Q What is the truth?
That would be nice to know, indeed. But the way this problem is formulated it is way too complex to be answered definitively with simple 'yes' or 'no'.
On the one hand, it's a really simple equation of input/output. If the substrate, fertilizer and water are lacking minerals, then the plants will be lacking them as well, as they generally do not manufacture minerals out of the air. But real world application of this seemingly simple truth is quite complicated.
Looking closely, the old problem of declining soil fertility wasn't solved by the fertilizer industry. In some ways it made it worse in the long term. So bad that that now we have Only 60 Years of Farming Left If Soil Degradation Continues.
At just the point when agriculture was running out of unexploited tillable lands, technological breakthroughs in the 1950s and 1960s allowed it to continue increasing production through the use of marginal and depleted lands. This transformation is known as the Green Revolution. The Green Revolution resulted in the industrialization of agriculture. Part of the advance resulted from new hybrid food plants, leading to more productive food crops.[…]
Soil erosion and mineral depletion remove about $20 billion worth of plant nutrients from US agricultural soils every year.
Dale Allen Pfeiffer: "Eating Fossil Fuels: Oil, Food and the Coming Crisis in Agriculture", 2006.
Many subproblems to the claim as presented can be answered "yes", for example "many soils are being depleted", "nutrient, here: mineral concentrations in produce, composition is changed compared to 100 years ago". But the certainty that whole string of claims present make it too to be precise about the end result of human health.
What exactly is meant with depletion? Also simple soil erosion? Loss of biodiversity and thus "soil health" or old-fashioned fertility? General downward trend or single constituents of soil? How to evaluate plant nutrients that are present in soil but becoming less available for plants? Do these 'depletions' result in plants that are deficient or just less yield as these nutrients are a limiting factor? How does this translate to what people eat? Are the nutrients diluted in fresh or dry weight? Is this the same across the world or with regional differences? The list goes on but I stop here.
From soil to plant to plate composition to nutritional value to health/deficiencies. This is just a bit n the broad side. "Food", "nutritious", "soil" all this needs to be narrowed down and defined. For example British bread is now drastically lower in Selenium compared to 40 years ago. But not because British soils are depleted of Selenium, but because it's now made more from British wheat instead of imported, which still has more Selenium than British wheat. And since this problem was identified, fertilizer compositions were changed so that now soils get enriched with Selenium.
A more meaningful answer might be derived from asking "Has the mineral content on the same plots of land decreased?" Which would lead to plants having a harder time accumulating stuff that's no longer there. Was soil and humus eroded?
This is not a binary problem and thus either "yes" or "no" are too simple. But quite a few soils are mismanaged, eroded and depleted, commercial artificial fertilisers are often deficient in compounds compared to what is removed from soils via harvests and degradation. Yes, that's often and in general a lesser problem in 'well managed' organic farming.
On the other hand, Cu is used in organic farming so much as pesticide that some soils are anthropogenically over-enriched as to be unsuitably polluted with it.
A big problem for answering this properly are the regional differences. Some soils are now way above N+P capacity, so that it gets washed into groundwater. This effects primarily Western Europe wheras Africa and South America tend to have the opposite problem. But this is again too simplified.
The human health angle is even more complicated than that. Vitamins and minerals and trace elemenst, the maro- and micronutirents in human nutrition are – again – in general not a widespread problem for affluent Westerners who eat a well balanced diet. "Well balanced" being the problem here.
Does it matter that potassium in local carrots declined so much that you now have to eat 12 carrots instead of 7 to obtain the same amount as from one half banana? Is a reduction in minerals in harvested wheat a problem if all of that is in those layers that are discarded for making white flour or junk food anyway? Is the reduced mineral content in broccoli a problem when 60 years ago it was boiled for 45 minutes on average while today it's down to 15 minutes after which the minerals leached into the water are discarded?
Then the secondary non-nutrients in plants, or phytochemicals. These cannot be classified across the board as beneficial, as some are also anti-nutrients, or outright poisons. Some go up, some go down, some are good, some are bad. It depends, and we do not know enough.
Even the basic minerals for themselves in plant products are not "more is better". What is the 'right amount' of nitrate, fluoride, selenium in salad, tomatoes, tea or nuts? Most of these can be overdosed with relative ease, so in some soils it would be beneficial if their levels were reduced so that plants do not accumulate them as much as they do.
Some facts that might help elucidate some subproblems:
Human activities impact several processes in soil that could lead to physical (accelerated erosion, deterioration of soil structure, crusting, compaction, hard-setting), chemical (nutrient depletion and imbalance, acidification, salinization) and biological (depletion of soil organic matter, loss of biodiversity) degradation of soil. Soil degradation directly affects food security through reduction in crop yields, decline in their nutritional quality and reduced input use efficiency. Plant availability of mineral nutrients in the soil is the main source of mineral supply to human beings.
Soil Quality and Human Health, p1.
Fig 1.6 Depletion of agricultural land and nutrient depletion (GLASOD) (Drawn from Oldeman et al. 1991)
World Asia Africa South North and Australasia Europe
America Central America
135 (7) 15 (2) 45 (9) 68 (28) 4 (3) 1 (–) 3 (2)
Table 1.4 Global Assessment of Human-induced Soil Degradation (GLASOD) for different regions (million ha). Numbers in parenthesis indicate percent of total degraded area (Adapted from Oldeman et al. 1991)
Global Assessment of Human-induced Soil Degradation (GLASOD) showed that worldwide 15% of the land covering an area of 1964 million ha is affected by human-induced soil degradation out of which 1642 million ha (84%) is affected by water and wind erosion (Table 1.4). Total annual production of dust by deflation of soils and sediments has been estimated to be 61–366 million Mg. The amount of dust arising from the Sahel zone has been reported to be around 270 million Mg per annum, which corresponds to a loss of a layer of 20 mm over the entire area (WMO 2005). Besides leading to loss of organic matter and plant productivity, wind erosion can cause serious health problems by blowing soil particles, pollutant and microbes into the air, aggravating allergies, asthma and opportunistic infection of the lungs (Korenyi-Both et al. 1992; Peters et al. 2001; Prahalad et al. 2001; Griffin and Kellogg 2004). Airborne bacterial and fungal spores and microbial molecules such as endotoxins and fungal mycotoxins can cause allergic reactions and respiratory stress in children (Braun-Fahrlander et al. 2002). Desert dust in Kuwait during the 1990s was reported to cause cellular membrane and DNA damage (Athar et al. 1998).
Chemical soil degradation covers about 239 million ha (12%) and physical soil deterioration, which includes compaction and water logging, occupies around 83 million ha (4%). Soils affected by pollution occupy an area of 22 million ha worldwide. Recent estimates made by Bai et al. (2008) show that 24% of the global land, often in very productive areas, has degraded during the period 1981–2003. Comparison of degrading areas with global land cover revealed that 19% of degrading land is cropland, 24% is broad-leaved forest and 19% needle-based forests. Comparison, of the new analysis with the previous GLASOD estimates show that much of the area estimated by two approaches does not overlap.
Loss of nutrients is the major sub-type of chemical deterioration of the soils followed by salinization. More than two-thirds of area affected by salinization (76 million ha) is located in Asia. Salinization leads to an excessive accumulation of water-soluble salts such as sodium, potassium, calcium, magnesium, chloride, sulphate, carbonate and bicarbonate in the soil and soil solution. The salinization could be caused through natural processes (primary salinization) or human interventions (secondary salinization). Primary salinization is caused due to high salt contents in parent material or groundwater particularly in arid regions. Secondary salinization develops due to inappropriate irrigation practices such as application of salt-rich irrigation water and/or insufficient drainage. Salinization is considered a major threat in the irrigation systems of the Indus, Tigris, and Euphrates River basins, in north eastern Thailand and China, in the Nile delta, in northern Mexico, and in the Andean highlands (Bai et al. 2008). Dryland salinity, which currently affects about 1 million hectare area in southwest Australia, has been linked to serious human health problems. Jardine et al. (2007) identified several potential human health impacts resulting from dryland salinity viz. wind-borne dust and respiratory health including altered ecology of the mosquito-borne disease Ross River virus and mental health consequences of salinity-induced environmental degradation.
Of the 135 million ha influenced by nutrient depletion worldwide, 68 million ha is located in South America followed by Africa (Fig. 1.6). The official report of the Earth Summit (1992) expressed concern over major declines in the mineral values in farm and range soils throughout the world. This concern was based on data showing that during the previous 100 years, average mineral levels in agricultural soils had declined worldwide, by 72% in Europe, 76% in Asia, 74% in Africa, 55% in Australia, and 85% in North America.
Nutrient depletion can be attributed to soil mining because of insufficient and imbalanced fertilizer use, soil erosion, and leaching. Nutrient depletion is predicted to cause serious problems in the mid-altitude hills of Nepal; in poor soil quality areas of north-eastern India and Myanmar, now undergoing transition to permanent agriculture, and in areas in north eastern Thailand. It is also expected to cause major problems in large areas of Africa under transition to short fallow or permanent cropping, in areas of reduced silt deposits in the Nile delta, in the sub-humid Mesoamerican hill sides, and in the semi-arid Andean valleys, north eastern Brazil, and the Caribbean Basin lowlands, where agriculture is undergoing intensification (Bai et al. 2008). Given the lack of alternatives available to smallholders and their limited resources, soil mining tends to be associated with poverty. In contrast, soils in many developed countries have excess nutrients. For example Western Europe has considerable surpluses of nitrogen, phosphorus and potassium (Bach and Frede 1998). These surpluses are the result of excessive mineral fertilizer input as well as due to addition of nutrients through imported food products that enter the nutrient cycle via animal dung or liquid manure. During the years 2008 and 2010, about 35 million Mg of soy and soybean products were imported into the EU. Soybeans are processed into soybean oil and soy flour. Virtually all the soy flour goes into animal feed (Kotschi 2013). In Asia, high nutrient surpluses occur as a consequence of excessive nitrogen and phosphorus fertilization such as in China, South Korea, and Malaysia (Lin et al. 1996; Tan et al. 2005). Globally, soil nutrient deficits for cereal production (wheat, rice, maize and barley) were estimated at an average rate (kg ha 1 year 1) of 18.7 N, 5.1 P, and 38.8 K, covering respectively 59%, 85%, and 90% of harvested area in the year 2000 (Tan et al. 2005).
Rolf Nieder & Dinesh K. Benbi & Franz X. Reichl: "Soil Components and Human Health", Spinger: Dordrecht, 2017. DOI
While 'mineral depletion in soils' is an almost inadequate oversimplification in itself, the more general and global outlook concerning possible health effects from degrading soils, mainly by that kind of mismanagement that is called conventional or industrialised farming, is a reason for concern. Not yet across the board in developed countries and not a reason for everyone to go out of their way to pop some pills because of undiagnosed but only suspected 'deficiencies'.
Soil degradation affects human nutrition and health through its adverse impacts on quantity and quality of food production. Decline in crops’ yields and agronomic production exacerbate food-insecurity that currently affects 854 million people globally, and low concentration of protein and micronutrients (e.g., Zn, Fe, Se, B, I) aggravate malnutrition and hidden hunger that affects 3.7 billion people, especially children. Soil degradation reduces crop yields by increasing susceptibility to drought stress and elemental imbalance. Strategies include: improving water productivity, enhancing soil fertility and micronutrient availability, adopting no-till farming and conservation agriculture and adapting to climate change. There are also new innovations such as using remote sensing of plant nutritional stresses for targeted interventions, applying zeolites and nanoenhanced fertilizers and delivery systems, improving biological nitrogen fixation and mycorrhizal inoculation, conserving and recycling (e.g., waste water) water using drip/sub-drip irrigation etc. Judiciously managed and properly restored, world soils have the capacity to grow adequate and nutritious food for present and future populations.
R. Lal: "Soil degradation as a reason for inadequate human nutrition", Food Sec. (2009) 1:45–57 DOI: 10.1007/s12571-009-0009-z
Regarding the nutritional supply of known important minerals in human food we've already seen a decline in for example magnesium:
John B. Marler & Jeanne R. Wallin: "Human Health, the Nutritional Quality of Harvested Food and Sustainable Farming Systems", Nutrition Security Institute, 2006. (PDF)
The alleged inadequacy of analytical methods for these comparisons might be addressed in David Thomas: "The Mineral Depletion of Foods Available to Us as a Nation (1940–2002) – A Review of the 6th Edition of McCance and Widdowson", Nutrition and Health, 2007, Vol. 19, pp. 21–55.
Although magnesium (Mg) is one of the most important nutrients, involved in many enzyme activities and the structural stabilization of tissues, its importance as a macronutrient ion has been overlooked in recent decades by botanists and agriculturists, who did not regard Mg deficiency (MGD) in plants as a severe health problem. However, recent studies have shown, surprisingly, that Mg contents in historical cereal seeds have markedly declined over time, and two thirds of people surveyed in developed countries received less than their minimum daily Mg requirement. Thus, the mechanisms of response to MGD and ways to increase Mg contents in plants are two urgent practical problems. In this review, we discuss several aspects of MGD in plants, including phenotypic and physiological changes, cell Mg2+ homeostasis control by Mg2 + transporters, MGD signaling, interactions between Mg2 + and other ions, and roles of Mg2 + in plant secondary metabolism. Our aim is to improve understanding of the influence of MGD on plant growth and development and to advance crop breeding for Mg enrichment.
Wanli Guoa et al.: "Magnesium deficiency in plants: An urgent problem", The Crop Journal, Volume 4, Issue 2, April 2016, Pages 83-91. DOI
The lack of overview currently only allows very limited conclusions to be drawn from that
Implies that a balance of the different essential nutrients is necessary for maintaining health. The eight minerals that are usually analysed are Na, K, Ca, Mg, P, Fe, Cu, Zn.
A comparison of the mineral content of 20 fruits and 20 vegetables grown in the 1930s and the 1980s (published in the UK Government’s Composition of Foods tables) shows several marked reductions in mineral content. Shows that there are statistically significant reductions in the levels of Ca, Mg, Cu and Na in vegetables and Mg, Fe, Cu and K in fruit. The only mineral that showed no significant differences over the 50 year period was P. The water content increased significantly and dry matter decreased significantly in fruit. Indicates that a nutritional problem associated with the quality of food has developed over those 50 years. The changes could have been caused by anomalies of measurement or sampling, changes in the food system, changes in the varieties grown or changes in agricultural practice. In conclusion recommends that the causes of the differences in mineral content and their effect on human health be investigated.
Anne-Marie Mayer: "Historical changes in the mineral content of fruits and vegetables", British Food Journal 99/6  207–211. (PDF)