The cultural connection that people have been making between soil and tranmission of pathogenic organisms, appears to be a result of the fact that for many years before the invention of the Haber Process and synthetic ammonia, animal excrement and decomposng animal organs and tissues, were routinely added to the garden and farming soil to increase the growth of plants. Although I am not an expert on the subject of soil pathogens, what I have learned is that soil from wildnerness areas and farmng and veganic soil that has only had green manures and compost made only from plant material, appears to be much less likely to be a vector for pathogens. This is why I do not use animal excrement or body parts in my own garden.
Hookworm and tetatanus, for example, have both, according to what I remember, been related to animal excrement, and appear to be unusual in wilderness soil and veganic soil. Although even today, most organic growers use considerable amounts of animal excrement and body parts, adding such materials to the soil is not necessary. While compost made from animal excrement is bacteriologically "hotter" than compost made from plant matter, the excrement from herbivorous animals is basically the same thing as compost made in a wooden compost bin. Think of the herbivorous animal's gastro-intestinal system as being a kind of compost bin -- one that speeds up decompostion, but also "robs" some of the nutrients from the compost, for "its own use." The gastro-intestinal bacteria that speed up the decomposition of the plant matter also introduces a risk of disease transmission that plant matter composted in a wooden bin does not have. The ratio of pathogenic to non-pathogenic bacteria in a "gastro-intestinal compost bin" is higher than that of a wooden compost bin. The pathogen ratio in feces from carnivorous animals is even higher than that of herbivorous animals. As is the amount of heavy metals in their urine. This difference causes Cooperative Extension Agents in the US to recommend strict avoidance of excrement from carnivorous animals. Veganic gardeners like myself have taken this one step further and avoid excrement from herbivorous animals, as well.
Although large commercial non-"organic" growers may use little or no animal matter in their soil, it is very common among organic growers. Many people have turned to organic produce, thinkng that commercial non-organic growers often use large amounts of pesticides, soil with little organic matter and poor tilth, that results in less than optimum root absorbtion by plants, and plants with less than optimum value as nutrients for humans. However by switching to conventional organic growers, they are risking an increased likelyhood of receiving soil-borne pathogens. The solution is veganic farming, with no animal materials, cautious and controlled use of pesticides, use of green manures, cover crops, and plant-based compost, and use of industrially produced sources of nitrogen to supplement that provided by compost, and increase yield per acre to the same standards as big agribusiness. By using as much compost as possible, the amount of industrially produced nitrogen sources that are needed, can be minimized. However eliminating it would be difficult if not impossible, if similar yields are desired.
I might add that good compost increases plant uptake of nitrogen 2 ways. 1. It supplies nitrogen. And 2. it improves soil tilth, so that nitrogen that is bound up in organic matter can become more available. It becomes more available 2 ways. 1. With a good tilth organic matter decomposes faster and 2. with a good tilth the contact between plant roots and soil particles is improved, allowing the roots better access to nutrients dissolved in soil moisture.
With better the soil tilth, the amount of nitrogen that is available to plants is increased, even tho the amount of nitrate and ammonical nitrogen as determined by tests of soil samples, may be the same. In fact, there are rather specific formulas that you can get from cooperative extension and other sources of soil-science information, that you can use to estimate how an increase in organic matter, humus, offsets the amount of nitrate and ammoniacal nitrates that would need to be added to soil, in order to get a specific yield, of various types of crops. With very high levels of humus, soil will provide sufficient nitrogen for many crops, even though the tested level of nitrogen is very low, or zero. Apparently if there is enough organic matter, the nitrogen bound up in the organic matter will be made available to the plants, quickly enough to produce maximum yield. This may not be the case with very voracious feeders, such as sweet corn or hybrid lettuce varieties. With such plants, in order to produce maximum yield, no amount of compost may be sufficient. Very nitrgoen rich excrement or industrially produced sources of N, may be needed. This is thought to be because such plants were selected by humans from plants grown in artifcially high-in-nitrogen soil, and have evolved to be adapted to such high-nitrogen soil.
I would suggest that perhaps a study could be made of micro-organisms populations that will speed the decompostion of various kinds of plant matter and production of nitrogen by decay bacteria, and at the same time will not be pathogenic. Perhaps such bacterial cultures could be added to plant matter to produce faster, better compost.
I am not against the use of industrially produce nitrogen plant food. I am however, for using it in moderation. I believe that composted plant matter may have materials that contribute to plant flavor, that industrially produced nitrogen would not have. Although a science of flavor chemistry exists, it seems that very little is known about the subject of plant flavor due to differences in growing medium, and that more research ought to be done. Althought there is the problem of "measuring" flavor. We simply do not know what chemicals are involved in many of the subtle flavors we seem to be able to taste; we often have difficulty finding words for these flavors, as well as difficulty identifying them chemically.