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Pea plant wrapping itself around the previous year vine |
Soil has a particular aroma but it is not the soil itself but an
actinobacteria which produces geosmin. I like the earthy taste of freshly dug
potatoes or carrots. There is a saying that a good farmer can know when to
start planting by picking up a handful of soil and smelling it. This is a true
statement considering the actinobacteria only thrives in warm soil. Since most
seeds need a soil temperature between 50-77F which is optimum for the life
cycle of the species of Streptomyces
that I studied for a semester in microbiology. Below is an excerpt from my
essay:
Description of
an actinobacterium isolate from soil sample taken in the vicinity of the
Oconaluftee River, Great Smoky Mountains National Park
12 December 2012
Discussion
There are over 500 recognized species of Streptomyces, which is a testament to
how important the genus is to humans. Many Streptomyces
species play important roles in the decomposition of organic matter and are
ubiquitous in soil accounting for 106-107 per gram of
soil. [10] The genus is an important source of antibiotics for both
animals and plants. The genome of Streptomyces
are typically large and that is attributed to the high number of genes required
for antibiotic synthesis.[7] Chromosomes are linear, much like
eukaryotes, and the chromosomal ends functions similar to the function of telomeres
in eukaryotic cells. [11]
The isolated colony used for the study on the
R2A agar was 1-2mm in size with an opaque consistency, circular appearance and
curled edges. There was a zone of inhibition around the first colony which was
undetectable with subsequent inoculated plates. The isolated colony appeared to
change color from white to dark pink-purple with time, possibly due to nutrient
depletion of the agar. The cause for the coloration of the colony is due to
pigmented conidia and sporophores. [7] Depending on the composition
of the medium, the colony can appear blue, gray, green, red, violet or yellow. [10]
The life cycle of Streptomyces
involves sporophores which form cross-walls in the multinucleate sporophores
produce conidia also known as conidiospores or spores. [7] Conidiospores
germinate to make substrate mycelium. [10] Dormant spores can
readily be dispersed by air currents. [9] The colony had a
particular earthy odor which was caused by a group of volatile organic
compounds known as geosmins. [10]
Gram staining techniques showed the Streptomyces spp. to be gram-positive. Because
gram-positive microorganism have cell walls a thicker layer of peptidoglycan,
the crystal violet-iodine complex gets trapped in the cell wall making the
cells appear dark purple. A negative staining technique was also performed to
enable viewing the microorganism morphology and cellular arrangement. With the
aid of a compound light microscope, the microorganism appeared filamentous with
diameter sizes of approximately 1µm and a variable length size of up to 80µm.
According to data collected about Streptomyces,
the filament sizes are typically 0.5-1µm in diameter and indefinite in length. [7]
Environmental parameter tests were performed to
find the optimal environment which the microorganism could grow. The tests
showed Streptomyces spp. to be a
facultative anaerobe, but the growth was slower than aerobic environments. Temperature
parameter testing was used to determine if the Streptomyces spp. could thrive with a range of temperatures. The
results showed the species does not tolerate extreme temperatures of 4°C or
50°C and only two of the three streaks grew in 37°C. The microorganism thrived
in the control condition of 25°C. A salt tolerance test was performed using
concentrations of 0%, 5%, 10% and 15% NaCl. The Streptomyces spp. is halointolerant and only grew under the control
conditions of 0% NaCl. A pH test also conducted and it was found the
microorganism can tolerate a range of pH and growth occurring from pH 5-9. The
pH test results show the growth of the microorganism in alkaline to neutral
soils is more favorable than acidic.
Results from the environmental parameters test
demonstrate the variable soil pH the Streptomyces
can tolerate. Since the microorganism can tolerate lower oxygen levels as a
facultative anaerobe, the depth at which the organism can grow varies. In one
study Streptomyces was found in a
three different locations of prairie soil at four depths. The study used
variation in the 16S rDNA sequence to determine the genetic variation among the
Streptomyces strains. There was
little variation found in the genetic diversity from the isolates taken at
differing soil depths. [5] An
extreme Streptomyces has been isolated
from the hyper-arid Atacama Desert. Streptomyces
desertai can grow in temperatures from 10°C to 35°C between pH 4 and 11 and
in the presence of 4% NaCl. [12]
A modified catalase test was used to determine
if the organism had the enzyme. Because the genus does not typically react with
the standard amount used for a slide test, a modification of using more of the
sample directly on the R2A plate was used. The Streptomyces spp. tested positive for catalase, which means the
microorganism has the ability to convert hydrogen peroxide into water and
gaseous oxygen. The microorganism does not have cytochrome c oxidase as a
respiratory enzyme because it the results were negative for oxidase test. [1]
An Enterotube II was used to determine the
metabolic characteristics of Streptomyces
spp. The test included possible reactions with glucose, adonitol, lactose,
arabinose, sorbitol and dulcitol fermentation, lysine and ornithine
decarboxylation, sulfur reduction, indole production, acetin production from
glucose fermentation, phenylalanine deamination, urea hydrolysis, or citrate
utilization. The organism tested positive for the characteristic to ferment
glucose and had a slow reaction with hydrolyzing urea.[1] The Streptomyces spp. uses the carbohydrate,
glucose, as a sources of carbon and energy. A positive result for the enzyme
urease means that the organism hydrolyzes urea to ammonia, CO2 and water. Despite
the Streptomyces spp. inability to
react with the majority of medium found in the Enterotube II, the microorganism
has the ability to decompose biopolymers like lignocellulose, starch, chitin,
pectin and latex. [8][10]
The rhizosphere zone in the soil profile is
defined as the zone of soil that adheres to plant roots. Streptomyces thrive in
the rhizosphere zone with the aerobic conditions and loose loamy soil. [9]
With 106-107 Streptomyces
per gram of soil, the microorganism is ubiquitous in the rhizosphere.[10] Because of the filamentous mode of growth,
the Streptomyces has a competitive
advantage in colonizing around plant roots. Streptomyces
decompose organic matter such as plant residues, but also benefit plants by
growing in close associating with the root system where they protect the plant
roots from potential invasion by fungal pathogens. Studies have shown with
legumes, the Streptomyces assimilate
iron from the soil and transfer it into root nodules where it is assimilated by
bacteroids. [8] Streptomyces
virginiae has been found to be beneficial in the prevention of tomato wilt
caused by a soil-borne plant pathogen called, Ralstonia solanacearum. [3] The use of microorganisms to
combat plant pathogens is only in the beginning stages, but using biocontrol
microbes is considered to be a less invasive alternative to pesticides and
fertilizers. The natural antibiotics produced in the rhizosphere are thought to
cause less stress on the indigenous microbes when compared with chemical
fungicides. Streptomyces can easily
colonize the plant root surfaces because of the filamentous growth pattern,
they can help protect roots against pathogens and can decompose organic matter.
The spores can also be dried, packaged into powdered products making it a
potential candidate for future commercial use. [8]
Within Actinobacteria
there are many organisms that have antibacterial and antifungal
characteristics. In a study involving fungus-growing termites, antibiotic
screening has shown that most Actinobacteria
throughout the termite nests produced molecules with antifungal activity. [6]
The zone of inhibition around the colony in the
original first colony collected for this study demonstrated the antibiotic
characteristics of the Streptomyces
spp. It is interesting to note an organism is sensitive to the antibiotics made
by other streptomycetes. The production of antibiotics is poorly understood,
but it is linked with sporulation which may be a mechanism to inhibit the
growth of nearby organisms competing for resources. There are over 500 distinct
antibiotics produced by stretomycetes. [7] Over half of the
commercially produced antibiotics originated from the genus. [10] Streptomycin
and is often used in patients who are allergic to penicillin. The antibiotic
Daptomycin is produced by Streptomyces
and is used against pathogenic
staphylococci and streptococci. Streptomyces platensis produces the
antibiotic, platensimycin, which is effective against methicillin-resistant Staphylococcus aureaus and vancomycin
resistant enterococci. The first treatment used against tuberculosis originated
from Streptomyces griseus. [7]
It is unclear if Streptomyces produce
antibiotics in their natural habitat.[10]
A possible change to the study could involve
using more cells for the metabolic tests. For example, by using more cells than
usually needed for the catalase test, a positive reaction with hydrogen
peroxide occurred. Using mediums other than those found in the Enterotube II
may result in finding more metabolic characteristics of Streptomyces spp. Studying why the color of the colony changed with
age would or possible advantages for the organism to have a variety of colors
may be an interesting focus for future studies. Further studies may also include
why humans are able to smell the compound and how it could have been useful to
humans from an evolutionary perspective.