Question 1

Biofilms:

Microbes in aquatic environments attached to surfaces are members of complex, slime-

encased communities called biofilms. Biofilms are ubiquitous in nature. They cause
corrosion which result in economic losses. These biofilms often cause serious illness
and failure of the medical device. Biofilms can form on virtually any surface once it has
been conditioned by proteins and other molecules present in the environment. Initially
microbes attach to the conditioned surface but can readily detach. Eventually they form
slimy matrix made up of various polymers called extra cellular polymeric substances
(EPS). The EPS matrix allows the microbes to stick more stably to the surface. As the
biofilms thickens and matures, the microbes reproduce and secrete additional polymers.
A mature biofilm is a complex, dynamic community of microorganisms. It exhibits
considerable heterogeneity due to differences in the metabolic activity of microbes at
various locations within the biofilm. The waste products of one microbe may be the
energy source for another microbes. The cells also use molecules to communicate with
each other. DNA present in the EPS can be taken up by members of the biofilm
community. Thus genes can be transferred from one cell to another. While in the
biofilm, microbes are protected from numerous harmful agents such as UV light and
antibiotics. The resistance of biofilm cells to antimicrobial agents has important
consequences. When biofilms form on a medical device, treatment with antibiotics often
fails, which can lead to serious systematic infections. The treatment failure is in part due
to the presence of persisters in the biofilm. The persisters survive antibiotic treatment
and then repopulate the biofilm once treatment ceases. Biofilm cells are regularly
sloughed off, which may serve as a source of contamination.
Microbial mats:

Microorganisms, through their metabolic activities, can create environmental gradients

resulting in layered ecosystem. Microbial mats are multilayered structures of
microorganisms, mainly bacteria, archaea, fungi and sometimes protozoans. They grow
at interfaces between different types of material, mostly on moist surfaces, but some are
found in dry environments. The colonized environments located in high altitude, they are
common in the deep biosphere, in subterranean environments with relatively low to high
temperatures. Microbial mats are characterized by intensive internal carbon cycling.
These highly striated communities of photoautotrophs and chemoautotrophs develop in
saline lakes, marine intertidal zones and hot springs. Some cold seeps are the sites of
microbial mats, which can sometimes cover several hundreds of meters. These mats
are dominated by giant vacuolated sulphur-oxidising bacteria in the genera Beggiatoa
and Thiomargarita.

Microbial loops:

Microorganisms play vital role in the ecosystem as primary producers, decomposers

and primary consumers. All bacterial and archaeal cells are consumed by protists which
also consume other protists. These microbes are then consumed by herbivores that
often select their food items by size, thereby ingesting both heterotrophic and
autotrophic microbes. Thus nutrient cycling is a complex system driven in large part by
microbes. The key to survival in the photic zones is the tight recycling of nutrients rather
than allowing them to sink to the seafloor. Within the microbial loop, photoautotrophic
microbes are the primarily procedures and heterotrophic microbes consume dissolved
organic matter (DOM) released as exudates by other microbes as well as larger plants
and animals. Marine viruses are also a source of DOM as the lysis of their host’s cells
contributes significantly to the return of nutrients into the microbial loop. This generates
a common pool of DOM that serves as a nutrient source for all osmotrophic organisms.
Protists including flagellates and ciliates consume smaller microbes, which may include
each other. Microbial cells, insoluble detritus and other solid organic material are called
particulate organic matter (POM). Because protists are then consumed by zooplankton,
both DOM and POM are recycled at a number of trophic levels. The net effect of the
microbial loop is the reuse of essential nutrients such as organic carbon, nitrate and
phosphate within the photic zone. Only a tiny fraction of the material sinks to the waters
below and resists degradation.
Question 2

2.1. Extreme environments – an environment in which physical factors such as

temperature, pH, salinity and pressure are outside of normal range for growth of most
organisms, these conditions allow unique organisms to survive and function.

2.2. Micro environment – the immediate environment surrounding a microbial cell or

other structure such as a root.

2.3. Benthos – the flora and fauna found on the bottom or in the bottom sediments of a
sea or lake.

2.4. Eutrophic – nutrient enriched and resulting in the rate of respiration greatly
exceeding that of photosynthesis, thus water becoming anoxic.

2.5. Geosmin – the filamentous actinomycetes, primarily of the genus Streptomyces,

produce an odor-causing compound, which gives soils their characteristic earthy odor.
Question 3
3.1. A simplified nitrogen cycle diagram:
3.2
Carbon cycle

 Important processes in the carbon cycle are photosynthesis, deposition and

decomposition.
 Carbon is absorbed by various plants and vegetation and converted into
carbohydrates via photosynthesis.
 Carbon travels through the food chain and eventually makes its way into the
atmosphere via cellular respiration, burning of fossil fuels or decay of
organisms.
 Carbon travels from the ground to the atmosphere
 The stage of fixation in the carbon cycle is made by plants and animals

Sulphur cycle

 Sulphur cycle involves the transformation of sulfur species through different

oxidation states, which plays an important role in both geological and biological
processes
 Enters the atmosphere in the form of sulphur dioxide and reacts with oxygen to
produce sulphur trioxide gas (SO3 ) to produce sulphur salt.
 Sulphur dioxide may also react with water to produce sulphuric acid ( H 2SO4),
which may also be produced from dimethyl-sulphide, which is emitted to the
atmosphere by plankton species.

Both carbon and sulphur cycle

 Both are involved in the ecosystem and the interaction of animals and nature.
That is carbon results by the burning of fossil fuels or decay of organisms and
sulphur by consequences of industrial processes where sulphur dioxide and
hydrogen sulphide ( H2S) gases are emitted on a wide scale.

Question 4
Soil microorganisms can be classified as bacteria, actinomycetes, fungi, algae and
protozoa and play essential roles in the nutrient cycles that are fundamental to life on
the planet.

Bacteria: are organisms that have only one cell and are therefore microscopic. They are
decomposers, eating dead plant material and organic waste. By doing this, the bacteria
releases nutrients that other organisms could not access. The process is essential in
the nitrogen cycle.

Actinomycetes: are soil microorganisms like both bacteria and fungi and have
characteristics linking them to both groups. Actinomycetes give soil its characteristics
smell and also been the source of several significant therapeutic medicines.
Fungi: are unusual organisms in that they are not plants or animals. They group
themselves into fibrous strings called hyphae. Hyphae then form groups called
mycelium which are less than 0.8mm wide but can get as long as several meters. Fungi
are helpful in a way that they have the ability to break down nutrients that other
organisms cannot. Fungi also attaches itself to plant roots and some plants grow better
when this happens and this is a beneficial relationship called mycorrhizal. Fungi can
also get food by being parasites and attaching themselves to plants or other organisms
for selfish reasons.
Algae: present in most of the soils where moisture and sunlight are available. They are
capable of photosynthesis, whereby they obtain carbon dioxide from atmosphere and
energy from sunlight and synthesise their own food.
Protozoa: these are colorless, single-celled animal-like organisms and larger than
bacteria. They derive their nutrition from feeding or ingesting soil bacteria and thus play
an important role in maintaining microbial /bacterial equilibrium in the soil. May also
cause diseases in human beings that are carried through water and other vector, for
example Amoebic dysentery.
Viruses: are of great importance as they may influence the ecology of soil biological
communities through both an ability to transfer genes from host to host and as a
potential cause of microbial mortality. Viruses are major players in the global cycles,
influencing the turnover and concentration of nutrients and gases
Soil microorganisms play an essential role in decomposing organic matter, cycling
nutrients and fertilizing the soil. The reactions involved in elemental cycling are often
chemical in nature, but biochemical reactions those facilitated by organisms also play
an important part in the cycling of elements.
Soil microorganisms are both components and producers of soil organic carbon, a
substance that locks carbon into the soil for long periods, improving the soil fertility and
water-retaining capacity. Research also supports the hypothesis that soil
microorganisms and fungi in particular can be harnessed to draw carbon out of the
atmosphere and sequester it in the soil.
Soil microorganisms may provide a significant means of reducing atmospheric
greenhouse gasses and help to limit the impact if greenhouse gas-induced climate
change.