Assessment of Microorganisms in Transitional Organic and Conventional Vegetable Farms
BIBLIOGRAPHY
ALIBUYOG, HECTOR C. APRIL 2007. Assessment of Microorganisms in
Transitional Organic and Conventional Vegetable Farms. Benguet State University, La
Trinidad, Benguet.
Adviser: Bernard S. Tad-awan, Ph.D
ABSTRACT
The study was conducted primarily to identify and assess population of
beneficial and pathogenic soil microorganisms in five transitional organic farms and four
conventional farms in Benguet, particularly Longlong, Madaymen, Loo, Englandad and
Sinipsip.
Four bacterial genera have been isolated and identified from two sampling sites
based on their morphological and physiological characteristics. Beneficial bacteria (based
on previous works) such as Pseudomonas sp. and Bacillus sp. have higher population in
transitional organic farms than in conventional farms. Conversely, the pathogenic
bacterium Ralstonia sp. has a higher population on conventional farms when compared to
transitional organic farms.
Eight fungal species have been identified based on colony appearance and
morphological characteristic of the conidiphore and conidia. Beneficial fungi (based on
previous works) such as Aspergillus niger, Trichoderma sp. and Gliocladium sp. have a
higher population on organic farms than on conventional farms. On the other hand,
pathogenic fungus such Fusarium sp., has a higher population than on conventional
farms.
Application of compost and manures, cover cropping and other practices of
organic farmers tend to be related to the increase in population of beneficial
microorganisms in the soil.
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TABLE OF CONTENTS
Page
Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i
Abstract . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i
Table of Contents . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iii
INTRODUCTION. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
REVIEW OF LITERATURE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
MATERIALS AND METHODS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
RESULTS AND DISCUSSIONS
Characteristics of Isolated Bacteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Bacterial Colony Counts in the Soil Sample . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Characteristics of the Isolated Fungi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Population of the Isolated Fungi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Organic Farmer Practices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
SUMMARY, CONCLUSION AND RECCOMENDATIONS . . . . . . . . . . . . . . . . . 27
Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Recommendations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
LITERATURE CITED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
APPENDIX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
A. Survey Questionnaire . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
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INTRODUCTION
It is noted that there is an agricultural intensification over the fast few decades.
Twenty-first century farmers become dependent on agrochemicals in stabilizing
agricultural production. These chemicals offer effective means in controlling pests,
diseases and in the replenishment of soil fertility.
However, agricultural intensification also causes several problems. Enormous
application of nitrogenous fertilizers to supply plant nutrition contributed to the problem
of soil acidity (Brady and Neil, 1996). This has brought about limited availability of some
nutrients and favors the growth of soil-borne pathogens. Moreover, extensive use of
chemicals has widespread damaging effects on non-target organisms, the level of species
biodiversity and the over all balance and healthy functioning of the environment.
Consequently, extensive use of agrochemicals to meet world food population demand
significantly altered natural soil microflora.
Several soil microorganisms are known to affect plant growth. Apart from the
decomposers of organic materials that released organically held nutrients, others promote
plant growth by colonizing root system and increasing the beneficial microbial activity in
the rhizosphere. Microbial activity in the soil improves soil structure, increase fixed
nitrogen and facilitate nutrient transfer to the higher plants (Tate, 1991). Furthermore,
beneficial microorganisms offer biocontrol activity against plant pathogens (Cook, 1991).
Due to the economic and environmental problems of agricultural intensification,
the sustainability of both agriculture and the environment is the main objective of today’s
agricultural policy (Anonymous, 2000). One viable alternative to the more traditional
approaches to agriculture is organic farming with the use of biological function and
Assessment of Microorganisms in Transitional Organic and
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substitution of chemical fertilizers with farm generated products. This farming system
relies in ecologically based practices (Greene and Kremen, 2001) that virtually exclude
the use chemicals in stabilizing agricultural production.
Asian governments have recently become interested in organic farming with the
expansion of the market for organic products and their potential for promoting sustainable
agriculture. Accordingly, almost all have put priority on organic certification and
accreditation, even though the major constraints in organic farming in Asia are still at the
level of farm production.
The Philippine government has been urged to reintroduce traditional organic
methods in crop production in a bid to boost the country’s ailing industry. Organic farmer
advocate Rivera (2001) insists that organic farming methods could help local farmers
address the pest and disease problems currently plaguing the production of the high-value
root crop.
In Benguet, 70% of the total vegetable needs of the country produced, farmers
continuously rely on using large amounts of synthetic fertilizers and chemical pesticides
(Anonymous, 2003). If the trend continues, little if not nil, beneficial microorganisms
may permanently be left in the soil. To reverse the trend, viable alternative farming
system without harming natural environment and the soil microflora need to be
established.
The study provides better understanding and use of beneficial microorganisms to
contribute in sustaining agricultural production. Such understanding would make farmers
realize the benefits of beneficial microorganisms in crop production. It identifies farm
Assessment of Microorganisms in Transitional Organic and
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practices that enhance beneficial microbial activity. Thus, it is important to show and
compare microorganisms present in farms practicing conventional and organic farming.
The study was conducted to primarily assess the microorganisms found in both
transitional organic and conventional farms. Specifically, it aims to 1) identify beneficial
microorganisms (according to Cook and Baker, 1983; Kloepper, 1991) present in the soil
under transitional organic and conventional farms; 2) compare for the presence of
beneficial and pathogenic microorganisms in transitionally organic farm and conventional
farm; and 3) determine cultural practices and organic amendments that enhance the
presence of beneficial microorganisms.
Soil samples were obtained from five transitional organic farms and four adjacent
conventional vegetable farms within Benguet particularly Loo, Longlong, Englandad,
Sinipsip and Madaymen from January to March 2007. Laboratory analysis to determine
and identify microorganisms was conducted at the Department of Plant Pathology
laboratory.
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REVIEW OF LITERATURE
Many microorganisms have enormous diversity of functions in the soil and
interact biologically in nature. Beneficial microorganisms play significant roles in the
growth and development of plants. In farming, these beneficial microorganisms are
fundamental in the mineralization of plant biomass as they improve soil aggregation
(Tate, 1991).
Walker (1975) cited that decomposition of organic matter is the primary function
of soil microorganism, which releases carbon dioxide, methane, and other volatile
compounds. This process releases nutrients, at the same time the glue-like intermediate
products and the more resistant portion humus enhanced the stability of soil aggregates.
According to Brady and Neil (1996), microbes convert organically bound forms
of Nitrogen, Sulfur, and Phosporus in plant available forms. However, these soil
microorganisms compete in nutrients such as Nitrogen, Phosphorus, Potassium, Calcium
and even Iron.
Cook (1991) reported that soil microorganisms offer biological control of soil-
borne pathogen. Cook and Baker (1983) define biological control as the reduction of
inoculom or disease producing activity of a pathogen in active or dormant state by one or
more organism accomplished naturally or through manipulation of natural environment,
host or antagonist or by introduction of more antagonists other than man.
Microorganisms that inhabit the soil include bacteria, actinomycetes, fungi and
protozoa. Alexander (1977) classified these microorganisms with respect to their carbon
and energy sources. Heterotrophic (or chemoorganotrophic), the first classification,
require preformed organic nutrients to serve as source of energy and carbon. On the other
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hand, autotrophic (or litotrophic) microorganisms obtain their energy from sunlight or by
the oxidation of inorganic compounds and their carbon by the assimilation of CO2.
Consequently, fungi, actinomycetes, protozoa, all animals and most bacteria are
heterotrophs.
Microbial Community
Several microorganisms are known to affect plant growth. Some beneficial
microorganisms isolated in the soil include bacteria, fungi, and actinomycetes.
Bacteria. These comprise a diverse group of singled-celled prokaryotic
microorganisms, which inhabit the soil of every terrestrial ecosystem (Alexander, 1998).
Their density is largely influenced by organic matter content of their habitat, wherein
cultivated land is higher than in virgin soil. Bacteria are classified based on their
ecological differentiation, physiological differentiation, the ability to grow in the absence
of oxygen, and on their cell structure (Alexander, 1961). On the other hand, Bergey’s
Manual of Determinative Bacteriology classifies bacteria into taxonomic group based on
the classical Linnaean concept of binomial nomenclature (Rao, 1999).
According to Rao (1999), order Pseudomonadales, Eubacteriales and
Actinomycetales contain species predominantly encountered in soil. Recent investigation
shows that strains of Pseudomonas, Arthrobacter, Clostridium, Achromobacter, Bacillus,
Micrococcus, Flavobacterium, Corynebacterium, Sarcina and Mycobacterium are the
most common soil bacteria.
Foster and Woodruff (1946), as cited by Raymundo et al. (1985) characterized
genus Bacillus as an important antibiotic-producing microorganism that occurs in soil,
water and air. The bacterium is spore forming rods, gram positive, motile and aerobic or
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facultative anaerobes. Subsequent studies reported successful isolation of antibiotic
producing Bacillus from the soil (Luke and Conell, 1954, and Tumanyan, 1958) as cited
by Raymundo et al., (1985). The bacterium has shown effective control against several
pathogens by the production of metabolites with biocontrol and antibiotic properties
(Madamba et al., 1991). Raymundo et al., (1985) successfully isolated Bacillus species
such as Bacillus cereus, B. pumilus, B. circulans, B. licheniformes, B. megaterium and B.
subtilis on Luzon area showing antagonism by the production of antibiotics. Mukerji and
Garg (1986) showed that Bacillus subtilis inhibits germination of Sclerotium cepivorum,
controls seedling blight caused by Fusarium roseum Graminearum and damping off
caused by Pythium ultimum.
Similarly,
Madamba
et al., (1991) identified Bacillus cereus, B.
stearothermophilus and B. circulans in the Philippine soil reducing root galls of nematode
infested plant. They identified Bacillus cereus as the most effective in controlling root-
knot nematode and even on several pathogens by colonizing root system of the plant.
Moreover, B. cereus produces probiotics that promote plant growth and induce nodulation
of some legume species. Due to these effects, plants grown in Bacillus treated nematode
infested soil were generally taller and show comparable effects to furadan treatment
(Selvadorai et al., 1981) cited by Madamba et al., (1991).
Rhizobacteria,
representing fluorescent Pseudomonads, classified by Kloepper
and Schroth (1978) cited by Kloepper (1991) as plant promoting bacteria by producing
metabolites independent to soil microflora. Pseudomonas fluorescence which is Gram
negative rod, catalase positive and produces soluble fluorescent pigments improve plant
growth of plants by colonizing root region aggressively that preempt the establishment of
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Deleterious Rhizosphere Mircoorganisms (DRMO) on roots (Rao, 1999) and by the
production of siderophore psuedobactin that deprives pathogens of iron, thereby
permitting the plant to grow better (Cook and Baker, 1983).
A comprehensive study was conducted in IRRI by Rosales et al., (1986) as cited
by Davide (1991) on the use of beneficial bacteria for the biological control of plant
pathogens. They showed that 50% of paddy field bacterial isolates in the germination test
were effective in suppressing bakanae disease caused by Fusariium moniliforme on rice.
Thus, naturally occurring beneficial bacteria demonstrate potential in controlling bakanae
disease (Davide, 1991).
Fungi. These are diverse group of multicellular organisms with incredible array
of vegetative and reproductive morphologies (Sylvia et al., 1998). The size, shape and
color of conidia or spores and the physiological characteristics of cultures in artificial as
well as in natural substrates provide taxonomic criteria in the classification of fungal
isolates (Rao, 1999). Fungi inhabit almost any niche containing substrates, take place in
degradation of organic matter, agent of disease, beneficial symbionts, agents of soil
aggregation, and important food sources for human and many organisms (Sylvia et al.,
1998).
The genera of fungi that are most commonly encountered in soils are
Acrostalagmus, Botrytis, Cephaloposrium, Gliocladium, Monilinia, Scopulariopsis,
Spicaria, Trichothecium, Verticilium, Pullularia, Cylindrocarpon, Fusarium, Absidia,
Cunninghamella, Mortierella, Mucor, Rhizopus, and Pythium. Germination, root growth
and uptake of minerals of plants are enhanced by the synthesis of humic acids by
Alternaria, Aspergillus, Cladosporium, Gliocladium and Humicola. In acidic soils,
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Penicillium and Trichoderma take part in the cellulose decomposition (Rao, 1999).
According to Tancangco et al., (1990), members of genus Trichoderma are important
sources of commercial cellulose and are natural agents of decomposition of plant
material, and have been reported by Cook and Baker (1983) to be very efficient
mycoparasite on a wide range of plant pathogens. Alcantara (1978), cited by Davide
(1991), observed that T. glaucum showed true hyperparasitism on hyphae of Rhizoctonia
solani and Trichoderma harzianum on Sclerotium rolfsii. Davide (1991) cited the study
conducted by Neypes et al., (1988) proves that the use of T. glaucum Abott in controlling
foot rot disease of seedling is more effective than fungicides under field condition, and it
gives significant increase in yield.
According to Davide (1991), Gliocladium spp. has been investigated for their
potencial as biocontrol agents against pathogen. Cook and Baker (1983) cited the ideas
of Webster and Lonas (1964) that these organisms are common in soil with antagonistic
activity against soil-borne diseases by producing potent antibiotics and mycoparasitism.
On the other hand, Huang (1978) and Hung Hoes (1976) found out that Gliocladium
catenulatum kill cells of Sclerotium sclerotivorum without direct penetration as cited by
(Cook and Baker, 1983).
Aside from the importance of beneficial microorganisms in controlling soil-borne
disease causing microorganisms, they also offer biological control on plant parasitic
nematodes. Jatala (1981) as cited by Villanueva and Davide (1984) discovered
Paecilomyces lilacinus fungus in Peru as biocontrol agent against root-knot nematode.
The fungus parasitizes egg masses and reduces hatching of larvae of Meloidogyne
incognita (Reyes and Davide, 1978) cited by Villanueva and Davide (1984).
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In the Philippines, Villanueva and Davide (1984) successfully isolated
Paecilomyces lilacinus Thom and Arthrobotrys cladodes Drechs from eggs of root knot
nematode infecting tomato, eggplant and in rabbit manure. P. lilacinus isolates
significantly reduced infection of Meloidogyne incognita from 75-82% compared to 90-
91 % reduction by the Peru isolate. Davide and Zorilla (1983) also reported that an isolate
of P. lilacinus significantly control cyst nematode Globodera rostocheinsis until harvest
of potato cv. Isola in Madaymen, Bugias, Benguet. From their experiment, they showed
that the effect of the fungus is generally comparable with those treated with nematicides
Ethoprop and Carbofuran.
Actinomycetes. These organisms constitute a specialized group of soil bacteria
that occur in soils. Actinomycetes form aerial mycelium and produce conidia, which give
the colonies powdery or chalky appearance (Alexander, 1998) and stick firmly to agar
surface (Rao, 1999). In the environment, they are involved in decomposition of organic
matter and they are also known as causative agent of animals, plants and human diseases
(Alexander, 1998).
The most common genera of Actinomycetes found in soil are Streptomyces,
Nocardia and Micromonospora (Rao, 1999). Cook and Baker (1983) claim that
Streptomyces are potentially very effective antagonist of plant pathogenic fungi especially
in environment too dry for bacteria by the production of potent antibiotic. In the Peoples
Republic of China, Yin and Associates (1957, 1965) cited by Cook and Baker (1983)
introduced Streptomyces sp. 5406 in cotton at planting and showed improvement in stand
and plant vigor.
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Natural suppressiveness of soil against soil-borne diseases is directly correlated to
soil microorganism, fertility level, and nature of soil and response of growing plants.
Adding compost, cover cropping, mulching and manuring foster a more diverse soil
environment for myriad soil organisms. Beneficial microorganisms including Bacillus
sp., Pseudomonas spp., Flavobacterium balastinum, Streptomyces, Penicillium,
Trichoderma, and Gliocladium virens, suppresses deleterious microorganisms that
inhabit compost (Sullivan, 2004).
The aforementioned studies and investigations show that microorganisms are chief
factors in sustaining crop production, and suggest that agricultural practices, which
significantly affect beneficial microorganisms in the soil, must look into account the viable
alternative practices that are ecologically friendly. Therefore, these serve as framework for
the analysis in the prevailing study on the assessment of the presence and absence of
beneficial microorganisms in conventional and organic farms.
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MATERIALS AND METHODS
Soil Sampling
Soil samples were randomly collected from five transitionally organic farms and
four adjacent conventional farms in Benguet particularly Loo, Longlong, Englandad,
Sinipsip and Madaymen at a depth of 15 cm and mixed evenly. About 1 kg of composite
soil samples was placed in a clean plastic for isolation.
Isolation of Soil Microorganisms
Bacteria and Fungi were isolated through the serial dilution method. A 10 gm of
soil was diluted with 90 ml of sterile distilled water in a sterile Erlenmeyer flask and
mixed using mechanical shaker for 20-30 minutes. While the suspension is in motion, 1
ml of the suspension was withdrawn and added to 9 ml sterile distilled water. Dilutions
such as 104 for bacteria and 102 for fungi were prepared. About 0.1 ml aliquot from each
dilution was plated in Nutrient agar (NA) for Bacteria and Potato Dextrose agar (PDA)
for fungi, spread using flamed L-shaped glass rod, incubated for 2-3 days and colonies
formed were counted. Single colonies that appeared on the medium were transferred on
the culture media as mentioned for the pure culture of the isolates.
Characterization of Isolated Microorganisms
Characterization of Isolated Fungi
Isolated fungi were plated on the center of PDA plates, incubated right side up to
30 ºC for 7-14 days. Colony color and surface structure were observed.
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Wet mount of each isolated fungus was prepared and examined under high power
objective. Microscopic structures were observed for presence or absence of septa, color
of mycelium, presence or absence of sexual and/or asexual spore, spore type and
arrangement of the phialiadies.
Characterization of Isolated Bacteria
Morphological and cultural examination. Isolated bacteria were streaked on
Nutrient agar (NA), King’s Medium B (KMB), which detects formation of water-soluble
fluorescent pigments and CPGA+TZC, medium that differentiates bacteria by their
ability to convert tetrazolium to a pink to red compound formazan. Different
characteristics of bacterial colonies were noted. These characteristics include color,
shape, size, elevation and consistency of the colony.
Following Gram staining procedure, the isolated bacteria were classified as
Gram-negative rod or coccus or Gram-positive rod or coccus.
Physiological Examination. Physiological characteristics of the isolates were
determined following the procedures of Raymundo et al., (1991).
1. Catalase test. A colony of the cultures was transferred on clean glass slide,
added with 1-2 drops of freshly prepared 3% hydrogen peroxide (H2O2). Bubble
formations were observed.
2. Oxidation/Fermentation of carbohydrates and other compounds. Using flamed
pin, the cultures were stab in freshly prepared Hugh and Leifson medium.
Formation of gas and growth were observed.
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3. Gelatin liquefaction test. Cultures were inoculate on tubes of NB +12% gelatin
and incubated for 72 hours. Inoculated tubes were placed in ice bath for 15
minutes and observed if the medium remains liquid or it solidifies. Reincubated
and observed again after several days.
Other Tests
Motility test. Hanging drop mount of each culture was prepared. A loopful of the culture
suspension was placed at the center of a clean cover slip and covered with
depression slides centered to the drop of the culture. Quickly and carefully, the
cover slip with depression slide was inverted right side up without touching the
bottom of the well and observed under low power objective (10x).
Staining Endospores. The prepared smear of the organisms was covered with absorbent
paper, flooded with malachite green and steamed for 7 minutes. The slide was
thoroughly washed with tap water and counterstained with safranin for 30-60
seconds, washed, blot dried and examined under oil immersion objective.
Determination of Cultural Practices by
Organic and Conventional Farmers
Cultural practices in transitional organic and conventional farms were determined
by interviewing organic and conventional farmers, following the interview schedule on
Appendix A. The information that was obtained is used to relate the presence and
absence of beneficial microorganisms in the different farms.
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Data Gathered:
1. Colony counts. Microbial population of bacteria and fungi.
a. Bacteria. CFU count was obtained using the formula after dilution at
1x104 for plating.
CFU/ml= Average No. of Colonies /Amount Plated
Total
Dilution
Factor
b. Fungi. Colony formed in 1x102 fold dilution using the following
criteria.
Abundant- average of 8 colonies
Medium – average of 5 colonies
Scarce – average of 2 colonies
Nil- no growth
2. Characteristics of bacterial and fungal isolates
a. Bacteria
1) Morphological characteristics- this includes colony color, shape,
consistency and capacity to transmit light.
2) Physiological characteristics- this includes catalase test, gelatin
liquefaction test and O/F test.
3) Biochemical test- this was done through Gram staining.
b. Fungi
1) Colony morphology- this was done mainly through colony color.
2) Morphological fungal structures- this was done through
microscopic examination.
3. Cultural practices in transitional organic farms. This was done through
interview schedule with four transitional organic farmers and five
conventional farmers.
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RESULTS AND DISCUSSION
Characteristics of the Isolated Bacteria
Four bacterial species were successfully identified in two transitional organic and
two conventional farms based on their morphological and physiological characteristics
(Figures 1-7). Isolate 1 characterized as gram-negative rod, occurs singly or in chain and
produces fluorescent pigment called pyoverdin (formerly called flourescin) which is a
type of siderophore in King’s B medium. Cook and Baker (1983) cited that these
characteristics are of limited to fluorescent pseudomonad. It grows oxidatively on O/F
test producing yellow colony color in open Hugh and Leifson agar tube. The organism
was observed to liquefy gelatin, which is one of the distinct characteristic of
Pseudomonas fluorescence against Pseudomonas putida.
Isolate 2 is gram-positive rod, motile and test positive on enzyme catalase.
Following endospore staining, the organism appears as rod, and a substantial portion
usually contain an oval endospore that makes it bulge. On nutrient agar (NA), colony
exhibited large, spreading, and dull to opaque type of colonies with irregular margins.
Bryan et al., (1962) identifies this bacterium as to Genus Bacillus.
Using CPGA+TZA medium, isolate 3 produces fluidal colonies with light pink to
light red centers after 48 hrs. incubation. The bacterium is characterized as gram-negative
rod, motile, catalase positive and does not form endospore, which is confirmed by Olson
(2005) as Ralstonia.
On NA, isolate 4 produces spread mycelia and filamentous gram-positive rod. It is
test positive on enzyme catalase and identified as Streptomyces sp.
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Fig.1. Formation of yellow color on O/F Fig. 2. Gelatin liquefies by Pseudomonas
test by Pseudomonas fluorescence
fluorescence on gelatin
liquefaction test
Fig. 3. Pseudomonas fluorescence producing
fluorescent
green
pigment
on
KMB medium
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Fig. 4. Stained oval endospore of Bacillus sp. Fig. 5. Spread colony with irregular
margins of Bacillus sp.
Fig. 6.Rasltonia sp. producing light Fig. 7. Streptomyces sp. forming
red to pink colony on spread mycelia
CPGA+TZA medium
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Bacterial Colony Counts in the Soil Samples
Classified beneficial bacteria based on previous studies such as Pseudomonas
fluorescence, Bacillus sp. and Streptomyces sp. have higher colony count in transitional
organic farms than in conventional farms. Conversely, a pathogenic bacterium such as
Ralstonia sp. shows higher population in conventional farms than on transitional organic
farms (Table 1). Soil microorganisms are known affected by agricultural operations. Nitta
(1991) stated that continuous monocropping and application of high doses of chemical
fertilizers, soil microflora are easy to become disorder in terms of normal plant growth.
Sullivan (2004) cited that adding compost, manure and cover cropping and mulching
fosters a more diverse soil environment in which myriad soil microorganisms exist.
Characteristics of the Isolated Fungi
From five transitional organic and four conventional vegetable farms, a total of 8
fungal species were identified (Figures 8-23). Table 2 summarizes the characteristics of
the isolated fungi.
Isolate 1 shows a dark green to yellow color in the middle reducing to yellow
green as it goes to the edge. Conidia forms in long chain from brushe-shape
conidiophores, glubose to ovoid and produce basipetally, which is characterize by
Quimio and Hanlin (1999) as Penicillium.
Isolate 2 are homogenously black and form large colony on PDA medium with
cream to whitish underside. Conidiophores are hyaline, erect, simple, and thick walled,
with foot cell basally, inflated at the apex forming glubose vesicles, bearing conidial
heads. Biseriate phialides on pale brown glubose vesicles, which is characterize as
Aspergillus niger.
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Table 1. CFU count (10 x 4 )
ORGANIC
CONVENTIONAL
MADAYMEN LOO MADAYMEN LOO
Pseudomonas sp. 1x106
--
--
--
Bacillus sp.
9x105 1.3x106
5x105
--
Streptomyces sp.
5x105 1x106
6x105
5x105
Ralstonia sp. 2.7x106 1.2x106 4.8x106 3.2x106
-- -nil
Isolate 3 appears in cottony, white to dull pink surface on culture media with
white to yellow underside. Conidiophores are erect bearing on brush-shaped conidial
bearing apparatus and forming determinate synemmata, branching biverticulate with
phialidic and cylindrical conidiogenous cells which is distinct characteristics of
Gliocladium sp. (Quimio and Hanlin, 1999).
Isolate 4 is characterized under the genus Trichoderma sp. producing pale green
and become blue green to yellow green colony color as it grows older forming patches
and appears in concentric rings. The phialides are converging and arrange approximately
at right angles on the conidiophores (Kifer and Morelet, 2000). Conidiophores are
branched and arranged in pyramidal order. Phialides are flask-shape and inflated at the
base.
Isolate 5 forms a pink colony surface and dark pink underside. Produces arched
phragmoconidia. Macroconidia are phragmosporate arched and microconidia are
amerosporate, which are limited characteristics of the Genus Fusarium (Kifer and
Morelet, 2000).
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Table 2. Colony Morphology and Microscopic Structures of Isolated Fungi
FUNGAL
COLONY
MICROSCOPIC
ISOLATES
MORPHOLOGY
STRUCTURE
Penicillium sp.
Greenish in the middle to Forms chain of conidia from
yellow green as it goes to the brush-shape phialides
edge with cream to brownish
underside
Aspergillus niger
Black surface and whitish to Long, smooth, colorless
cream color at the back of the
conidiophores, bisereate
plates
phialides with round and
radiate head
Gliocladium sp.
Cottony, white to dull pink Conidiophores erect, borne on
and white to cream underside
brush-shaped conidial bearing
apparatus, verticillium-like
conidiophores on young
cultures
Trichoderma sp.
Whitish in early growth, Conidiophores hyaline,
becoming blue green or branched, arranged in
yellow green patches and pyramidal order, phialides
appears in concentric rings as hyaline, flask-shaped and
it grows mature, cream to inflated at the base
yellowish green underside
Fusarium sp.
Having pink surface and Macroconidia didymo or
brownish pink underside
phragmosporate erect or
curved with asymmetrical foot
cell, microconidia
amerosporate
Pythium sp.
Spread type colony, surface Mycelium coenoncytic,
and back of the culture sporangiophore indeterminate,
appears in white color
sporangia glubose
Rhizopus sp.
Raised mycelia from the
Mycelia aerial, stolon and
surface of the medium with rhizoids present,
grayish surface and underside
sporangiophores long and
upright, sporangia spherical
containing minute
aplanospores
Cladosporium sp.
Grayish colony color, slow Spores occurs in chain arising
growing, forming black color from dark conidiophores,
underside
produces prominent scar
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Fig. 8. Penicillium sp. with greenish to Fig. 9. Penicillium sp.forming chain of conidia
yellow green mycelia on PDA from brush-shaped phialides (400x)
yellow green
Fig.10. Aspergillus niger with homogenous Fig. 11. A. niger with biseriate phialides
black mycelia
with round and radiate head (400x)
Fig. 12. Gliocladium sp. showing cottony, Fig. 13. Gliocladium sp. with verticillium-
Assessment of Microorganisms in Transitional Organic and
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white to pale pink colony color
like conidiophores (400x)
Fig. 14. Trichoderma sp. forming green to yellow Fig. 15. Trichoderma sp. with flask-shape
green colony with concentric rings
and inflated phialides (400x)
F
Fig.16. Fusarium sp. having pink colony
Fig.17. Fusarium sp. with arched macro
surface
conidia
and amerosporate microconidia
(400x)
Fig. 18. Pythium sp. with white spread type Fig. 19. Pythium sp. forming glubose
colony
sporangia
(400x)
Assessment of Microorganisms in Transitional Organic and
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Fig.20. Rhizopus sp. with grayish raised
Fig.21. Rhizopus sp. with spherical
mycelia
sporangia containing minute
aplanospores (400x)
Plate 12. Trichoderms sp. formings
Fig. 22. Cladosporium sp. showing brown Fig. 23. Cladosporium sp. showing a
to grayish colony, forming lines from a prominent scar (400x)
the middle extending to the edge
Isolate 6 forms spread type white colony on PDA. Mycelium appears as
coenocytic and sporangiophores are indeterminate with globuse sporangia, which are
typical characteristics of Pythium sp.
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Isolate 7 shows a raised mycelia with dark to white color and yellow underside
which is known to be as Rhizopus sp. Sporangiophores are upright and long, sporangia
appears to be spherical containing minute aplanospores.
Isolate 8 is slow growing, forming dark green to grayish colony color.
Spores occurs in chain arise from dark conidiophore producing prominent scar.
Conidiophores are macronematous, polyblastic conidiogenous cells usually discrete that
is known to belong on Genus Cladosporium sp. as stated by Quimio and Hanlin (1999).
Population of the Isolated Fungi
Similar to the bacteria, the beneficial fungi (based on previous works), which
include Trichoderma sp., Gliocladium sp. and Aspergillus niger, have a higher population
on transitional organic farms as compared to conventional farms (Table 3). Conversely,
pathogenic fungi such as Fusarium sp. have a lower population on transitional organic
farm than on conventional farms surveyed. However, fungal species such as Pythium sp.,
Rhizopus sp., Cladosporium sp. and Penicillium sp., were observe to have almost the
same population in transitional and conventional farms. As stated by Nitta (1991),
agricultural practices such as application of high doses of chemical fertilizers, soil
microflora are easy to become disorder in terms of normal plant growth. Applying
compost, manures, and cover cropping and mulching that adds organic matters to the soil
fosters a more diverse soil environment in which a myriad soil organisms exist (Sullivan,
2004).
Assessment of Microorganisms in Transitional Organic and
Conventional Vegetable Farms / Hector C. Alibuyog. 2007
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Table 3. Colonies of isolated fungi on transitional organic and conventional farms
COLONY COUNT
FUNGAL GENERA
ORGANIC FARM
CONVENTIONAL FARM
Penicillium sp
8
8
Aspergillus niger
8
2
Trichoderma sp
5
2
Cladosporium sp.
5
5
Gliocladium sp.
2
*
Pythium sp. 2
2
Fusarium sp.
2
5
Rhizupos sp. 2
2
Legend:
* - nil
Organic Farmers Practices
All transitional organic farmers interviewed maintain the fertility level of their
farms by applying compost, chicken dung, organic fertilizers and do mulching and other
practices that add organic matter to the soil. Some of the farmers introduced beneficial or
effective microorganisms available in the market such as Trichoderma sp. and Virtouso,
which contain Bacillus sp. According to the farmers, they use Trichoderma to control
Assessment of Microorganisms in Transitional Organic and
Conventional Vegetable Farms / Hector C. Alibuyog. 2007
26
soil-borne diseases and as plant growth promoter. For controlling pest and diseases,
organic farmers use resistant varieties, botanical pesticides and biofungicides such as
Virtouso.
These practices may explain the presence or absence as well as the population of
beneficial fungi and bacteria as earlier presented in Table 1 and Table 3. In a nutshell,
transitional organic farm have a higher population of beneficial microorganisms than in
conventional farms.
Assessment of Microorganisms in Transitional Organic and
Conventional Vegetable Farms / Hector C. Alibuyog. 2007
27
SUMMARY, CONCLUSION AND RECCOMENDATIONS
Summary
The microorganisms found in transitional organic farms and conventional farms
are Bacillus sp., Streptomyces sp., Ralstonia sp., Penicillium sp., Trichoderma sp.,
Gliocladium sp., Fusarium sp., Cladosporium sp., Pythium sp., Rhizopus sp., Aspergillus
niger and Pseudomonas fluorescence, which is only found on transitional organic farm.
Of these microorganisms, those classified beneficial based on previous works
include P. fluorescence, Bacillus sp., Trichoderma sp., Gliocladium sp., and A. niger.
These beneficial microorganisms have greater population in transitional organic farms
than in conventional farms. Conversely, pathogenic microorganisms, which include
Ralstonia sp. and Fusarium sp. have a greater population on conventional farms than in
transitional organic farms. Microorganisms such as Pythium sp., Penicillium sp.,
Rhizopus sp. and Cladosporium sp. have the same population on both transitional and
organic farms.
Conclusion
There are beneficial microorganisms (based on previous works) present in
transitional organic farms in Benguet. Said beneficial microorganisms have higher
population in transitional organic farms than in conventional farms. Conversely, some
pathogenic microorganisms have a higher population in conventional farms.
Assessment of Microorganisms in Transitional Organic and
Conventional Vegetable Farms / Hector C. Alibuyog. 2007
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Recommendations
Based from the results of the study, the following are suggested.
1. Pathogenicity test need to be conducted among the isolates to determine their
efficacy against certain pathogenic species.
2. Further characterization of the isolates including DNA analysis need to be
undertaken.
3. There is a need to investigate the mode of action of beneficial microorganisms
on pathogenic microorganisms.
Assessment of Microorganisms in Transitional Organic and
Conventional Vegetable Farms / Hector C. Alibuyog. 2007
29
LITERATURE CITED
ANONYMOUS. 2003. Organic Farming in Benguet. AGSHAN News. P.11.
ANONYMOUS. 2000. European Commission Agriculture. Retrieved March 6, 2007
from http://ec.europa.eu/agriculture/qual/organic/index_en.htm
RIVERA, R. 2001.Philippines: Organic Farming could Up Cassava Production, says
Expert.
Retrieved
January
8, 2007 from http://www.just-
food.com/article.aspx?art=48445&type=1
ALEXANDER, M. 1977. Introduction to Microbiology (2nd ed.). John Wiley and Sons
Inc. New York. Pp.16-52
ALEXANDER, M. 1961. Introduction to Microbiology. John Wiley and Sons Inc. New
York. Pp.3-85
ALEXANDER, D. B. 1998. Bacteria and Archea: Principles and Application of Soil
Microbiology. Prentice Hall Inc. New Jersey. Pp.44-45.
BRADY, N. C. and R. R. NIEL.1996. The Nature and Properties of Soil (11th ed.).
Prentice Hall, Upper Sadler River, New Jersey. Pp. 340-355
BRYAN, A. H., C. G. BRYAN, and C. A. BRYAN. 1962. Bacteriology, Science and
Practice (6th ed.). Barnes and Noble Inc. New York. Pp. 109-110
COOK, J. R. 1991. Biological Control of Plant Diseases: Broad Concept and Application.
Proceedings of the International Seminar on Biological Control of Plant Diseases
and Virus vectors, Tsukuba Japan. Pp. 1-5
COOK, J. R. and K. F. BAKER. 1983. The Nature and Practice of Biological Control of
Plant Diseases. APS Press, Minnesota USA. Pp.312-389
DAVIDE, R. G. 1991. Biological Control of Plant Diseases in the Philippines.
Proceedings of the International Seminar on Biological Control of Plant Diseases
and Virus vectors, Tsukuba Japan.
DHINGRA, O. D. and J. B. SINCLAIR. 1986. Basic Plant Pathology Methods. CRC
Press, Inc. Boca Raton, Florida. Pp.179-200
GREENE, C. and A. KREMEN, 2001. Organic Farming System. Retrieved March 6,
2007 from http://www.ers.usda.gov/publications/aib780/aib780d.pdf U.S.
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30
HALOS, P. M. and R. A. ZORILLA. 1979. Vesicular-Arbuscular Mycorrhizae Increase
Growth and Yield of Tomatoes and Reduce Infection by Pseudomonas
solanacearum. Phil. Agric. Vol. 62. Pp. 309-314.
KIFER, E. and M. MORELET. 2000. The Deuteromycetes. Science Publisher Inc.
Enfield New Hampshire, USA. Pp.167-187
KLOEPPER, J. W. 1991. Plant Growth Promoting Rhizobacteria as Biological Control
agents of Soil-Borne diseases. Proceedings of the International Seminar on
Biological Control of Plant Diseases and Virus Vectors, Tsukuba Japan.
MADAMBA, C. B, E. N. CAMAYA, D. B. ZENAROSA, H. M. YALER. 1991. Soil
Bacteria as Potential Biocontrol agents against Root knot Nematode. The Phil.
Agric. Vol. 82 No.1
MUKERJI, K. G. and K. L. GARG. 1986. Biocontrol of Plant Diseases. Vol. 1. CRC
Press, Inc. Boca Raton, Florida. Pp.16-25, 54-80.
NITTA, T. 1991. Diversity of Root Fungal Floras: Its implication for Soil-borne Diseases
and Crop Growth. JARQ. Vol. 25 No.1. Pp. 6-10
OLSON, H. A. 2005. Ralstonia solanacearum. www.cals.ncsu.edu/course pp728.
QUIMIO, H. T. AND HANLIN, R. T. 1999. Illustrate Genera and Species of Plant
Pathogenic Fungi in the Tropics. College of Agriculture, Universtity of the
Philippines. College of Agriculture Publication program. Pp. 58
RAO, N.S. 1999. Soil Microbiology, Soil Microorganisms and Plant Growth (4th ed.).
Science Publisher Inc. Enfield, New Hampshire USA. Pp.21-69, 253-267
RAYMUNDO, A.K., E. T. SERRANO, G. D. REYES and T. O. ZOLAYBAR. 1985.
Isolation and Identification of Antibiotic Producing Bacillus from the Soil. Phil.
Agric. Vol. 68. Pp. 394-401.
RAYMUNDO, A. K., A. F. ZAMORA, and I. F. DAMACIO.1991. Manual on
Microbiological Techniques. Technology and Livelihood Resource Center and
University of the Philippines, Los Banos. Media Communication Group, Makati
Metro Manila, Philippines.
SYLVIA, D. M., J. FUHRMANN, P. G. HARTEL and D. A. ZUBERA (ed). 1998.
Principles and Application of Soil Microbiology. Prentice Hall Inc. Simon and
Schuster, Upper Sadler River New Jersey.
SULLIVAN, P. 2004. Sustainable Management of Soil-borne Plant Diseases. Retrieved
July 2004 from ATTRA Publication #IP173http://www.attra.org/attra-
pub/soilborne.html#strategies
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31
TANCANGCO, C. P., V. C. CUEVAS and L. M. ENGLE. 1990. Two improve cellulase-
producing strains of Trichoderma harzianum rifai. Phil. Agric. Vol. 73. No.2. P.
271.
TATE, R. 1991. Soil Microbiology. John Wiley and Sons Incorporated, USA. Pp.171-
191
VILLANUEVA, L. M. and R. G. DAVIDE. 1984. Evaluation of Several Isolates of Soil
Fungi for Biological Control of Root-Knot Nematode. Phil. Agric. Vol. 67. Pp. 361-
370.
WALKER, N. (Ed.) 1975. Soil Microbiology. Butterworths Co. Ltd. London
Assessment of Microorganisms in Transitional Organic and
Conventional Vegetable Farms / Hector C. Alibuyog. 2007
32
APPENDIX
Appendix A. Survey Questionnaire
I. Personal information
1. Name:
2. Sex:
3. Address:
Farm
Location:
4. Educational attainment
a. no formal education
g.college graduate (degree)
b. elementary level
c. elementary graduate
h. vocational/ diploma
d. high school level
e. high school graduate
f. college level
5. Trainings and seminars attended:
II. Farm Management
1. How many years have you been in farming?
2. How many years have you been farming organically?
Conventionally?
3. Is your farm certified? Yes No
4. Is all your production organic/conventionally produce? Yes No
Or do you mixed organic and conventional farm? Yes no
5. Do you farm full time or part time?
6. What is the total area devoted to organic farming?
On vegetable organic farming?
7. Crops grown:
Estimated area:
8. Cropping pattern
Monocropping:
Mixed cropping:
Crop rotation:
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33
III. Production Management
1. Tillage operation
Cultivate land using ٱ grabhoe ٱ machines
ٱothers
No tillage
2. Pest and Disease Management
a. Weeds:
Management
measures
Mechanical tillage
Weeding by hand
Cover crops:
Mulches:
Burning:
Chemicals:
Other control:
b.
Insects:
Management measures
Use of resistant varieties:
Crop
rotation:
Mixed
cropping:
Beneficial
insects:
Botanical
pesticides:
Chemical
pesticides:
Use of traps ٱplants ٱpheromones
ٱothers
(specify)
c.
Diseases:
Management
measures
Use of resistant varieties:
Crop
rotation:
Mixed cropping with:
Beneficial microorganisms:
Botanical
pesticides:
Chemical
pesticides:
Other
control:
3. Fertility management
Materials used
Compost
application
Green
manuring
Organic fertilizers
Assessment of Microorganisms in Transitional Organic and
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Mulching
Cover
cropping
Fermented
products
Effective
microorganisms
Balancing
soil
pH
Synthetic
fertilizers
Others (Specify)
Assessment of Microorganisms in Transitional Organic and
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ALIBUYOG, HECTOR C. APRIL 2007. Assessment of Microorganisms in
Transitional Organic and Conventional Vegetable Farms. Benguet State University, La
Trinidad, Benguet.
Adviser: Bernard S. Tad-awan, Ph.D
ABSTRACT
The study was conducted primarily to identify and assess population of
beneficial and pathogenic soil microorganisms in five transitional organic farms and four
conventional farms in Benguet, particularly Longlong, Madaymen, Loo, Englandad and
Sinipsip.
Four bacterial genera have been isolated and identified from two sampling sites
based on their morphological and physiological characteristics. Beneficial bacteria (based
on previous works) such as Pseudomonas sp. and Bacillus sp. have higher population in
transitional organic farms than in conventional farms. Conversely, the pathogenic
bacterium Ralstonia sp. has a higher population on conventional farms when compared to
transitional organic farms.
Eight fungal species have been identified based on colony appearance and
morphological characteristic of the conidiphore and conidia. Beneficial fungi (based on
previous works) such as Aspergillus niger, Trichoderma sp. and Gliocladium sp. have a
higher population on organic farms than on conventional farms. On the other hand,
pathogenic fungus such Fusarium sp., has a higher population than on conventional
farms.
Application of compost and manures, cover cropping and other practices of
organic farmers tend to be related to the increase in population of beneficial
microorganisms in the soil.
ii
TABLE OF CONTENTS
Page
Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i
Abstract . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i
Table of Contents . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iii
INTRODUCTION. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
REVIEW OF LITERATURE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
MATERIALS AND METHODS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
RESULTS AND DISCUSSIONS
Characteristics of Isolated Bacteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Bacterial Colony Counts in the Soil Sample . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Characteristics of the Isolated Fungi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Population of the Isolated Fungi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Organic Farmer Practices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
SUMMARY, CONCLUSION AND RECCOMENDATIONS . . . . . . . . . . . . . . . . . 27
Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Recommendations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
LITERATURE CITED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
APPENDIX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
A. Survey Questionnaire . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
iii
INTRODUCTION
It is noted that there is an agricultural intensification over the fast few decades.
Twenty-first century farmers become dependent on agrochemicals in stabilizing
agricultural production. These chemicals offer effective means in controlling pests,
diseases and in the replenishment of soil fertility.
However, agricultural intensification also causes several problems. Enormous
application of nitrogenous fertilizers to supply plant nutrition contributed to the problem
of soil acidity (Brady and Neil, 1996). This has brought about limited availability of some
nutrients and favors the growth of soil-borne pathogens. Moreover, extensive use of
chemicals has widespread damaging effects on non-target organisms, the level of species
biodiversity and the over all balance and healthy functioning of the environment.
Consequently, extensive use of agrochemicals to meet world food population demand
significantly altered natural soil microflora.
Several soil microorganisms are known to affect plant growth. Apart from the
decomposers of organic materials that released organically held nutrients, others promote
plant growth by colonizing root system and increasing the beneficial microbial activity in
the rhizosphere. Microbial activity in the soil improves soil structure, increase fixed
nitrogen and facilitate nutrient transfer to the higher plants (Tate, 1991). Furthermore,
beneficial microorganisms offer biocontrol activity against plant pathogens (Cook, 1991).
Due to the economic and environmental problems of agricultural intensification,
the sustainability of both agriculture and the environment is the main objective of today’s
agricultural policy (Anonymous, 2000). One viable alternative to the more traditional
approaches to agriculture is organic farming with the use of biological function and
Assessment of Microorganisms in Transitional Organic and
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substitution of chemical fertilizers with farm generated products. This farming system
relies in ecologically based practices (Greene and Kremen, 2001) that virtually exclude
the use chemicals in stabilizing agricultural production.
Asian governments have recently become interested in organic farming with the
expansion of the market for organic products and their potential for promoting sustainable
agriculture. Accordingly, almost all have put priority on organic certification and
accreditation, even though the major constraints in organic farming in Asia are still at the
level of farm production.
The Philippine government has been urged to reintroduce traditional organic
methods in crop production in a bid to boost the country’s ailing industry. Organic farmer
advocate Rivera (2001) insists that organic farming methods could help local farmers
address the pest and disease problems currently plaguing the production of the high-value
root crop.
In Benguet, 70% of the total vegetable needs of the country produced, farmers
continuously rely on using large amounts of synthetic fertilizers and chemical pesticides
(Anonymous, 2003). If the trend continues, little if not nil, beneficial microorganisms
may permanently be left in the soil. To reverse the trend, viable alternative farming
system without harming natural environment and the soil microflora need to be
established.
The study provides better understanding and use of beneficial microorganisms to
contribute in sustaining agricultural production. Such understanding would make farmers
realize the benefits of beneficial microorganisms in crop production. It identifies farm
Assessment of Microorganisms in Transitional Organic and
Conventional Vegetable Farms / Hector C. Alibuyog. 2007
3
practices that enhance beneficial microbial activity. Thus, it is important to show and
compare microorganisms present in farms practicing conventional and organic farming.
The study was conducted to primarily assess the microorganisms found in both
transitional organic and conventional farms. Specifically, it aims to 1) identify beneficial
microorganisms (according to Cook and Baker, 1983; Kloepper, 1991) present in the soil
under transitional organic and conventional farms; 2) compare for the presence of
beneficial and pathogenic microorganisms in transitionally organic farm and conventional
farm; and 3) determine cultural practices and organic amendments that enhance the
presence of beneficial microorganisms.
Soil samples were obtained from five transitional organic farms and four adjacent
conventional vegetable farms within Benguet particularly Loo, Longlong, Englandad,
Sinipsip and Madaymen from January to March 2007. Laboratory analysis to determine
and identify microorganisms was conducted at the Department of Plant Pathology
laboratory.
Assessment of Microorganisms in Transitional Organic and
Conventional Vegetable Farms / Hector C. Alibuyog. 2007
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REVIEW OF LITERATURE
Many microorganisms have enormous diversity of functions in the soil and
interact biologically in nature. Beneficial microorganisms play significant roles in the
growth and development of plants. In farming, these beneficial microorganisms are
fundamental in the mineralization of plant biomass as they improve soil aggregation
(Tate, 1991).
Walker (1975) cited that decomposition of organic matter is the primary function
of soil microorganism, which releases carbon dioxide, methane, and other volatile
compounds. This process releases nutrients, at the same time the glue-like intermediate
products and the more resistant portion humus enhanced the stability of soil aggregates.
According to Brady and Neil (1996), microbes convert organically bound forms
of Nitrogen, Sulfur, and Phosporus in plant available forms. However, these soil
microorganisms compete in nutrients such as Nitrogen, Phosphorus, Potassium, Calcium
and even Iron.
Cook (1991) reported that soil microorganisms offer biological control of soil-
borne pathogen. Cook and Baker (1983) define biological control as the reduction of
inoculom or disease producing activity of a pathogen in active or dormant state by one or
more organism accomplished naturally or through manipulation of natural environment,
host or antagonist or by introduction of more antagonists other than man.
Microorganisms that inhabit the soil include bacteria, actinomycetes, fungi and
protozoa. Alexander (1977) classified these microorganisms with respect to their carbon
and energy sources. Heterotrophic (or chemoorganotrophic), the first classification,
require preformed organic nutrients to serve as source of energy and carbon. On the other
Assessment of Microorganisms in Transitional Organic and
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hand, autotrophic (or litotrophic) microorganisms obtain their energy from sunlight or by
the oxidation of inorganic compounds and their carbon by the assimilation of CO2.
Consequently, fungi, actinomycetes, protozoa, all animals and most bacteria are
heterotrophs.
Microbial Community
Several microorganisms are known to affect plant growth. Some beneficial
microorganisms isolated in the soil include bacteria, fungi, and actinomycetes.
Bacteria. These comprise a diverse group of singled-celled prokaryotic
microorganisms, which inhabit the soil of every terrestrial ecosystem (Alexander, 1998).
Their density is largely influenced by organic matter content of their habitat, wherein
cultivated land is higher than in virgin soil. Bacteria are classified based on their
ecological differentiation, physiological differentiation, the ability to grow in the absence
of oxygen, and on their cell structure (Alexander, 1961). On the other hand, Bergey’s
Manual of Determinative Bacteriology classifies bacteria into taxonomic group based on
the classical Linnaean concept of binomial nomenclature (Rao, 1999).
According to Rao (1999), order Pseudomonadales, Eubacteriales and
Actinomycetales contain species predominantly encountered in soil. Recent investigation
shows that strains of Pseudomonas, Arthrobacter, Clostridium, Achromobacter, Bacillus,
Micrococcus, Flavobacterium, Corynebacterium, Sarcina and Mycobacterium are the
most common soil bacteria.
Foster and Woodruff (1946), as cited by Raymundo et al. (1985) characterized
genus Bacillus as an important antibiotic-producing microorganism that occurs in soil,
water and air. The bacterium is spore forming rods, gram positive, motile and aerobic or
Assessment of Microorganisms in Transitional Organic and
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facultative anaerobes. Subsequent studies reported successful isolation of antibiotic
producing Bacillus from the soil (Luke and Conell, 1954, and Tumanyan, 1958) as cited
by Raymundo et al., (1985). The bacterium has shown effective control against several
pathogens by the production of metabolites with biocontrol and antibiotic properties
(Madamba et al., 1991). Raymundo et al., (1985) successfully isolated Bacillus species
such as Bacillus cereus, B. pumilus, B. circulans, B. licheniformes, B. megaterium and B.
subtilis on Luzon area showing antagonism by the production of antibiotics. Mukerji and
Garg (1986) showed that Bacillus subtilis inhibits germination of Sclerotium cepivorum,
controls seedling blight caused by Fusarium roseum Graminearum and damping off
caused by Pythium ultimum.
Similarly,
Madamba
et al., (1991) identified Bacillus cereus, B.
stearothermophilus and B. circulans in the Philippine soil reducing root galls of nematode
infested plant. They identified Bacillus cereus as the most effective in controlling root-
knot nematode and even on several pathogens by colonizing root system of the plant.
Moreover, B. cereus produces probiotics that promote plant growth and induce nodulation
of some legume species. Due to these effects, plants grown in Bacillus treated nematode
infested soil were generally taller and show comparable effects to furadan treatment
(Selvadorai et al., 1981) cited by Madamba et al., (1991).
Rhizobacteria,
representing fluorescent Pseudomonads, classified by Kloepper
and Schroth (1978) cited by Kloepper (1991) as plant promoting bacteria by producing
metabolites independent to soil microflora. Pseudomonas fluorescence which is Gram
negative rod, catalase positive and produces soluble fluorescent pigments improve plant
growth of plants by colonizing root region aggressively that preempt the establishment of
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Deleterious Rhizosphere Mircoorganisms (DRMO) on roots (Rao, 1999) and by the
production of siderophore psuedobactin that deprives pathogens of iron, thereby
permitting the plant to grow better (Cook and Baker, 1983).
A comprehensive study was conducted in IRRI by Rosales et al., (1986) as cited
by Davide (1991) on the use of beneficial bacteria for the biological control of plant
pathogens. They showed that 50% of paddy field bacterial isolates in the germination test
were effective in suppressing bakanae disease caused by Fusariium moniliforme on rice.
Thus, naturally occurring beneficial bacteria demonstrate potential in controlling bakanae
disease (Davide, 1991).
Fungi. These are diverse group of multicellular organisms with incredible array
of vegetative and reproductive morphologies (Sylvia et al., 1998). The size, shape and
color of conidia or spores and the physiological characteristics of cultures in artificial as
well as in natural substrates provide taxonomic criteria in the classification of fungal
isolates (Rao, 1999). Fungi inhabit almost any niche containing substrates, take place in
degradation of organic matter, agent of disease, beneficial symbionts, agents of soil
aggregation, and important food sources for human and many organisms (Sylvia et al.,
1998).
The genera of fungi that are most commonly encountered in soils are
Acrostalagmus, Botrytis, Cephaloposrium, Gliocladium, Monilinia, Scopulariopsis,
Spicaria, Trichothecium, Verticilium, Pullularia, Cylindrocarpon, Fusarium, Absidia,
Cunninghamella, Mortierella, Mucor, Rhizopus, and Pythium. Germination, root growth
and uptake of minerals of plants are enhanced by the synthesis of humic acids by
Alternaria, Aspergillus, Cladosporium, Gliocladium and Humicola. In acidic soils,
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Penicillium and Trichoderma take part in the cellulose decomposition (Rao, 1999).
According to Tancangco et al., (1990), members of genus Trichoderma are important
sources of commercial cellulose and are natural agents of decomposition of plant
material, and have been reported by Cook and Baker (1983) to be very efficient
mycoparasite on a wide range of plant pathogens. Alcantara (1978), cited by Davide
(1991), observed that T. glaucum showed true hyperparasitism on hyphae of Rhizoctonia
solani and Trichoderma harzianum on Sclerotium rolfsii. Davide (1991) cited the study
conducted by Neypes et al., (1988) proves that the use of T. glaucum Abott in controlling
foot rot disease of seedling is more effective than fungicides under field condition, and it
gives significant increase in yield.
According to Davide (1991), Gliocladium spp. has been investigated for their
potencial as biocontrol agents against pathogen. Cook and Baker (1983) cited the ideas
of Webster and Lonas (1964) that these organisms are common in soil with antagonistic
activity against soil-borne diseases by producing potent antibiotics and mycoparasitism.
On the other hand, Huang (1978) and Hung Hoes (1976) found out that Gliocladium
catenulatum kill cells of Sclerotium sclerotivorum without direct penetration as cited by
(Cook and Baker, 1983).
Aside from the importance of beneficial microorganisms in controlling soil-borne
disease causing microorganisms, they also offer biological control on plant parasitic
nematodes. Jatala (1981) as cited by Villanueva and Davide (1984) discovered
Paecilomyces lilacinus fungus in Peru as biocontrol agent against root-knot nematode.
The fungus parasitizes egg masses and reduces hatching of larvae of Meloidogyne
incognita (Reyes and Davide, 1978) cited by Villanueva and Davide (1984).
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In the Philippines, Villanueva and Davide (1984) successfully isolated
Paecilomyces lilacinus Thom and Arthrobotrys cladodes Drechs from eggs of root knot
nematode infecting tomato, eggplant and in rabbit manure. P. lilacinus isolates
significantly reduced infection of Meloidogyne incognita from 75-82% compared to 90-
91 % reduction by the Peru isolate. Davide and Zorilla (1983) also reported that an isolate
of P. lilacinus significantly control cyst nematode Globodera rostocheinsis until harvest
of potato cv. Isola in Madaymen, Bugias, Benguet. From their experiment, they showed
that the effect of the fungus is generally comparable with those treated with nematicides
Ethoprop and Carbofuran.
Actinomycetes. These organisms constitute a specialized group of soil bacteria
that occur in soils. Actinomycetes form aerial mycelium and produce conidia, which give
the colonies powdery or chalky appearance (Alexander, 1998) and stick firmly to agar
surface (Rao, 1999). In the environment, they are involved in decomposition of organic
matter and they are also known as causative agent of animals, plants and human diseases
(Alexander, 1998).
The most common genera of Actinomycetes found in soil are Streptomyces,
Nocardia and Micromonospora (Rao, 1999). Cook and Baker (1983) claim that
Streptomyces are potentially very effective antagonist of plant pathogenic fungi especially
in environment too dry for bacteria by the production of potent antibiotic. In the Peoples
Republic of China, Yin and Associates (1957, 1965) cited by Cook and Baker (1983)
introduced Streptomyces sp. 5406 in cotton at planting and showed improvement in stand
and plant vigor.
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Natural suppressiveness of soil against soil-borne diseases is directly correlated to
soil microorganism, fertility level, and nature of soil and response of growing plants.
Adding compost, cover cropping, mulching and manuring foster a more diverse soil
environment for myriad soil organisms. Beneficial microorganisms including Bacillus
sp., Pseudomonas spp., Flavobacterium balastinum, Streptomyces, Penicillium,
Trichoderma, and Gliocladium virens, suppresses deleterious microorganisms that
inhabit compost (Sullivan, 2004).
The aforementioned studies and investigations show that microorganisms are chief
factors in sustaining crop production, and suggest that agricultural practices, which
significantly affect beneficial microorganisms in the soil, must look into account the viable
alternative practices that are ecologically friendly. Therefore, these serve as framework for
the analysis in the prevailing study on the assessment of the presence and absence of
beneficial microorganisms in conventional and organic farms.
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MATERIALS AND METHODS
Soil Sampling
Soil samples were randomly collected from five transitionally organic farms and
four adjacent conventional farms in Benguet particularly Loo, Longlong, Englandad,
Sinipsip and Madaymen at a depth of 15 cm and mixed evenly. About 1 kg of composite
soil samples was placed in a clean plastic for isolation.
Isolation of Soil Microorganisms
Bacteria and Fungi were isolated through the serial dilution method. A 10 gm of
soil was diluted with 90 ml of sterile distilled water in a sterile Erlenmeyer flask and
mixed using mechanical shaker for 20-30 minutes. While the suspension is in motion, 1
ml of the suspension was withdrawn and added to 9 ml sterile distilled water. Dilutions
such as 104 for bacteria and 102 for fungi were prepared. About 0.1 ml aliquot from each
dilution was plated in Nutrient agar (NA) for Bacteria and Potato Dextrose agar (PDA)
for fungi, spread using flamed L-shaped glass rod, incubated for 2-3 days and colonies
formed were counted. Single colonies that appeared on the medium were transferred on
the culture media as mentioned for the pure culture of the isolates.
Characterization of Isolated Microorganisms
Characterization of Isolated Fungi
Isolated fungi were plated on the center of PDA plates, incubated right side up to
30 ºC for 7-14 days. Colony color and surface structure were observed.
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Wet mount of each isolated fungus was prepared and examined under high power
objective. Microscopic structures were observed for presence or absence of septa, color
of mycelium, presence or absence of sexual and/or asexual spore, spore type and
arrangement of the phialiadies.
Characterization of Isolated Bacteria
Morphological and cultural examination. Isolated bacteria were streaked on
Nutrient agar (NA), King’s Medium B (KMB), which detects formation of water-soluble
fluorescent pigments and CPGA+TZC, medium that differentiates bacteria by their
ability to convert tetrazolium to a pink to red compound formazan. Different
characteristics of bacterial colonies were noted. These characteristics include color,
shape, size, elevation and consistency of the colony.
Following Gram staining procedure, the isolated bacteria were classified as
Gram-negative rod or coccus or Gram-positive rod or coccus.
Physiological Examination. Physiological characteristics of the isolates were
determined following the procedures of Raymundo et al., (1991).
1. Catalase test. A colony of the cultures was transferred on clean glass slide,
added with 1-2 drops of freshly prepared 3% hydrogen peroxide (H2O2). Bubble
formations were observed.
2. Oxidation/Fermentation of carbohydrates and other compounds. Using flamed
pin, the cultures were stab in freshly prepared Hugh and Leifson medium.
Formation of gas and growth were observed.
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3. Gelatin liquefaction test. Cultures were inoculate on tubes of NB +12% gelatin
and incubated for 72 hours. Inoculated tubes were placed in ice bath for 15
minutes and observed if the medium remains liquid or it solidifies. Reincubated
and observed again after several days.
Other Tests
Motility test. Hanging drop mount of each culture was prepared. A loopful of the culture
suspension was placed at the center of a clean cover slip and covered with
depression slides centered to the drop of the culture. Quickly and carefully, the
cover slip with depression slide was inverted right side up without touching the
bottom of the well and observed under low power objective (10x).
Staining Endospores. The prepared smear of the organisms was covered with absorbent
paper, flooded with malachite green and steamed for 7 minutes. The slide was
thoroughly washed with tap water and counterstained with safranin for 30-60
seconds, washed, blot dried and examined under oil immersion objective.
Determination of Cultural Practices by
Organic and Conventional Farmers
Cultural practices in transitional organic and conventional farms were determined
by interviewing organic and conventional farmers, following the interview schedule on
Appendix A. The information that was obtained is used to relate the presence and
absence of beneficial microorganisms in the different farms.
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Data Gathered:
1. Colony counts. Microbial population of bacteria and fungi.
a. Bacteria. CFU count was obtained using the formula after dilution at
1x104 for plating.
CFU/ml= Average No. of Colonies /Amount Plated
Total
Dilution
Factor
b. Fungi. Colony formed in 1x102 fold dilution using the following
criteria.
Abundant- average of 8 colonies
Medium – average of 5 colonies
Scarce – average of 2 colonies
Nil- no growth
2. Characteristics of bacterial and fungal isolates
a. Bacteria
1) Morphological characteristics- this includes colony color, shape,
consistency and capacity to transmit light.
2) Physiological characteristics- this includes catalase test, gelatin
liquefaction test and O/F test.
3) Biochemical test- this was done through Gram staining.
b. Fungi
1) Colony morphology- this was done mainly through colony color.
2) Morphological fungal structures- this was done through
microscopic examination.
3. Cultural practices in transitional organic farms. This was done through
interview schedule with four transitional organic farmers and five
conventional farmers.
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RESULTS AND DISCUSSION
Characteristics of the Isolated Bacteria
Four bacterial species were successfully identified in two transitional organic and
two conventional farms based on their morphological and physiological characteristics
(Figures 1-7). Isolate 1 characterized as gram-negative rod, occurs singly or in chain and
produces fluorescent pigment called pyoverdin (formerly called flourescin) which is a
type of siderophore in King’s B medium. Cook and Baker (1983) cited that these
characteristics are of limited to fluorescent pseudomonad. It grows oxidatively on O/F
test producing yellow colony color in open Hugh and Leifson agar tube. The organism
was observed to liquefy gelatin, which is one of the distinct characteristic of
Pseudomonas fluorescence against Pseudomonas putida.
Isolate 2 is gram-positive rod, motile and test positive on enzyme catalase.
Following endospore staining, the organism appears as rod, and a substantial portion
usually contain an oval endospore that makes it bulge. On nutrient agar (NA), colony
exhibited large, spreading, and dull to opaque type of colonies with irregular margins.
Bryan et al., (1962) identifies this bacterium as to Genus Bacillus.
Using CPGA+TZA medium, isolate 3 produces fluidal colonies with light pink to
light red centers after 48 hrs. incubation. The bacterium is characterized as gram-negative
rod, motile, catalase positive and does not form endospore, which is confirmed by Olson
(2005) as Ralstonia.
On NA, isolate 4 produces spread mycelia and filamentous gram-positive rod. It is
test positive on enzyme catalase and identified as Streptomyces sp.
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Fig.1. Formation of yellow color on O/F Fig. 2. Gelatin liquefies by Pseudomonas
test by Pseudomonas fluorescence
fluorescence on gelatin
liquefaction test
Fig. 3. Pseudomonas fluorescence producing
fluorescent
green
pigment
on
KMB medium
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Fig. 4. Stained oval endospore of Bacillus sp. Fig. 5. Spread colony with irregular
margins of Bacillus sp.
Fig. 6.Rasltonia sp. producing light Fig. 7. Streptomyces sp. forming
red to pink colony on spread mycelia
CPGA+TZA medium
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Bacterial Colony Counts in the Soil Samples
Classified beneficial bacteria based on previous studies such as Pseudomonas
fluorescence, Bacillus sp. and Streptomyces sp. have higher colony count in transitional
organic farms than in conventional farms. Conversely, a pathogenic bacterium such as
Ralstonia sp. shows higher population in conventional farms than on transitional organic
farms (Table 1). Soil microorganisms are known affected by agricultural operations. Nitta
(1991) stated that continuous monocropping and application of high doses of chemical
fertilizers, soil microflora are easy to become disorder in terms of normal plant growth.
Sullivan (2004) cited that adding compost, manure and cover cropping and mulching
fosters a more diverse soil environment in which myriad soil microorganisms exist.
Characteristics of the Isolated Fungi
From five transitional organic and four conventional vegetable farms, a total of 8
fungal species were identified (Figures 8-23). Table 2 summarizes the characteristics of
the isolated fungi.
Isolate 1 shows a dark green to yellow color in the middle reducing to yellow
green as it goes to the edge. Conidia forms in long chain from brushe-shape
conidiophores, glubose to ovoid and produce basipetally, which is characterize by
Quimio and Hanlin (1999) as Penicillium.
Isolate 2 are homogenously black and form large colony on PDA medium with
cream to whitish underside. Conidiophores are hyaline, erect, simple, and thick walled,
with foot cell basally, inflated at the apex forming glubose vesicles, bearing conidial
heads. Biseriate phialides on pale brown glubose vesicles, which is characterize as
Aspergillus niger.
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Table 1. CFU count (10 x 4 )
ORGANIC
CONVENTIONAL
MADAYMEN LOO MADAYMEN LOO
Pseudomonas sp. 1x106
--
--
--
Bacillus sp.
9x105 1.3x106
5x105
--
Streptomyces sp.
5x105 1x106
6x105
5x105
Ralstonia sp. 2.7x106 1.2x106 4.8x106 3.2x106
-- -nil
Isolate 3 appears in cottony, white to dull pink surface on culture media with
white to yellow underside. Conidiophores are erect bearing on brush-shaped conidial
bearing apparatus and forming determinate synemmata, branching biverticulate with
phialidic and cylindrical conidiogenous cells which is distinct characteristics of
Gliocladium sp. (Quimio and Hanlin, 1999).
Isolate 4 is characterized under the genus Trichoderma sp. producing pale green
and become blue green to yellow green colony color as it grows older forming patches
and appears in concentric rings. The phialides are converging and arrange approximately
at right angles on the conidiophores (Kifer and Morelet, 2000). Conidiophores are
branched and arranged in pyramidal order. Phialides are flask-shape and inflated at the
base.
Isolate 5 forms a pink colony surface and dark pink underside. Produces arched
phragmoconidia. Macroconidia are phragmosporate arched and microconidia are
amerosporate, which are limited characteristics of the Genus Fusarium (Kifer and
Morelet, 2000).
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Table 2. Colony Morphology and Microscopic Structures of Isolated Fungi
FUNGAL
COLONY
MICROSCOPIC
ISOLATES
MORPHOLOGY
STRUCTURE
Penicillium sp.
Greenish in the middle to Forms chain of conidia from
yellow green as it goes to the brush-shape phialides
edge with cream to brownish
underside
Aspergillus niger
Black surface and whitish to Long, smooth, colorless
cream color at the back of the
conidiophores, bisereate
plates
phialides with round and
radiate head
Gliocladium sp.
Cottony, white to dull pink Conidiophores erect, borne on
and white to cream underside
brush-shaped conidial bearing
apparatus, verticillium-like
conidiophores on young
cultures
Trichoderma sp.
Whitish in early growth, Conidiophores hyaline,
becoming blue green or branched, arranged in
yellow green patches and pyramidal order, phialides
appears in concentric rings as hyaline, flask-shaped and
it grows mature, cream to inflated at the base
yellowish green underside
Fusarium sp.
Having pink surface and Macroconidia didymo or
brownish pink underside
phragmosporate erect or
curved with asymmetrical foot
cell, microconidia
amerosporate
Pythium sp.
Spread type colony, surface Mycelium coenoncytic,
and back of the culture sporangiophore indeterminate,
appears in white color
sporangia glubose
Rhizopus sp.
Raised mycelia from the
Mycelia aerial, stolon and
surface of the medium with rhizoids present,
grayish surface and underside
sporangiophores long and
upright, sporangia spherical
containing minute
aplanospores
Cladosporium sp.
Grayish colony color, slow Spores occurs in chain arising
growing, forming black color from dark conidiophores,
underside
produces prominent scar
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Fig. 8. Penicillium sp. with greenish to Fig. 9. Penicillium sp.forming chain of conidia
yellow green mycelia on PDA from brush-shaped phialides (400x)
yellow green
Fig.10. Aspergillus niger with homogenous Fig. 11. A. niger with biseriate phialides
black mycelia
with round and radiate head (400x)
Fig. 12. Gliocladium sp. showing cottony, Fig. 13. Gliocladium sp. with verticillium-
Assessment of Microorganisms in Transitional Organic and
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white to pale pink colony color
like conidiophores (400x)
Fig. 14. Trichoderma sp. forming green to yellow Fig. 15. Trichoderma sp. with flask-shape
green colony with concentric rings
and inflated phialides (400x)
F
Fig.16. Fusarium sp. having pink colony
Fig.17. Fusarium sp. with arched macro
surface
conidia
and amerosporate microconidia
(400x)
Fig. 18. Pythium sp. with white spread type Fig. 19. Pythium sp. forming glubose
colony
sporangia
(400x)
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Fig.20. Rhizopus sp. with grayish raised
Fig.21. Rhizopus sp. with spherical
mycelia
sporangia containing minute
aplanospores (400x)
Plate 12. Trichoderms sp. formings
Fig. 22. Cladosporium sp. showing brown Fig. 23. Cladosporium sp. showing a
to grayish colony, forming lines from a prominent scar (400x)
the middle extending to the edge
Isolate 6 forms spread type white colony on PDA. Mycelium appears as
coenocytic and sporangiophores are indeterminate with globuse sporangia, which are
typical characteristics of Pythium sp.
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Isolate 7 shows a raised mycelia with dark to white color and yellow underside
which is known to be as Rhizopus sp. Sporangiophores are upright and long, sporangia
appears to be spherical containing minute aplanospores.
Isolate 8 is slow growing, forming dark green to grayish colony color.
Spores occurs in chain arise from dark conidiophore producing prominent scar.
Conidiophores are macronematous, polyblastic conidiogenous cells usually discrete that
is known to belong on Genus Cladosporium sp. as stated by Quimio and Hanlin (1999).
Population of the Isolated Fungi
Similar to the bacteria, the beneficial fungi (based on previous works), which
include Trichoderma sp., Gliocladium sp. and Aspergillus niger, have a higher population
on transitional organic farms as compared to conventional farms (Table 3). Conversely,
pathogenic fungi such as Fusarium sp. have a lower population on transitional organic
farm than on conventional farms surveyed. However, fungal species such as Pythium sp.,
Rhizopus sp., Cladosporium sp. and Penicillium sp., were observe to have almost the
same population in transitional and conventional farms. As stated by Nitta (1991),
agricultural practices such as application of high doses of chemical fertilizers, soil
microflora are easy to become disorder in terms of normal plant growth. Applying
compost, manures, and cover cropping and mulching that adds organic matters to the soil
fosters a more diverse soil environment in which a myriad soil organisms exist (Sullivan,
2004).
Assessment of Microorganisms in Transitional Organic and
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Table 3. Colonies of isolated fungi on transitional organic and conventional farms
COLONY COUNT
FUNGAL GENERA
ORGANIC FARM
CONVENTIONAL FARM
Penicillium sp
8
8
Aspergillus niger
8
2
Trichoderma sp
5
2
Cladosporium sp.
5
5
Gliocladium sp.
2
*
Pythium sp. 2
2
Fusarium sp.
2
5
Rhizupos sp. 2
2
Legend:
* - nil
Organic Farmers Practices
All transitional organic farmers interviewed maintain the fertility level of their
farms by applying compost, chicken dung, organic fertilizers and do mulching and other
practices that add organic matter to the soil. Some of the farmers introduced beneficial or
effective microorganisms available in the market such as Trichoderma sp. and Virtouso,
which contain Bacillus sp. According to the farmers, they use Trichoderma to control
Assessment of Microorganisms in Transitional Organic and
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soil-borne diseases and as plant growth promoter. For controlling pest and diseases,
organic farmers use resistant varieties, botanical pesticides and biofungicides such as
Virtouso.
These practices may explain the presence or absence as well as the population of
beneficial fungi and bacteria as earlier presented in Table 1 and Table 3. In a nutshell,
transitional organic farm have a higher population of beneficial microorganisms than in
conventional farms.
Assessment of Microorganisms in Transitional Organic and
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SUMMARY, CONCLUSION AND RECCOMENDATIONS
Summary
The microorganisms found in transitional organic farms and conventional farms
are Bacillus sp., Streptomyces sp., Ralstonia sp., Penicillium sp., Trichoderma sp.,
Gliocladium sp., Fusarium sp., Cladosporium sp., Pythium sp., Rhizopus sp., Aspergillus
niger and Pseudomonas fluorescence, which is only found on transitional organic farm.
Of these microorganisms, those classified beneficial based on previous works
include P. fluorescence, Bacillus sp., Trichoderma sp., Gliocladium sp., and A. niger.
These beneficial microorganisms have greater population in transitional organic farms
than in conventional farms. Conversely, pathogenic microorganisms, which include
Ralstonia sp. and Fusarium sp. have a greater population on conventional farms than in
transitional organic farms. Microorganisms such as Pythium sp., Penicillium sp.,
Rhizopus sp. and Cladosporium sp. have the same population on both transitional and
organic farms.
Conclusion
There are beneficial microorganisms (based on previous works) present in
transitional organic farms in Benguet. Said beneficial microorganisms have higher
population in transitional organic farms than in conventional farms. Conversely, some
pathogenic microorganisms have a higher population in conventional farms.
Assessment of Microorganisms in Transitional Organic and
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Recommendations
Based from the results of the study, the following are suggested.
1. Pathogenicity test need to be conducted among the isolates to determine their
efficacy against certain pathogenic species.
2. Further characterization of the isolates including DNA analysis need to be
undertaken.
3. There is a need to investigate the mode of action of beneficial microorganisms
on pathogenic microorganisms.
Assessment of Microorganisms in Transitional Organic and
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APPENDIX
Appendix A. Survey Questionnaire
I. Personal information
1. Name:
2. Sex:
3. Address:
Farm
Location:
4. Educational attainment
a. no formal education
g.college graduate (degree)
b. elementary level
c. elementary graduate
h. vocational/ diploma
d. high school level
e. high school graduate
f. college level
5. Trainings and seminars attended:
II. Farm Management
1. How many years have you been in farming?
2. How many years have you been farming organically?
Conventionally?
3. Is your farm certified? Yes No
4. Is all your production organic/conventionally produce? Yes No
Or do you mixed organic and conventional farm? Yes no
5. Do you farm full time or part time?
6. What is the total area devoted to organic farming?
On vegetable organic farming?
7. Crops grown:
Estimated area:
8. Cropping pattern
Monocropping:
Mixed cropping:
Crop rotation:
Assessment of Microorganisms in Transitional Organic and
Conventional Vegetable Farms / Hector C. Alibuyog. 2007
33
III. Production Management
1. Tillage operation
Cultivate land using ٱ grabhoe ٱ machines
ٱothers
No tillage
2. Pest and Disease Management
a. Weeds:
Management
measures
Mechanical tillage
Weeding by hand
Cover crops:
Mulches:
Burning:
Chemicals:
Other control:
b.
Insects:
Management measures
Use of resistant varieties:
Crop
rotation:
Mixed
cropping:
Beneficial
insects:
Botanical
pesticides:
Chemical
pesticides:
Use of traps ٱplants ٱpheromones
ٱothers
(specify)
c.
Diseases:
Management
measures
Use of resistant varieties:
Crop
rotation:
Mixed cropping with:
Beneficial microorganisms:
Botanical
pesticides:
Chemical
pesticides:
Other
control:
3. Fertility management
Materials used
Compost
application
Green
manuring
Organic fertilizers
Assessment of Microorganisms in Transitional Organic and
Conventional Vegetable Farms / Hector C. Alibuyog. 2007
34
Mulching
Cover
cropping
Fermented
products
Effective
microorganisms
Balancing
soil
pH
Synthetic
fertilizers
Others (Specify)
Assessment of Microorganisms in Transitional Organic and
Conventional Vegetable Farms / Hector C. Alibuyog. 2007
Document Outline
- Assessment of Microorganisms in
Transitional Organic and Conventional Vegetable Farms.
- BIBLIOGRAPHY
- ABSTRACT
- TABLE OF CONTENTS
- INTRODUCTION
- REVIEW OF LITERATURE
- MATERIALS AND METHODS
- RESULTS AND DISCUSSION
- Characteristics of the Isolated Bacteria
- Bacterial Colony Counts in the Soil Samples
- Characteristics of the Isolated Fungi
- Population of the Isolated Fungi
- Organic Farmers Practices
- SUMMARY, CONCLUSION AND RECCOMENDATIONS
- Summary
- Conclusion
- Recommendations
- LITERATURE CITED
- APPENDIX