ay in hExam 2014 (The exam was the same for everyone, but these are the questions that each student reported)
1st exam (studend a):
1) 10 questions (short reply) – genomics questions are easy – Characteristics of cyanobacteria
2) Koen Sabbe (easy & nice): biodiversity – endosymbiosia
3) Wim W. : explain the distribution of organism in the water column from the surface to the level of 0% oxigen and which are the characteristic that can conditioned the distribution (ie, light, pigment composition)
2nd exam (student B)
DGGE XLD lyofilization Biocorrosion DGGF blooms why do they flourish?
plus 10 concepts to write
3rd exam: (student C)
a) the first one asked for concepts (short definitions) and also for quorum sensing and something else
b) the second part asked for the organization of microbial communities along the water column and other things
c) third part for the endosymbiosis theory and the primary, secondary and tertiary endosymbiosis
Exam 2015
10 Concepts to describe in three lines:
1. meta-omics
2. lyophilization
3. Tara oceans
4. Photobacterium profundum
5. XLD agar
6. DGGE
7. Comparative genome hybridisation
8. Biocorrosion
9. …
10. …
11. …
Plus two questions:
a)
b) Vibrio cholerae
——————–
Part. Koen Sabbe
a) Two theories of biodiversity (ubiquity model and island biogeography theory)
b) endosymbiosis theory and the primary, secondary and tertiary endosymbiosis
——————–
Part Wim W.
a) organization of microbial communities along the water column according to oxigen
b)
Exam 6/01/2015
G.Huys/ G. Lima-Mndez:
1) definitions: pufM, DGGE, Tara Oceans, meta-omics, CGH, lyophilization, biocorossion, Photobacterium profundum, …
2) V. cholerae: 2 cellular mechanisms that help the bacterium to survive in the environment
3) metagenomics in context of habitat preference organisms + give example conection with evolution
K. Sabbe:
1) 1, 2nd, 3th endosymbiosis
2) 2 theories about biodiveristy
W. Vyverman:
1) vertical stratification micro organisms in the watercolumn, correlation OMZ
2) why cam some algae become HAB?
Geert Huys/ Lima Mendez:
Ten Questions on Definitions. Answer in 3 Lines (Short replies):
Characteristics of Cyanobacteria
Quorum Sensing
Genomic Questions
DGGE
XLD
Biocorrosion
DGGF
Why do blooms flourish?
metagenomics
Lyophilization
Tara oceans
Photobacterium profundum
XLD agar
Comparative genome hybridisation
Other Questions on:
1. Vibrio cholerae: 2 cellular mechanisms that help the bacterium survive in the environment
2. Metagenomics in context of habitat preference organisms + give example conection with evolution
Koen Sabbe:
1. Two Theories of Biodiversity
2. Endosymbiosis theory and the primary, secondary and tertiary endosymbiosis
Wim:
1. Explain the organization of microorganism in the water column from the surface to the level of 0% oxygen. What are the characteristics necessary for the distribution (ie, light, pigment composition).
2. Why can algae become HABs?
The pufM gene encodes a pigment-binding protein in the photosynthetic reaction center of all purple phototrophic bacteria, as well as Chloroflexus
Question: Metagenomics in context of habitat preference organisms + give example conection with evolution
The choice of the microbial community to study will be driven by the underlying scientific question being addressed. However, the more information one has about the study habitat—physical, chemical, and ecological—the more insight can be derived from the metagenomic data. Specific hypotheses can be posed and genes sought in genomic data from a well-characterized site. The acid mine drainage study is a case in point. The geochemical conditions that create and maintain that habitat were delineated before the researchers embarked on their metagenomics journey. As a result, the information gleaned in studying the genomes could be placed in a phylogenetic, biochemical, and physiological context. For example, knowledge of the nitrogen budget of the site impelled the researchers to seek nitrogen-fixation genes in the metagenome. When they did not find candidate genes in the dominant members, they examined the minor components of the community and discovered that one of the least abundant members of the community, Leptospirillum ferrodiazotrophum, carried the nif operon. They then cultured that bacterium by providing N2 as the only nitrogen source to ensure that only nitrogen-fixing bacteria would grow. The discovery of the keystone species (a community member whose significance to the community is larger than its relative abundance) was made possible by an ecological inference that depended entirely on knowledge of the site.
Exploring habitats that have been well studied by other methods will accelerate progress in metagenomics.
• Well-characterized habitats will leverage the value of metagenomic data.
• Interdisciplinary collaborations with scientists studying the non-microbial aspects of the habitat will inform the analysis.
• Different habitats require different depths of sequencing depending on their complexity and the degree of completeness needed to address the questions being posed. Pilot studies to determine the required depth of sequencing may be necessary.
Habitat change over time is one of the most interesting aspects of communities. Their responses to changing conditions are central to understanding community structure, function, and robustness. Understanding the role of host-associated microbial communities in host development and health requires not only sampling from the same host over time, but also understanding host-to-host variation.
Bicorrosion
Biocorrosion refers to corrosion influenced by bacteria adhering to surfaces in biofilms. Biocorrosion is a major problem in areas such as cooling systems and marine structures where biofilms can develop.
The term microbially influenced corrosion, or biocorrosion, refers to the accelerated deterioration of metals owing to the presence of biofilms on their surfaces. The detailed mechanisms of biocorrosion are still poorly understood. Recent investigations into biocorrosion have focused on the influence of biomineralization processes taking place on metallic surfaces and the impact of extracellular enzymes, active within the biofilm matrix, on electrochemical reactions at the biofilm-metal interface.
Why do blooms flourish?
As sunlight is a vital component for the development of algae cells, they usually occur in summer, when there is increased light intensity and warmer water, which favors their development. Another essential ingredient for rapid growth and multiplication of algae is the availability of nutrients. Nitrates and phosphates occur naturally in ecosystems and are important building blocks for the development of primary producers (plants and algae).
However, when excessive nutrients flow into a water body, the algae cells multiply exponentially to form dense blooms. Nutrients can enter the system from various sources:
• Runoff from fertilizers used in crop production or maintenance of recreation facilities (golf courses, sports fields, etc)
• Sewage overload into the water body, animal waste products (e.g. runoff from farm lands), or animal waste from aquaculture.
This is exacerbated when heavy rains are experienced during spring and summer, or after heavy snowfalls when the snow starts to melt in summer, increasing runoff from land sources.
Why do harmful algal blooms occur?
Harmful algal blooms (HABs) occur when colonies of algae—simple plants that live in the sea and freshwater—grow out of control while producing toxic or harmful effects on people, fish, shellfish, marine mammals, and birds.
While we know of many factors that may contribute to HABs, how these factors come together to create a 'bloom' of algae is not well understood.
Studies indicate that many algal species flourish when wind and water currents are favorable.
In other cases, HABs may be linked to 'overfeeding.' This occurs when nutrients (mainly phosphorus, nitrogen, and carbon) from sources such as lawns and farmlands flow downriver to the sea and build up at a rate that 'overfeeds' the algae that exist normally in the environment.
Some HABs have also been reported in the aftermath of natural phenomena like sluggish water circulation, unusually high water temperatures, and extreme weather events such as hurricanes, floods, and drought.
People often get sick by eating shellfish containing toxins produced by these algae. Airborne HAB toxins may also cause breathing problems and, in some cases, trigger asthma attacks in susceptible individuals.
HABs can also be costly in economic terms as well. At present, HABs cause about $82 million in economic losses to the seafood, restaurant, and tourism industries each year. HABs reduce tourism, close beaches and shellfish beds, and decrease the catch from both recreational and commercial fisheries.
NOAA scientists continue to monitor and study HABs to determine how to detect and forecast the location of the blooms. The goal is to give coastal communities advance warning, so they can adequately plan and deal with the adverse environmental and health effects associated with a harmful bloom.
Photobacterium profundum
Deep sea Gammaproteobacerium, under the family vibrionaceae and genus photobacterium.
G(-) Rod, flagellates, mesophilics, barophilic and halophilic bacteria.
Like other vibrio species it also have two chromosomes
Chromosome 1 contains the most “established” genes, and it is stable. Chromosome 2 serves as the “genetic melting pot” or a target of gene transfer, containing a high number of unknown genes. The majority of transcription takes place in chromosome 1, where a minimal amount of transcription occurs in chromosome 2 since genes are poorly expressed there.
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