
Experimental plots of 16x24m each will be used in each subsystem and all sampling will be done simultaneously on three treatment plots of crop-planted bunds and on two treatment plots of bund distancing (see Appendix).
3

The three treatment plots of crop-planted bunds are as follows:
1). Plot without plants on the bunds (control),
2). Plot with legumes on the bunds, and
3). Plot with cassava on the bunds, while the two treatment plots of bund distancing are :
1). Plot with bund distance of 3 m, and
2). Plot with bund distance of 6 m.
All of the experimental plots should be located in a homogenous area. Such an area is described by its soil texture and usually exhibits one soil type and uniform habitat characteristics (Öhlinger 1996). a). Study of two important macrofauna (earthworms and termites) dynamics
The diversity and density of two important macrofauna groups (earthworms and termites) will be studied during the whole study period. To evaluate the effect of cropplanted bunds on macrofauna diversity and density, the macrofauna will be collected both in the fields and in the bunds for the treatment plots of crop-planted bunds (no plants, cassava and legumes), while to asses the effect of bund distancing on fauna in the fields, the macrofauna will be collected in the fields for the treatment plots of bund distancing (3 and 6 m). The soil macrofauna will be sampled by using a soil corer of 21 cm diameter
(Meyer 1996) from 8 randomized points of the fields and the bunds, respectively, per plot at 30, 60 and 90 days after planting. Population of soil macrofauna in each season are then extracted in a Berlese apparatus (heat extraction) (Beck et al . 1998). Handsorting methods will also be done especially for larger animals (Anderson and Ingram 1989). The extracted animals will then be identified by stereomicroscope in laboratory.
The number of individuals (abundance) of extracted animal will be calculated as followed (Meyer 1996):
IS

= I.cm
-3 *)
V
IS mean number of individuals per sample
V volume of the corer (cm
3
)
I number of individuals
*) The number of individuals per volume can be converted to numbers of individuals per area (I.m
-2 or I.ha -1 ) from the radius of the corer (area of the corer = r 2 .

).
The diversity index will be calculated as Simpson’s Index of D diversity
(Bhadauria et al . 1997):
l-S ni(ni – 1)
I – D =

{ 
i=1 N(N – 1)
} ni = number of individuals of species i in the sample
N = total number of individuals in the sample
S = number of species in the sample
I - D = Simpson’s index of diversity
4

b). Study of organic matter decomposition
The organic matter decomposition will be studied by using polyethylene litter bags of size 25 x 25 cm with the following mesh sizes which is suitable for tropical regions:
0.02, 0.25 and 10 mm (Beck et al . 1998). Mesh size of 10 mm will allow access to all meso- and macrofauna; mesh size of 0.25 mm will exclude the soil macrofauna and mesh size of 0.02 mm will exclude meso- and macrofauna, respectively. Five to ten grams of air-dried litter will be filled into each mesh size of litter bags. The two sides of bags are then sewn up with nylon thread. The fine and medium bags are marked with individual numbers using a water-proof pen, while the coarse bags are marked using a metal plates with numbers. The bags will then be exposed on the top of soil surface and they should have close contact with the soil surface (no air spaces due to plant cover) (Schinner
1996). The litter decomposition rate will be calculated from the loss of weight after exposition, using the formula for the negative exponential regression.
Fallow and upland crop subsystems . In the subsystems of fallow and upland crop, rice straw will be used as site-specific litter or standard litter, while legume prunings will be used for comparison, because legumes are present in the location under study. The decomposition rate of rice straw and legumes pruning will be studied in the treatment plots of crop-planted bunds (no plants, cassava and legumes) and in the treatment plots of bund distancing (3 and 6 m). Five to ten grams of air-dried rice straw will be filled into litter bags with mesh sizes of 0.02, 0.25 and 10 mm, respectively. For comparison, 5 to
10 grams air-dried legume prunings will similarly be filled into different litter bags with each mesh sizes as above. Twenty four litter bags of each mesh size will then randomly be distributed on the soil surface in each plot as mentioned above. The remaining dry matter in retrieved bags (24 bags) in each plot will be collected and evaluated at 30, 60 and 90 days after exposure to the field.
Paddy field subsystem . Rice straw will also be used as standard litter in paddy field subsystem. As comparison, azolla will be used as litter source, because farmers in this area are used to using azolla as source of organic matter. Rice straw and azolla as source of litter and their decomposition rate will be studied in the treatment plots of cropplanted bunds (no plants, cassava and legumes) and in the treatment plots of bund distancing (3 and 6 m). The same procedure with subsystems above to measure decomposition rate will also be done in this subsystem. c). Study of nitrogen turn-over
Nitrogen turn-over will be evaluated on all treatment plots of crop-planted bunds
(no plants, cassava and legumes) and bund distancing (3 and 6 m) in fallow, paddy field and upland crop subsystems, respectively. Soil samples will be collected from 4 randomized points per plot at 30, 60 and 90 days. Nitrogen mineralization will be studied by using undisturbed soil columns confined within PVC tubes, the accumulation of ammonium and nitrate will be measured after 3-4 weeks. An ion-exchange resin buried at the bottom of intact soil cores will be used to account for nitrate leaching. Nmineralization or immobilization in field soils is calculated as the sum of changes in
NH
4
+ -N (net ammonification) and NO
3
-N (net nitrification) ( Kandeler, 1996).
The potential of nitrification and denitrification will be studied by measuring the microbial activity involved in that processes by using most probable number (MPN) methods (Trolldenier, 1996).
5

III. TIME TABLE
Activities
Preparation
Days ( May 2000)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
1.Selection of location x
2.Soil fauna population
*soil sampling
- soil corer
- others
*Berlese-extractor
-basic frame
-funnels
-bottles
-sieves
-others
3.Litter decomposition
*Preparation of litters :
- to collect litters
- air dried
-ash-free dry weight
*Preparation of bags :
- materials
-sewing
* weighing of litters
* preparation of others
4. Study of N-turn-over
* preparation of materials
and equipment x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x
6

EXPERIMENT
Activities 2000
June July Aug Sept Oct Nov Dec Jan
Fallow Paddy field
2001
Feb Mar Apr May Jun Jul
Upland crop
1. Screening of soil fauna
2. Study of soil
fauna dynamic
-soil sampling
-heat extraction
-identification
3. Study of litter
decomposition
-exposure bags to the
field
-retrieved bags
-weighing
4. Study of N turn-over
-soil sampling
-analysis of N-
mineralization xxxx xxxx xxxx xxxx xxxx xxxx xxxx xxxx xxxx xxxx xxxx xxxx xxxx x
x x
x x
x x
x x
x x
x x
x x
x x
x
x x x x x x x x x xxxx xxxx xxxx xxxx xxxx xxxx xxxx xxxx xxxx xxxx xxxxx xxxx x x x
x
xx
x
xx
x
xx
x
xx
x x
xx xx
x
xx
x
xx
x
xx xxxx xxxx xxxx xxxx xxxx xxxx xxxx xxxx xxxx xxxx xxxx xxxx
x x x x x x x x x
xx xx xx xx xx xx xx xx xx
-analysis of
nitrification
and denitrification
5. Data analysis
xx xx xx xx xx xx xx xx xx xxx
7

IV. REFERENCES
Anderson, J.M. and J.S. Ingram. 1989. Tropical Soil Biology and Fertility, a handbook of methods. Commonwealth Agricultural Bureau, Oxon. 171 pp
Bardgett, D. Richard and R. Cook. 1998. Functional aspects of soil animal diversity in agricultural grasslands. Appl. Soil Ecol. 10(3): 263-267
Bhadauria, T., P.S. Ramakrishnan, K.N. Srivastava. 1997. Population dynamics of earthworms during crop rotation under rainfed agriculture in central Himalayas,
India. Appl. Soil Ecol. 6(1997): 205-215
Beck, L., H. Höfer, C. Martius, M.B. Garcia, E. Franklin and J. Römbke. 1998. Soil fauna and litter decomposition in primary and secondary forests and a polyculture system in Amazonia- study design and methodology. Proceeding of the Third
SHIFT-Workshop, Manaus, March 1998. BMBF, Bonn.
Eggleton, P. 1996. Termite Diversity and its Role in Tropical Ecosystems. In Witt, B.
Using Soil Fauna to Improve Soil Health. http://www.hort.agri.umn.edu/h5015/97papers/witt.html
Kandeler, E. 1996. In situ studies of N-Mineralization. In : Schinner, F, R. Ohlinger, E.
Kandeler, R. Margesin (Eds.). 1996. Methods in Soil Biology. Springer-Verlag,
Berlin, Heidelberg, NewYork. p. 136-143
Lavelle, P., D. Bignell, M. Lepage, V. Wolters, P. Roger, P. Ineson, O.W. Heal and S.
Dhillion. 1997. Soil function in a changing world: the role of invertebrate ecosystem engineers. Eur. J. Soil Biol. 33(4), 159-193.
Martius, C. 1997. Decomposition of Wood. In : Junk (ed.). 1997. The Central Amazon floodplain. Springer-Verlag, Berlin, Heidelberg. p. 267-276
Meyer, E. 1996. Endogeic Macrofauna. In : Schinner, F, R. Ohlinger, E. Kandeler, R.
Margesin (Eds.). 1996. Methods in Soil Biology. Springer-Verlag, Berlin,
Heidelberg, NewYork. p. 346-354
Öhlinger, R. 1996. Soil Sampling and Sample Preparation.
In : Schinner, F, R. Ohlinger,
E. Kandeler, R. Margesin (Eds.). 1996. Methods in Soil Biology. Springer-Verlag,
Berlin, Heidelberg, NewYork. p. 7-11
Schinner, F. 1996. In Situ Studies of Litter Decomposition. In : Schinner, F, R. Ohlinger,
E. Kandeler, R. Margesin (Eds.). 1996. Methods in Soil Biology. Springer-Verlag,
Berlin, Heidelberg, NewYork. p. 114-116
8

Schulte, A. 1996. Dipterocarps forest ecosystem theory based on matter balance and biodiversity. In : Schulte, A and Dieter Schöne (Eds.). 1996. Dipterocarp Forest
Ecosystems. World Scientific, Singapore. p. 3-28
Syamsiah, I., Suprapto, A.M. Fagi, and S.I. Bhuiyan. 1994. Collecting and conserving rainwater to alleviate drought in rainfed ricelands of Indonesia. In : Bhuiyan, S.I.
(Ed.). 1994. On-Farm Reservoir Systems for Rainfed Ricelands. International Rice
Research Institute, Los Banos, Philippines.
Tian, G. Long. 1992. Biological effects of plant residues with contrasting chemical compositions on plant and soil under humid tropical conditions. Ph.D. thesis,
Wageningen Agricultural University, The Netherlands.
Trolldenier, G. 1996. Denitrifiers by MPN Methods. In : Schinner, F, R. Ohlinger,
E. Kandeler, R. Margesin (Eds.). 1996. Methods in Soil Biology. Springer- Verlag,
Berlin, Heidelberg, NewYork. p. 28-31
Trolldenier, G. 1996. Nitrifiers by MPN Methods. In : Schinner, F, R. Ohlinger,
E. Kandeler, R. Margesin (Eds.). 1996. Methods in Soil Biology. Springer-Verlag,
Berlin, Heidelberg, NewYork. p. 32-35
Watanabe, I. And P.A. Roger. 1985. Ecology of flooded rice fields. Proceedings of
Wetland Soils : Characterization, classification and utilization. International Rice
Research Institute, Los Banos, Philippines, 26 March to 5 April 1984
9

Appendix
I. Experimental plots in fallow, paddy field and upland crop subsystems
1. Bund Distance of 3 m a). Bunds without plants (control)
3m
4m b). Bunds with cassava
3m
4m c). Bunds with legumes
3m
4m
10

2. Bund Distance of 6 m a). Bunds without plants (control)
6m
4m b). Bunds with cassava
6m
4m c). Bunds with legumes
6m
4m
11

12