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This is a hive that has made very little progress in the last 30 days. After 90 days of great growth, the third brood box (where this frame came from) still has several frames that have no draw-out at all.

Here's a close up of some cells:



There are a lot of medium brown empty cells, and the bottoms of the cells don't look right to me.

I was thinking foulbrood, but there is absolutely no off-smells at all. I'm just worried about a perceived lack of vitality of growth, and now the third brood box has a darkly-colored frame, with mostly empty cells surrounded by honey cells.
 

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Where I live, this is the time of year brood rearing will start to slow down, & upper brood boxes will start to be filled with honey.
Does all look good in the lower boxes?
 

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If you're going to worry about foulbrood you need to look at cells that have brood in them, not nectar cells. How does the open brood look? If it's nice and white and glossy looking you don't have foulbrood. If brown and stinking you might! Do a rope test on any brown nasty looking brood or else go drink a beer and relax. :D
 

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I'm gonna say either your queen has stopped laying or your hive is queenless. This time of year I would guess your queen has stopped laying. Looks like larva around the edges of the brood.

As for the cells looking "funny", I'm not seeing any indication of disease just from this one picture. If there were foulbrood on this frame, you would have partially capped brood where the center looked sunken in or broken. Prying away the rest of the capping to expose the brood would reveal a brownish gooey mess slumped in the bottom of the cell (bottom as in toward the bottom of the frame). Inserting a small stick or toothpick and "stirring" the contents of the cell would result in something the consistency of thick snot. Withdrawing the stick or toothpick would draw with it a string of goo - roping they call it.

A question for you. Why do you have three deep brood boxes on? Two should be sufficient. You need to look a little further than this box if you suspect a problem. Two boxes is easier to search thru.

I see nice stores on the frame. I don't see drone brood scattered amongst the worker brood, so I'll assume that if your queen is there, she's not a drone layer.

You may be panicking just a little...
 

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You should check both the lower boxes for fresh open brood. If there is no flow they won't draw foundation. If they have enough room in the bottom boxes of drawn comb they will use that instead of drawing foundation. What I see in the frame you show is that the bees are backfilling the brood cells as they hatch with nectar. The dark cells are caused by the brood that was raised in it.
 
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