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I've been filling planter boxes (PB5s to PB12s) with organic soil mixes, with a tiny amount of synthetic fertlizer.

Is this bad for my lungs? The environment wasn't windy, and the soil was moist enough so that any airborne dust was unnoticable, however I've found very fine particles turning my mucus black after work. I was unable to wear a mask for other reasons.

I'm not sincerely concerned with this due to the brevity of the job, however i'm wondering from a theoretical perspective if this would ever be an issue if I held the job long enough? Could it be carcinogenic or reduce lung capacity as it blocks alveolae?

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It is not harmful to get some 'dust' in your lungs, sporadically. Your lungs will remove it via mucus, like you have noticed.

It becomes dangerous, when it becomes chronic instead of sporadic. So every day, or during a day job (think of mine workers, or smokers).

Also when the compound is carcinogenic then it becomes dangerous, but as far as I know fertilizer is not. Fertilizer is usually a salt (or mineral), containing NP and K. Carcinogenic compounds are for example benzene, and asbestos. These molecules fit exactly in the alveoli (the lung sacs).

So don't worry about it!

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If working with organic soil mixes that include compost you need to work outside preferably with any wind blowing the contents away from you. If working inside you need to wear an approved antibacterial mask. A high percentage of compost available in various markets contains legionella and I know of several people who have contracted legionella pneumonia in such circumstances. http://www.bbc.com/news/uk-scotland-glasgow-west-24348811

When working with dry vermiculite and perlite you should use a dust respirator when working inside. Vermiculite may contain trace amounts of crystalline silica, and chronic exposure can lead to silicosis. Levels above 0.1% should be marked as carcinogenic.

This paper describes reactive airways disease appearing after accidental inhalation of perlite. https://www.researchgate.net/publication/41452213_Acute_Expanded_Perlite_Exposure_with_Persistent_Reactive_Airway_Dysfunction_Syndrome

Update: seems the most common cause of summertime pneumonia in the Bay of Plenty, NZ is legionella from potting mixes https://www.stuff.co.nz/life-style/homed/community/101482988/how-a-love-of-gardening-led-to-a-potentially-lethal-bout-of-legionnaires-disease

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