Need help identifying problem. Bacterial infection?

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Hi everyone, 

I have been having a slow die off of my CRS over the last few of months. I am fairly new to this so I am not sure how to deal with this. 

Tank: 28L

Substrate: Fluval shrimp stratum (buffered to ~6.5)

Current GH: 5

KH: 0

Temperature: 22 C

Ammonia, nitrates, nitrites: ~0 ppm

Bit of background:

I started with 12 juvenile shrimp that I bought off a breeder in February this year. I started off using tap water (treated) with no problems. I got my first two berried females at the beginning of May. To this point I had had no deaths. At the beginning of June I had a couple (2) of deaths that I am still not sure the cause of. GH was low (2) at this time as I hadn't been testing for it, so that may have been the cause. Following those deaths I got some shrimp specific gh booster (saltyshrimp mineral GH+) and things seemed to recover. Berried females' eggs hatched at the beginning of June. One female became berried again in July. 

Now the tank was a bit overgrown at this stage so it was hard to keep tabs on the shrimp. I didn't notice any more deaths until a recent move. Before moving the tank I removed a lot of the overgrown plants. Once getting it to the new place I only saw 6 shrimp (2 females, 4 male) so it seems there were a few lost between June and August. There was one small shrimp in there as well (seems the only baby who survived). 

Since the move there was one death shortly after getting the tank set up. I chalked this one up to stress from the move. I haven't seen the baby shrimp since the second or so day after the move so I suspect that it has died as well. More recently I had a female die (at least I think it asa  female). See the first picture below. I noticed one day that she was behaving strangely. My shrimp haven't gone up to ride the floating frogbit since the first month I had them but a few days ago I noticed one up there. I went and had a look and she was just standing there. I also noticed that she seemed to be missing her long antennae. I snapped the below photo and went to work. When I got home, she was still there in the exact same spot. A few hours later, she was on the ground lying on her side. I poked at her and it was clear she was almost dead. Once I was sure she was dead, I removed her immediately. I did a test of the water and all parameters were good except pH which was high (around 7.2). Seems my buffered substrate had run out of buffering capacity due to the use of high PH tap water. I added some fresh substrate and did a water change with RO water and the pH is back to 6.5. Water change was done over the course of the day 1 litre at a time to avoid rapid swings in parameters. 

My berried female was still doing well and her eggs hatched two days ago. She was active and seemed healthy the next day. Today I noticed her in the corner tipped over and not moving much. I snapped the below photo. I know the colour of the internal organs are meant to be a sign of bacterial infection, but I don't know what to really look for in a CRS. The colour in the second photo below looks odd to me. All limbs and antennae intact.

EDIT: Just checked and the shrimp is dead. Anything I can do to try to determine the cause before I dispose of it?

I am just at a loss at this stage. I feel like a bad shrimp keeper and I don't know what else to do. 

Does this look/sound like a bacterial infection to you? What can I do to fix this?

Thanks for your help and let me know if you need any more info!



Edited by EBC

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Here are a couple of close ups now that I have pulled her out of the tank. Her organs seem very black and there is a black spot in her mouth area. Thoughts?



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@EBC, sorry for the loss of the nice female CRS

Have you tested for ammonia / nitrites?

The move of tanks might have caused a spike in ammonia. 

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Any updates @EBC ?

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No real updates unfortunately. All water parameters (ammonia, nitrites, nitrates, KH, GH, pH) were perfect on the day she died. All I can think is that the lack of buffering capacity left in the soil resulted in pH swings that killed her. 

I added more soil and the water is back to being buffered at pH 6.4. I have switched to only using RO water now (bought 20L for now but have an RO unit on the way). Hopefully the substrate will buffer a bit longer now and this won't happen again.

Just a shame as there are only 3 adult male CRS left in the tank plus the shrimplets from the female that just died. Could be a while before the numbers get back up on their own so I may need to replenish them (also a bit of genetic diversity would be good).

How do people usually handle switching out substrate? Especially with baby shrimps around, that sounds like a real hassle and you are bound to lose some. Is there some special technique?


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When you added soil can I ask what soil it was ? Did you pre-cycle it? Also it's worth noting that if that shrimp had been through some stress while exposed to high pH they will have weakened immune systems and so other little issues can tip them over the edge.


More than once I've discovered problems and corrected them as carefully as I could only to still watch the occasional shrimp die over the following days and weeks still despite conditions being ideal I believe.





PS Just as an aside - ¥others will have different opinions and prefer to do multiple smaller waterchanges but my modus operandi when I feel that a tank is "stuffed" is to do one or two huuuuuuge waterchanges - carefully allowing the new water to drip in slowly over 24-48 hours and then leave it be. The three times now that I've done this to get myself out of a bad spot I have found that although some already weak shrimp may continue to pass away over the following days even up to 2 or 3 weeks later but the healthier ones bounce back quickly and are breeding already within a few weeks.

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It was Fluval Shrimp Stratum which I have learned tends to have a relatively short life span compared to other soils. Will probably just replace it all in about 6 months when I move again. Any recommendations for one that will last the longest? And one that I can actually buy in Australia?

But yes, I imagine that she was just weak from the pH swings from before. The three remaining males all seem perfectly healthy for now at least. I'll give it some time to make sure there are no more deaths and then maybe find a nice female to add.

I have seen varying opinions on this, but how often would you suggest doing water changes (standard, not emergency) on a small tank like mine (28L)? I was doing them pretty infrequently before (~monthly; 20%) as I was using tap water so I wanted to avoid too many. Now that I will have an RO system would ~10% weekly be better? Or something else?

Thanks again.

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There are a few options for buffering substrate that you can try next.

Benibachi black soil, ADA Amazonia, ADA Amazonia lite, Cal Labs Black Earth Premium are some substrates that you can use which last a lot longer than Fluval shrimp stratum.

10% weekly water changes is a good water change routine. 

Like Will, I will occasionally (say every 6 months) do a huge water change of 80-90%. I will tear down the tank, gravel vac, trim all plants, and clean filter media at that 6 monthly massive clean-out. It's usually done at the change of seasons, from Summer-Winter. And I will usually also remove my aquarium chillers for cleaning. Or reinstall the chiller between Winter-Summer. 

Resetting the water parameters to remove built up minerals occasionally seems to do the shrimp good.

Edited by jayc

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How do your shrimp fare when you do a big tear down like that? Do you generally expect to lose a couple? Or do you put them in another tank while you do it? I am currently renting one bedroom apartments so I only have the one small tank. With such a small tank I would be worried I would crush some shrimp in the process. 

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The shrimp seem to not mind it at all, in fact they seem to be thinking ... "Ooo, look! New foraging areas" whenever I disturb the substrate. But of course, I match the new water parameters to the old as much as I can except for TDS (generally the new water is lower in TDS). Every other parameter, like pH, GH, and temperature will be a very close match. So the shrimp don't notice it much.

I catch as many as visibly possible into a bucket temporarily while I clean the tank. And they are returned to the tank after acclimating them slowly.

I filter the water I drain into a net first to catch any baby shrimplets. 

If you want to add substrate without removing the old substrate, it can be done easily ... one scoop at a time. Use those plastic takeaway containers. The shrimp will scatter.  Don't be too worried, they are faster than you think when the need arises.

5 hours ago, EBC said:

Do you generally expect to lose a couple?

I aim to never loose any ? ?


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Good solid advice@jayc :-)


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Thanks for the input guys! Really appreciate it.

Having a bit of a nitrate problem right now (~5ppm). Probably because I didn't cycle the soil first and once in the cycled tank all the ammonia ended up as nitrate. Didn't notice any ammonia from the soil last time, but I can't think what else it would be. Also just pulled out a bunch of plants which I am sure didn't help. Doing water changes to get it back down for now. Need my RO filter to get here though as I just ran out of my stock of RO water! Meant to be here tomorrow so hopefully that won't be too long.

One last question while I have got you. Since I am going to be moving again within six months, do you have any suggestions for how to best move a shrimp tank? Do you remove as many shrimp as you can for the move? Or do you just lower the water level and let them hang on for dear life during the move. 

The second option is what I went with in my most recent move and it seemed to work okay (apart from all the issues now, but I think the move isn't related to these issues) but keen to hear if you have any suggestions!

Oh and I suppose one more. Any suggestions for the best place to buy an adult female CRS? Breeders, LFS, etc? And if I decide to go for juveniles again, any suggestions for where to get maybe a dozen?


EDIT: So I just did a bit of a test to see whether the nitrates came from the Fluval Shrimp Stratum. Turns out that it leeches both ammonia and nitrate. I am sure it could be done more scientifically, but roughly 20 grains of the soil were put in 2.5mL of water and shaken for a bit and then left to sit for about an hour. Reading for ammonia was about 0.50ppm and nitrate was about 10-20ppm. Just thought that might be useful one day for someone googling Fluval Shrimp Stratum. Keep in mind that those are approximate numbers as the water was a bit cloudy from the stratum so it was a bit tougher to read the test.

Edited by EBC
Update on Fluval Shrimp Stratum

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6 hours ago, EBC said:

Or do you just lower the water level and let them hang on

for a tank your size, go with this option.

Just remove any ornaments or driftwood that might roll around and crush shrimp.

Keep all the tank water you can however. And make sure you keep ALL filter media in water. 

So, if you drain some water out of the tank into a bucket, move your filter media into that bucket as well. Cause the beneficial bacteria also need oxygen to survive. Aerating that bucket with the filter is the best option. But if you can't, then a large volume of water will hold more oxygen than keeping the media inside the filter. Same goes for air driven sponge filters too.  This should minimise the risk of the bacteria dying out and causing more deaths due to ammonia.

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