The Pangea of Commerce Part 1: What lives here?
What is the impact of trade on biodiversity?
Over the past few years I've become interested in this question. I've become interested enough that I've decided to pursue this topic as a graduate student in the Marine and Environmental Biology department at the University of Southern California. I've decided to start writing out the process of putting this project together, as well as everything involved in carrying it out, for two reasons. One, if I try and explain what I'm working on I should hopefully get a better idea of what it is I'm doing in the first place. Two, I'm interested in this topic I just like to share my work on it.
Now the impact of trade on biodiversity is a really broad topic. In the interest of getting a thesis completed at some point in my lifetime I'm going to need to define some terms and narrow the scope of what I want to look for.
First, how to define trade? Humans have been exchanging goods and services, often with some medium of exchange like cash, for millenia. Since current data is often the easiest to collect I'm going to go with studying the most common current form of trade, cargo ships. At this point in human history about 80% of the volume of global trade is carried on ships, and it turns out the bulk of those ships can be tracked in near real time using various databases.
Now how to define biodiversity? There are a number of metrics used in ecology to quantify biodiversity, but does it make sense to look at the biodiversity of every organism at every location. Again, I have the issue of a finite lifespan so I will need to narrow the scope here a few more times. If I'm focusing on marine shipping traffic I can assume that the impact on biodiversity should be greatest, geographically speaking, where there is the highest level of shipping traffic. This then means I should be focusing in on the marine environment immediately in and around ports. As for what type of organisms to focus on, given what can be done in a few years, I would want to focus on what will respond the fastest to changes in the environment. In marine environments, or really any environment, this means focusing on single-celled organisms. Marine microbes have generation times on the order of a day. This means one can study populations of microbes in harbor waters over the course of a few years and expect to go through about 1000 generations of microorganisms, enough time to see the evolution of individual species and shifts in the populations of species.
Now microorganisms, by definition, are incredibly small. If I'm going to measure their diversity in a port's waters how would I go about even telling what was there in the first place? After all humans have a hard enough time counting other humans, and we have the benefit of being visible. Thankfully there have been a few key developments in biology over the past few decades that make this a very manageable problem. The first is PCR, which allows for a large number of copies of a particular strand of DNA to made in order for there to be enough genetic material to study. The second is 16S and 18S rDNA sequencing.
Both 16S and and 18S are short sequences of genes which are involved in coding for ribosomes, structures which help convert the instructions from DNA into proteins. While 16S genes are found in prokaryotic cells, those which lack a nucleus, and 18S genes are found in eukaryotic cells, those with a nucleus, all cells have to synthesize proteins. This means that anything you scoop out of the sea will have some version of these genes. What is even more useful to biologists is that every species has a unique version of these genes, which means you can identify every species found in a sample of seawater. A number of research groups have been doing this in recent years, uploading their data to various public servers such as Silva. Performing such sequencing on a sample also gives the relative levels of each unique 16S / 18S gene sequence, which in turn gives both the relative number of each species found in that particular volume of water.
Now I've started to get a handle on how to get a microbial census in a port's water, which in turn is an indicator of the biodiversity in that region.
Next up, how to tell if what you're sequencing is living it up or pining for the fjords.
Over the past few years I've become interested in this question. I've become interested enough that I've decided to pursue this topic as a graduate student in the Marine and Environmental Biology department at the University of Southern California. I've decided to start writing out the process of putting this project together, as well as everything involved in carrying it out, for two reasons. One, if I try and explain what I'm working on I should hopefully get a better idea of what it is I'm doing in the first place. Two, I'm interested in this topic I just like to share my work on it.
Now the impact of trade on biodiversity is a really broad topic. In the interest of getting a thesis completed at some point in my lifetime I'm going to need to define some terms and narrow the scope of what I want to look for.
First, how to define trade? Humans have been exchanging goods and services, often with some medium of exchange like cash, for millenia. Since current data is often the easiest to collect I'm going to go with studying the most common current form of trade, cargo ships. At this point in human history about 80% of the volume of global trade is carried on ships, and it turns out the bulk of those ships can be tracked in near real time using various databases.
Now how to define biodiversity? There are a number of metrics used in ecology to quantify biodiversity, but does it make sense to look at the biodiversity of every organism at every location. Again, I have the issue of a finite lifespan so I will need to narrow the scope here a few more times. If I'm focusing on marine shipping traffic I can assume that the impact on biodiversity should be greatest, geographically speaking, where there is the highest level of shipping traffic. This then means I should be focusing in on the marine environment immediately in and around ports. As for what type of organisms to focus on, given what can be done in a few years, I would want to focus on what will respond the fastest to changes in the environment. In marine environments, or really any environment, this means focusing on single-celled organisms. Marine microbes have generation times on the order of a day. This means one can study populations of microbes in harbor waters over the course of a few years and expect to go through about 1000 generations of microorganisms, enough time to see the evolution of individual species and shifts in the populations of species.
Now microorganisms, by definition, are incredibly small. If I'm going to measure their diversity in a port's waters how would I go about even telling what was there in the first place? After all humans have a hard enough time counting other humans, and we have the benefit of being visible. Thankfully there have been a few key developments in biology over the past few decades that make this a very manageable problem. The first is PCR, which allows for a large number of copies of a particular strand of DNA to made in order for there to be enough genetic material to study. The second is 16S and 18S rDNA sequencing.
Both 16S and and 18S are short sequences of genes which are involved in coding for ribosomes, structures which help convert the instructions from DNA into proteins. While 16S genes are found in prokaryotic cells, those which lack a nucleus, and 18S genes are found in eukaryotic cells, those with a nucleus, all cells have to synthesize proteins. This means that anything you scoop out of the sea will have some version of these genes. What is even more useful to biologists is that every species has a unique version of these genes, which means you can identify every species found in a sample of seawater. A number of research groups have been doing this in recent years, uploading their data to various public servers such as Silva. Performing such sequencing on a sample also gives the relative levels of each unique 16S / 18S gene sequence, which in turn gives both the relative number of each species found in that particular volume of water.
Now I've started to get a handle on how to get a microbial census in a port's water, which in turn is an indicator of the biodiversity in that region.
Next up, how to tell if what you're sequencing is living it up or pining for the fjords.
 |
| Market research suggest that people like pictures. Please enjoy this image of some charismatic microbes. |
Comments
Post a Comment