Isolation and Identification of an Unknown Bacteria Found in Ski Gloves
Click here for lab report.
Click here for lab report.
Planococcus sp. Isolated from sub-artic decomposing wood.
Morgen Southwood April 26, 2017
After learning about some extreme life styles that microbes could have, I was curious if I could find one in my own home. I sampled two places, a piece of wood from my fire wood stack (which is exposed to the extreme cold temperatures of Alaskan winters) and the ashes from my stove. If any microbes grew from the firewood it would mean that they were able to withstand temperatures below -50 degrees Celsius and be psycrophiles, if any microbes grew in my wood stove they would have had to be thermophiles. I was unable to grow any microbes from the wood stove but the growth from the previously frozen wood was abundant. Each of those colonies represented a microbe that had the physiological capability of surviving those conditions, and I was interested in observing them in the lab. The identification of this microbe would add to the depth of knowledge of what bacteria are and can be found on decomposing wood in the sub-artic.
The firewood pile was slowly decomposing, and it is likely that the microbe that was isolated from it was a part of the community that was utilizing the wood as an energy source. Decomposing communities frequently have a mix of fungi and bacteria. These communities emit extracellular enzymes to decay the wood, this results in an environment with high acidity and enzymes that are producing free radical oxygen species7. To thrive in this community it would be helpful to have mechanisms to process radical oxygen species. One such mechanism is the use of Catalase to catalyze the transformation of the reactive species hydrogen peroxide into O2. It is natural for bacteria in these community’s to be adapted to oxidative stress8
Throughout the course of this study I isolated one colony and performed many physiological and genomic tests to identify what species my isolate was. Considering the environment in which it was found, there were a few expected results: such as the microbe’s oxygen class and catalase test results. Once identified, I could then research the species and compare it’s physiology and genomic data to current literature to confirm the taxonomic assignment.
Collecting sample and isolation process
The sample was collected from a dry piece of wood. Sterile water was used to moisten the wood and a sterile swab was rolled along the wood’s surface. The sample was streaked using the quadratic method to grow pure isolated colonies onto a tryptic soy agar (TSA) plate. To control growth rates the plates were grown in incubators for 2-4 days at 37 degrees Celsius then moved to a refrigerator to ensure colonies did not grow large enough to touch. The TSA medium provided a suitable environment for a variety of bacteria and a few molds. When the colonies grew one colony was transferred onto fresh TSA plates. The quadratic streak was used 4 times to ensure a pure culture. At this time the culture was transferred into an agar slant. Tests were performed on the isolate by obtaining cells from either the TSA plates or from the slant agar.
The gram stain was performed to assess the thickness of the peptidoglycan wall. The sample was stained using the provided protocol, gram-positives and negative controls were compared to the isolate to determine its gram-state (lab 4). While the cells were prepped in slides some characteristics were observed with the microscope, such as cell alignment shape and length. Colony morphology including color, size, margin and elevation was observed from growth on the TSA agar.
Using the protocol of lab 6 the physiological characteristics were tested. A suspension of the microbe in broth was tested simultaneously in all 21 of the tests included in the API 20E test strip. Additionally the isolate underwent the thioglycolate test- for oxygen class, oxidase test- for the presence of cytochrome c-oxidase, and lastly the catalase test- for the presence of catalase enzyme.
The cells inoculated onto Eosin Methylene Blue (EMB) and MacConkey Agar (MAC) plates. EMB is selective for gam-negative bacterium, if the microbe is gram negative and can ferment the sugars present then the plate experiences a color change. MAC plates are also selective for Gram-negative microbes and differentiates between lactose fermenters (agar turns pink) and non-lactose-fermenters (agar turns colorless).
The susceptibility of the isolate to 8 different antibiotics was tested using the Kirby-Bauer Method agar and the disk diffusion test per the protocol of Lab 9. The antibiotics tested were Amikacin, Cefazolin, Cefoperazone, Gentamicin, Piperacillin, Tobramycin, Trimethoprim and Vancomycin. After a two-day waiting period while the microbe was given the opportunity to develop where it could, the diameter of prohibited growth was measured and compared to standard antibiotic specific diameters and then classified as either susceptible, intermediate or resistant.
Dna was extracted and purified from the isolates cells using protocol from lab 5. Cell lysis was accomplished through adding sodium dodecyl sulfate (SDS), which is a surfactant that chemically weakened the cell walls, and the use of PowerBeads and the centrifuge to mechanically break the cell walls. A series of patented solutions C1-4 were added following the protocol to purify and remove inhibitors and proteins until all that remained was a pure solution of DNA. The DNA was then sent to the UAF’s DNA Core Lab sequenced using the Illumina MiSeq DNA sequencer which utilized the next-generation sequencing methodology.
Using Illumina’s BaseSpace dashboard to handle the data, the isolate’s genome was analyzed and compared to an existing database to search for similar sequences of DNA. BaseSpace has many apps that provide different information about the genomic data. The SPAdes Genome Assembler provided the overall result of the genomes assembly. Of this information, only the number of contigs that were greater than 1000 base pairs long [# contigs (>=1000bp)], The total length of the assembled genome, the longest contig and the guanine and cytosine percentage in the genome (GC%) were observed. The next app that was used was the Kraken Metagenomics, which provided taxonomic assignment. This app provided sample information such as the total number of reads that were used for classification and the percent of reads that were classified. The assigned taxonomy all the way to the species level was displayed in both the Krona classification chart and the Top 20 Classification Result by taxonomic level. Both sources have specific classification percentages that confer certainty. The final app Prokka Genome Annotation assigned gene regions that likely code for either tRNAs, rRNAs, CRISPRs and coding genes (CDs) and the abundance of them. The APP provides an extensive list of regions that were specifically identified as the above elements.
Further analysis of the genomic information was necessary. The contig.fasta file from the SPAdes Genome Assembly produced by Illumina’s BaseSpace was analyzed by BLAST. BLAST had a different database and could possibly have the genome of the isolates species if base space did not. BLAST suggested Genus and species with associated query cover percentage and identity percentage.
The Isolate appeared to be a pure culture by the third quadratic streak; a fourth was performed for certainty. The Microbes transfer to the agar slant was successful: Image 1, and was successfully re-cultured from the slant when necessary.
Image 1: Microbe growing on TSA agar
Image 2: Gram-stained microbe
The gram-stain was repeated three times before a successful stain was accomplished. The gram-stain revealed that the isolate was a gram-positive coccid: Image 2. While under the microscope it was observed that the cells could be aligned linearly, in pairs or quads but not in a longer strep chain. The purity of the isolate was confirmed with the microscopic observation of a mono-culture. The cells were measured to be 1 micrometer in diameter. Colony morphology on the TSA agar revealed a yellow colony that’s size increased with time, a smooth round margin and the colony was an elevated domed.
Image 3: API 20E test results
The API 20e tests had negative results for all for the 21 tests: Image 3. Considering that the API 20e test is designed for enteric gram negative microbes these results are confirmation that the microbe is gram-positive. The thioglycolate test had growth throughout the agar with thicker growth at the surface, which revealed that the microbe’s oxygen class was facultative aerobe. The catalase test produced bubbles and the oxidase test produced a blue color change on the strip indicating that the microbe was positive in both tests. These results reveal that the cells contained both cytochrome c-oxidase and the catalase enzyme respectively. The isolate failed to grow on EMB or MAC plates, considering that both plates are selective for gram negative, these results confirm the results of the gram positive test: Image 4.
|Cell morphology||1 micrometer diameter, coccus, cells divide linearly|
|Colony Morphology||Yellow colonies that’s size increases with time, a smooth round margin, elevated dome.|
|API 20e||All negative results|
|Fluid thyioglycolate||Facultative anaerobe|
Table 1: Physiological Test Results
The microbe was susceptible to all eight antibiotics tested. The Inhibition Zones exceed the antibiotic specific threshold diameter for susceptibility see table 2 for details.
|Antibiotic Name||Minimum Inhibition zone for susceptibility (mm)||Microbe exceed inhibition zone
Table 2: Antibiotic Susceptibility Results
The analysis of the DNA with BaseSpace revealed unreliable data. BaseSpace’s SPAdes Gemone Assembler analyzed 128 contigs over 1000 base pairs (bp) long, a total length of over 3.7 million bp, the longest contig was 196 thousand bp, and the GC% was 44.4%. Kraken Metagenomics app was only able to classify 2.67% of reads, and of those reads only 17% of those reads identified the microbe as Lysinibacillus sphaericus. The Prokka Genome Annotation app identified 64 tRNAs, 0 rRNAs, 1 CRISPR, and 3739 CDS. Image 5 and 6 are from the Kraken app.
Image 5: Krona Classification Chart from BaseSpace displays the large portion of unclassified reads.
Image 6 To 20 Classification Results by Taxonomic Level from BaseSpace
A second analysis of the DNA was performed using the BLAST genomic database. BLAST classified the organism as Planoccus donghaensis with a query cover of 77% and a 78% identity. Several other species had similar query cover, including Planococcus antarticus: Image 7.
Image 7: BLAST Genomic Results
The genotypic test results for this microbe were vague, the results of BaseSpace had a low number of reads that could be classified and of those reads there was little consensus. The results of the SPAdes Genome Assembler were above required values; # contigs >=1000 bp should be in the hundreds, total length should be at least a million bp and the longest contig should be at least 100000 bp. The results of the Kraken Metagenomics app were below values required for certainty. The percent of contigs read needed to be greater than 80% and the percent of those reads that needed to agree upon a classification to trust that classification to the genus level was 80% and to the genus level was 60%. The results did not meet these thresholds, and this is the reason that the BaseSpace indentified taxanomy of Lysinibacillus sphaericus was rejected.
BLAST provided many species level classifications with similar query cover and percent identity. The species classification with the highest query cover is poorly documented in literature. The first publication of a species under the genus Planococcus was P. citreus. It was identified in 1894, and was only approved in 19806. This genus is relatively young and is currently growing with many of the species being described within the last ten years. Of the few documents that relate to Planococcus donhaensis, there is one that notes the origin of the sample, the South Korean Sea. There are some qualities that are consistent between my sample and P. donghaensis, they are both, gram-positive, aerobic, coccus and oxidase positive 1. However these similarities are not enough to convince me that they are the same species. A hallmark of the genus Planococcus is that they are usually halo-tolerant gram-positive bacteria that frequently inhabit Antartica4. The isolates holotolerance was not tested but the similar cellular membrane composition and habitat conditions indicate that this genus is likely correct.
The negative results and lack of growth in the API 20e, MAC, and EMB are all consistent with the microbe’s gram-positive cell wall. These tests reveal nothing more than a conformation that it is indeed a gram-positive microbe. The oxygen class determined by the fluid thioglycolate test and the positive results of the Oxidase and Catalase test are both consistent with the oxygenic environment that the microbe was isolated from. These tests proved that the microbe could thrive in an oxygenated as well as an anoxic environment, that it contained cytochrome c oxidase which is a part of the electron transport chain found in microbes that utilize oxygen, and that it contained the catalase mechanism for dealing with oxidative damage, respectively.
At the genus level, morphology can vary greatly. Many of the morphological and physiological analyses made on the isolate are not held by every species in the Planoccocus genus. The morphological characteristics that are consistent with the isolate and across the genus are: gram-positive membranes, cocci cell shape, colonies are yellow orange in color, catalase positive and an aerobic oxygen class5. My isolate was not just aerobic but a facultative aerobe, which is inconsistent with two articles that state the genus is strictly aerobic5. The isolate was found to be susceptible to all antibiotics tested with the disk diffusion test. This is consistent with a study that found, to the level of the genus, that Planococcus’ were susceptible to all antibiotics tested3.
The second most likely species suggested by was P. antarticus, at least this species shares a similar environment. P. antarticus thrived in an Antarctica, my sample would likely have similar mechanisms for surviving temperatures around -45 degrees Celsius in Faribanks winters. P. donghaensis may have had the ability to deal with these temperatures in its genome, but it is not certain since it’s environment doesn’t select for such characteristics.
The literature on the Planococcus species like donghaensis, kocurii, halocryophilus and antarticus often notes how closely related the species are and how further analysis like G-C content, fatty acid strains, DNA-DNA hybridization etc1,2 are needed to differentiate the species. To conclusively Identify the taxonomy of this isolated microbe, it would be advisable to repeat DNA isolation and genomic analysis that was preformed in this project, and to additionally perform other genotypic analyses like, DNA-DNA hybridization and 16s rRNA analysis and fatty acid identity. Considering the limit of species identified to this date, there is the potential that this microbe could be a new species.
5. Fackrell, H. (n.d.). Planococcus. Retrieved April 11, 2017, from Uwindsor.ca website: https://web2.uwindsor.ca/courses/biology/fackrell/Microbes/17375.htm
This is my abstract interpretation of the decomposition of spruce and the interacting systems in a subarctic climate such as Fairbanks, with a focus on the fungi you may find on a piece of decomposing (as well as living) spruce (left to right: lichens, slime mold, and turkey tails). The array of color in the background serves as a reminder of the diversity of the interacting systems, both biotic and abiotic. The plants on this piece represent the living features in an healthy ecosystem, such as the different plants, animals, fungi, bacteria, archaea, and viruses that inhabit that ecosystem. The soil on this piece is in reference to nutrient cycling within a system of decomposition, as well as the soil the wood will ultimately become part of and that many decomposing microbes inhabit. The symmetry and mixture of media serve to show the balance between the biotic/abiotic factors in a healthy subarctic habitat.
I chose this as my project because the there are so many components that go into the decomposition [of wood] that I had previously underestimated. Also, when you typically envision “nature” in Fairbanks, you may think: birch, spruce, squirrels, ravens, fireweed, etc., but the great diversity of microbes within the environment is typically less prominent. I felt it was important to highlight the interactions and results of microbes in a forest system.
I picked these fungi because as I was choosing a log from my wood pile to cut for this project, I saw 2/3 of these fungi on some of the logs. All of the plants in this piece are were found outside of my house.
**After painting this I found out slime molds(middle log) are no longer categorized as fungi, but eukaryotes… so it’s really the interactions of fungi and eukaryotes.
My name is Kjersten Williams. For my art project, I decided to go with mixed media. I constructed the microbes’ background environments out of paper and colored pencil, and made the microbes themselves out of modeling clay, giving the project a bit of visual depth. For my subject, I decided to focus on a specific group of microbes: the temperature extremophiles. I wanted to showcase the variety of different morphologies and habitats of these microbes (through the relatively accurate depiction of the microbes and their respective environments), while also making a statement against the general belief that all microbes are “bad’ (hence, the added shaky eyes to make them cuter and more personable). These microbes live in environments which would be deemed uninhabitable to the majority of life forms on Earth. Due to their resilience and adaptability, they represent the type of organism which astrobiologists may be most likely to find on other planets!
There are a couple mesophiles included for the sake of contrast. The microbes represented are: Chloroflexus aurantiacus (the red snake-like thermophilic bacterium represented against the background of a hot spring area), Methanopyrus kandleri (the blue, rod-shaped hyperthermophilic archaea set against the background of hydrothermal vents), Deinococcus radiodurans (a mesophilic bacteria represented by the green tetrad set against the forest background), Acidithiobacillus thiooxidans (a mesophilic bacterium represented by the purple, rod-shaped microbe with the pink flagellum), Psychrobacter arcticus (the blue diploid psychrophilic coccobacillus bacterium with pink spots, which is set against the aquatic background underneath the ice layers), and Planococcus halocryophilus (the blue-green diploid cocci bacterium set against the polar background).
From The New York Times on June 3rd, 2016 – Educate Your Immune System
This article summarizes recent research done on the development of autoimmune diseases (Type I diabetes, celiac disease, severe allergies, etc.) in children who grew up in different microbial environments – represented by households in Finland, Estonia, and the Karelia region of Russia. Studies found that, when factors such as diet and breastfeeding were controlled for, toddlers who grew up in Finland were four times as likely as those in Karelia to develop precursors for Type I diabetes, and the two groups had very few similarities between their microbiomes. Karelia is a significantly poorer area than most of Finland, and many households drink untreated well water, so researchers hypothesized that early exposure to microbes from the environment “taught” the toddlers’ immune systems how to respond appropriately to common environmental pathogens, and so they developed fewer autoimmune issues.
We’ve discussed acquired immunity in class, but this area of research takes it a bit farther, and suggests that our microbiomes and when we are exposed to certain microbes may play a larger role in our immune development than previously thought. Other studies mentioned in this article found that children who were exposed to certain pathogens at a young age were much less likely to develop autoimmune diseases than those that first encountered the same pathogens as teenagers or adults. This updates the hygiene hypothesis (which I think we discussed briefly?), which essentially says that people exposed to fewer kinds of microbes during their development tend to be sicker than those that were exposed to a wider variety of microbes.
I appreciated the angle this article took, describing autoimmune diseases and decreased exposure to diverse microbial communities as an issue of the 21st century. The author did an excellent job of defining terms and ideas that may be foreign to the lay reader, and I think this article is accessible to a wide range of audiences. However, the article implicitly assumed that the relationship between early microbial exposure and autoimmune disease was proven, and I don’t think any of the studies examined in the piece proved a causal relationship. Popular science writing needs to be careful not to assume causation when it has not been proven!
How might we (ethically) prove a link between childhood microbial exposure and autoimmune disease?
— Article and link: “Too Clean for Our Children’s Good? The Checkup’ by Perri Klass, MD, The New York Times, April 17, 2017.
— Summary: This article talks about the many various ways in which our children are protected from interaction with microbes, including giving birth by caesarian section, bottle-feeding, and possible exposure to antibiotics. Such protection on the one hand affords protection from disease but on the other hand offers greater risk that children may experience complications of the “built environment.’ It is a concern that living in such a clean, controlled environment could lead to an underdeveloped immune system and subsequent health problems which may have otherwise been avoidable had the body been exposed to a diverse array of microbes at a young age. In order to combat this problem, it is recommended that young children be introduced to these microbes in the outside environment through “controlled exposures’ in the form of either “natural exposure’ consisting of interaction with their environment or through a type of vaccine yet to be developed.
— Connections: This article include discussion of the development of the human microbiome, its importance in the overall health of an individual, the avenues by which children are typically first exposed to microbes, and also the concept of vaccination with microbes in order to improve health. All of these are topics which have been mentioned or discussed over the course of the semester.
— Critical analysis: I liked the contrast that the author provided between the microbes found outdoors as opposed to those found within the “built environment.’ While I had naturally assumed that the inside of a house or apartment may be “cleaner’ than the outside world, I had not given much thought to the members of the microbial populations to be found in each of the two environments; in reality, the inside of a dwelling is not necessarily any more microbe-free than the outside, it is instead simply inhabited by a different, and possibly narrower, variety of microbes. I did not detect anything scientifically inaccurate or confusing in this article, and think that it did perform an adequate job in relaying this information to the public. The author did not get too technical in any of their explanations, yet clearly stated the anticipated problem, reasons behind that belief, and also the possible solutions to the problem.
— Question: Are researchers suspecting that the health problems mentioned are primarily due to inadequate exposure to pathogenic bacteria? Or do interactions with the non-pathogenic bacteria also play a role in shaping the immune system of children? What kinds of “natural exposures’ are parents advised to pursue in order to assist their child’s immune system to develop properly?
From The Atlantic on April 12th, 2017 – Air Pollution Might Make Dangerous Bacteria Harder to Kill
This article discusses a recent study that examined the effects of black carbon (a major component of air pollution) on the growth and antibiotic resistance of common opportunistic pathogens within the human microbiome – Staphylococcus aureus and Streptococcus pneumoniae. The researchers found that the addition of black carbon to plated cultures of the two species changed the morphology of their respective biofilms and increased their antibiotic resistance, as well as increasing their pathogenicity when applied to the nasal mucosa of mice.
We’ve discussed how bacteria develop resistance to antibiotics in class, and while we don’t know which kinds of antibiotics were tested (other than penicillin), we can conjecture as to the mechanism through which the bacteria developed their resistance. Since I imagine black carbon is not a favored carbon source of bacteria, it may encourage the survival of bacteria with more efflux pumps, to remove the black carbon from the cells.
It’s fascinating that research into the effects of air pollution on the microbes affecting human health was not done until so recently – especially when the effects of air pollution on disease are already well-documented. This article didn’t contain any factual errors (as far as I know), and was careful not to generalize the results of mouse studies to humans. The author also did a good job of defining terms that the lay reader may not be familiar with (biofilm, microbiome, etc.), and was careful to represent the results of the study accurately. Now, if only more science writing was this clear!
What mechanisms are used by bacteria to adapt to air pollution that also increase their pathogenicity?
Summary: In a cooperative research effort between the Israeli and US universities, a hydrogel was developed to coat exisiting commercial ultrafiltration membranes in order to increase their ability to repel and filter viruses, specifically Adenovirus and norovirus. The impetus for its development, and the advantage over normal methods of filtering viruses, is because it can function without amounts of energy and without additional chemical disinfecting products.
Connections: This article relates to our discussions in class regarding both water purification in the form of filtration of pathogens, as well as food/water safety methods on a large scale.
Critical Analysis: This article is interesting because it addresses the issue of public waste water as a critical entry point for microbes into municipal drinking water. In our lecture discussion during class we did not delve much into the that particular issue. The article highlights the cost of current methods of waste filtration and treatment, but does not give much in the way of details for the size of the issue, nor the extent of contamination that these cities are facing. To that same point, they fail to explain how effective the hydrogel is at ‘repelling’ viruses. Though the article seems to be a brief overview for the layman, I don’t believe the readers would have been bored by statistics to reinforce the information they provided. However, if this is an effective method that can be applied to control measures already in place, the results could be outstanding for reuse of potable water.
Question: How long are the researchers expecting the hydrogel coating to maintain efficacy? Will the gel last as long as the existing filter it is applied to, and what will the added costs for cities planning to implement this extra barrier in their water supply?
— Article and link: “Zika-Fighting Sterile Mosquitoes Released Near Key West’, NBC News, April 19, 2017.
— Summary: This article aims to describe the testing of new experimental methods for the reduction of Aedes aegypti mosquito populations, a species which has been previously linked to the spread of multiple diseases, including the Zika virus. The ultimate goal of this testing is to control the spread of the Zika virus through controlling these insect vector populations. One such method has recently been tested in Key West, Florida, where lab-raised male mosquitoes infected with Wolbachia spp. of bacterium were released into habitats known to harbor populations of Aedes aegypti. The lab-raised male mosquitoes will breed with the wild female mosquitoes; however, due to the Wolbachia spp. carried by the male parent, the young produced by this coupling cannot survive to adulthood. While this method involves the use of microbes, there is another technique mentioned which instead involves genetic modification of lab-raised male mosquitoes to obtain a similar result.
— Connections: This article related to the material in class through its association with Zika virus, which was covered both in our course material and also in the guest lecture given by Dan Stinchcomb. The use of these microbes by humans to alter a detrimental aspect of an environment is also an example of microbes functioning in environmental bioremediation, another topic covered in class.
— Critical analysis: I found this method for mosquito population control extremely interesting. We had learned in class that certain microbes can be used to confer certain health benefits to a host organism through the transfer of particular genes, but I had not yet heard much of this particular strategy involving using members of a population as hosts for the microbe with the aim of stopping the spread of a disease from an insect vector to a human population. Both this method as well as the genetic engineering process mentioned towards the end of the article, if such methods prove effective in their goal and also harmless to the environment, would be extremely useful in inhibiting the spread of the Zika virus and thereby preventing further human infections.
This article was written in such a way as to inform the general public. As such, the scientific details and mechanisms behind the ideas discussed are not mentioned in great detail. In terms of the limited scientific details provided, I believe the article was scientifically accurate, though somewhat vague. The explanation of the science involved was somewhat simplified, and I did not detect any confusing aspects. While I personally feel that they could have included more detail behind the processes mentioned, I can see that the inclusion of too much detail could have been confusing to someone not well-versed in biological concepts. I think the article adequately communicated the highlights of the science to the public, as it stuck to the main ideas and results of the testing in an attempt to be clear and to communicate their ideas effectively.
— Question: What is the mechanism by which Wolbachia spp. inhibits the development of the next generation of mosquito? Would the inhibition of mosquito populations through such methods reduce their numbers to the point where other organisms in the food chain might be affected (most specifically those organisms in the food chain which utilize mosquitoes as a food source)? In reference to the genetic engineering method for the control of mosquito population, what is altered or added in the genome of the mosquitoes in order to obtain the desired effect?
Source: Science Magazine
Date: April 4th, 2017
Summary: Currently, big chemical plants use nitrogen and methane to make ammonia (i.e fertilizer), which is not typically a viable option for developing countries, not only because they are expensive to run and maintain, but also because they lack the resources to distribute the produced fertilizer. While we know of some microbes that are capable of nitrogen fixation, researchers from Harvard have genetically engineered a bacterium to be able to convert nitrogen (N2) to ammonia or other forms that plants can use, with the hope it could be used on a widespread commercial scale, which India has started to work on.
Connections: Throughout the semester, we have learned about and tested the physiological capabilities of microbes. We did test to see if our microbial isolates were capable of denitrification (whether it be partial or complete).
Critical Analysis: I do think this article was scientifically accurate and it did answer some of my questions (how/where does the energy for this come from? what enzymes are involved in the process?). However, the article does fail to discuss the fact that there are existing microbes that convert N2 to ammonia or nitrates/nitrites and does not explain why this specific genetically engineered bacterium is better than any of the preexisting microbes capable of this same process. It conveys a message that this is somehow a new concept, even though it is not. It also discusses the scientific conclusions that the genetically engineered bacterium, Xanthobacter autotrophicus, works outside of the lab because the researchers put it in solution, watered a sample of radishes with it, and noted the radishes grew 150% more than the controls. They did this in the lab though. I’m not saying this conclusion isn’t valid, just that it doesn’t sound as if anyone has attempted to replicate this, or test this in an environment with several other factors that a lab cannot account for. They have a ways to go before this could lead to feeding the worlds poor. Overall, I think the author means well and conveys the science itself fairly well, but misleads the public as to what exactly the science means in the grand scheme of things.
Question(s): If we’re wanting to commercialize nitrogen fixating bacteria, why not use one that does not require genetic modifications? Do Xanthobacter autotrophicus have greater diversity in the environments in which they can survive/thrive (i.e a variety of climates)?