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This one is relevant for the first 80 days (at day 80 they switched it to salt water to see if the same bacteria lived, for the record they are different bacteria)

It's from the Dr Tim paperNitrospira-Like Bacteria Associated with Nitrite Oxidation in Freshwater Aquaria
I've seen other charts that are similar in other places, but this one pops to mind fastest.
I do think you are supposed to SEE nitrItes by day 10. I get concerned if someone says they haven't seen them by 2 weeks.

Yeah, they eat alkalinity and produce acid.
 
I've just been looking at an article. It states that 80% of bacteria energy goes on co2 fixation as part of the Calvin cycle. Lower ph has more c02 so it could mean that co2 takes precedence over ammonia in this instance. Maybe why the cycle slows at 6? I'm at work so can't look in to this with more detail. Another question I have is does lower ph mean less oxygen? Oxygen is already reduced by turning the heat to 30 degrees and increase bacteria metabolism meaning more oxygen demand more reduction in alkalinity and more production of acid = ph crash?
 
Does this mean lower doses of ammonia would still cycle and reduce the possibility of a ph crash?


That's what I would of thought. I've seen anywhere from 2 up to 5ppm suggested as a dosing rate. I thought 4 was just to bullet proof for a tank at stocking capacity. However most shop stock is (over here anyway) not fully grown.
 
I was also under the impression that as well as consuming alkalinity, acidity was produced by the bacteria during the breakdown if ammonia. I need to find this also. That would be doubly important if this was the case. What surprises me though is that people with relatively normal ph struggle. Jen can you find the paper that gives average times for ammonia levels to decrease and nitrites to appear then decrease? I can't find it anywhere but I also think a lot of people are expecting nitrites to drop sooner.


The 7.1 mg CO3/mg NH4 number that Jen quoted is just the alkalinity consumed buffering the protons created by ammonia oxidation. Any direct carbonate consumption would be in addition to that.


Calibran07 said:
I've just been looking at an article. It states that 80% of bacteria energy goes on co2 fixation as part of the Calvin cycle. Lower ph has more c02 so it could mean that co2 takes precedence over ammonia in this instance. Maybe why the cycle slows at 6? I'm at work so can't look in to this with more detail.

CO2 levels are mostly related to air concentration of CO2 and water temperature; that is to say, CO2 impacts pH much more than pH impacts CO2. CO2 would essentially be constant at all pHs for an open system like what we have (where atmospheric CO2 can't be reduced/increased). At lower pHs, you will drive off your carbonate buffers in the form of CO2, but that's the buffering system working as intended.

Also important to note is that the calvin cycle is separate from ammonia/nitrite oxidation, so I don't think that they would interact in the way you think they would (although I might be misunderstanding you).

If I had to guess why the cycle starts to sputter at low pH, I would probably guess that it had something to do with the bacteria maintaining a proton gradient across their membrane (which is part of the nitrification process) or due to sequestration of ammonia in the ammonium form where it can't be as easily accessed by bacteria's machinery (similar to the detoxification of ammonia at low pH in fish).

Another question I have is does lower ph mean less oxygen?

No. I don't know of anything off the top of my head that relates oxygen concentration to pH. Like CO2, the main factors in oxygen level is mainly temperature and atmospheric levels, with surface consumption and surface agitation being secondary (but still important) factors.
 
An interesting idea would be to recommend dosing bicarbonate (baking soda) whenever you dose ammonia in accordance with the acid production/base consumption of the ammonia dosed. That would be about 1 dKH per 2.5 ppm ammonia, give or take a bit. That way you'll only be consuming the buffer you add and not be limited to whatever's in your tap.
 
Just something that really ought to be said. I've seen several comments regarding 'the forums guide' and things of that nature. Just wanted to make sure that nobody is under the assumption that there is a guide written or endorsed by the site, nor will there be.


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An interesting idea would be to recommend dosing bicarbonate (baking soda) whenever you dose ammonia in accordance with the acid production/base consumption of the ammonia dosed. That would be about 1 dKH per 2.5 ppm ammonia, give or take a bit. That way you'll only be consuming the buffer you add and not be limited to whatever's in your tap.

Since posing those questions earlier today I have been doing lots of reading. We are not scientists or even close. Im just asking questions as they crop up. I read a lot today and understand now that co2 effects ph. I read a lot about yhe importance of ph stability and buffering capacity and was going to suggest the addition of baking soda as a mandatory as to eliminate the possibity of a ph crash.

If people were cycling in a tank that had plants, we would expect ph to drop further at night since the nitrification process would continue round the clock. At 4ppm ammonia bacteria would be using buffering capacity up. Co2 levels would increase at night which may cause a crash? I know oh would go back to normal levels during the day but what if it got to a level that stopped bacteria from working? If someone had a low ph and kh to begin with or normal ph but not a great buffering capacity.

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Just something that really ought to be said. I've seen several comments regarding 'the forums guide' and things of that nature. Just wanted to make sure that nobody is under the assumption that there is a guide written or endorsed by the site, nor will there be.


From the TOS:

Ok

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If people were cycling in a tank that had plants, we would expect ph to drop further at night since the nitrification process would continue round the clock. At 4ppm ammonia bacteria would be using buffering capacity up. Co2 levels would increase at night which may cause a crash? I know oh would go back to normal levels during the day but what if it got to a level that stopped bacteria from working? If someone had a low ph and kh to begin with or normal ph but not a great buffering capacity.


CO2 levels would increase somewhat at night, but it would be a transient effect. As CO2 leaves the system, the CO2 would be restored. I'm not convinced that the CO2 levels at night in a planted tank would be that significant in a buffered tank either, considering the amount of CO2 we need to add with a pressurized system to achieve the levels that we do. Additionally, people who use DIY CO2 inject CO2 24/7 without a dramatic pH crash at night.
 
CO2 levels would increase somewhat at night, but it would be a transient effect. As CO2 leaves the system, the CO2 would be restored. I'm not convinced that the CO2 levels at night in a planted tank would be that significant in a buffered tank either, considering the amount of CO2 we need to add with a pressurized system to achieve the levels that we do. Additionally, people who use DIY CO2 inject CO2 24/7 without a dramatic pH crash at night.


Ok point taken. Surely running the co2 at night would have had to have been considered during a fishless cycle? Would have at least made people question the ph of there water before doing so? 4ppm is a lot if alkalinity being removed. Is there a way to calculate how much? Do you have any thoughts on why cycles stall or take longer? You mentioned nutrient depletion. I haven't really gone in to this in too much detail. Maybe you could expand a little on this? Do you think people who's water is softer are more susceptible? Do we know how much nutrients would be required to sustain the BB? If it's something you are keen on then we could encourage people to change do a single water change.

I still think 1 dose of 4ppm ammonia would see you to the end I the cycle. You could then just dose another 4 at the end to see how long it takes to be reduced now you have established a colony.
 
Long post ahead. Plan accordingly.


Ok point taken. Surely running the co2 at night would have had to have been considered during a fishless cycle?
I'm not sure that it has really. A lot of people that do CO2-injected planted tanks will do a 'silent cycle', which is essentially a fish-in cycle with plants and a light stocking with fast growing plants, wherein the plants consume most of the ammonia produced. There remains a small amount of ammonia, below the detection limits of liquid test kits, that will cycle the filter. Remember that in the initial stages of cycling, the ammonia consumption is exceptionally small. Eventually the bacteria will overtake the plants for ammonia consumption and the cycle repeats for nitrite. I'm not sure that I've ever heard of CO2 per se stalling a cycle. Considering the fact that some people inject CO2 directly into their filter, I don't think it is an issue.

Would have at least made people question the ph of there water before doing so? 4ppm is a lot if alkalinity being removed. Is there a way to calculate how much?
Napkin math gives about 17 ppm KH per 2.5 ppm ammonia or 1.5 dKH (27 ppm KH)/4 ppm.It's pretty obvious where people can get into problems with buffer consumption with this level of repeated ammonia dosing. That being said, people with planted tanks should be doing water changes, which will be replenishing buffer. Same thing with fish-in cycles. This certainly raises a problem with the 'no WC' philosophy of fishless cycling.

Do you have any thoughts on why cycles stall or take longer? You mentioned nutrient depletion. I haven't really gone in to this in too much detail. Maybe you could expand a little on this?

I think most of the help threads in our 'getting started' section fall into one of a few categories: nutrient limitation, pH 'crash'/buffer consumption, nitrite toxicity, 'user error', psychological.

Nutrient limitation is exactly what you think it is with regards to phosphate block. The only thing I'm saying in addition to this is that the number of potentially 'limiting' nutrients extends well beyond phosphates to include potassium and various metals/micronutrients, eg iron. That being said, the majority are probably phosphate due to the large phosphate demand of a rapidly proliferating bacterial colony. Phosphate is used for many things in a functioning cells, notably in DNA synthesis which a proliferating bacteria colony will be doing a lot of. No phosphate = no DNA for new bacteria. Iron, sulfur, magnesium, potassium are all also needed in less significant but non-trivial amounts. Unfortunately, people with soft water (as well as others) might have very low levels of these minerals available, as might a planted tank without fertilization wherein plants will take up much of the available nutrients (WCs will reduce or eliminate this). This kind of 'what am I missing?' problem comes up all the time on the planted side of the hobby. I have seen multiple cases of people cycling tanks fishlessly with plants that present with very classic phosphate deficiencies in plants not particularly susspetible to nutrient issues such as anubias (eg here).


I think that a 'pH crash', so to speak, is a real possibility in tanks with low to moderate alkalinity that repeatedly redose ammonia to a higher concentrations. Fortunately, it is pretty easy to figure out if this is the cause, as pH tests are pretty common these days. It would be interesting for someone to monitor KH over a cycling period though to see if the drop in alkalinity is roughly in line with what we predict mathematically.

Nitrite toxicity... It's just what it sounds. If you've dosing 4 ppm of ammonia daily, you'll create 75 ppm of nitrite in a week's time. The longer the cycle takes, the higher levels take. I'm willing to argue that 12-20 ppm of nitrite won't cause toxicity issues, but 100+? Much more likely.

User error is... probably much more common than we realize. I'm putting things like improper water dechlorination, ammonia with surfactant, improper use of test kits, etc, in this category; things that we wouldn't necessarily think to ask and that posters wouldn't mention that they are (or aren't) doing. If you consider that many people are that are fishless cycling are completely new to the hobby, it's completely reasonable to expect them to make so called 'beginner' mistakes. This might be a cynical perspective on the matter, but it happens more often than you would think.

For the last one, I think a little background might be in order to fully understand where I'm coming from.

Everyone on this forum brings their own background to the hobby, even if it's just a perspective and not necessarily direct knowledge of the hobby. In my case, I bring a science background (chemistry, biochemistry, and biology mostly) as well as a medical perspective. I'm constantly seeing parallels between the aquarium hobby/participating and clinical practice. Let me give you a few examples.

In case #1, I have someone come in for a yearly checkup. Now, if I were so inclined, I could run a battery of unindicated tests, I will eventually find something outside of normal ranges. I can then run a bunch more tests to work up this incidental finding to make sure it's not something important, but it's A) a waste of money and resources and B) incredibly taxing on the patient from a psychological perspective. To this extent, we caution against running unnecessary tests that don't have much benefit or direct indication. How does this relate to aquaria? Liquid test kits are the MRI of fish tanks. You see a lot of posts on this site that are essentially "Help, my pH is 8.2, how do I get it down?" This hypothetical person probably tested his tank for really no reason other than he could, found something outside the 'normal range', and is now worried about the health of his fish. In reality, his fish are probably well adapted to the somewhat higher pH and are doing just fine. The flipside of this is if he's having trouble with Rams (or something) dieing in his tank, and he tests his pH to find that it's 8+. At this point, there's a reasonable reason to intervene. Same thing with fishless cycling. People will test their ammonia every day for the first two weeks to see if their tank is cycling. It's just obsessive really. Similarly, you give someone enough test kits and they will find something out of whack with their tank. High GH, high phosphate, etc, and they'll worry about if this parameter is harming their fish. A more medically-minded method for testing in a fishless would be to wait until the three week mark and check ONLY nitrite. Nitrite showing up? Fine, put it away the test kit for a few more weeks. No nitrite? Check ammonia, check nitrate. That will let you know if you've cycled early or have a hangup somewhere.

TL;DR: Put down the test kits, step away from the tank, breath.

In the second example, we have a process called 'watchful waiting'. In essence, this means that we've observed something that's could require intervention, but may resolve on its own or not need intervention for some time. Examples of this would be some slow growing cancers, like some forms of prostate or DCIS. Another example would be a sore throat that looks viral (no antibiotics needed). People are often impatient though, and want surgery/antibiotics/whathaveyou. Same thing with cycling a tank. Say your test comes up with no nitrites at 2 weeks (which is pretty common judging from submissions to this forum). At this point, I think the best course would probably be to check for red flags (ammonia with surfactants, cycling in RODI, etc) but otherwise reassure the poster until 3-4 weeks without ammonia. A lot of tanks are 'late bloomers', if you will, and take 2+ weeks to cycle while others see ammonia drops in the first week. Unfair maybe, but no reason for worry until later.


I guess what I'm trying to say in the rambling dialog is that many, many cases of 'stalled' cycles are actually within the realm of individual variation and very possibly not stalled at all, but rather a result of the poster's anxiety. I took a quick survey of the last 11 fishless cycle 'stall' threads and attempted to classify them as to the nature of the problem, as I saw it. I got one case of 'user error', one that was bonafide 'stalled' (4 weeks w/o ammonia), one that could very possibly have been nitrite toxicity, and 8 that were either cycling normally or within reasonable tank to tank variation.


Do you think people who's water is softer are more susceptible? Do we know how much nutrients would be required to sustain the BB? If it's something you are keen on then we could encourage people t change do a single water change.

Most of the mineral content in ground water is from the water stripping it from surrounding rock and minerals. The ideal is that water will pick up other minerals from the ground in proportion to how much calcium/magnesium it picks up. Seems reasonable enough to me, although it might not be the case. This would really be a question for someone with a stronger geology or limnology background that me.


I still think 1 dose of 4ppm ammonia would see you to the end I the cycle. You could then just dose another 4 at the end to see how long it takes to be reduced now you have established a colony.

I would mostly agree. I might add 2 ppm or so every week or every other week for peace of mind though, especially if you don't have anything else in the tank.
 
Very interesting read and much appreciated.

Just a quick add that water passing through rock, etc will pick up elements at different ratios. So you might find silica is more mobile (for example) then iron.
 
Very interesting read and much appreciated.

Just a quick add that water passing through rock, etc will pick up elements at different ratios. So you might find silica is more mobile (for example) then iron.

I realIze that. My logic is that they are dissolved at a constant ratio, such that if hard water has 200 ppm calcium and soft water has 20 ppm, the levels of magnesium in hard water should be 10x that of soft water, ie, the same relative ratio as calcium.
 
I realIze that. My logic is that they are dissolved at a constant ratio, such that if hard water has 200 ppm calcium and soft water has 20 ppm, the levels of magnesium in hard water should be 10x that of soft water, ie, the same relative ratio as calcium.


Ah, got it. Yes that makes sense. We might have some bore well tests over winter and summer - I'll see if we still have them.

As the elements are mobilised, preferentially re-deposited and mixed during transport then I think the ratios would modify.
 
Certainly humic substances would preferentially bind some metals, but once again, it would be different for each metal. I wish I had a limnobotonist on hand that would know more about water column vs sediment distribution of metals or a geologist that had a better knowledge of groundwater.
 
I did not read this whole thread but wanted to ask if while doing a water change is it good to run an air stone?
 
Certainly humic substances would preferentially bind some metals, but once again, it would be different for each metal. I wish I had a limnobotonist on hand that would know more about water column vs sediment distribution of metals or a geologist that had a better knowledge of groundwater.


Unfortunately no luck, all the records were thrown out. I'll ask around but offhand can't think of anyone - bit of a long shot.
 
Long post ahead. Plan accordingly.



I'm not sure that it has really. A lot of people that do CO2-injected planted tanks will do a 'silent cycle', which is essentially a fish-in cycle with plants and a light stocking with fast growing plants, wherein the plants consume most of the ammonia produced. There remains a small amount of ammonia, below the detection limits of liquid test kits, that will cycle the filter. Remember that in the initial stages of cycling, the ammonia consumption is exceptionally small. Eventually the bacteria will overtake the plants for ammonia consumption and the cycle repeats for nitrite. I'm not sure that I've ever heard of CO2 per se stalling a cycle. Considering the fact that some people inject CO2 directly into their filter, I don't think it is an issue.


Napkin math gives about 17 ppm KH per 2.5 ppm ammonia or 1.5 dKH (27 ppm KH)/4 ppm.It's pretty obvious where people can get into problems with buffer consumption with this level of repeated ammonia dosing. That being said, people with planted tanks should be doing water changes, which will be replenishing buffer. Same thing with fish-in cycles. This certainly raises a problem with the 'no WC' philosophy of fishless cycling.



I think most of the help threads in our 'getting started' section fall into one of a few categories: nutrient limitation, pH 'crash'/buffer consumption, nitrite toxicity, 'user error', psychological.

Nutrient limitation is exactly what you think it is with regards to phosphate block. The only thing I'm saying in addition to this is that the number of potentially 'limiting' nutrients extends well beyond phosphates to include potassium and various metals/micronutrients, eg iron. That being said, the majority are probably phosphate due to the large phosphate demand of a rapidly proliferating bacterial colony. Phosphate is used for many things in a functioning cells, notably in DNA synthesis which a proliferating bacteria colony will be doing a lot of. No phosphate = no DNA for new bacteria. Iron, sulfur, magnesium, potassium are all also needed in less significant but non-trivial amounts. Unfortunately, people with soft water (as well as others) might have very low levels of these minerals available, as might a planted tank without fertilization wherein plants will take up much of the available nutrients (WCs will reduce or eliminate this). This kind of 'what am I missing?' problem comes up all the time on the planted side of the hobby. I have seen multiple cases of people cycling tanks fishlessly with plants that present with very classic phosphate deficiencies in plants not particularly susspetible to nutrient issues such as anubias (eg here).


I think that a 'pH crash', so to speak, is a real possibility in tanks with low to moderate alkalinity that repeatedly redose ammonia to a higher concentrations. Fortunately, it is pretty easy to figure out if this is the cause, as pH tests are pretty common these days. It would be interesting for someone to monitor KH over a cycling period though to see if the drop in alkalinity is roughly in line with what we predict mathematically.

Nitrite toxicity... It's just what it sounds. If you've dosing 4 ppm of ammonia daily, you'll create 75 ppm of nitrite in a week's time. The longer the cycle takes, the higher levels take. I'm willing to argue that 12-20 ppm of nitrite won't cause toxicity issues, but 100+? Much more likely.

User error is... probably much more common than we realize. I'm putting things like improper water dechlorination, ammonia with surfactant, improper use of test kits, etc, in this category; things that we wouldn't necessarily think to ask and that posters wouldn't mention that they are (or aren't) doing. If you consider that many people are that are fishless cycling are completely new to the hobby, it's completely reasonable to expect them to make so called 'beginner' mistakes. This might be a cynical perspective on the matter, but it happens more often than you would think.

For the last one, I think a little background might be in order to fully understand where I'm coming from.

Everyone on this forum brings their own background to the hobby, even if it's just a perspective and not necessarily direct knowledge of the hobby. In my case, I bring a science background (chemistry, biochemistry, and biology mostly) as well as a medical perspective. I'm constantly seeing parallels between the aquarium hobby/participating and clinical practice. Let me give you a few examples.

In case #1, I have someone come in for a yearly checkup. Now, if I were so inclined, I could run a battery of unindicated tests, I will eventually find something outside of normal ranges. I can then run a bunch more tests to work up this incidental finding to make sure it's not something important, but it's A) a waste of money and resources and B) incredibly taxing on the patient from a psychological perspective. To this extent, we caution against running unnecessary tests that don't have much benefit or direct indication. How does this relate to aquaria? Liquid test kits are the MRI of fish tanks. You see a lot of posts on this site that are essentially "Help, my pH is 8.2, how do I get it down?" This hypothetical person probably tested his tank for really no reason other than he could, found something outside the 'normal range', and is now worried about the health of his fish. In reality, his fish are probably well adapted to the somewhat higher pH and are doing just fine. The flipside of this is if he's having trouble with Rams (or something) dieing in his tank, and he tests his pH to find that it's 8+. At this point, there's a reasonable reason to intervene. Same thing with fishless cycling. People will test their ammonia every day for the first two weeks to see if their tank is cycling. It's just obsessive really. Similarly, you give someone enough test kits and they will find something out of whack with their tank. High GH, high phosphate, etc, and they'll worry about if this parameter is harming their fish. A more medically-minded method for testing in a fishless would be to wait until the three week mark and check ONLY nitrite. Nitrite showing up? Fine, put it away the test kit for a few more weeks. No nitrite? Check ammonia, check nitrate. That will let you know if you've cycled early or have a hangup somewhere.

TL;DR: Put down the test kits, step away from the tank, breath.

In the second example, we have a process called 'watchful waiting'. In essence, this means that we've observed something that's could require intervention, but may resolve on its own or not need intervention for some time. Examples of this would be some slow growing cancers, like some forms of prostate or DCIS. Another example would be a sore throat that looks viral (no antibiotics needed). People are often impatient though, and want surgery/antibiotics/whathaveyou. Same thing with cycling a tank. Say your test comes up with no nitrites at 2 weeks (which is pretty common judging from submissions to this forum). At this point, I think the best course would probably be to check for red flags (ammonia with surfactants, cycling in RODI, etc) but otherwise reassure the poster until 3-4 weeks without ammonia. A lot of tanks are 'late bloomers', if you will, and take 2+ weeks to cycle while others see ammonia drops in the first week. Unfair maybe, but no reason for worry until later.


I guess what I'm trying to say in the rambling dialog is that many, many cases of 'stalled' cycles are actually within the realm of individual variation and very possibly not stalled at all, but rather a result of the poster's anxiety. I took a quick survey of the last 11 fishless cycle 'stall' threads and attempted to classify them as to the nature of the problem, as I saw it. I got one case of 'user error', one that was bonafide 'stalled' (4 weeks w/o ammonia), one that could very possibly have been nitrite toxicity, and 8 that were either cycling normally or within reasonable tank to tank variation.




Most of the mineral content in ground water is from the water stripping it from surrounding rock and minerals. The ideal is that water will pick up other minerals from the ground in proportion to how much calcium/magnesium it picks up. Seems reasonable enough to me, although it might not be the case. This would really be a question for someone with a stronger geology or limnology background that me.




I would mostly agree. I might add 2 ppm or so every week or every other week for peace of mind though, especially if you don't have anything else in the tank.

Ok co2 doesnt have much to do with it.

Like I said i read alot. Which leads me to ask questions. I really havent been a member of this site that long and to be honest, I wasnt even aware of the fish less cycle.

These past few weeks I would have to agree and i have said it before now that I do think a lot of people are being impatient, now if the guide doesnt enforce patience then this is going to cause problems.

As I mentioned, I did read a lot on phosphate block and is one of the reasons I change water when I fish in cycle. This is the only reason though. TAN has never gone above 0.25ppm when I have done fish in cycles. I have also read much about toxicity of nitrite to fish and can say that at 0.25ppm ammonia, nitrite will not harm my fish and ive never even recorded nitrites. As for nitrites toxicity to bacteria, again, tests were conducted at levels as high as 50mM which equates to a ridiculously high ppm with still no stall so I think this would have to be well in the hundreds.

Ph crash I think is the most important where constantly adding ammonia with low buffers. There is a guy on a thread now who has to let his water gas off before ph rises from 6,5 to just above 7. He added a rainbow shark. The increased bioload may have have caused his ph to fall. He said his shark was dead and recorded 2 ppm ammonia and ph was at 6.4. Its unlikely the ammonia killed the fish at this ph as the toxicity would be minimal but maybe the ph swing due to the ammonia being processed? Could have been many reasons I guess.

Anyway I know people are obsessed with testing and constant testing will throw up an anomily sooner or later and testing should be minimal, I would only test for nitrates to be honest and check where my nitrites were at when I had recorded the former.

My point is, if patience and the complications of over testing are not enforced in the guide then people will get frustrated. All in all, I think a lower dosing of ammonia and less often would be better to further increase the success rate of the fish less cycle.

However, I think this thread may be waning slightly. I have learned a lot for myself personally and I feel like I can do more to help people in cycling situations. Both with or without fish. I still think the stickie could be tweaked slightly to improve things but I dont know if thats something I will pursue.

I also dont like it when senior members who dont even have the decency to introduce themselves plaster parts of the terms of use on the thread with out kindly explaining the situation to fellow members who may be a little unaware. A kind inbox would have sufficed.

Thanks for all your help aqua_chem ill be about if I dont get kicked. Hope threnjen is ok.

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