Instructor: Stjepko Golubic,
Tel. (617) 353-2436,
Prerequisites: BUMP - Core, and consent of instructor or director.
Course description: The course promotes understanding of the impact of microorganisms and their metabolic activities on marine environments today, and considers the importance of microbial activities in the geological past. It deals with interactions between microorganisms and their environment from microscopic to global scale. It explains biocatalytic enhancement of bio-geo-chemical processes. The course deals with case histories that illustrate how nutrient requirements determine the selection of microorganisms and their distribution in the habitat and how metabolic products of different microorganisms modify the environment they live in. Such modifications trigger microbial successions and lead to development of complex microbial consortia with complementary metabolic systems so that the product of one organism is used as a resource by another, thus promoting nutrient cycling.
Special attention is paid to interactions between microorganisms and sediments, involved in stabilization of loose sediment and construction of biosedimentary structures, such as microbialites and stromatolites through processes of biosedimentation and biomineralization. Different specialized microorganisms are involved in bioerosion, a process of integrated action of a number of different trophic modes and levels. These interactions leave recognizable signatures in sediments, and are significant over geological time.
The assessment of microbial diversity combines molecular phylogenetic information with the ecological roles and adaptations. Students learn elements of sedimentology, geochemisty and paleontology in conjunction with microbial life in the oceans. The role of microorganisms and applied microbiology in the abatement of coastal pollution is discussed.
Course organization: The course is organized around three basic activities: (a) Field work and laboratory exercises (b) Student projects and (c) Lectures with discussion.
Field trips are planned to be an integral part of the course. They will provide material for analytical
and/or experimental student projects.
When organized around
Student projects dealing with processes in microbial ecosystems will be generated mostly during the field trips. They will select particular problems encountered in aquatic environments and sedimentary systems. The projects will start with analyses in the field, followed by laboratory analyses of the materials collected. Additional projects are planned to concentrate on existing collections from the tropics. Students will learn and use analytical tools and technologies including light, fluorescence and scanning electron microscopy. Students will present the results of their projects in the style of professional meetings. Best presentations will be displayed on BUMP web site.
Lectures deal with topics referring to principles and processes in microbial ecology as supported by the textbooks. The Lectures promote basic understanding of microbial activities, distribution and diversity. They are accompanied and illustrated by case histories from research in microbial ecology as supported by original primary publications. The case histories illustrate the principles covered by the formal lectures.
Textbook: Konhauser, K. 2007. Introduction to Geomicrobiology.
425 pp. Blackwell Publishing. 350
Main str.
The topics to be covered by the lectures are listed below with the titles of Case Histories in italics. The actual sequence of topics may be re-arranged from year to year in accordance with the schedule of the field work.
1. The study of microbial ecology and
diversity. (a) Culture-dependent methods: From enrichment to axenic
culture Kochs principles and ecology Enrichment cultures Experimental
value of cultures Controlled conditions or controlled responses? Relevance of laboratory experiment results to
conditions in nature. (b) Culture independent methods: Molecular approaches to microbial diversity
in nature (PCR, FISH, DGGE). Relations between
genotypic characters (potential) and their phenotypic expresion
(realization) (c) Polyphasic pheno-genetic approach in microbial ecology. Evaluation of phylogenetic, metabolic and morphotypic diversity of
prokaryotic and eukaryotic microorganisms. Historic retrospect via
molecular sequence analysis vs. paleontological
record.
Corals as
microbial consortia past, present and future of coral reefs
Microbiology
of deep seeps and hydrothermal vents
2. Microbial diversity in marine
environments. Microorganisms as primary producers,
consumers and decomposers in the sea Redox systems
and energy generation. Environmental
requirements, metabolic systems and diversity: Chemolithotrophs
Organotrophs anoxygenic
and oxygenic Phototrophs. Anoxic and oxygenatged environments. Origins and consequences of oxygenic phototrophy The age of Prokaryotes: Primary production,
consumption and nutrient recycling in the prokaryotic world Microbial metabolism
and metal solubility Prokaryotes and N-cycling Picoplankton and picobenthos The
origins of eukaryotic organization and the age of Eukaryotes Prokaryotes in
extreme environments Evaporitic sequences Return
of Prokaryotes: Pasteurs prophecy.
Cyanobacteria:
Nature and diversity of Greater Bacteria
Extreme
environments and prokaryote dominance
Solar lake
and hypersaline ponds - geobiochemistry
of salt production
3. Microorganisms as architects of
sedimentary structures. Microbial biofilms,
mats and stromatolites Biomineralization
and skeletogenesis Chemistry of mineral deposition
Microbially influenced calcification Organically infuenced calcification Trapping and binding of sediment
particles Stromatolites in fossil record Early
and late diagenesis and microfossil preservation
Modern models to explain ancient occurrences.
Stromatolites and microbial fossils: windows into distant past
Biomineralization in modern stromatolites: 3
case histories.
4. Microbial weathering and bioerosion. Lithobiontic ecological
niches Microbial
endoliths and coastal bioerosion
Diversity and distribution of prokaryotic and eukaryotic endoliths Microbial
endoliths have a long history. Co-evolution of microbial endoliths and grazing
invertebrates and ertebrates The cumulateive impact of endolith-grazer
interactions on coastal erosion and generation of fine grain sediments Finishing student
projects Presentation of the results.
Environments,
agents and effects of coastal Bioerosion
The
life in a grain of sand: today and 800 My ago
The background color approximates
that of anaerobic green sulfur bacteria
Updated Feb., 2007.
Go to:
S. Golubic Home Page
BU Marine Program - information
BUMP - course description
BUMP - faculty page