Nature’s Element…and it’s not Oxygen.

Nitrogen! A relatively inert, triple-bonded element that makes up 70% of the atmosphere. An integral part of our biological make up. It can be found in almost, if not, every living organism on this earth. If we look at the nitrogen cycle, we can see why:

From the atmosphere it falls to the ground where it is reduced and oxidised into more reactive forms and plants take them up. Then up the food chain they go…and back down, if you get what I mean. If we eat it, we release it and when we do, it’s in the form of organic nitrogenous compounds. Some of these compounds include urea, amines and amides. Along with human and animal waste, there are other nitrogen contributors like decaying plant matter, agricultural, industrial and pharmaceutical runoffs. When released they undergo different processes including ammonium oxidation and denitrification. 

As discussed in my last post ammonium oxidation is carried out by ammonium oxidising bacteria (AOB) and results in the formation of nitrite. It is half of the nitrification process which is the complete oxidation of ammonium to nitrate. This process occurs in the soil naturally and in wastewater treatment (WWT) in the activated sludge tank. 


After nitrification is denitrification and this is the reduction of nitrate to nitrogen gas which is re-released to the atmosphere. This is carried out by denitrifying bacteria. In my research project, I didn’t measure for this process because it was not in my original plan. However, there was a strong possibility that it was occurring. Remember in the last post, I stated that carbon dioxide was being produced within the reactor despite it being a fully closed system. The process responsible for this could have been heterotrophic denitrification which is carried out by ordinary heterotrophic organisms. One could argue that this step is the most important in a wastewater treatment process due to the fact that it completely removes the toxic nitrogenous compounds from the water, rendering it “clean”.

Nitrogen assimilation

Algae are efficient at consuming nitrogen in its different forms and the nitrogen is usually incorporated into the biomass. This is quite an advantageous reality which is why algae is widely researched for more than just bio-fuels. In my research, I didn’t expect for the algae to make much of an impact in assimilating the ammonium because of the stoichiometry of the photosynthesis reaction when compared to that of nitrification. However, it played a very important role by aerating the reactor.

My two cents…

Nitrogen is one of the most important nutrients in this world but it can be toxic in different forms. Carbon dioxide is also beneficial to photosynthetic organisms however it is a dangerous greenhouse gas. It is absolutely beneficial to combine the nitrogen removal properties of bacteria and carbon dioxide consumption properties of algae. This is biotechnology that can assist us in adapting to climate change. But, how do we make affordable for countries to use it? How do you convince governments to fund it? If I did it in a temperate country with fake sunlight, then how much better do you think it would be to kick-start in Barbados, the land of eternal summer?

Let me know what you think.


Carbon dioxide: algal growth & ammonium oxidation

We’re running the most dangerous experiment in history right now, which is to see how much carbon dioxide the atmosphere… can handle before there is an environmental catastrophe.” – Elon Musk

In 1896, Arrhenius posited that the carbon dioxide (CO2) produced from fossil fuel combustion would be directly proportional to the increase in global temperature. We can see from today’s events that his hypothesis was very much proven. One of my previous posts, about Earth day, highlighted the importance of photosynthesis in the consumption of CO2 from the atmosphere. Algae, much like trees, photosynthesise consuming inorganic carbon (dissolved CO2 or bicarbonate) from their aquatic environment. Another process countering the rising CO2 concentrations is ammonium oxidation which is carried out by ammonium oxidising bacteria (AOB). As the name states, these bacteria oxidise ammonium into nitrite (NO2). The energy produced from this oxidation is used to fix CO2 into their biomass through the Calvin Cycle.

Image result for infographic of calvin cycle
The Calvin Cycle

Algal growth

IMG_9203For this research project, the 2 green alga species (Chlorella and Scenedesmus) were documented in literature to be excellent at nutrient fixation while the other 2 species (Anabaena and Spirulina) were relatively unknown. In terms of COconsumption, the 2 different types of algae had 2 different ways of consuming dissolved CO2 .They differed in efficiency too because by the end of the study, only Anabaena remained. The other species died out from the reactor as a result of low dissolved COconcentrations and Anabaena survived due to the species utilising a carbon concentrating mechanism (CCM). This CCM is characterised by the conversion of bicarbonate (from the environment) to COby the enzyme carbonic anhydrase. The COis then consumed through photosynthesis therefore, maintaining function even in a below optimum environment.



Ammonium oxidation

Ammonium oxidation, or nitritation, is part of a very important process (nitrification) in biological nitrogen removal from wastewater. When I first learnt of ammonium oxidation I thought AOB had the same metabolic pathway as most bacteria which was to release CO2. However, much like a photosynthetic organism, AOB consumed CO2 to incorporate into biomass. In order to ensure ammonium oxidation was occurring in the bioreactor, the dissolved oxygen (DO) concentration had to be 3 mg/L and above. Photosynthesis made it easy to maintain this concentration however, it still caused one of the bigger challenges for me which was to create an environment where AOB thrived above all the other oxidising microorganisms. Since that DO concentration was optimal for all “oxidisers”, I was constantly manipulating the lights which controlled photosynthesis and subsequently the DO concentration.

An observation…

After reviewing the dissolved CO2 profiles in the bioreactor, we noticed that there was an increase in the concentration which meant that CO2 was getting into the reactor after feeding. Now, when dealing with algae and bacteria biomass, the reactors are usually completely sealed to reduce the introduction of new microorganisms that could present as competition to the ones inside. Thus CO2 was being produced inside the reactor by the ordinary heterotrophic organisms (OHOs) that break down organic matter resulting in CO2 as one of the byproducts. This should have been a a positive for the algal strains that died out but I believe Anabaena was already taking over by this time.

My two cents…

In the mitigation of climate change, these processes would be beneficial but on a very large scale. This research also showed me that perfecting (CO2) consumption and wastewater treatment is quite challenging but quite necessary. Imagine reducing (CO2) concentrations in the atmosphere and simultaneously cleaning water that could be reused instead of continuously depleting the already low fresh water reserves. What a way to change the tide.

the Awkward Chemist

My research project: carbon dioxide, algae and bacteria…

“If we knew what we were doing, it would not be called research, would it?” – Albert Einstein

The great Einstein really knew what he meant when he said that and I sure found out when I did my research project/thesis for my Masters degree. I definitely had no clue what I was getting myself into but I can confidently say that the end result was more than gratifying. This project opened my eyes to the benefits of resource recovery, the intricacies of natural metabolic pathways and the large impacts the smallest organisms can have on the environment.

I remember saying that I’d share my journey with you and I think it’s time I keep up my end of the bargain. So, to do that, I’ll be publishing a series of posts on the different topics my research rested on just to give you an idea of what I got up to in the laboratory.

But first, I’ll give an overview of my research:

I evaluated the effects of carbon dioxide concentration on algal growth and ammonium oxidation. To accomplish this, a mixed biomass of algae and bacteria was inoculated with a medium called BG11 in a sequencing batch reactor (SBR). The algal species were 2 green (Chlorella and Scenedesmus) and 2 blue-green (Anabaena and Spirulina) strains. The bacteria was provided by activated sludge from a dutch wastewater treatment plant. For those who do not know, activated sludge is sewage which is being (actively) broken down by aerobic (need oxygen to function) microorganisms. BG11 is a growth medium containing all essential nutrients, inorganic and organic, needed for algal and microbial proliferation (assimilation into biomass). In this study however, the BG11 medium was used to mimic municipal wastewater. Simulation of day/night scheduling was achieved by timer-controlled lights and the SBR operated under 24 and 12 hr cycles in 2 different phases of research. IMG_7524

Further, nitrogen and carbon compound concentrations and other physico-chemical parameters were measured and used to determine the success of the mixed biomass. Based on those measurements, I concluded that the mixed biomass excellently removed ammonium from the “wastewater” and that the carbon dioxide concentration did not affect the rates of algal growth or ammonium oxidation.

Another aspect was one which I knew nothing about, computer modelling. I used the results from the experiments to predict the values of the half saturation constant for both algal and bacteria, separately. I used a program called AquaSim. This was a challenge but a challenge I welcomed.

Now that you have a general idea of what I did, below is a list of the topics I wish to cover in the coming weeks:

  1. Carbon dioxide: algal growth, ammonium oxidation
  2. Nitrogen cycling: ammonium oxidation/nitrification, denitrification, nitrogen assimilation
  3. AquaSim and simulation of natural processes
  4. Resource recovery and biological wastewater treatment
  5. Rationale, major challenges and something new

I’m so glad to be sharing this with you in hopes that you learn just like I did.  And remember,

Science is gorgeous. Chemistry is a beauty best observed in a laboratory. The colours, the textures, the smells (some not pleasant), the unpredictability, the laughs, the tears, the encouragement…nothing compares. You might find you enjoy some areas in chemistry more than others, and that is okay. But enjoy…ENJOY!” – the Awkward Chemist

Short Post: Keep Barbados Clean

I’m a part of the Caribbean Youth Environment Network (Barbados) and every year we put on a National coastal clean up called the Barbados International Coastal Clean-Up (BICC). This Sunday we did the northern beaches. Myself and my CYEN colleague Alex (shown in picture), along with members of the St. Peter Parish Committee, tackled Six Men’s Beach. The pictures I have, show no real indication of the amount of garbage littered across the beach however, it would be remiss of me not to say something about it.
We, as a nation, need to do A LOT better with our garbage disposal and our regard for the environment. The majority of the garbage collected was plastics: bottles, caps, bags, straps, forks. I engaged a member of the community, asking him if we asked for community help what the response would be like. His answer to me was,” they would only help to dirty it up more.” Horrible. We MUST do better. Imagine how much of this loose garbage was deposited into the sea after the passage of Tropical Storm Matthew. Barbadians take pride in your surroundings, please. It will not kill you to find a garbage can to dispose of your waste. 

–  the Awkward Chemist

#KeepBarbadosClean #FindAGarbageCan #BICC2016Chronicles#WhatAboutOurBeaches #WhatAboutOurMarineLife14516330_348905712112898_7451737847075857727_n

Ocean Acidification

“Ocean Acidification is just the evil twin of global warming…” As if global warming isn’t evil enough… Disappointed-Meme-Face-08

Being from a country where glass bottom boats, snorkeling and coral reef exploration are parts of tourism, Ocean Acidification is one of the global warming effects we need to discuss. Before we dive into that, let’s first understand pH, acids, bases & indicators, and the importance of pH balance.

What is pH?

pH is the measure of the hydrogen ion concentration of a compound. It is a logarithmic scale which ranges from 0-14 where 7 is neutral, >7 is basic (alkaline) and <7 is acidic.

pH= -log[H+]

pH scale (1)
pH Scale

Acids & Bases

From corrosive and sour to soapy and bitter, acids and bases make up the world as we know it. They are many different types of acids but for the simplicity’s sake, it can be defined as a chemical substance that neutralises bases, dissolves some metals, and turns litmus red or a molecule or entity that can donate a proton or accept an electron pair in reactions.

For a more in depth explanation of the pH Scale, click here!

Bases (a.k.a Alkalis) can be defined as a chemical compound that neutralises or effervesces (bubbles) with acids & turns litmus blue. Also, by being the opposite of acids, it is subsequently a compound that accepts protons or donates electron pairs in reactions.


These are compounds which change colour and structure when exposed to certain environments. Litmus, mentioned above, is an example of an indicator; it is the first indicator you will ever learn about in science. There are many other indicators which are used in chemical tests such as methyl red, phenolphthalein (common), methyl orange and many more.

pH Importance

For every biological system, pH plays a very important role in keeping the balance. The slightest change in pH can have adverse effects. For this post, I will use aquatic environments as an example. The pH of most aquatic environments ranges between 6-8 and in these conditions organisms, both at the top and the bottom of the food chain, thrive. pH can determine how well some organisms carry out their regular day-to-day processes with said water and unsustainable changes result in decreased numbers and in extreme cases, death. For other organisms, they grow to levels which may continue to inhibit the ones already struggling. This is why keeping the balance is paramount.

What’s there to know about the Ocean?

Ocean pH, seawater composition and the general equilibrium of the ideal ocean would help to show how different things can become or are becoming via Ocean Acidification. As Caribbean natives, we tend to just go to the beach and never think about what we’re stepping into. I think it’s high time we changed that.

Ocean pH

Unaffected by anthropogenic (man-made) emissions, the pH of sea water was a basic 8.2. After the rise in carbon dioxide concentrations in the atmosphere, it has decreased to 8.1 thus, increasing in acidity. A 0.1 change in pH may seem so minuscule but the pH scale and the Richter Scale are alike in that a change of 1.o is actually 10 times that of the original value. So, this change represents a considerable decrease in the comfort of marine life.

“What is seawater even made of?”, you ask?

Seawater Composition

Ions found in seawater originate either from inside the earth (seismic/volcanic activity), the atmosphere (gases floating around in the atmosphere) or from the many organisms (coral reef, excrement or decomposing) which call the ocean their home. It is because of these above salts that the ocean tastes ‘salty’.

“How does the ocean maintain a basic pH?”

Ideal Ocean Equilibrium

You were probably thinking that a body of water should be neutral but by now I’m sure that has changed and wondering how it is basic and how does it stay basic. The answer, a Carbonate Buffer (a solution that resists pH changes when volumes of acid or alkali are added to it). A buffer usually consists of a weak acid and its salt; the carbonate buffer consists of carbonic acid (H2CO3) – formed when carbon dioxide dissolves in seawater – and the bicarbonate ion. Since carbonic acid is unstable, it breaks down into the bicarbonate and carbonate ions which are now responsible for the buffering/pH regulation of the ocean. The percentage presence of the bicarbonate ion (HCO3– ) and carbonate ion ( CO32-)make up part of the “other” percentage. Even though their percentages are scanty, they play the most important role in the ocean. All aquatic life is sensitive to the pH of the ocean therefore the buffer must be supreme.


The entire process of the Carbonate Buffer. In more basic conditions, the Carbonate Ion is formed. Ideally, equilibrium should be between the bicarbonate & carbonate ions.

“So! What is Ocean Acidification?” 

Ocean Acidification (OA)

Now that you have enough knowledge on the Carbonate Buffer, we can now take a look at the acidification process. Buffers are usually resistant to additions of acids and bases but given enough of one, the equilibrium will definitely shift. Since the amount of carbon dioxide in the atmosphere has increased over the years due to industrialisation, more and more carbon dioxide has been dissolving into the ocean. Therefore, the abundance of carbonic acid in the ocean is increasing, causing the buffer to become unbalanced thus, lowering the pH.

Before, the absorption of carbon dioxide by the world’s oceans was seen as natural mitigation to our climate change issue. But now it is proving to be yet another head of the hydra.


Calcium Carbonate Breakdown

Remember that carbonate ion which is formed in more basic conditions? Well when it reacts with the calcium ions in the ocean it forms a salt called calcium carbonate. This compound is one of the building blocks used by organisms to build shells and coral reefs amongst other things. When it reacts with the carbonic acid, it dissociates causing a weakening of the shells of snails, clams and any other like organisms, as well as the destruction of coral reef. The coral reef cannot use the calcium carbonate to keep their skeletons strong, therefore they dissolve. In Barbados, damage to our coral reefs will impact on our eco-tourism package. Imagine the larger world renowned reefs. How will they survive?

Ecosystem Imbalance

With calcium carbonate out of the picture, there is the problem of organism survival. Some juveniles of aquatic organisms have hard shells to protect them making them extremely vulnerable to OA. When the mortality rate of juveniles increase, the rate of survival decreases thus, an overall decrease in populations. This causes a domino effect in the food web. Where there is a shortage of food, a shortage of feeders arises.

Socio-Economic Impact

As I mentioned before, coral reefs are a part of many tropical destinations’ eco-tourism. With them being destroyed by OA, economic problems come to the light. Not only are the coral reefs gone, but the fish that frequented them are gone too. The big fishing companies that catch the mussels and shellfish for restaurants and supermarkets can go out of business if OA goes on long enough. Jobs, livelihoods and maybe even communities could be lost taking a toll on the economy causing it to tumble, yet again.

My Two Cents

“In the last 150 years or so, the pH of the oceans has dropped substantially, from 8.2 to 8.1–equivalent to a 25 percent increase in acidity. By the end of the century, ocean pH is projected to fall another 0.3 pH units, to 7.8.” (ScienceDaily, June 2014 )

We have discussed what pH, acids & bases and indicators are, everything you need to know about the ocean (for the purpose of this blog), and what is OA as well as its consequences. You have read for yourself, the situation is a serious one. I cannot stress enough how dangerous climate change (& its family) is to the planet and how much we have taken for granted. A step in the right direction would be to become more aware of what’s going on around you. There is no such thing as too much information when it comes to something as serious as this. Once you know, you can always do better.

– the Awkward Chemist

“It is a curious situation that the sea, from which life first arose, should now be threatened by the activities of one form of that life. But the sea, though changed in a sinister way, will continue to exist: the threat is rather to life itself.” –Rachel Carson


Sites Used for this Post:


Teach Ocean Science

National Science Foundation




“David & Goliath”

“David and Goliath? Wuh she really talking bout?”

I know that is what some of you are thinking. But, that popular bible story can be applied to many real life situations and today I choose to apply it to mankind and the skyscrapers of the environment, trees. Earth Day is being celebrated today, April 22nd 2016, and I want to shed some light on the movement and it’s purpose as well as highlighting the importance of trees and the processes which make them our saviours.

Hey Peoples! I hope you’re coping well with life. Thanks for continuing to rock with me; let’s get into my newest post.

 “David and Goliath? Wuh she really talking bout?”

I know that is what some of you are thinking. But, that popular bible story can be applied to many real life situations and today I choose to apply it to mankind and the skyscrapers of the environment, trees. Earth Day is being celebrated today, April 22nd 2016, and I want to shed some light on the movement and it’s purpose as well as highlighting the importance of trees and the processes which make them our saviours.

What Is Earth Day?

Earth Day is a movement which was started in 1970 to bring awareness to the quickly growing environmental issues through participation from the world’s population. Their aim was really to increase the international environment movement and use it as a tool to “build a healthy, sustainable environment, address climate change, and to protect the world for future generations.” (For more information about Earth Day, please visit their website : About Us | Earth Day Network)

This year’s theme is: “Trees for the Earth. Let’s get planting.”

Countries the world over host rallies, forums, tree planting ceremonies, educational fairs and many other events to celebrate Earth Day and to bring awareness to the movement. Here in Barbados, the Caribbean Youth Environment Network (NPO) is hosting their own Earth Day activity called, “Shining Light on Climate Change”. It will be held at Brandon’s Beach, St. Michael, from 6:00 p.m. (For more information about the event, visit the event’s page on Facebook: Shining Light on Climate Change ) [CYEN – Barbados]

Trees : The Silent Saviours


Simply put, a tree can be defined as a woody plant usually with a single trunk and a branched top.
There are 2 types of trees:

  1. Deciduous Trees: These trees spread out as they grow with a rounded shape and their leaves are very broad. During Autumn, they tend to drop their leaves because of the change in weather and the difficulty to carry out photosynthesis properly.
  2. Coniferous Trees: These trees are referred to as “Evergreen” trees. This is because their leaves remain green throughout the changing seasons only dropping off if old. They grow upwards and tend to have a triangular shape. (Bajan example: Casuarina Tree/Mile Tree)

Forests make up some of the largest ecosystems of the world by being home to thousands of organisms; these organisms range from vertebrates to invertebrates. Imagine what happens to them when we carry out intentional deforestation (forest fires can be accidental). How would you live without your home?

What is Photosynthesis?

Trees also act as filters of the atmosphere through Photosynthesis. Photosynthesis is the process by which green plants create their food by combining Carbon Dioxide and Water using sunlight. All of which occurs in the chloroplasts of the leaves’ cells.

Chemical Equation of Photosynthesis: The sub-scripted numbers represent the number of atoms of the particular element needed to bond with the other to form a stable molecule. The large numbers represent the number of moles of each molecule needed and produced in the process; they balance the equation. [EVERY CHEMICAL EQUATION MUST BE BALANCED]
From there the sugar goes on to form polymers (a substance consisted of large numbers of similar units bonded together) like cellulose and lignin which make up the plant’s structure.

Let's Explore Science... Food from the Sun plantcell1

The above images represent the Process of Photosynthesis (left) and an image of a plant cell showing the Chloroplasts and other important cell structures.

With carbon dioxide emissions being one of the prominent environmental issues, photosynthesis is one of the best natural processes to clean up the atmosphere. Another great feature about trees and photosynthesis, is the expulsion of oxygen as a byproduct. Therefore, photosynthesis acts as a critical balance between carbon dioxide and oxygen. Who wouldn’t want decreased carbon dioxide levels for good clean oxygen to respire?

Now you know the some of the benefits of trees and why it is important to help preserve them. Not just on Earth Day but any day of the year. Trees help to save our lives every day and with deforestation & acid rain occurring, their duties are becoming more and more difficult.

My Two-Cents

I chose to go into a little detail about trees because photosynthesis can be represented chemically, with ease of description while all other issues discussed on Earth Day seem more social (this does not make them any less important)[Earth Day Campaigns]. In showing the actual process of photosynthesis, both chemical and biological, I aimed to give you an idea of what really happens and why it is as important as people say it is.

I used David and Goliath as the analogy because we,as small as we are, cut down the tallest and widest trees for our gain. In this case, David isn’t the hero, he is the villain. In another way, by planting more trees and creating more forests, we strike a detrimental blow to the body of that which is climate change; David remains a hero. My question to you is, which one would you rather be? The hero or the villain?

– the Awkward Chemist

“The good man is the friend of all living things.”Gandhi

Sites used for this post:

Earth Day Network

Help Save the Climate

The Different Types of Trees