MIKROBIOLOGI PERTANIAN
AGRICULTURAL MICROBIOLOGY
INTRODUCTION
Prof.Dr.Agr.Sc.Ir. Vita Ratri Cahyani, MP
Faculty of Agriculture
Sebelas Maret University
Academic Norms
1.Minimal class attendance: 75%
2.Completing all evaluations:
➢ take-home work, paper, presentation
➢ written test: quiz, mid-term test, final exam
3. Completing practicum
4. No cheating
5. No plagiarism
6. Scoring : process-evaluation and test-score
MICROORGANISMS and MICROBIOLOGY
1.1 Microbiology and You
1.2 Microorganisms as Cells
1.3 Elements of Cell and Viral Structure
1.4 Evolutionary Relationship Among Living Organisms
1.5 Microbial Populations, Communities, and Ecosystems
1.6 Laboratory Culture of Microorganisms
1.7 The Impact of Microorganisms on Human Affairs
1.8 The Historical Roots of Microbiology : van Leeuwenhoek, Pasteur, and Koch
1.9 Transition into the Twentieth Century
1.1 Microbiology and You
Microbiology :
➢ is about living cells and how they work
➢ is the study of microorganisms, a large and diverse group of microscopic
organisms that exist as single cells or cell clusters; it also includes viruses,
which are microscopic but not cellular. (+Meso- & makro-fauna)
Microorganisms are generally able to carry out their life processes of growth,
energy generation, and reproduction independently of other cells, either of the
same kind or different kind.
The cells of animals and plants are unable to live alone in nature and can exist
only as parts of multicellular organisms.
Microbiologists study microbiology for two major reason
1. As a basic science, biological science
2. As an applied biological science
Not everyone that studies microbiology aspires to be a microbiologist.
But everyone should know some microbial facts.
Why should you study microbiology?
1. Without microorganisms, all higher life forms on Earth would cease to exist.
2. Although individual microorganisms are very small, collectively their metabolic
power is very great. The sum total of their protoplasm constitutes the greatest source
of biomass on Earth.
3. Only a very limited number of microorganisms are pathogens, that is, capable of
causing disease. Their activities can lead to the death of plants and animals.
4. Microorganisms do not exist as individuals in nature, but instead with other organisms
in microbial communities. Their small size & rapid growth & ready ability to
exchangegenes, allow them to adapt rapidly to changing environmental conditions.
5. Microorganisms were the first life on Earth and that all living organisms share an
evolutionary link to microbial world.
6. Microorganisms show the greatest genetic and physiological diversity of all living
organisms. Microorganisms, especially the bacteria, are Earth’s greatest chemists.
Microorganisms are a key part of your life.
To survive on planet Earth, we clearly need to know everything we can about microbial life.
The Impact of Microorganisms on Human Affairs
1. Microorganisms as Diseases Agents
a. Identifying new diseases
b. Treatment and cure
c. Disease prevention
2. Microorganisms and Agriculture
a. N2 fixation
b. Nutrient cycling
c. Animal husbandry
3. Microorganisms and the Food Industry
a. Food preservation
b. Fermented foods
c. Food additives
4. Microorganisms, Energy, and the Environment
a. Biofuels (methane and ethanol)
b. Bioremediation
c. Microbial mining
5. Microorganisms and the Future (Biotechnology)
a. Genetically modified organisms
b. Production of pharmaceutical
c. Gene therapy for certain diseases
Development of the major subdisciplines of Microbiology
A. The applied aspects:
1. Medical microbiogy and imunology
2. Agricultural microbiology
3. Industrial microbiology
4. Aquatic microbiology
5. Microbial ecology
B. The basic aspects:
1. Bacterial physiology
2. Bacterial cytology
3. Bacterial chemistry
4. Bacterial genetics
5. Molecular biology
6. Bacteriophages
7. Biotechnology : a good example of how basic and applied research advance
together.
References:
Madigan T et al. 2019. Brock Biology of Microorganisms-Pearson
Alberts,B, Bray D, Johnson A, Lewis J, Raff M, Roberts K, Walter. 1998.
Essential Cell Biology. An Introduction to the Molecular Biology of the Cell.
Garland Publishing, Inc. New York.
Alexander M. 1977. Introduction to Soil Microbiology. John Wiley & Sons, Inc.
New York .
Bardgett RD, Usher MB, Hopkins DW 2005: Biological Diversity and Function
in Soils. Cambridge University Press, Cambridge
Buscot F, Varma A 2005: Microorganisms in Soils: Roles in Genesis and Function.
Springer, Berlin
Deacon, JW. 1997. Modern Mycology. Third Ed. Blackwell Science Ltd. London
Kimura M 2000: Anaerobic microbiology in waterlogged rice fields.
In Soil Biochemistry, Vol. 10. Eds JM Bollag and G Stotzky, pp. 35–138,
Marcel Dekker, New York.
Kimura M, Jia Z-J, Nakayama N, Asakawa S 2007. Ecology of viruses in soils:
past, present, and future perspectives. Review. Soil Science and Plant Nutrition,
54, 1–32
Madigan MT, Martinko JM, Parker J. 2000. Brock Biology of Microorganisms.
Ninth Ed. Prentice Hall International, Inc. New Jersey
Metting ,FB, Jr. 1993 (Ed). Soil Microbial Ecology. Application in Agricultural and
Environmental Management. Marcel Dekker, Inc. New York.
Nelson,DL , Cox,MM. 2000. Lehninger Principles of Biochemistry. Third Edition.
Worth Publisher. New York
Paul EA 2007: Soil Microbioloy, Ecology, and Biochemistry. 3rd Edition.
Elsevier Inc, MA
Van Elsas JD, Trevors JT, Wellington EMH 1997: Modern Soil Microbiology.
Marcel Dekker, Inc. New York
My researches & publications for
supporting the lecture:
Cahyani VR and Kimura M: Succession and phylogenetic composition of microbial
communities responsible for the composting process of rice straw.
In Joseph C. Pereira, and John L. Bolin (eds.), Composting: Processes, Materials and
Approaches. pp.69-112. Nova Science Publishers, Inc. New York, USA
ISBN: 978-1-60741-438-4
Cahyani VR, Murase J, Asakawa S, Kimura M 2009: Change in T4-type
Bacteriophage communities during the composting process of rice straw:
Estimation from the major capsid gene (g23) sequences. Soil Science and Plant
Nutrition,
55, 468-477
Cahyani VR, Murase J, Ishibashi E, Asakawa S, Kimura M 2009: T4-type
Bacteriophage communities estimated from the major capsid genes (g23) in
manganese
nodules in Japanese paddy fields. Soil Science and Plant Nutrition, 55, 264-270
Cahyani VR, Murase J, Ishibasi E, Asakawa S, Kimura M 2009: Phylogenetic
Positions of Mn2+-oxidizing bacteria and fungi isolated from Mn nodules in rice field
subsoils. Biology and Fertility of Soils, 45, 337-346
Watanabe T, Cahyani VR, Murase J, Ishibashi E, Kimura M, Asakawa S 2009:
Methanogenic archaeal communities developed in paddy fields in the Kojima bay
polder, estimated by denaturing gradient gel electrophoresis, real time PCR and
sequencing analyses. Soil Science and Plant Nutrition, 55, 73-79
Cahyani VR, Murase J, Ikeda A, Taki K, Kimura M: 2008: Bacterial communities in
iron mottles in the plow pan layer in a Japanese rice field: Estimation using
PCR-DGGE and sequencing analyses. Soil Science and Plant Nutrition, 54, 711-717
Cahyani VR, Murase J, Ishibasi E, Asakawa S, Kimura M 2007: Bacterial
Communities in manganese nodules in rice field subsoils: estimation using
PCR-DGGE and sequencing analyses. Soil Science and Plant Nutrition, 53, 575-584
Cahyani VR, Matsuya K, Asakawa S, and Kimura M. 2004. Succession and
Phylogenetic profile of eukaryotic communities in the composting process of
rice straw estimated by PCR-DGGE analysis. Biology and Fertility of Soils, 40, 334-344
Cahyani VR, Matsuya K, Asakawa S, and Kimura M. 2004. Succession and
Phylogenetic profile of methanogenic archaeal communities during the composting
process of rice straw estimated by PCR-DGGE analysis. Soil Science and Plant
Nutrition, 50, 555-563
Cahyani VR, Matsuya K, Asakawa S, and Kimura M. 2003. Succession and
Phylogenetic composition of bacterial communities responsible for the
composting
process of rice straw estimated by PCR-DGGE analysis. Soil Science and
Plant
Nutrition, 49, 619-630
Cahyani VR, Watanabe A, Matsuya K, Asakawa S, and Kimura M. 2002.
Succession of microbiota estimated by phospholipid fatty acid analysis and
changes in organic constituents during the composting process of rice straw.
Soil Science and Plant Nutrition, 48, 735-743
