Trials in Taxonomy: Popcorn, Spirals, and Roses
by Robyn Granger
In 2016, I worked as a teaching assistant to a group of biology and conservation undergraduates. Despite my taxonomy knowledge being rather limited (having done my Master's degree in Palaeoclimatology), the students never seemed to tire of asking me to identify various species in the field. It wasn't long before they began to affectionately quip “Robyn is a palaeoclimatologist - she knows nothing,” whenever I informed them that I was unable to tell them the difference between a plant that might kill them, and one that would be good rolled up in a cigarette.
Figure 1: Both of these organisms are the same species? Now I'm really confused...[1]
They would probably laugh if they could see me now. Two years later, I have found myself nose-deep in a PhD with a significant biological component, which involves picking out the subtlest of differences between tiny ocean-dwelling organisms called foraminifera. My project involves refining one of the chemical proxy methods scientists use to infer oceanic changes in variables like temperature and nutrients.
Luckily for the scientists, these little guys are stubborn creatures: when they die, they sink to the ocean floor but refuse to decompose in ocean sediments even after millions of years. Their chemical makeup reflects that of the environment in which they lived and died, so the immaculate preservation of their shells means that with a bit of detective work, one can effectively “look back in time” to reconstruct the ocean environment over hundreds, thousands or even millions of years.
Unluckily for me, there is an exhaustive amount of different species - and I'm finding out just how murky taxonomy can be. How does one define a new species, as opposed to morphological differences within a single type?
Not only that, but it seems like scientists find new reasons to reclassify organisms every few years. How can anyone keep up?! To keep some semblance of order, and on the advice of another PhD student, I decided to start with classifying them into what I felt they resembled. Petri dishes 1, 2 and 3 were thus labelled “Popcorn,” “Spiral,” and “Rose” respectively. But the philosophy of taxonomy is a debate for another time.
Over the past few months, my primary concern has been to pick out foraminifera from modern seawater samples in the hope of obtaining their chemical composition - a key step towards validating my methodology. Hundreds of hours spent bent over a microscope have yielded several thousand foraminifera (and chronic backache) but has still left me wondering how best to distinguish between them.
I was delighted when I came across a website that claimed to be a taxonomic guide. Perfect, I thought. I could just enter in the characteristics of the foraminifer, and the computer would spit out the answer. This proved to be a failure: either I was putting in the wrong characteristics, or the list of available species was generated based on Northern Hemisphere samples (which can be very different to those found in the South African waters where I am working). Either way, I kept coming up with “no matches,” despite my protests to the internet that my foraminifera definitely existed.
Textbook photographs of foraminifera helped, but the images were almost too good; the stereo microscope that I was using could in no way show the detail depicted and described in those pages.
So I changed strategy - I sourced a Scanning Electron Microscope, and although this required a painstaking amount of work matching up images shot from the SEM, the stereo's camera and my cellphone, slowly, the murky world of foraminifera taxonomy started to become less so.
Strangely enough, the difficulties I've had in identifying the foraminifera have only made me love studying them even more. It's become like a puzzle, or a game entitled “Name that Foraminifer!”, and I am determined to uncover their secrets. To this end, I've registered to attend this year's International School on Foraminifera. People tell me I'm a nerd to be excited about this, but I know they're just saying that to cover their burning jealousy.
If I were to come across my biology students again, perhaps they would still remind me that I know nothing. But no longer can I plead the excuse that I am not a biologist; somewhere along the way and without fully realising it, I stepped into the world of biogeochemistry.
by Robyn Granger
In 2016, I worked as a teaching assistant to a group of biology and conservation undergraduates. Despite my taxonomy knowledge being rather limited (having done my Master's degree in Palaeoclimatology), the students never seemed to tire of asking me to identify various species in the field. It wasn't long before they began to affectionately quip “Robyn is a palaeoclimatologist - she knows nothing,” whenever I informed them that I was unable to tell them the difference between a plant that might kill them, and one that would be good rolled up in a cigarette.
Figure 1: Both of these organisms are the same species? Now I'm really confused...[1]
They would probably laugh if they could see me now. Two years later, I have found myself nose-deep in a PhD with a significant biological component, which involves picking out the subtlest of differences between tiny ocean-dwelling organisms called foraminifera. My project involves refining one of the chemical proxy methods scientists use to infer oceanic changes in variables like temperature and nutrients.
Luckily for the scientists, these little guys are stubborn creatures: when they die, they sink to the ocean floor but refuse to decompose in ocean sediments even after millions of years. Their chemical makeup reflects that of the environment in which they lived and died, so the immaculate preservation of their shells means that with a bit of detective work, one can effectively “look back in time” to reconstruct the ocean environment over hundreds, thousands or even millions of years.
Unluckily for me, there is an exhaustive amount of different species - and I'm finding out just how murky taxonomy can be. How does one define a new species, as opposed to morphological differences within a single type?
 |
| Figure 2: A disheartening result for my search. a a |
Over the past few months, my primary concern has been to pick out foraminifera from modern seawater samples in the hope of obtaining their chemical composition - a key step towards validating my methodology. Hundreds of hours spent bent over a microscope have yielded several thousand foraminifera (and chronic backache) but has still left me wondering how best to distinguish between them.
I was delighted when I came across a website that claimed to be a taxonomic guide. Perfect, I thought. I could just enter in the characteristics of the foraminifer, and the computer would spit out the answer. This proved to be a failure: either I was putting in the wrong characteristics, or the list of available species was generated based on Northern Hemisphere samples (which can be very different to those found in the South African waters where I am working). Either way, I kept coming up with “no matches,” despite my protests to the internet that my foraminifera definitely existed.
Textbook photographs of foraminifera helped, but the images were almost too good; the stereo microscope that I was using could in no way show the detail depicted and described in those pages.
 |
| Figure 3 (Left): Using a stereo microscope, I could see my foraminifera up close, but these didn't look like the beautiful SEM pages found online and in textbooks (Right). Left: An educated stab at identification! Some of my SEM images include (a) Globorotalia inflata, aka Rose, (b) Globorotalia truncatulinoides, also known to me as Spiral; and (c) Globigerina bulloides, which looks rather like Popcorn. |
So I changed strategy - I sourced a Scanning Electron Microscope, and although this required a painstaking amount of work matching up images shot from the SEM, the stereo's camera and my cellphone, slowly, the murky world of foraminifera taxonomy started to become less so.
Strangely enough, the difficulties I've had in identifying the foraminifera have only made me love studying them even more. It's become like a puzzle, or a game entitled “Name that Foraminifer!”, and I am determined to uncover their secrets. To this end, I've registered to attend this year's International School on Foraminifera. People tell me I'm a nerd to be excited about this, but I know they're just saying that to cover their burning jealousy.
If I were to come across my biology students again, perhaps they would still remind me that I know nothing. But no longer can I plead the excuse that I am not a biologist; somewhere along the way and without fully realising it, I stepped into the world of biogeochemistry.
by Robyn Granger
Oceanography, University of Cape Town, South Africa
If you have questions or comments concerning Robyn's post, please leave a comment below, or send her an email. You are also encouraged to visit her department's website.
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[1] Thirumalai K, Richey J N, Quinn T M, Poore R Z. 2014. Globigerinoides ruber morphotypes in the Gulf of Mexico: A test of null hypothesis. Scientific Reports 4:6018. DOI: 10.1038/srep06018
If you have questions or comments concerning Robyn's post, please leave a comment below, or send her an email. You are also encouraged to visit her department's website.
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Reference:
[1] Thirumalai K, Richey J N, Quinn T M, Poore R Z. 2014. Globigerinoides ruber morphotypes in the Gulf of Mexico: A test of null hypothesis. Scientific Reports 4:6018. DOI: 10.1038/srep06018
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