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So I was wondering is there a benefit to adding sand to a pleco setup vs keeping it bare bottom? That is fine river sand or similarly sized filter sand not gravel or coarse sand (those are a nightmare to keep clean). I know it would contribute to the total surface area of the tank and provide for nitrifying bacteria, but I mean would a thin (<2cm) layer of sand benefit fish in any way? Other than the aesthetics and what I mentioned earlier, would it have a positive effect on stress or anything? I know that Pseudohemiodon species would want sand to borrow in, but my context in non-borrowing species like Hemiancistrus, Panaque, Panaqolus, Hypancistrus etc...

I know from the past, and a search in the forum here should bring something up, when a layer of sand is left in with fry of many species, there is less chance of losing those fry to bacteria. Glass bottoms seem to get a film of bacteria on them that can be harmful to fry. I always kept about 1 to 2 centimeters of sand in my tanks which was very beneficial against losses for myself.

In addition to the points raised by Birger above, plecos kept over some type of natural substrate also appear more at ease (less stressed) than those kept with no substrate at all. For messy plecos I prefer cutting a piece of slate to use as a "false bottom" substrate. I have spawned several spp with this arrangement and it is super easy to keep the aquarium clean.
-Shane

I have done it both ways. I used to be all bare bottom and over time I began using a bit of sand. This is as much because it hosts the bacteria we want and because, in some cases, it helps to keep the wastes in easy to spot places.

While I have read about fry and a bacterial layer, I have never witnessed it in any of my bare bottom tanks. However, because I have to break down a tank to as little as possible to inventory fish, to nab babies or to move them to grow or selling tanks, most bare bottom tanks got the bottom glass cleaned twice a year.

I moved to mostly having sand bottoms in my pleco tanks over the 6 years or so. I also moved towards more aire driven Poret foam filters in tanks. These do not tend to move sand around a tank the way canisters, power filters and powerheads can. But I also notice how many claimed caves have a bare patch exposing the bottom glass in front of them from the male waving its tail about.

I have lost more fry to piles of gunk that built up between weekly maint. and into which they unknowingly wandered in search of food.

@Shane
How do you prevent or deal with the gunk that wants to accumulate under or along the perimeter of the slate?

I just go around the edges with my trusty siphon during water changes. Every six months to a year I also pull out the slate and siphon out any built up detritus. Many of the faster water plecos seem to enjoy as they are basically living on a flat rock. In terms of ease of maintenance, I have also spawned woodeaters in these set ups with no issues.
-Shane

Thanks guys!

I got a group of L264's close to a month ago. They are eating but they are extremely shy and would never come out when I'm near. They are in a bare bottom tank with nothing with them, would adding sand make them more or less shy? Or should I look into adding dithers (bristlenose?, a single apisto male?)

Sand would most likely help, just as dithers. But you have wrong examples of dithers.

Dithers are fishe swimming around, near the surface, telling other fish no predatory birds are around. Bristlenoses are hiding themselves and an Apisto would need dithers to know it's safe hinself.

However, any Tetra would suffice.

I added a thin layer of river sand and they got out of their hides immediately, I think they're pissed of or confused at first. I also added a black background in an attempt to make them feel safer.

And about dithers, would a group of rainbowfish work or are they too much? Since I already have them in another tank.