Bacteria...let's really start understanding them! part one

[GlassMunky]

Well unfortunately I'm not sure the operation is going to help you much. There can be a completely different microbiome in every nook and cranny of your tank. Basically miniature ecosystems throughout. That being said I think the info is pretty fun, and if you get joy out of it doesn't matter.



You know when a fish dies it sometime floats? Gas build up from the fish being digested from the inside. That's all anaerobic. The first barrier that tends to give way in a dead animal is it's digestive tract. So don't think a hunk of salmon is going to be representative

Well unfortunately I'm not sure the operation is going to help you much. There can be a completely different microbiome in every nook and cranny of your tank. Basically miniature ecosystems throughout. That being said I think the info is pretty fun, and if you get joy out of it doesn't matter.

Yea it’s not really for joy per se, was more hoping to be able to watch trends and make anecdotal inferences About how the corals/fish are doing and see if there’s any Correlation. Unfortunately you’re Not the first person to say that the testing is pretty useless in reality (my paraphrasing, not to put words in your mouth) and more a gimmick than say ICP testing.

couple this with the fact that it takes 1.5-2 months to even get the results, I might be done with it sooner than later.
Seems I may not be the only one feeling this way either with the email they sent around this month.... I’ll be interesting to see weather they can stay in business or not.
It’s kind of a shame though because good testing and understanding of this stuff would be a big change in the right direction for the hobby if anyone is able to achieve it

 

[flampton]

Yea it’s not really for joy per se, was more hoping to be able to watch trends and make anecdotal inferences About how the corals/fish are doing and see if there’s any Correlation. Unfortunately you’re Not the first person to say that the testing is pretty useless in reality (my paraphrasing, not to put words in your mouth) and more a gimmick than say ICP testing.

couple this with the fact that it takes 1.5-2 months to even get the results, I might be done with it sooner than later.
Seems I may not be the only one feeling this way either with the email they sent around this month.... I’ll be interesting to see weather they can stay in business or not.
It’s kind of a shame though because good testing and understanding of this stuff would be a big change in the right direction for the hobby if anyone is able to achieve it

I think I saw they weren't doing great. If I were them I would change their game plan.

I was wondering if you could share your results with me? I could tell you what's cool, but again I won't be able to say how healthy your tank is. Btw anything in your tank come directly from the ocean?

 

[chaostactics]

Great write up, laughed a bit at the used of the term "edgy science". I'm imagining edge lords in lab coats.

If you really want to stir the pot address the difference in the organisms that are commonly referred to as cyano and "red slime" and all the confusion.

 

[flampton]

Great write up, laughed a bit at the used of the term "edgy science". I'm imagining edge lords in lab coats.

If you really want to stir the pot address the difference in the organisms that are commonly referred to as cyano and "red slime" and all the confusion.

Thanks!!
And I probably will since I'm going to try culturing a few strains of cyanobacteria to feed my own aquarium

 

[SMSREEF]

Thanks! I have to add pics as r2r wants it as an article. Bonus though is that I'm going to add a little bit more info to part one because of it acheiving article status.

I might add pics of bacteria but unfortunately they won't be too helpful. The bacteria in your tank are too small for you to identify under a microscope as to get good pics you need an electron microscope.

I think for one of the pics I'll make a figure with an aquarium and show where the different groups are found.

Love the idea of pic of where each kind is normally found. This would help us understand why disturbing a certain section can lead to certain outcomes.

This makes me think of another possible pic for your article too. A basic “size” of bacteria relative to other common aquarium organisms. Comparing to things we can see with the scope.

bacteria-chrysophyte-Phytoplankton, dinoflagellate-protist-Cyanobacteria, copepod,etc (not sure ordering is right here)

I’m really excited about your threads!

 

[taricha]

You know when a fish dies it sometime floats? Gas build up from the fish being digested from the inside. That's all anaerobic. The first barrier that tends to give way in a dead animal is it's digestive tract. So don't think a hunk of salmon is going to be representative

Thanks. Yeah, I'm gonna go ahead and say I was probably wrong here just from a stoichiometric argument...

So a dead something that causes the tank to have a bloom probably kills more organisms by depleting oxygen rather than ammonia spike. Because dangerous O2 levels happen well before dangerous ammonia levels.

thinking through the stoichiometry in rough numbers - what could happen to 10mg/L of protein:
10mg/L of protein at 50% carbon - if the carbon were fully oxidized to CO2 would consume ~13mg/L of O2 or twice what the water can hold.
for ammonia, 10mg/L protein at 16% nitrogen, if it were released when the carbon is oxidized gets you to about ~2ppm ammonia.
a loss of 13mg/L O2 or a release of 2ppm ammonia are both problematic, but I'm guessing more systems could handle the O2 replacement in a few hours than the ammonia. And that doesn't take into account the anaerobic processes (you pointed out) or bacteria building biomass which would both skew the ratios more towards ammonia release and less O2 consumption.

(Originally I was thinking about some tests I did with fish flake consuming O2 and releasing ammonia and forgot that flake has a lot of extra carbon and isn't just protein - and generally is not a fish.)

 

[taricha]

Photoautotrophs- these are your favorite because this is where we find the cyanobacteria. ...Don't know anyone who sells cyanobacteria.

funny thing is how many foods are "enriched with spirulina" - which is technically cyano and in fact some nuisance cyano mats in tanks are spirulina. But I've never seen the same kinds in a cyano mat as is grown in bulk for the industry. So I doubt one ever seeds the other.

 

[Snoopdog]

1. can a cat litter box next to a reef tank, even a rank one, transmit enough ammonia waft to legit register a spike in a reef next to it, this is the greatest reef mystery naturally we'd start there. Reefcentral alone took years on that one matter

I am intrigued. You have a link?

 

[Graffiti Spot]

I am curious to see the carbon dosing part! Good thread

 

[brandon429]

Snoop
Lemme check old archives sec. that issue Is among the litany of causes we attribute to .25 free ammonia reads in reefkeeping


sustained .25 ammonia noncontrol is the biggest misconception against bacteria we have going for us. We can thank api + folks forgetting to do TAN conversions before reporting suspected levels, my chemistry friends remind me that nh3 is in the hundredths ppm in most of the reported cases where tenths ppm nh3 was the original concern

Cat liter boxes and ammonia - Reef Central Online Community

Cat liter boxes and ammonia The Reef Chemistry Forum

www.reefcentral.com

His levels reported for .8 ppm

lol
not digital, thats a human mind making up the best number to reference a color someone else would read as .2

i don’t buy it, they didn’t have access to a calibrated seneye they had Red Sea ammonia, 85% as bad at indicating false reads as api

gaseous ammonia gets in no doubt, and then is nearly instantly oxidized just like when a seneye owner has a fish die in the tank and the readings dont spike, the systems handle variation in ammonia just fine. Red Sea will report the lost fish for the next four months and the owner will certainly buy four bottles of bacteria to offset the risk, and dose bacteria that certainly could not make it without us.

 

[Snoopdog]

Snoop
Lemme check old archives sec. that issue Is among the litany of causes we attribute to .25 free ammonia reads in reefkeeping, yet that condition can not occur. Not one time has a reef tank hit and sustained .25 it’s biggest misconception of bacteria we have going for us. We can thank api + folks forgetting to do TAN conversions before reporting suspected levels.

Cat liter boxes and ammonia - Reef Central Online Community

Cat liter boxes and ammonia The Reef Chemistry Forum

www.reefcentral.com

i don’t buy it, they didn’t have access to a calibrated seneye they had Red Sea ammonia, 85% as bad at indicating false reads as api

Yeah that is the one I am reading right now, good read.

 

[brandon429]

See how we do not know the basics of bacteria but we can tell you their atcg genetic ordering and divisional lineage lol thats awesome. We are about to go forty years not even knowing if cat urine can overcome our filter systems, or if wet pack sand dosed with bacteria is viable like we know bottled bacteria to be



There is a bigger thread than that one but it’s hard to find. At least twenty people posting positive reads due to cat box proximity

thankfully there is an array of retail doser$ available to remedy our knowledge gaps. we feel good buying and adding those items

Fascinating: water treatment plants that use the exact same science we use to keep reefs alive don't have trouble keeping cycles in place or attaining them per charts or having uncontrollable ammonia, that's solely an issue for our hobby + the test kits we have. a massive retail machine runs to fill in where we're unsure

 

[Graffiti Spot]

I have never heard of the cat box “issue” but always worried about the litter dust, NOT ammonia vapors? How would that even work. The zeolites the cats use should take care of that. Maybe it’s time to read the thread if I get bored enough, I am guessing it’s long.

 

[terraincognita]

We build ecosystems but then focus on individual occurrences as if they’re not part of a hugely intricate web of interdependence. I am avidly following your thread friend!

well said.

 

[AcanthurusRex]

Thanks!!
And I probably will since I'm going to try culturing a few strains of cyanobacteria to feed my own aquarium

You can save time and take my cyano...

 

[Randy Holmes-Farley]

I have never heard of the cat box “issue” but always worried about the litter dust, NOT ammonia vapors? How would that even work. The zeolites the cats use should take care of that. Maybe it’s time to read the thread if I get bored enough, I am guessing it’s long.

If you can smell ammonia, it will get into the water.

Not enough to be a problem, I expect, however.

 

[Butcher333]

Darn it! The posts have been read and I will have to revisit.
-The algae and the bacteria of the Great Salt Lake are exciting. (But not for sale unfortunately)
-PNS Pro Bio is exciting.

 

[Hans-Werner]

Nothing is simple, everything is complex (or complicated?). To make things a bit more complicated and to add complexity: Will you mention Archaea separately?

 

[brandon429]

Flampton

I hope in future works we get to see practical application of bacteria alongside their metabolic differences and classifications

Cycle stalled

This is the first time I've ever used a product to aid in cycling a tank and I'm confused by where I'm at today. I used Red Sea Reef Mature Pro and things seemed on track at first but now I'm way off the targets. I'm at 5 weeks now and have .2 Ammonia, 1+ Nitrite, and 50+ Nitrate. I've been...

www.reef2reef.com

That thread is very impactful to me.

It is a microcosm of today's hobby view on what cycling bacteria do, whether classic nitrifiers or heterotrophs stepping up to the plate can carry a bioload, in the end people simply want to know when they can start to reef.


False notions in what filter bacteria are doing drive sales in this hobby to the tune of hundreds of thousands of dollars spent to unstick cycles that never were stuck. bottle bac sellers tell us cycles can stall, and have a product ready to remedy.

Our hobby cannot even agree of whether nitrite testing should factor. https://www.reef2reef.com/threads/nitrite-toxicity.402708/
of course everyone says it should, but they will ignore 200 nitrite positive reef starts we have on file with updates as well, rules are broken daily in reef tank cycling and we need formal works on that. We have enough data to permanently exclude nitrite measurement in reef tank cycling, but it is ignored. Offsetting stuck nitrite readings is a large driver of bottle bac sales...we collect those reaction purchase threads for pattern study as well.


It is very important to state that in understanding bacteria, we must be able to simply cycle reef tanks consistently. That is currently not the case for the hobby, nobody is in agreement on what we should measure, how long we should wait etc


there are some people in agreement: the twenty thousand or so reef tanks set up at MACNA conventions all to meet the start date, the sales date, of the convention. given the right motivation and bacterial understanding, we can either be stuck in a cycle for 80 days or we can have the reef ready by this friday, two days from now, and never fail.

I say until we can cycle reef tanks consistently in this hobby, we don't really understand the bacteria though they might classify in different ways and perform known functions when evaluated alone/not in a meshing of tank life.

 

[flampton]

Nothing is simple, everything is complex (or complicated?). To make things a bit more complicated and to add complexity: Will you mention Archaea separately?

Well they asked me to write this up as an article so will be including Archaea. However it is actually not important to this discussion to split the prokaryotes up as different Archaea species also fit within the aforementioned roles (except as known pathogens). I'm really want the entry point to be simplistic but not overly simplistic, and that is a fine line

However it might be interesting down the road to talk differences, e.g. can we grow a biofilter that withstands antibiotics and some other chemicals by utilizing Archaea? Probably.