Sample Research Paper: Microscopes

Research PaperScience
Apr 18, 2022

Microscopes are important instruments that play integral roles in scientific research methods . They allow scientists to observe microscopic samples that are otherwise invisible to the human eye. Microscopes help biologists to see cell-sized organisms and observe their behavior; Pathologists utilize the tools to identify diseases and help in patients’ diagnoses; Forensic scientists use microscopes to analyze evidence and aid in criminal cases; Even jewelers use these instruments to clean and craft jewelry and gemstones. This sample  research paper will discuss the functions and principles of a microscope as well as include a research review of a study that utilized microscopes in the methodology.

Microscope Definition and Purpose

A microscope is a scientific tool that allows an individual to observe objects at a microscopic level. Through the tool’s lenses, an individual can observe any object whether it is a single-cell organism or part of a larger sample, such as the head of a match stick. Most individuals are familiar with microscopes since they are common scientific instruments and are always present in science classes. For a microscope to be in working condition, it must be able to magnify the sample, separate details in an image to increase resolution, and render the details visible to the human eye (Abramowitz & Davidson, n.d.). If a microscope fails in any of these tasks, it is likely that it has damage and does not function properly.

The purpose of a microscope varies depending on the professional who is using it. According to Abramowitz & Davidson (n.d.), microscopes are useful in photography, biology, medicine, physics, the semiconductor industry, forensics, and other sciences because of their effectiveness as quantitative tools to gather optical data. Each field, however, utilizes a different type of microscope that is fit to its needs. Biologists and medical practitioners use compound microscopes to observe cells while engineers rely on metallurgical microscopes to help with manufacturing. These show that a microscope’s ability to observe in a highly magnified resolution has multiple uses outside of laboratories.

How Microscopes Work

Microscopes are integral in scientific research because they can see objects that are invisible to the human eye. Humans can only see objects that are within the visible spectrum of the eye. Colors like violet, green, blue, and red are visible while ultraviolet and infrared rays are outside the spectrum  For the human eye to see outside the spectrum or see an object at a higher magnification, light must hit the retina at a specific angle (Abramowitz & Davidson, n.d.). Since the human eye does not have this ability, individuals require the use of scientific tools like microscopes to see at a higher magnification.

The most common type of microscope, which is the compound microscope, utilizes convex lenses to create a magnified image of an object. These objective lenses have a focal point that the observer can manipulate to increase or decrease magnification. Moving the point away from the sample creates a real image while manipulating it closer resulting in a microscopic detailed image (Rawline, 1992). These convex lenses are integral parts of the instrument since they allow the rendering of detailed images. 

A microscope’s lenses and other parts also deal with magnification, resolution, and numerical aperture. Magnification refers to the manipulation of the image to create a more detailed picture (Shannon & Ford, 2022). Resolution refers to the separation of two points to create separate images. Resolution is necessary for the creation of detailed images since failing to separate a point from the bigger object will result in two close objects appearing as one. The numerical aperture is a microscope’s ability to gather light and establish good resolution (Education in Microscopy, n.d.). A good lens will have an effective numerical aperture and create maximum image resolution. Additionally, there are also the concepts of depth of field, depth of focus contrast, and illumination which are related to light and numerical aperture. These concepts are integral to the proper function of microscopes and any issue with them can lead to poor image quality.

Parts of a Microscope

The common compound microscope has a variety of parts that work to hold samples and manipulate resolution. These parts are the eyepiece lens, tube, arm, base, illuminator, stage, stage clips, nosepiece, objective lenses, rack stop, condenser lens, and diaphragm or iris. The eyepiece lens, not to be confused with the objective lens, is the top part of the instrument and where an individual will look to see the image. The tube, arm, and base are part of the supporting body of the microscope and ensure that the other parts are in place. The illuminator is the source of light for the microscope. Some microscopes do not have this part and use a mirror to reflect external light into the objective lens. They may also have a diaphragm or iris that can help manipulate the intensity of light. Once there is light in the objective lens, the condenser lens focuses the light into the specimen. The stage is the platform where an individual will place the sample and use the stage clips to stabilize the slide. The nosepiece holds the objective lenses and allows the user to change magnification by rotating to another lens. Lastly, the rack stop is responsible for setting the distance between the objective lens and slide. It helps avoid the lens from making contact with the slide, potentially breaking it or the lens.

Sample Research Utilizing Microscopes

To better understand microscopes, discussing a study that utilized the instruments can be beneficial. This study is Wang et al.’s (1993) “Effects of pH in Arbuscular Mycorrhiza, Field Observations on the Long-Term Liming Experiments at Rothamsted and Woburn”. In the study, the proponents measured the percentage of arbuscular mycorrhizal Fungi (AMR) colonization in the roots of spring oats (Avena Sativa) and maincrop potatoes (Solanum Tuberosum). Arbuscular mycorrhizal fungi are known to infest plant roots and penetrate the root cortex. The fungi then produce hyphae, filamentous fungal branches that extend further into the surrounding soil than the host’s roots. The increased absorption area from this behavior increases the host’s nutrient uptake and drought resistance (Schenck, 1982). The fungi then receive sugar from the host which is its sole carbon source. Arbuscules, which are the structures within the plant roots that the fungi create, are the sites of this two-way exchange.


This study aimed to determine whether soil acidity affected AMF colonization, either directly or selectively by species. Since there are acid-tolerant species in the original population there can be varying results. AMF has been shown to increase the host’s defenses against heavy metal concentrations in the soil (Wiesenhorn, 1994). Robson & Abbott (1989) conducted a study that showed that pH and heavy metal concentration affected AMF spore germination, with spores of different species having differing pH optima (cited in Wang et al., 1993). This further supports the notion that increasing acidity in the soil can increase the presence of aluminum and manganese which may or may not affect AMF colonization.

Materials and Methods

The setting of the study, which was Rothamsted Experimental Station and Woburn, had a serif of plots that have been maintained at four different pH values for 22 years. Preliminary studies have shown that soil pH had no effect on the percentage of roots colonized in oat and potato but did affect the species of the colonizing AMF fungi (Wang et al., 1985, cited in Wang et al., 1993). Oat and potato were chosen for their ability to tolerate a wide range of soil pH. Three soil cores (7.5 x 30cm) were taken from each site. Roots were washed from the cores and cut into lengths of 1cm from which a subsample was taken. Roots were cleared and stained and the percentage of AMF colonization was assessed using the gridline intersect method of Giovannetti & Mosse (1980). AMF spores were extracted from fresh soil by wet sieving and decanting. Spores over 50mm were counted on a nematode-cyst counting dish.

In the preparatory stage, the proponents used specific techniques to preserve the integrity of the samples. The proponents utilized the clearing and staining technique of Philips and Hayman (1970). The procedure was a breakthrough in AMF research because it was specifically adapted to mycorrhizal fungi. The drawback, however, includes the use of phenols and saturated chloral hydrate (Schenck, 1982). The fumes of these chemicals are hazardous even at room temperature, and the procedure required them to be heated. Newer procedures can adequately stain AMF infection using only lactic acid instead of phenols. (Kormanik, 1980). The gridline intersects method of Giovannetti and Mosse (1980) can be used to estimate both the proportion of root length colonized and the total root length of the sample. 

The procedure involves spreading the washed root sample in a petri dish. The dish is placed on a grid of 1.27cm squares and viewed through a dissecting microscope. Vertical and horizontal gridlines are scanned and the presence or absence of colonization at each root/line intersection is recorded. A high accuracy of colonization percentage can be determined if at least 100 intersections are tallied. For estimates of total root length, all intersections must be recorded. The total number of root/gridline intersections will represent the total root length in centimeters. Many other procedures have been developed to assess AMF colonization. McGonigle et al.’s (1990) magnified intersect method involves scanning roots at higher power (200x) using an eyepiece with two perpendicular crosshairs. Researchers reported that this particular technique results in a more objective and accurate representation of AMF colonization.

Results and Discussions

The study concluded that soil pH levels affected the crop yields of spring oats and potatoes and that the percentage of AMF root colonization could account for the differences. The percentage change can be a result of changes in root growth or fungal growth rate.  The highest percentage of colonization was observed in soils with a pH of 6.5, but changes within the range of 5.5-7.5 were small. On the most acidic plots (pH 4.5) colonization was reduced by half over the pH 7.5 plot. The percentage of colonization increased only slightly over time. 

Overall, available phosphorous seemed to affect the percentage of colonization more than soil pH. At sites with a greater amount of available phosphorus, root colonization was strongly suppressed. The results were similar for potatoes except that the lowest percentage of colonization was observed at pH 7.5 site at Woburn and at pH 4.5 site at Rothamsted. This may be the result of the difference in soil chemistry between the two sites. Rothamsted has a greater concentration of has a higher concentration of oxides of aluminum, iron, and manganese in the soil, which would become more available at low pH. This could account for the suppression of colonization. However, a similar effect was not observed in oats.

The identification of AMF species proved to be difficult for the proponents since there were also non-mycorrhizal species invasions in the test plants’ roots. Additionally, the spore number of a particular species in the soil and a species’ colonization percentage are not necessarily related, adding to the difficulty of the task. The proponents, however, found out that only the fine endophyte species were found in the acidic soils and only the course type was found at pH 7.5. No resting spores of the course endophytes were found in any soil at pH 4.5, but since spores, less than 50mm were not sampled and some species of AMF are known to have smaller spores at maturity, species of course endophyte may have been present.

For the other pH sites, the proponents found that nine different species were present and successfully identified six of the species. They also found that the species Glomus Caledonium, G. Albino, and G. Etenicatum were present in both sites. The shift in species across the pH sites appeared to have a very limited effect on the percentage of colonization. The proponents suggested that the uniformity of colonization suggests mechanisms within the host plant rather than the concentrations of inoculum in the soil, affecting colonization. Additionally, natural selection may alter species composition in response to long-term changes while leaving concentrations of inoculum relatively unchanged.


There are no questions about the significance of microscopes to science and human innovation. The instrument’s ability to see outside the human eye’s visible spectrum makes it an irreplaceable tool in any field. Scientists do not have any alternative to microscopes for observing microscopic samples; Jewelers cannot reach the tool’s magnification level just by using magnifying glasses; Engineers and physicists can only rely on microscopes to visually analyze small technology. Furthermore, Wang et al.’s (1993) research showed the effectiveness of using microscopes to identify and investigate small organisms. Fungi spores are very small objects and identifying them from each other would have been an impossible task without microscopes. As technology experience more innovations, microscopes can become more powerful and obtain more functions.

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Reference List

Abramowitz, M. & Davidson, M. (n.d.). Anatomy of a Microscope [Online]. Olympus. Available at . Accessed May 4, 2022. 

Ames, R., E. Ingham & C. Reid (1982) Ultraviolet Induced Autofluorescence of Arbuscular Mycorrhizal Root Infections: An Alternative to Clearing and Staining Methods for Assessing Infections. Canadian Journal of Microbiology. 28:485-488

Giovennetti, M., & B. Mosse (1980) An Evaluation of Techniques for Measuring VAM Infection in Roots. New Phytol. 71:287-295.

Kormanik, P., W. Bryan & R. Schultz (1980) Procedures and Equipment for Staining Large Numbers of Plant Roots for Mycorrhizal Assay. Can J. Microbiol. 26:536-538

McGonigle, T., M. Miller, D. Evans, G. Fairchild and J. Swain (1990) A New Method Which Gives an Objective Measure of Colonization of Roots by Vesicular-Arbuscular Mycorrhizal Fungi. New Phytologist 33:115 (n.d.). Microscope Parts & Specifications [Online]. MicroscopeWorld. Available at Accessed May 4, 2022.

Mosse, B., D. Stribley & F. LeTacon (1981) Ecology of Mycorrhiza and Mycorrhizal Fungi. Advances in Microbial Research. 5:137-210.

Phillips, J., & D. Hayman (1970) Improved Procedures for Clearing and Staining Parasitic and VAM Fungi for Rapid Assessment of Infection. Transactions of the British Mycological Society. 55:158-161

Rawlins, D. (1992) Light Microscopy. BIOS Scientific Publishers Ltd, Oxford, UK.

Schenck. N. C. (1982) Methods and Principles of Mycorrhizal Research. American Phytopathological Society, St. Paul, Minn.

Shannon R., & Ford, B. (2022).Microscope. Encyclopedia Britannica. Available at Accessed May 4, 2022.

Wang, G., D. Stribley, P. Tinker and C. Walker (1993) Effects of pH in Arbuscular Mycorrhiza, Field Observations on the Long-Term Liming Experiments at Rothamsted and Woburn. New Phytologist 124:3

Zeiss-campus.magnet.fsu.edi. (n.d.). Education in Microscopy and Digital Imaging [Online]. Zeiss. Available at . Accessed May 4, 2022.

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