Aquatic ecosystems, biodiversity and DNA barcoding

How to understand it in the larger picture?

Science has created various systems to identify the living organisms around us. The first formal system, Linnaean classification and binomial nomenclature, was created around 1753 to help humans understand the living organisms around them.

DNA barcoding, is a modern identification system designed to help humans preserve the ecosystem and its biodiversity at a time of constant and serious threat by human impacts.

DNA Barcoding Identification System.
A way to preserve ecosystems by creating the Library of Life

The Canadian Centre for DNA Barcoding (CCDB) founded the DNA barcoding concept and is the "analytical hub for the International Barcode of Life (iBOL) " that has over 50 collaborating countries. They describe the DNA Barcoding and its importance this way:

• "DNA Barcoding combines taxonomy, genetics and computer science into a process that obtains expert species identification. Genetic markers identify unknown samples like Human Criminal Forensic DNA Fingerprinting."
  
• The International Barcode of Life (iBOL) ambitiously aims to build a DNA based reference library of all multi-cellular life. Within it's first just completed phase, it aimed to barcode 5 million specimens, that represent over 500,000 species.
  
• Why is this important? Scientific models can be built using the iBOL database that can aid in ecosystem monitoring, conservation, forensics, the impact of invasives and so much more. Examples include the possibility to measure the impact that humans have on the ecosystems, and the potential impacts through proposed development. If invasives are identified, the origin of the invasive can be discovered thanks to multi-national participation.
• Why is this important for Georgian Bay? While Georgian Bay Forever is supporting iBOL to help with the bigger picture of ecosystem health with specimen collection and identification from Georgian Bay, our main purpose for participation is to have a library of multi-cell aquatic organisms to help with protection of Georgian Bay ecosystems in the future. Learn more by reading on.

The elimination of invasive Phragmites is one example that helps protect the biodiversity of wetlands, but it is very difficult to protect ‘biodiversity’ when we don’t know or have a record of what comprises our ecosystems.

How can we measure the impacts of humans (whether through invasive species, pollution, development etc.), if we don’t understand what’s there.

GBF has been working for the past 4 years with Dr. Kevin McCann of the University of Guelph, and the Canadian Centre for DNA Barcoding to catalogue all the aquatic organisms in Georgian Bay. Once these have been catalogued, we have the ability to aid conservation management, ecosystem monitoring, forensics, and invasives for Georgian Bay.

Some specific examples of what we can do with DNA barcoding include the ability to:

• Monitor the impact of changes on diversity and document hotspots in biodiversity that need protection. If we find areas of high quality diversity that are exceptional candidates for protection we will be able to prove it scientifically; or if development pressure arise in an area, we will have the means to support mitigation strategies to avoid adverse impacts.


• Uncover food webs, which can aid in management decisions such as understanding the impact of increasing cage aquaculture (net-pen aquaculture) in Lake Huron/Georgian Bay to native fish populations. This is something GBF is beginning to look at. By understanding the contents of the feed of the fish through biotracers (stable isotopes, DNA,etc, fatty acids), it can be determined for instance if aquaculture operations are changing the food web in some areas. Through research we are able to see the nutrients from the aquaculture operation entering the food web through one specific pathway in the food web rather than a diffuse entry throughout the entire food web. This new understanding will be shared with appropriate government oversight agencies. Please go here for more information.

• Determine relative abundance of organisms in an area. Once all the species have been identified, the quantity of each species in an area can be identified through simplified sample testing in the environment. This will be far more efficient and less expensive than hiring multiple specialists in biology to go into each region and identify the specific organisms in which they have expertise. This will be important to help understand how populations of species are impacted by different stressors in the ecosystem.

We have identified that DNA barcoding is a species identification system that will help create a library of the aquatic biodiversity in Georgian Bay. This library will help stakeholders with stewardship of the ecosystem in the future as scientists will be able to monitor impacts and create models that will inform managers about ecosystem risks from anthropogenic or human sources.

How can it do this?

Over 500 specimens have been collected for the Georgian Bay Forever project (Sept 2019 to date) and 180 taxonomic groups identified. See the 2019 Sept update from the professors at this link. There is so much more of The Bay to go.

To give you an idea, here is what the looked at the breakdown looked like in 2017 when there was about 399 specimens sampled.

Of those collected to Sept 2017, 236 were identified to the species level, with all but 41 having some taxonomy level of identification. The samples have been collected from Big Sound, Shawanaga Bay, Sturgeon Bay, and some from Wiarton and Owen Sound. The biggest proportions of the specimens fall in these classes.

Insecta - 37%.0, class of insects invertebrates with 3-part body, 3 pairs of jointed legs, compound eyes, 1 pair antennae
Actinopterygii - 27.1%, class of bony fishes
Malacostraca - 10.1%, largest of 6 classes of crustaceans, segmented organisms with 20 body segments (sometimes 21), with a head, thorax, and abdomen
Maxillopoda - 6.1%, crustaceans, no single character common to all, mostly small. Eg. Barnacles
Gastropoda - 5.0%, snails and slugs from micro to large
Branchiopoda - 4.6%, crustaceans, mostly small freshwater creatures that eat plankton and detritus. Gills are present on mnay of their appendages, including the mouth parts
Bivalvia - 4.4%, molluscs whose bodies and protected by a shell of 2 hinged parts. They have no head or radula (which is like a tongue)
(and others) - 5.7%

Read about some of the specific species in the next segment named "Meet the species barcoded in Georgian Bay."

How are the species determined from specimens?

The specimens that are collected have a tiny tissue extracted. According to iBOL, this tissue is used to isolate a part of the DNA. In 2003, Paul Herbert's research group at the University of Guelph, found that a short section of DNA from a standardized region of the genome could be used for identifying species - comparable to a barcode on a product that you purchase. Most animal groups use a 648 base-pair region in the mitochondrial cytochrome c oxidase 1 gene ("CO1"). This small part is the information used to make the barcode. The bonus to this identification method opposed to others (like isoptope analysis) is that it is fast and cheap and able to determine variations in species. Once the barcode region of the DNA is isolated, it is reproduced and sequenced.

What does DNA sequencing mean?
There are the four bases or subunits (nucleotides) of DNA including adenine, guanine, cytosine, and thymine. DNA sequencing is the process of determining the precise order of these nucleotides within a DNA molecule. In DNA barcoding each of these units is assigned a letter A G C T, and the order is extracted.
iBol provides this example for the Arctic Warbler.
CCTATACCTAATCTTCGGAGCATGAGCGGGCATGGTAGGC....
This code is translated into this image.

If the species already exists in the database, the specimen will be identified immediately. If the specimen does not exist in the database, scientists will determine its classification for future like specimens that are submitted. In this way, we are building an entire catalogue of the aquatic organisms of Georgian Bay!