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Would you like to add information to this article? Interested in writing or submitting an article? Have a question about this article? Bacterial Action in Wood 
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Large bodies of standing water like lakes undergo a process called benthic turn-over. Cold, oxygen depleted water rises to the surface, displacing the warmer, oxygen rich water on top, creating a cycle. Rivers (except for a few very deep, slow rivers like the Amazon) have a large surface area to depth ratio that allows for high oxygen diffusion as well as rapids and whitewater that mix in O2. As for the fatty deposits, I'm not sure to what you are referring. The fatty (lipid) structure of the wood cells is different than the fatty deposits around my mid-section! Rancidity is caused by a specific group of bacteria that thrive under very narrow conditions. All in all, it comes down to microbe populations and the conditions in which they thrive. Did I answer your question or get off on the wrong track?
From the original questioner: In another posting a person was having problems with a cabinet made from luan that smelled like vomit. Gene explained this as fat deposits from bacteria turning rancid, a well known problem. I developed my questions from that discussion and my curiosity about sunken wood salvage. Thank you - you answered my question perfectly. From contributor J: I see. I can see how fatty deposits could come from some groups of bacteria. Some fats will release butyric acid that smells like vomit or rotting meat. I thought we were talking about fats in the tree. My mistake. From Professor Gene Wengert, forum technical advisor: The fatty acids indeed come from bacteria. I believe that temperature is much more a factor than the oxygen level in the water. From contributor J: Yes, there are three things necessary: environment, host, and pathogen. Without one of these, you have no "disease," for lack of a better term. So your oxygen levels, temperature, and such fall into the environment part of the equation. From the original questioner: Thanks. So, in summary, pathogens and hosts are always present, but wood taken from the depths of the Great Lakes is salvageable because of the cold environment and availability of oxygen. On the other hand, wood salvaged or even stored for cutting in a warm water environment like a shallow lagoon with little flow would be afoul of rancid bacteria, provided that wood had been there for several months. In such an environment, anaerobic bacteria release methane and H2S into the wood and in addition, in warm water, bacteria whose fat will turn rancid. The only solution for logs that exude diseased odors is to not buy them in the first place. Do these bacteria reach the center of hardwood logs? From Professor Gene Wengert, forum technical advisor: Logs at the bottom of Lake Superior (which can no longer be harvested) got there often times because the wood was bacterially infected in the first place. The bacterial activity increases the MC and decreases the amount of air in the wood, so the logs sink (they are called sinkers) and do not float, as would all uninfected logs in North America. There is little oxygen on the bottom of Lake Superior. The Clostridium bacteria in wood create fatty acids which do indeed turn rancid. Again, I do not believe the oxygen content of the water has much to do with this problem, as I have seen aerated ponds with infected logs. I believe the main factor is temperature of the water and the wood. The ability of the water to support anaerobic bacteria may influence the process, but most infected logs will already have bacteria in them - the bacteria move too slowly for a log pond to infect and then spread in the wood over a short time. The bacteria are found initially at the heartwood/sapwood junction. As the tree ages, this infected zone will be in the heartwood as the sapwood converts to heartwood. I doubt that heartwood already formed will support a new infestation of bacteria.
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