Q2.

Activities of microbes in natural environments are studied in the field of microbial

ecology. Describe the importance of this field of study by identifying two different
locations and what the impact of microbes can be on that location or on any other living
organism in that location. The impact that you describe can be a positive impact or a
negative impact.

Introduction:
Microbial ecology is the study related to the interactions of microorganisms between the and
their impact and interactions with their environment.
Microbial ecology stands out to be very important in the regards of importance of
microorganism in the very settings of an environment. In an environment microorganism can
leave either a devastating or a contrastive role microbiota for example plays an important role
while interacting with the human GIT and on the other hand the same microorganism can play
a destructive role in a pond with algal bloom. Microorganism plays a role in the whole
biosphere of planet earth, specially maintaining the biogeochemical cycles. As a consequence
of the quantitative magnitude of microbial life (calculated as 5.0×1030 cells; eight orders of
magnitude greater than the number of stars in the observable universe [5][6]) microbes, by virtue
of their biomass alone, constitute a significant carbon sink.
Importance:
Microorganisms are the backbone of all ecosystems, but even more so in the zones where
photosynthesis is unable to take place because of the absence of light. In such zones,
chemosynthetic microbes provide energy and carbon to the other organisms. These
chemotrophic organisms can also function in environments lacking oxygen by using other
electron acceptors for their respiration. Other microbes are decomposers, with the ability to
recycle nutrients from other organisms' waste products. These microbes play a vital role in
biogeochemical cycles. The nitrogen cycle, the phosphorus cycle, the sulphur cycle and the
carbon cycle all depend on microorganisms in one way or another. For example, the nitrogen
gas which makes up 78% of the earth's atmosphere is unavailable to most organisms, until it is
converted to a biologically available form by the microbial process of nitrogen fixation. Due
to the high level of horizontal gene transfer among microbial communities, microbial ecology
is also of importance to studies of evolution.

Location of microbes and their Ecology:

1. Human Microbiome:
The human gut harbour diverse microbes that play a fundamental role in the well-being of
their host. The constituents of the microbiota—bacteria, viruses, and eukaryotes—have been
shown to interact with one another and with the host immune system in ways that influence
the development of disease
The Healthy Microbiota
Characterizing the Human Gut Microbiota:
Determining what constitutes a healthy microbiota and the variability found across
populations is a prerequisite for assessing deviations that are associated with disease
states. Microbes colonize all of the surfaces of the human body that are exposed to the
environment, with the majority residing in the intestinal tract, which is the focus of
this Review. Distinct microbial communities are also found in the mouth in the vagina,
and

The human microbiota affects host physiology to a great extent. Trillions of microbes
colonize the human body, including bacteria, archaea, viruses, and eukaryotic
microbes. The body contains at least 1000 different species of known bacteria and
carries 150 times more microbial genes than are found in the entire human genome [2].
Microbiotic composition and function differ according to different locations, ages,
sexes, races, and diets of the host [27]. Commensal bacteria colonize the host shortly
after birth. This simple community gradually develops into a highly diverse ecosystem
during host growth [28]. Over time, host-bacterial associations have developed into
beneficial relationships. Symbiotic bacteria metabolize indigestible compounds,
supply essential nutrients, defend against colonization by opportunistic pathogens, and
contribute to the formation of intestinal architecture [29]. For example, the intestinal
microbiota is involved in the digestion of certain foods that cannot be digested by the
stomach and small intestine, and plays a key role in maintaining energy homeostasis.
These foods are primarily dietary fibers such as xyloglucans, which are commonly
found in vegetables and can be digested by a specific species of Bacteroides [30].
Other non-digestible fibers, such as fructooligosaccharides and oligosaccharides, can
be utilized by beneficial microbes, such as Lactobacillus and Bifidobacterium [31].
Studies have clarified the role of the gut microbiota in lipid and protein homeostasis as
well as in the microbial synthesis of essential nutrient vitamins [32]. The normal gut
microbiome produces 50–100 mmol·L-1 per day of short-chain fatty acids (SCFAs),
such as acetic, propionic, and butyric acids, and serves as an energy source to the host
intestinal epithelium [33]. These SCFAs can be quickly absorbed in the colon and
serve many diverse roles in regulating gut motility, inflammation, glucose
homeostasis, and energy harvesting [34,35]. Furthermore, the gut microbiota has been
shown to deliver vitamins to the host, such as folates, vitamin K, biotin, riboflavin
(B2), cobalamin (B12), and possibly other B vitamins. A previous study demonstrated
that B12 can be produced from delta-aminolevulinate (ALA) as a precursor [36]. In
addition, gut-colonizing bacteria stimulate the normal development of the humoral and
cellular mucosal immune systems [37]. The signals and metabolites of microorganisms
can be sensed by the hematopoietic and non-hematopoietic cells of the innate immune
system and translated into physiological responses [38]. Studies comparing normal
mice with GF mice have found that GF mice show extensive defects in the
development of gut-associated lymphoid tissue and antibody production [29,39]. A
report has also demonstrated that the gut microbiota generates a tolerogenic response
that acts on gut dendritic cells and inhibits the type 17 T-helper cell (Th17) anti-
inflammatory pathway [40]. However, not all microbiota lead to health benefits. Some
induce inflammation under certain conditions.
3. The human microbiota in disease
3.1. The human microbiota and infectious diseases

Infection is one of the most common diseases caused by dysbiosis of the microbiota.
Importantly, infectious disease and its treatment have a profound impact on the human
microbiota, which in turn determines the outcome of the infectious disease in the
human host (Fig. 2). Offending pathogens colonize the intestinal mucosa, thus
resulting in the induction of a strong inflammatory response, followed by the
translocation of the intestinal bacteria Numerous studies have demonstrated the
intimate relationship between infection and dysbiosis of the microbiota, and have
shown that infection is associated not only with the microbiome, but also with viruses.
For example, the intestinal microbiota of patients with Clostridium difficile (C.
difficile) infection (CDI) is significantly altered. Disturbance of the microbiota is also
associated with the progression of human immunodeficiency virus (HIV) [44,47],
hepatitis B virus (HBV), and other diseases.
3.1.1. Infection with Clostridium difficile

The pathological overgrowth of C. difficile is usually related to antibiotic-associated

diarrhoea, which is one of the most frequent complications following antibiotic
administration and which is now a growing public health threat. C. difficile is an
anaerobic, gram-positive, spore-forming bacillus that is a component of the human gut
microbiota. Antibiotics disturb intestinal mucosa homeostasis, thus decreasing
resistance against toxin-producing C. difficile and promoting the progression of CDI.
faecal bacterial diversity is reduced, and the microbial composition dramatically shifts
in patients following antibiotic administration, whether or not CDI is present. A
decrease in putative butyrate-producing anaerobic bacteria and an increase in
endotoxin-producing opportunistic pathogens and lactate-producing phylotypes have
been detected in patients following antibiotic administration, whether or not CDI is
present. Putative butyrate-producing anaerobic bacteria are significantly depleted in
patients with antibiotic treatment when compared with healthy controls. The above
changes in microbial communities may increase susceptibility to C. difficile
colonization. Ling et al. found that different toxigenic C. difficile strains have different
effects on fecal microbiota in children. C. difficile strains that are both toxin A-
positive and toxin B-positive reduce fecal bacteria diversity to a greater degree than
strains that are only toxin B-positive.
3.1.2. Infection with Helicobacter pylori
Helicobacter pylori (H. pylori) is a pathogen that induces peptic disease. It was recently found
to be related to the progress of periodontitis [49]. Hu et al. [49] investigated the correlation of
H. pylori infection with periodontal parameters, periodontal pathogens, and inflammation.
Their study showed that the frequencies of Porphyromonas gingivalis, Prevotella intermedia,
Fusobacterium nucleatum, and Treponema denticola are significantly higher in patients
infected with H. pylori than in those without infection, whereas the frequency of
Aggregatibacter actinomycetemcomitans is lower. The results indicate that patients with H.
pylori show significantly higher probing depth and attachment loss, and that H. pylori might
promote the growth of some periodontal pathogens and aggravate the progress of chronic
periodontitis

2. Environmental Microbes and their role in geochemical cycles

Nutrients move through the ecosystem in biogeochemical cycles. A biogeochemical cycle is a
pathway by which a chemical element (such as carbon or nitrogen) circulates through the
biotic (living) and the abiotic (non-living) factors of an ecosystem. The elements that move
through the factors of an ecosystem are not lost but are instead recycled or accumulated in
places called reservoirs (or “sinks”) where they can be held for a long period of time.
Elements, chemical compounds, and other forms of matter are passed from one organism to
another and from one part of the biosphere to another through these biogeochemical cycles.

Ecosystems have many biogeochemical cycles operating as a part of the system. A good
example of a molecule that is cycled within an ecosystem is water, which is always recycled
through the water cycle. Water undergoes evaporation, condensation, and then falls back to
Earth as rain (or other forms of precipitation). This typifies the cycling that is observed for all
of the principal elements of life.

Figure: The Water Cycle: Water is recycled in an ecosystem through the water cycle.

Although biogeochemical cycles in a given ecosystem are coordinated by the full complement
of living organisms and abiotic factors that make up that system, microorganisms play a
primary role in regulating biogeochemical systems in virtually all of our planet’s
environments. This includes extreme environments such as acid lakes and hydrothermal vents,
and even includes living systems such as the human gut. The key collective metabolic
processes of microbes (including nitrogen fixation, carbon fixation, methane metabolism, and
sulfur metabolism) effectively control global biogeochemical cycling. Incredibly, production
by microbes is so immense that global biogeochemistry would likely not change even if
eukaryotic life were totally absent!
Microbes comprise the backbone of every ecological system, particularly those in which there
is no light (i.e. systems in which energy cannot be collected through photosynthesis ). Two
key examples of critical biogeochemical processes carried out by microorganisms are
discussed below.

The Carbon Cycle

Figure: Cyanobacteria: Cyanobacteria, also known as blue-green bacteria, blue-green

algae, and Cyanophyta, is a phylum of bacteria that obtain their energy through
photosynthesis

Carbon is critical for life because it is the essential building block of all organic compounds.
Plants and animals utilize carbon to produce carbohydrates, fats, and proteins, which can then
be used to build their internal structures or to obtain energy.

Carbon in the form of carbon dioxide (CO 2) is readily obtained from the atmosphere, but
before it can be incorporated into living organisms it must be transformed into a usable
organic form. The transformative process by which carbon dioxide is taken up from the
atmospheric reservoir and “fixed” into organic substances is called carbon fixation. Perhaps
the best-known example of carbon fixation is photosynthesis, a process by which energy
derived from sunlight is harnessed to form organic compounds. Photosynthesis depends on the
activity of microorganisms such as cyanobacteria; indeed, the fact that there is oxygen in the
Earth’s atmosphere at all is a consequence of the photosynthetic activity of ancient microbes.

The Nitrogen Cycle

Nitrogen is essential for all forms of life because it is required for synthesis of the basic
building blocks of life (e.g., DNA, RNA, and amino acids). The Earth’s atmosphere is
primarily composed of nitrogen, but atmospheric nitrogen (N2) is relatively unusable for
biological organisms. Consequently, chemical processing of nitrogen (or nitrogen fixation) is
necessary to convert gaseous nitrogen into forms that living organisms can use. Almost all of
the nitrogen fixation that occurs on the planet is carried out by bacteria that have the enzyme
nitrogenase, which combines N2 with hydrogen to produce a useful form of nitrogen (such as
ammonia). Thus, microorganisms are essential for plant and animal life forms, which cannot
fix nitrogen on their own.

Conclusion

Microbial ecology stands out to be a very important player in the whole of the biosphere
and plays very important role in keeping the biosphere balanced. It has both negative
and positive interactions with the rest of the organisms.