There's an interesting discussion of this issue at Biology Fortified blog. The post is by my first MS student, Andy McGuire, who also has interesting things to say on a blog from Washington State University, where he works.
Andy's post was apparently inspired partly by something I wrote last year, showing my estimates of how much nitrogen flows from synthetic fertilizer to conventional corn to chicken manure to organic farms.
I don't get too excited about whether organic farmers should be allowed to use manure from conventional farms, or whether we should "blame" them for the fertilizer used to grow the corn to feed the chickens. My point was simply that this dependence limits the potential for expanding organic agriculture. (So advocates of organic farming should be showering me with money for research on nitrogen-fixing legume crops and forages -- but that's another story.)
More interesting is this open-access paper, titled "To what extent does organic farming rely
on nutrient inﬂows from conventional farming?" The paper has some actual numbers on nutrient fluxes to organic farms from conventional ones in France. While my earlier diagram assumed that an organic farm relied entirely on manure whose nitrogen originally came from synthetic fertilizer, the French study estimated that only 23% of nitrogen (though 73% of phosphorus) supply to organic farms came from conventional sources. But let's look at some details.
First, there are apparently some differences from US practices:
"European regulations recommend to use organically produced animal manure but allow the use of conventionally produced manure, provided that it is not the output of 'factory farming'."
I don't think we have that restriction in the US. Second, they found that:
"More than 80% of nutrient inﬂows through manures (82%, 85% and 81% for N, P and K, respectively)... came from conventional farming"
So 82% of N in manure came from conventional farms, but that was only 23% of estimated total N supply. The rest (almost 60% of total N inputs) was mostly estimated to come from biological nitrogen fixation:
"N ﬁxation was estimated using the model proposed by Høgh-Jensen et al (2004)... based on the total N amount in leguminous crop biomass, multiplied by the ratio between the amount of symbiotically ﬁxed N and the total N amount in the crop
That seems to be about all they said about biological nitrogen fixation -- I would have liked a little more detail. They also say that unsustainable "soil nutrient mining" (failure to replace nutrients exported in crops or otherwise lost from soil) was "not considered." A simple approach to that problem would have been to estimate nitrogen and phosphorus contents of products sold off-farm, and compared that to total inputs. If inputs exceed outputs, some of the difference may end up polluting groundwater, although some may be accumulating in soil, at least for a while. If outputs exceed inputs (including biological nitrogen fixation), over the long term, they will not be able to continue farming over the long term.
My conclusion is that organic farms that rely on manure from other farms (or on manure from their own animals, which are fed grain or hay from other farms) are dependent on conventional farms and therefore not a model that can be scaled up. That doesn't mean they are not making a positive contribution, if they are using manure that would otherwise end up polluting rivers.
If we can believe the nitrogen-fixation estimates in this paper, French farms are already getting a majority of their nitrogen from symbiotic rhizobia in the root nodules of their legume crops and forages. Maybe that could be scaled up. But if 75% of their phosphorus is coming from manure from conventional farms anyway, there may be little point in trying to replace the nitrogen in that manure with biological nitrogen fixation.