Planococcus sp. Isolated from sub-artic decomposing wood

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Planococcus sp. Isolated from sub-artic decomposing wood.

Morgen Southwood April 26, 2017

 

Introduction

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.

 

Methods

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.

 

Physiological Characteristics

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.

 

Bioinformatics

                      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.

 

Results

Physiological Characteristics

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.

 

 

Physiological Tests Results
Gram Positive
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
Oxidase Positive result
Catalase Positive result
MAC No growth
EMB No growth

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

(yes/no)
Amakicin >=17 Yes
Cefazolin >=18 Yes
Cefoperazone >=21 Yes
Gentamicin >=15 Yes
Piperacillin

    Enterobacteriaeae

    S. pneumoniae

  

>=21

>=18

  

Yes

Yes
Tobramycin >=15 Yes
Trimethoprim >=16 Yes
Vancomycin >=17 Yes

Table 2: Antibiotic Susceptibility Results

Bionformatics

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

Discussion

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.

 

 

 

Work Cited

  1. Jeong-Hwa C, Wan-Taek I, Qing-Mei L, Jae-Soo Y, Jae-Ho S, Sung-Keun R, Dong-Hyun R. Planococcus donghaensis nov, a starch-degrading bacterium isolated from the East Sea, South Korea. Int J Syst Evol Microbiol. 2007;57:2645—2650. doi: 10.1099/ijs.0.65036-0.

 

  1. Reddy G, Prakash J, Vairamani M, Prabhakar S, Matsumoto G. Shivaji S. Planococcus antarcticus and Planococcus psychrophilus nov. isolated from cyanobacterial mat samples collected from ponds in Antarctica. Extremophiles. 2002;6:253—261.

 

  1. Tuncer, I. (2016). Antibiotic resistance of bacterial isolates from sediments of eastern Mediterranean Sea in association with environmental parameters. Journal of Bacteriology and Parasitology, 7(6), 51. https://doi.org/10.4172/2155-9597.C1.025

 

  1. See-Too, W. S., Ee, R., Lim, Y.-L., Convey, P., Pearce, D. A., Yin, W.-F., & Chan, K.-G. (2017). AidP, a novel N-Acyl homoserine lactonase gene from Antarctic Planococcus Scientific Reports, 7, 42968. https://doi.org/10.1038/srep42968

 

5.         Fackrell, H. (n.d.). Planococcus. Retrieved April 11, 2017, from Uwindsor.ca website: https://web2.uwindsor.ca/courses/biology/fackrell/Microbes/17375.htm

  1. Euzeby, J. P., & Parte, A. C. (2017, April 1). Genus planococcus. Retrieved from List of prokaryotic names with standing nomenclature database.

 

  1. Valášková V., de Boer W., Gunnewiek P. J. K., Pospíšek M., Baldrian P. (2009).  Phylogenetic composition and properties of bacteria coexisting with the fungus  Hypholoma fascicularein decaying wood.  ISME J.  3  1218—1221. 10.1038/ismej.2009.64
  2. de Boer W., van der Wal A. (2008).  “Interactions between saprotrophic basidiomycetes and bacteria,’ in  British Mycological Society Symposia Series 8  eds Lynne Boddy J. C. F., van Pieter W., editors. (Cambridge, MA: Academic Press; )  28  143—153.

 

 

 

 

Art Project: “Extreme Environments”

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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).

 

Abandoned Toxic Pit Might Have Next Antibiotic

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Article Title:  Fungal duo isolated from toxic lake produce novel antibiotic

Source:  C&En

Date: 4-19-17

Link:  https://cen.acs.org/articles/95/i17/Fungal-duo-isolated-toxic-lake-produce-novel-antibiotic.html

Summary: In Montana there is an abandoned mining pit called  Berkeley Pit. Since it was abandoned in 1983 water has leaked in and make it into a toxic pool with a pH of 2.5. It is so toxic that thousands of snow geese died last winter after they landed in it. However microbes love the pit. Two scientist from the University of Montana Andrea A. Stierleand  and Donald B. Sterile who have been studying the fungus in the lake have found that two  Penicillium fungus together make a new antibiotic. The antibiotic isn’t really a super new shape but it seems to act differently from know antibiotics.

Connection:  Antibiotics we learned we discovered  from a penicillin fungus by Alexander Fleming, so I thought it was really cool that we still find antibacterials like that. Could it be that fungus are adapting their antibacterials to fight resistant bacteria? This article also connects to the section on what bacteria use as energy sources, as finding life in an inhospitable place like an abandoned mining pit with pH2.5 is incredible and show how microbes can adapt to use almost anything.

Critical Analysis:  The article doesn’t give much on the antibacterial agent it’s self, however it does provide us with a picture of the its chemical structure and a link to the article that the scientists published. The purpose of the post must have been to inform the public of a new discovery in science and I think it does this very well. How the article starts by describing the location of the discovery really draws readers and helps the mission of the article.

Question:  We have learned a bit about how bacteria survive in inhospitable places like this pit, but how do fungus do it? How do fungus deal with low pH and high concentrations of heavy metals? Also what do the fungus use as an energy source?

A2: Microbes in the News

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Article: 7 Alien ‘Earths’ May Be Swapping Life via Meteorites

Link: National Geographic, Mar 22, https://news.nationalgeographic.com/2017/03/earth-planets-aliens-life-panspermia-space-science/

Summary: On Feb 23, NASA reported that they found other solar system about 39 light years away from our solar system, called TRAPPIST-1 and some of planets in TRAPPIST-1 have liquid water. This release gave a shock to the world and someone may think that extraterrestrial life is existing now. According to the new research from Manasvi Lingam and Abraham Loeb of the Harvard-Smithsonian Center for Astrophysics released on Mar 15 that seven planets in TRAPPIST-1 is condensed around the stellar host so that the seeds of life can jump from one planet to other planet by debris. This research support the theory of panspermia, which maintains the origin of life came from the space to Earth. In TRAPPIST-1, all planets are located close to each other and distance between them is much shorter than the distance between Earth and Mars, so it’s easy to approach to other planets in TRAPPIST-1. Also, three planets out of seven planets may have liquid water and is located in habitable zone, so they think if they have moderate temperature and atmosphere, life can exist there. However, some astronomers are suspicious of this because they think life can’t stand the harsh condition while they are traveling. In the space, there are lots of cosmic rays and they can be exposed for more than million years. In addition, they receive a huge shock when they land on some planets. Though some member in the team says it’s really difficult to survive in the harsh condition, but some organism like extremophiles can overcome it. They don’t find plausible evidence yet, but it is a good chance for us to think about what is panspermia theory and where life come from.

Connection: The idea of ubiquitous is relate to this article. It is also relate to the origin of life(LUCA).

Critical analysis: Discovering of the TRAPPIST-1 was amazing. However, I’m wondering how microbes can jump from one planet to the other. This news said some researchers thinks it’s difficult for some microbes to survive in the space for long time due to UV or cosmic rays. While, other researchers says extremophiles can survive because some has tolerance for UV or heat. I’m suspect for this idea. If microbes can jump to other planet, we can find microbes from meteorites which come to the earth. Inside the meteorites, there are lots of Carbon sources, but their shock when land on some planet or heat can sterile them. However, the distance between one planet to the other is shorter than the distance between the Earth and Mars. Therefore, maybe, if their travel is short, some may survive and land on other planet, but it’s rarely happened.

Question: Why it support panspermia theory? How to jump to other planet from the ocean in the planets in TRAPPIST-1?

A2: Microbes in the News

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Article: 60,000-year-old microbes found in Mexican mine: NASA scientist

Link: PHYS, https://phys.org/news/2017-02-year-old-microbes-mexican-nasa-scientist.html

Summary: The research team from NASA found some microbes which is 60,000-year-old in the Naica mine in Mexico and revived them. Penelope Boston of NASA’s Astrobiology Institute said that in that mine, they found some crystals and inside of that, they found lots of microbes and viruses and they were alive, but they were locked by the crystal. Naika is the mine region and inside the mine, temperature is so high, so those area is extreme environment. When the researchers conducted research, they wore a spacesuit and an ice bag. Then, those microbes and viruses were picked up. They are really different from other well known microbes in terms of genome. It’s 10% difference between them and some microbes which has the closest genome sequence and this difference is like between humans and mushrooms. Those microbes lay dormant in the layer of minerals. Penelope said they adapted to their harsh environment and this discovery is just an one example how organisms in the earth are strong.

Connections: It’s relate to microbial ubiquitous and some extrememophiles.

Critical analysis: This mine is really hot and dark and nutrient are limited, so for almost all of organisms, it’s absolutely extreme environment. However, some microbes and viruses can exist in those environment. I was surprised when I read this article, but I am wondering why genome became different from others due to living inside crystals? This article said they are different like human to mushrooms. However, human and mushrooms are completely different from the shape, complexity, habitat and foods etc and they are microbes, but genome is different at 10%, so I’m confused.

Question: How to survive in the crystal even they can’t move? Why they are totally different from other microbes in terms of genome?

A2: Lack of oxygen not a showstopper for life

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https://phys.org/news/2017-04-lack-oxygen-showstopper-life.html
Lack of oxygen not a showstopper for life April 17, 2017.
Phys.org
Charles Q. Choi

Summary: Scientists sampled organisms from 15 different hot pools to see how many different chemosynthetic communities are thriving in the springs. The team focused on the oxidants present in communities, and worked on nailing down what type of bacteria are in those communities. They found that microaerophiles dominated mainly planktonic communities. This information helps provide a look at what kind of life may have been present in early earth, and if this life may be possibly survive on other planets.

Connections: In class we have talked about how microbes may have lived in an anoxic environment, and how they evolved with earth’s evolving environment. Eric Collin’s lecture gave an insight on how and why microbes should be able to survive on other planets.

Critical analysis: I like this article because I find it fascinating that so much science can be going on in one of the worlds most natural wonders. People visit Yellowstone all year round just to see these hot springs, and it is so interesting to think that these pools of water can offer so much insight on our environments future and past. I find this article to be accurate because we have learned a lot about how and why archaea that can survive in harsh environments, and how that can be an insight into life on other planets.

Question: This team focused on a small amount of microbial communities and were able to come up with plenty of information. Do you think it is even possible to find, analyze, and classify all of the microbes that could be living in just one hot springs?

A2: Microbes in the news

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Article title: Behind the iron curtain: How the methan-making microbes kept early Earth warm Behind the iron curtain: How methane-making microbes kept the early Earth warm

 

Date: Arpil 17, 2017

Article author was not listed but the research’s author was: m S. Bray. The article was provided by the Georgia institute of Technology.

Source: Phys.org

Link: https://phys.org/news/2017-04-iron-curtain-methane-making-microbes-early.html

Assignment author: Morgen Southwood

Summary-

Marcy Bray and his team simulated early earth conditions to try and explain why the oceans could be liquid in the first two billion years. The prevailing theory is that methanogens provided enough methane for the green house effect to maintain liquid oceans. The problem with this theory is that, as we learned in class, methanogenesis is an inefficient system, and can be out competed when alternatives are possible. One major competitor in this time period was the rust-breathing microbes, they would dominate any environment when iron was available. The term iron curtain, refers to the potential for rust-breathing microbes to repress methane emissions when rust is plentiful. If methane was completely suppressed then the planet would likely have cooled. The microbiologists simulated early earth to study microbial diversity and methane emissions in varying conditions. They found that in iron free pockets of the oceans, methanogens could have thrived and been enough of a source of methane for keeping early Earth warm.

Connections-

This article strongly related to our lectures on the methane cycle It also related to some exam 1 material, when we learned about the ferrous and ferric iron signatures that signaled changes in early earth microbial diversity.

Critical analysis-

This article could have used some more explanations. I understood the conclusions it drew, but I wouldn’t have been able to without material I learned in this class. I would have needed someone to fill in the blanks for me. It was important to understand why rust-breathing microbes would have outcompeted methanogens, and the significance of shifts in microbial diversity with different conditions etc. The article assumed/required the reader to know this supplementary information, and therefore it was not accessible to the general public.  I think the article was scientifically accurate in the way it described the idea proposed by the results of the study, however the title is misleading. The title seems portray that the study was a confirmation, when it was only supportive of the idea.

Since I did have some background information, this article was very interesting to me. When I thought about the major shifts in microbial diversity of the planet , I always thought about microbes relating to oxygen. These rust breathing microbes and methanogens were just as important stepping stones in shaping the Earth.

Question-

The conclusion of the article is that methane emissions could have come from microbial communities that were in rust free patches of the ocean. I thought that the ocean was well mixed. How could there be sections of the early ocean that were so poorly mixed that they lacked iron, while other areas had high levels of iron?

 

A2: Microbes in the news

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Article Title: Deepest Life on Earth May Be Lurking 6 Miles Beneath Ocean Floor

Author: Thea Ghose

Date: April 11, 2017

Source: Live Science

Link: https://www.livescience.com/58632-deepest-life-on-earth-possibly-found.html

Assignment author: Morgen Southwood

Summary-

There are mud volcanoes under the sea floor and they may be inhabited. Biological signatures in material that has risen to the surface could possibly be coming from microbial life 32,800 feet under the surface of the ocean floor. The organic matter are good indicators of the presence of life, but could also have been produced by abiotic processes.

Connections-

Reading this article reminded me of earlier in the semester when we discussed the origins of life and more recently in the semester when we discussed Bas-Becking’s idea. When we discussed the origins of life near under water vents we discussed the kinds of organic chemicals that could have been precursors for the first life forms, those same compounds were found in these mud deposits. When we discussed that life could/would be everywhere, I considered the presence of life beyond our atmosphere, but not beneath the crust of the earth. This article made me wonder what microbial super power could survive in those conditions.

Critical analysis. —

This article only spends one half of it’s very short article discussing the new discovery. I wish that there had been more details on the discoveries methods. Apparently the compounds came from rocks that were “spewed’ onto the surface, there was no explanation on how the scientists could be sure that any signs of life originated in the mud volcano, and wasn’t the product of contamination as the mud progressed to the surface.

My favorite sentence in this paper isn’t referring to the recent discovery; it’s within a paragraph summarizing other research on deep sub surface microbial life. The sentence reads, “ the deeper that scientists have looked the deeper life has seemed to go.’     I wonder if there is a limit to this, if scientist will one day conclusively say: no more life past this point. The researchers of the under sea mud volcano seem to think so. They made an estimate for the maximum depth that could support life. Considering a maximum temperature of 122 degrees Celsius and 1000x atmospheric pressure, the deepest Achaean environment would be about 32,800 feet below the surface.

This article was presented both scientifically, and in a way that could be digested by an interested member of the general public. Its lack of depth was compensated by links to relevant background information and relevant studies.

Question-

Will scientists ever be able to definitively state that an environment/ location is completely free of life without having to clarify “that we know of’?

 

A2: Microbes in the News Assignment

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Microbes in the News !

Over the course of the semester, post 3 different stories involving microbes  from the popular media and then read and comment on 3  posts by other students.

 

Points: Total possible = 30 points. Earn up to 8 pts for making a post and 2 points for posting a comment. Create 3 posts and 3 comments over the course of the semester.

Deadline: All posts and comments must be made by April 24 to receive credit.

 

Learning Objectives:

– Increase your awareness of microbiology and its role in society

– Expand and apply your knowledge of microbiology

– Practice critical thinking by analyzing popular news media for scientific accuracy

– Develop questions about microbiology

– Help your peers and yourself understand microbiology by answering their questions

 

Instructions:

Over the course of the semester, create 3 separate Microbes in the News posts on the course website, and then read and comment on 3 Microbes in the News posts by other students. Be sure to follow the guidelines below in order to qualify for  full credit.

 

Guidelines for creating a post:

– Article and link: Enter the title, source, and date of the article and create a link to it. Articles should be from any popular media source (newspaper, magazine, podcast, blog,  etc.) that others can access without hitting a paywall. Any relevant story is acceptable, but challenge yourself to find stories that are current (~within the last 3 months) and that haven’t yet been posted by your peers, whenever possible.

– Summary: Write a short summary of the story (just a few sentences is sufficient).

– Connections: Explain briefly how this connects to what we’ve covered in class.

– Critical analysis: Explain what you found interesting about this story, and what (if anything) you learned. Comment on whether you think the story was scientifically accurate or not. If you noticed any factual inaccuracies or aspects of the story that might inadvertently confuse or misinform readers, identify those and provide a more accurate explanation. Also comment on how this was written. Do you think it did a good job of communicating science to the public? Why or why not?

– Question: Write a question about microbiology that you had as a result of reading this story.

– Categorize: Categorize your post as “A2: Microbes in the News’ using the categories menu on the right. This will ensure I can find it and give you credit.

– Tag: Tag your post based on any relevant microbiological themes by choosing from the tag menu (below categories on the right). Use existing tags when possible, but you can add new ones if needed by clicking “+Add New Category’ link just below the list of tags. This will help us find stories on relevant themes. You can also use these tags to search for other students’ stories on themes that interest you.

Guidelines for commenting on a post:

– Read the news story and the students’ post about it

– Create a comment and write a response to their critical analysis. Do you agree, disagree, or have more to add?

– In your comment, answer their question to the best of your ability. This might require some independent research.