Bacterial Analysis.
- Thread starter ShaunW
- Start date
- Location
- Brooklyn, NY
Oooh I scored another point with the scientist!!!!
RD
RD
- Location
- Long Island, NY
Ok all, I have sent out the first batch of packages--Sanjay and Pierce (cali-reef) were the first on the list, so theirs went out today. Randy and Kedd are next--probably next Tuesday depending on my regular workday (eh, earning a living ).
And I am in agreement with Shaun--MR gets first dibs on the results/posting etc.
I am alos willing to explain any and all results to whomever wants to hear them, at length, at the appropriate time. By this I mean when we actually have reproducible results. While it is difficult not to share interesting results midway (and I'm sure we will want to do that), the last thing I want to do is to say "our results are X" when we haven't quantified, analyzed etc etc. Research is by nature methodical, and unfortunately time-intensive. Shaun and I have been working at this stuff long enough to know that the preliminary data often doesn't mean much--
So please be patient with us and we will keep you all updated.
And thanks everyone for your support, interest, and fellowship.
Christine
).And I am in agreement with Shaun--MR gets first dibs on the results/posting etc.
I am alos willing to explain any and all results to whomever wants to hear them, at length, at the appropriate time. By this I mean when we actually have reproducible results. While it is difficult not to share interesting results midway (and I'm sure we will want to do that), the last thing I want to do is to say "our results are X" when we haven't quantified, analyzed etc etc. Research is by nature methodical, and unfortunately time-intensive. Shaun and I have been working at this stuff long enough to know that the preliminary data often doesn't mean much--
So please be patient with us
and we will keep you all updated.And thanks everyone for your support, interest, and fellowship.
Christine
- Location
- Union Square, NY
....and always under scrutiny by the entire community (scientists and amateurs alike).
In the words of the SOS Band, "take your time, do it right."
So please be patient with us
And thanks everyone for your support, interest, and fellowship.
Christine
Christine, no one will pressure you for the results, but we will be excited to hear them. I hope rich won't have to change his sig line
- Location
- Upper West Side
Ummm... I dont really agree with this statement. I know several people that maintain incredible SPS reefs with no skimming. The more I study my tank, the more I realize that skimming is not as important as thought. I have MINIMAL skimming but DO use a filter sock and EVERYTHING in my tank is growing faster than I can cut it.
-Alfred
-Alfred
- Location
- Upper West Side
Hey, if it is of any use, I would be willing to collect water AND provide clippings of my SPS and octocorals for analysis.
-Alfred
-Alfred
Sure, since your tank seems an interesting addition. As for my skimmer statement, I am speaking in the "general" sense. Depending on husbandry, I am sure that you could have a very successful reef tank without one. There are no giant skimmers located somewhere in nature,
. But in our overfeed, nutrient rich (with the wrong nutrients) aquariums, in general a skimmer is needed.Can you PM me your address?
This is a fine question. But what will you do with the answer? Say you find that bacteria counts in tanks is higher than 1x106 bacteria/mL. What does that mean? Is it good? Is it bad? I think this may be a fine place to start, but it's not a very sexy question in that the answer probably isn't going to satisfy you very much.
Ahh... now I think we're getting somewhere! These are sexy questions! But I'm thinking (as you probably are too) that you may have to set up a study for each one.
marry me
Maybe one day, if we hobbyists, as a community, can get our act together and show the scientific/academic community that we're not just a bunch of hacks (that we do respect science and established knowledge), they'll be more willing to open their hearts and their vast resources to helping us answer these questions. Aaaa... dare I dream of it?
I also have a friend who's going to soon be working at Mote Marine who is working with coral symbiotes. Maybe I can ask her about this too.
Regarding skimmers... I recently talked with one of the only actual protein fractionation experts (a prof at Vanderbilt) in the world (there really aren't that many). Basically I asking him a whole lot of questions about skimming and he was kind enough (with the help of one of his reefer students) to answer them.
However, this is something of an "article" that will be on a website I'm developing that won't be officially "launched" until Febuary. So please don't copy and paste or otherwise threaten the intellectual property of this Q&A. I swore I wasn't going to share it until the website was done, but you guys are asking so many intelligent questions, I can't take it anymore. So here it is, maybe it will help, maybe it won't. In any case, it's an interesting read...
Protein Skimmer Q&A
questions answered by Chris Stowers and Dr. Robert D. Tanner of Vanderbilt University
Proteins can range greatly in size and chemical nature. What kinds of proteins do protein skimmers remover?
Protein skimmers can remove a wide range of proteins depending on their size and type. In general, larger proteins, proteins with hydrophobic appendages, and linear natured proteins (not coiled) will be removed easier. The efficiency of a skimmer will determine the rate and extent that a certain protein will be removed. Most coral and fish waste has potential to be removed by foam fractionation (skimming).
What determines what kinds/sizes of proteins a skimmer will remove?
Bubble contact time- The time which a bubble generated from a skimmer spends in contact with the water and proteins. The longer the time a protein spends in contact with a bubble, the more likely it will be adsorb to the surface of the bubble and removed.
Salinity- Higher salinity can increase bubble production and therefore increase the amount of proteins removed.
Skimmer Size- Larger skimmers generally have longer contact times and process more water leading to more efficient skimming.
Water Chemistry- Certain chemicals such as surfactants have been shown to greatly skew the ability for proteins to be removed from water by foam fractionation. Other chemicals such as tannins have led to similar results. Thus, one should be aware that the presence of a chemical that greatly modifies bubble production will affect protein skimming.
What else (if anything) do protein skimmers remove?
Protein skimmers can remove any substance that is hydrophobic in nature. Most chemicals other than proteins in the reef water column are hydrophilic. However, proteins often complex with nutrients such as Mg allowing them to be removed along with the protein.
Do skimmers remove bacteria and algae too?
Yes, but not efficiently. Although bacteria and algae can be removed by skimming, they are encompassed by a cellular membrane which is hydrophilic on the exterior making them practically immune to skimming.
How do protein skimmers remove phosphates?
Protein skimmers can remove organic phosphate, but will likely not remove vast amounts of inorganic phosphate.
How do protein skimmers remove heavy metals?
Heavy metals can often form chemical complexes with organic content (i.e. proteins) which can in turn be removed by skimming.
Is there any way to tell what my skimmate is or how concentrated it is?
Generally, the darker the skimmate, the more concentrated. It is possible to run a BOD (biological oxygen demand) analysis on your skimmate, but these can be costly and timely.
Does the color/shade of the skimmate mean anything?
See above
My skimmer produces bubbles faster sometimes than others, does that mean that sometimes my tank is "dirtier" and sometimes it's "cleaner?"
Yes. This can mean that your tank water is dirtier. However, it can also mean that either your skimmer needs cleaning or there is a chemical (i.e. a surfactant) in your tank water that has modified bubble formation.
Does the size of the bubbles produced by the skimmer make a difference? If so, how?
The smaller the bubble, the higher the efficiency of skimming will be. This is due to the increased bubble residence time. This is because smaller bubbles take longer to rise to the surface.
Can we make our skimmers produce smaller/larger bubbles? Which kinds of skimmers produce smaller bubbles?
Some skimmers such as Beckett skimmers and needle wheel skimmers have adjustable air intakes whereas other skimmers do not. Adjusting the skimmer air intake will change bubble size and effect skimming.
Does the column size (the distance the bubbles have to travel up before they are traped by the skimmer cup) make a difference?
Yes. See explanation above.
Is there any way to control our skimmers such that they pull out more of the proteins we don't want and less of the proteins we might want?
Not that I am aware of.
To what extent do protein skimmers oxygenate water? What else is there to know about gas exchange and protein skimming?
Protein skimmers greatly oxygenate the water in a tank. Skimmers can also modify the tank pH by allowing the CO2 in air to reach equilibrium with the CO2 in tank water. In the winter, CO2 concentrations can build up within a home. For this reason, it is often wise to use outside air for the skimmer air intake. Using air high in CO2 content can lead to too low of pH values.
Do protein skimmers remove biologically toxic substances (like the toxic terpenoids leather corals produce)?
It has been widely speculated that skimmers can remove many toxic substances. Some substances such as oils and detergents will certainly be removed by a skimmer. However, other chemicals that may be released from coral would need to be investigated on a case by case basis.
Can I tell if I'm over-skimming my tank?
Not that I am aware of.
Dr. Tanner is one of the few remaining experts in the country studying foam fractionation. Chris Stowers is a graduate student and reef aquarium hobbyist pursuing a PhD in Chemical Engineering.
However, this is something of an "article" that will be on a website I'm developing that won't be officially "launched" until Febuary. So please don't copy and paste or otherwise threaten the intellectual property of this Q&A. I swore I wasn't going to share it until the website was done, but you guys are asking so many intelligent questions, I can't take it anymore.
So here it is, maybe it will help, maybe it won't. In any case, it's an interesting read...Protein Skimmer Q&A
questions answered by Chris Stowers and Dr. Robert D. Tanner of Vanderbilt University
Proteins can range greatly in size and chemical nature. What kinds of proteins do protein skimmers remover?
Protein skimmers can remove a wide range of proteins depending on their size and type. In general, larger proteins, proteins with hydrophobic appendages, and linear natured proteins (not coiled) will be removed easier. The efficiency of a skimmer will determine the rate and extent that a certain protein will be removed. Most coral and fish waste has potential to be removed by foam fractionation (skimming).
What determines what kinds/sizes of proteins a skimmer will remove?
Bubble contact time- The time which a bubble generated from a skimmer spends in contact with the water and proteins. The longer the time a protein spends in contact with a bubble, the more likely it will be adsorb to the surface of the bubble and removed.
Salinity- Higher salinity can increase bubble production and therefore increase the amount of proteins removed.
Skimmer Size- Larger skimmers generally have longer contact times and process more water leading to more efficient skimming.
Water Chemistry- Certain chemicals such as surfactants have been shown to greatly skew the ability for proteins to be removed from water by foam fractionation. Other chemicals such as tannins have led to similar results. Thus, one should be aware that the presence of a chemical that greatly modifies bubble production will affect protein skimming.
What else (if anything) do protein skimmers remove?
Protein skimmers can remove any substance that is hydrophobic in nature. Most chemicals other than proteins in the reef water column are hydrophilic. However, proteins often complex with nutrients such as Mg allowing them to be removed along with the protein.
Do skimmers remove bacteria and algae too?
Yes, but not efficiently. Although bacteria and algae can be removed by skimming, they are encompassed by a cellular membrane which is hydrophilic on the exterior making them practically immune to skimming.
How do protein skimmers remove phosphates?
Protein skimmers can remove organic phosphate, but will likely not remove vast amounts of inorganic phosphate.
How do protein skimmers remove heavy metals?
Heavy metals can often form chemical complexes with organic content (i.e. proteins) which can in turn be removed by skimming.
Is there any way to tell what my skimmate is or how concentrated it is?
Generally, the darker the skimmate, the more concentrated. It is possible to run a BOD (biological oxygen demand) analysis on your skimmate, but these can be costly and timely.
Does the color/shade of the skimmate mean anything?
See above
My skimmer produces bubbles faster sometimes than others, does that mean that sometimes my tank is "dirtier" and sometimes it's "cleaner?"
Yes. This can mean that your tank water is dirtier. However, it can also mean that either your skimmer needs cleaning or there is a chemical (i.e. a surfactant) in your tank water that has modified bubble formation.
Does the size of the bubbles produced by the skimmer make a difference? If so, how?
The smaller the bubble, the higher the efficiency of skimming will be. This is due to the increased bubble residence time. This is because smaller bubbles take longer to rise to the surface.
Can we make our skimmers produce smaller/larger bubbles? Which kinds of skimmers produce smaller bubbles?
Some skimmers such as Beckett skimmers and needle wheel skimmers have adjustable air intakes whereas other skimmers do not. Adjusting the skimmer air intake will change bubble size and effect skimming.
Does the column size (the distance the bubbles have to travel up before they are traped by the skimmer cup) make a difference?
Yes. See explanation above.
Is there any way to control our skimmers such that they pull out more of the proteins we don't want and less of the proteins we might want?
Not that I am aware of.
To what extent do protein skimmers oxygenate water? What else is there to know about gas exchange and protein skimming?
Protein skimmers greatly oxygenate the water in a tank. Skimmers can also modify the tank pH by allowing the CO2 in air to reach equilibrium with the CO2 in tank water. In the winter, CO2 concentrations can build up within a home. For this reason, it is often wise to use outside air for the skimmer air intake. Using air high in CO2 content can lead to too low of pH values.
Do protein skimmers remove biologically toxic substances (like the toxic terpenoids leather corals produce)?
It has been widely speculated that skimmers can remove many toxic substances. Some substances such as oils and detergents will certainly be removed by a skimmer. However, other chemicals that may be released from coral would need to be investigated on a case by case basis.
Can I tell if I'm over-skimming my tank?
Not that I am aware of.
Dr. Tanner is one of the few remaining experts in the country studying foam fractionation. Chris Stowers is a graduate student and reef aquarium hobbyist pursuing a PhD in Chemical Engineering.
Yeah I know. He seemed to jump on the "bandwagon" after I mentioned what I was planning to do on one of his threads awhile back.Btw, did you all know that Mr. Borneman is now trying to do the same thing (at least with skimmate): http://www.marshreef.com/modules.php?name=Forums&file=viewtopic&t=19023
Maybe you guys can help him out.
I wonder if he will perform his tests with the same "rigor" :lol2: as his salt study.
Based on analyzing the water column for bacterial counts from my tank, I think this will actually be a very sexy question. I am finding that my tank is 10-100 fold less bacterial/mL than wild reefs.
Also getting this question answered is the base line for all further studies to compare skimmer uptakes, bacterial fluctuation, etc..
LOL I don't want to pick on him much more than I already have, but it is hard to ignore his track record sometimes... with the salt study, the elegance coral project, the Model Systems Committee Calhoun CDHC project (which still no one knows what happened to), etc. Whatever he's doing, I doubt we'll see "results" anytime soon... if ever.
But anyway... I don't think just testing skimmate is the way to go. Even if one were to collect 100s of samples of skimmate and thoroughly analyses them all, there's no way to ensure all the samples were collected the same way and analyzed within the same amount of time, etc.
I think it would be better to tests a few samples of skimmate and use that info to narrow down what you want to look at (or look for). I would also think it far easier (and possibly more meaningful) to test tank water before and after skimmer use (for both brief use and long term use). I think it's the only way to ensure that you're not getting stuff that's living or reproducing in the skimmer itself.
This is what I proposed (hypothetically) to Dr. Toonen when I was asking him about study design:
1) Take 6 experimental tank setups, starting 3 with skimmers and 3
without skimmers.
2) Take measurements of various relevant parameters and observable,
quantifiable factors on a daily or weekly basis for X months.
3) After X months, take the skimmers off the skimmed tanks and put
skimmers on the un-skimmed tanks (keeping all else the same).
4) Continue taking measurements for another X months to see how things change.
He replied basically saying that, prima facie, there's nothing wrong with such a design (so long as a control group was added).
Oh WOW! Are you serious? How much confidence do you have in the bacterial count? I wonder if that's characteristic of closed systems or just your tank or just reef tanks or just skimmed tanks...? And when you say "than in wild reefs", that number you use, is it for open water? or actually physically on the reef/rock/sandbed? Aaaa.... too many questions! lol This is what I meant... despite the shock value, knowing that just frustrates me because I don't know what it means or what to think of it.
The other issue is, skimmers might decrease bacterial counts not because they take out the bacteria themselves, but because they take out the organics/compounds that bacteria need. Now how are you going to figure that one out?!
lemme ask you something shaun, i was reading a article on serratia marcescen how it has formed a pigment allowing it to stay in water better. When bubbles pop and surface agitation the pigment has something to do with keeping it in the water without throwing the bacteria into the air? I mean bacteria are very light if a skimmer wants to push them out of the water it's possible right?
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