The manure would be collected from your domesticated animals and then applied to your farm plots to help decrease growth time and/or increase quality of your crops. Maybe something like a beehive where you could store the manure and within a certain radius the crops would be effected and an amount of manure would be consumed. Imo applying the manure by hand wouldnt be as impactful unless it was more of a thing you would use on small patches of crops just to increase quality faster than the current method.
Could be used to remove tree stunting though. Like, to make it more 'fun', make trees require manure to grow. For this to work wild animals would have to take dumps too...
Maybe just slow down current speed/quality gain and with added manure it would be the same as pre-patch.
Or make quality growth speed like 0-50 100% speed with or without manure 50-100- 50% speed without manure, 100% speed - manure is required 100+ - 50% speed compared to 50-100 with manure 150+ - 25% speed compared to 50-100 with manure