MICROBIAL ECOLOGY

Module Code
Credits
Pre-requisites
Lecturer(s)
Module Description

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BIO-60506
2-1 Credits
Microbiology BIO-60502
Prof. Dr. A. Endang Sutariningsih Soetarto, MSc.
The module consists of six Topics: Introduction in which
describes concepts and applications in ecology of
microorganisms in natural and engineered environments;
Advances in molecular-based understanding of microbial
behavior principles and interactions in ecosystem; Microbially
driven biogeochemical processes interactions among microbial
populations and communities; Microbial processes and
interactions in extreme or unusual environments associated with
environmental pollution; Methods and parameters of determining
diversity and functioning; Economic Microbial ecology and
Microbial ecology in Biotechnology

Kuliah Ekologi Mikrobia meliputi enam pokok bahasan, yaitu:

Pengantar yang membahas tentang konsep dan arti penting serta
aplikasi ekologi mikrobia di alam dan lingkungan terekayasa;
Prinsip perilaku dan interaksi mikrobia di dalam ekosistem pada
aras dan berdasarkan pemahaman molekular; Aktivitas mikrobia
dalam proses biogeokimia hasil interaksi antara populasi dan
komunitas mikrobia; Proses mikrobia dan interaksi yang terjadi
pada lingkungan ekstrim atau lingkungan yang terkait dengan
polusi; Metoda dan parameter untuk menentukan keanekaragaman
dan fungsi mikrobia di alam; Nilai ekonomi Ekologi mikrobia dan
Ekologi mikrobia dalam bioteknologi

.Daftar Pustaka:
Atlas, R.M. and R. Bartha. 1998. Microbial Ecology: Fundamentals and Applications, 4th
ed. Benjamin/Cummings Science Publishing.
Cappuccino J.G. & Sherman N. (2002) Microbiology, a Laboratory Manual (6th edit).
Benjamin Cummings.
Lynch, J.M. and Hobbie, J.E. 1988. Micro-organisms in Action: Concepts and Applications
in Microbial Ecology. Blackwell Scientific Publications
Madigan, M.T., J.M. Martinko, and J. Parker. 2000. Brock Biology of Microorganisms, 9th
ed. Prentice Hall.
Yogyakarta, 1 Oktober 2012
Dosen Pengampu

Prof. Dr. A. Endang Sutariningsih Soetarto, MSc

TENTATIF JADWAL KULIAH EKOLOGI MIKROBIAI (BIO 6057/2-1)

PROGRAM STUDI S2-BIOLOGI FAK. BIOLOGI UGM 2015/2016
Hari Rabu, 10.00 - 11.40
1.

Tanggal
16-9-15

2.

23-09-16

3.

30-09-16

4.

07-10-15

5.

14-10-15

6.
7.
8.
9.

21-10-15
28-10-15

Mingg

10
11.

I.

Pokok Bahasan
Pengantar

II. Prinsip perilaku mikrobia di

dalam ekosistem dan
interaksi mikrobia di dalam
ekosistem pada aras dan
berdasarkan pemahaman
molekular

III. Aktivitas mikrobia dalam

proses biogeokimia hasil
interaksi antara populasi
dan komunitas mikrobia;
MIDTERM
IV. Proses mikrobia dan
interaksi yang terjadi pada
lingkungan ekstrim atau
lingkungan yang terkait
dengan polusi;
V. Metoda dan parameter
untuk menentukan
keanekaragaman dan
fungsi mikrobia di alam

12.

VII. Nilai ekonomi Ekologi

mikrobia dan Ekologi
mikrobia dalam bioteknologi

13.
14.
15.

Liburan
Minggu tenang
UJIAN AKHIR

Sub Pokok Bahasan

1. Arti penting dan Manfaat ekologi mikrobia serta
ruang lingkupmya
2. Konsep ekosistem dan aplikasi ekologi mikrobia
di alam dan lingkungan terekayasa;:
3. Keanekaragaman mikrobia dan metabolik :
mikrobia di alam
4. Faktor lingkungan yang mempengaruhi aktivitas
MO
1. Adaptasi dan Seleksi alam populasi Mikrobia
2. Dinamika komunitas dan populasi mikrobia
3. Perkembangan dan suksesi komunitas MO
Kolonisasi dan suksesi (Suksesi mikrobia
pada pembusukan dan fermentasi
Suksesi mikrobia di dalam tubuh hewan dan
tumbuhan
Homeostatis dan Suksesi sekunder
4. Potensi interaksi mikrobia dengan jasad lain
1. Aktivitas Mikrobia pada proses biogeokimia:
Daur karbon, nitrogen di alam
2. Interaksi mikrobia di lingkungan
3. Pengendalian hayati
1. Proses mikrobia di Lingkungan alam : terestian,
akuatik, dan udara (Biodegradasi,
Biodeteriorasi, dll)
2. Proses mikrobia di dalam tubuh hewan
3. Pencemaran lingkungan air dan
pencegahannya

1. Parameter ekologi mikrobia

Pengenalan teknik pengambilan sampel

Estimasi populasi mikrobia dengan metoda
biokimia (Protein, ATP, Klorofil, LPS dan
asam muramat
2. Penentuan biomasa Mikrobia (teknik molecular)
1.
Masalah logam, xenobiotik dan senyawa
rekalsitran
2.
Aplikasi komersial bioproses pada
lingkungan bermasalah: bioremediasi lingkungan
tercemar dan biomineralogi (mendapatkan
kembali mineral dan logam); biosensor, biofuel,
plastik yang biogradable, penangan limbah dan
biokontrol.
3.
Manfaat ekologi mikrobia bagi bioteknologi

Aktivitas Kelas
Minggu 1 Diskusi kelompok::
1.
How do you see microbial ecology as being relevant in your life and

work?
2. What are some of the key questions you would like to explore
this lecture?
Diskusi dikerjakan sesuai latar belakang ilmiah mengapa anda memilih
matakuliah ini.
The Microbial World -- general overview, roles on our planet, history of life
Brock xxi-37; 322-329
Minggu 5

Genetika: molekular Mikrobia (masing-masing mahasiswa menyiapkan diri

untuk membahas materi kuliah merupakan prinsip dan konsep dasar
(dengan topic terkait) untuk memahami aktivitas mikrobia di lingkungan)

Minggu 7

Presentasi mahasiswa:
1. Nitrogen, sulfur, Carbon and iron cycles
2. Microbial bioremediation of natural compounds

(build from 669-676) Carbon cycle: 652-662; Plant interactions: 679-694

Minggu 9

Presentasi tentang ** how much deeply you understand the relationship

between microbial physiology and energetics
1. Colonization and microbial succesion (on deterioration and fermentation
2. The biodegradation of pesticides and polynuclear aromatic
hydrocarbons,
3. microbial ecology and biogeochemistry of acid mine drainage,
4. microbial solubilization and weathering of minerals, and
5. Microbial processes in landfills.

Presentasi dibarengi dengan diskusi, dalam bentuk tulisan ilmiah (maksimal 1000 kata)
Minggu 11

Presentasi tentang

1. Marine microbiology
2. Essentials of Viruses and Phages:

B. Practical work schedule

Practical work in the laboratory is to combine microbial metabolism and ecology
with environmental disciplines and starts after three week lectures
Topics for laboratory experiment
1)
microbial ecology and biogeochemistry of mineral soil (Iron sand)
2)
the biodegradation of pesticides and polynuclear aromatic hydrocarbons
Topic
1. Microbial ecology and biogeochemistry of iron sand (mineral soil)
The scope of the study
Mine drainage constitutes a serious water pollution problem in mine areas.
Treatment methods of acid mine water include constructed wetland systems
to remove acidity and metal ions.
The approach to elucidating microbial ecology in constructed acid mine
wetlands is based on using 16S rDNA-based techniques. With emphasis on
non-culturable approaches, genetic stains (using fluorescent in situ
hybridization (FISH) is used to characterize microbial communities
Geochemical and mineralogical changes with time are described by analysis
of pore water and iron precipitates in aerobic and anaerobic zones.
Topic
2. The biodegradation of pesticides and polynuclear aromatic hydrocarbons
The scope of the study
Biodegradation is the most important factor in the attenuation of pesticides in
soils.
Biodegradation rates vary with presence of microorganisms with degradative
capabilities and bioavailability in soils and subsurface environments.
Annual applications of this herbicide may enhance biodegradation rates in
agricultural soils.
Biodegradation rates reflect the growth of microorganisms. The growth
kinetics reflects phenotypic and genotypic variation in soil microbial
communities.
Complete biodegradation of this herbicide involves dehalogenation, Ndealkylation, deamination, and ring-cleavage steps.
The genes provide the basis for the characterization of soil microbial
communities by molecular techniques such as DNA probes and PCR
amplification, cloning, and sequencing.
To assess the biodegradation potential of polynuclear aromatic hydrocarbons
in water sediments impacted by hydrocarbon pollution and storm water
runoff.
The biodegradation potential yields useful information for assessing the fate
and kinetics of the biodegradation of these compounds in environments
impacted by anthropogenic sources.
Such information may be useful in designing bioremediation strategies for
solid waste materials.
Aims

Introducing techniques how to design an experiment

Introducing modern molecular techniques to detect, phylogeny and tracking
of microbial community active in biodegradation.

Laboratory activities
1. Field surveys and sampling of water sediment

Location: South beach of Yogyakarta:

Samples: Sea water and mud or sediment

Collecting environment data : pH, temperature of

samples
2. Lobotomy experiment:
Set-up equipments for running experiment
Isolation of bacterial strains through an enrichment culture technique
Enumeration mineral or pollutant degrading bacteria
Detection and characterization of microbial communities by molecular
techniques using genetic stain (FISH).
3. Parameter measurement:
Bacterial population involved in the biodegradation and biodegradation
rates