Exploring Aquarium Eukaryotes With Aquabiomics tankDNA

[Clarkjw2002]

These types of mass sequencing results are only as good as the libraries they are being blasted against. I'd inquire as to what libraries they use if you are interested in actual identifications. I suspect they use an open source site like NCBI Genbank. If this is the case I can tell you from experience to take the results with a grain of salt. Anyone can post sequences to genbank, mis-identified or not.

That being said, I'd expect eDNA results from your tank and refugium to be similar, even if the species composition is different because of the shared recirculating water source.

 

[LovinlifeinGuam]

These types of mass sequencing results are only as good as the libraries they are being blasted against. I'd inquire as to what libraries they use if you are interested in actual identifications. I suspect they use an open source site like NCBI Genbank. If this is the case I can tell you from experience to take the results with a grain of salt. Anyone can post sequences to genbank, mis-identified or not.

That being said, I'd expect eDNA results from your tank and refugium to be similar, even if the species composition is different because of the shared recirculating water source.

The researchers have a different opinion, but you're just as entitled to yours as they are. There's not much of a debate to be made since I'm not one of the researchers myself.

 

[Clarkjw2002]

If they are just doing mass sequencing and then blasting results, my comment applies. If they are actually using DNA fragments to bind and identify what is in the mass sequenced sample that is a different story. In this case, your detection abilities are limited by what DNA fragments you have on the reading chips/platform.

Been 10 or more yrs since I oversaw research utilizing these methods so I am sure a lot has advanced/changed. Back then MagPix beads were the new thing for large scale identification beyond just blasting sequences against Genbank.

Retired now so take my comments with a grain of salt as well! Oh, and by the way, most researchers think their methods are the greatest thing since sliced bread.

 

[LovinlifeinGuam]

If they are just doing mass sequencing and then blasting results, my comment applies. If they are actually using DNA fragments to bind and identify what is in the mass sequenced sample that is a different story. In this case, your detection abilities are limited by what DNA fragments you have on the reading chips/platform.

Been 10 or more yrs since I oversaw research utilizing these methods so I am sure a lot has advanced/changed. Back then MagPix beads were the new thing for large scale identification beyond just blasting sequences against Genbank.

Retired now so take my comments with a grain of salt as well! Oh, and by the way, most researchers think their methods are the greatest thing since sliced bread.

Oh, I'm with you 100% in saying that whatever the most modern method is will be claimed to be far superior to those used previously and extraordinarily accurate. Id imagine this will always be a trend. I just read a study published this year which I believe did use DNA fragments, but that obviously still doesn't guarantee flawless results.

 

[Dan_P]

These types of mass sequencing results are only as good as the libraries they are being blasted against. I'd inquire as to what libraries they use if you are interested in actual identifications. I suspect they use an open source site like NCBI Genbank. If this is the case I can tell you from experience to take the results with a grain of salt. Anyone can post sequences to genbank, mis-identified or not.

That being said, I'd expect eDNA results from your tank and refugium to be similar, even if the species composition is different because of the shared recirculating water source.

Thanks for the observations.

I had assumed the shared water would erase potential differences. Actually seeing differences might be a finding that needs confirming. I might consider temporarily separating the two compartments before sampling next time. What do you think?

 

[Clarkjw2002]

You could but the question would be how long does eDNA in your water column stay detectable? Might need to separate by months or more, at which point differences may develop due to isolation that may not otherwise have existed--if that makes sense.

I suspect, at the microbiome level, the two tanks are similar so if you separate they may begin to drift apart over time. Any differences at the macro level you probably already know.

What would be more interesting is to compare tanks across regions to see how similar our tanks really are at the micro level, both within regions and across. Or maybe compare established tanks started with live rock to those started with dry, and combinations in between, to see if there are any long term differences.

 

[Dan_P]

You could but the question would be how long does eDNA in your water column stay detectable? Might need to separate by months or more, at which point differences may develop due to isolation that may not otherwise have existed--if that makes sense.

I suspect, at the microbiome level, the two tanks are similar so if you separate they may begin to drift apart over time. Any differences at the macro level you probably already know.

What would be more interesting is to compare tanks across regions to see how similar our tanks really are at the micro level, both within regions and across. Or maybe compare established tanks started with live rock to those started with dry, and combinations in between, to see if there are any long term differences.

Had similar thoughts after mulling it over.

Separating the two for a day or two might provide a glimpse of DNA decay rate. Assumes no drastic change in populations. Removal of DNA from other compartment makes the differences between the two compartments stronger.

Longer separation of the two compartments will as you point out cause them to drift apart. Water chemistry will definitely be affected by removing nitrogen and phosphorous input from the algae pond and nitrate and phosphate removal from the aquarium. Also, algae exudates also removed from the aquarium. Following the population drift would be interesting, but what would I learn from such an uncontrolled experiment.

While I am not a fan of aquarium experiments, this type of study has the potential to generate interesting questions. Maybe a better use of the research budget is something along the lines of what you suggested. I would really like to know how the microbiome evolves in new aquaria with and without live rock and with varying nutrient inputs. I will continue to think this through and listen to suggestions while studying variation in replicate microbiome tests.