Advances in irrigation and soil management techniques, along with the application of chemical fertilizers and pesticides introduced by the Green Revolution in farming, resulted in a substantial increase in food production over the last 50 years. However, the potential of chemical fertilizers to disrupt soil health, the food chain, and ultimately human health has led to renewed interest in the consequences of their application, and has resulted in a substantial increase in the number of certified organic farms. Organic systems, defined by management practices lacking the application of synthetic fertilizers and pesticides, appear to reduce the burden of xenobiotics in the food chain, but there is still controversy regarding the nutritional advantages of organic versus conventionally produced food. Irrespective of the impacts on food quality, the potential for organic farming to impact soil health has been expounded as a significant benefit. However, only a few studies have explored these phenomena while taking into account all the confounding variables. Synthetic fertilizers can result in disrupted soil health, and may negatively impact plant growth as well as soil and plant microbial diversity and structure. Therefore, the cumulative use of such compounds could lead to the loss of productivity and economic revenue. Organic fertilizers are known to have several advantages to improve soil fertility, such as the ability to increase organic matter content in soil, improve the soil structure, enhance soil nitrogen content,planting blueberries in a pot enhance nutrient availability, and improve nutrient mobilization as well as increase root growth.

Organic practices rely upon crop rotations, crop residues, animal and/or green manure, off-farm organic wastes, mechanical cultivation, mineral bearing rocks, and aspects of biological pest control to maintain soil productivity and supply plant nutrients. It is generally assumed that greater soil microbial species’ richness promotes enhanced functional stability and thus soil health, but it is unknown whether short-term synthetic fertilizer application versus organic fertilizer will have a substantial impact on these ecological properties. Organic systems have previously been associated with either an increase in soil microbial richness or no significant change. Some of this variance may be explained by differences in the composition of the organic amendment, the time of harvesting, the studied time span, the rotation of crops planted, and so on. However, in general, studies suggest that short-term organic fertilizer amendment leads to a copiotrophic microbial community, while long-term application will result in a more stable community. Overall, Proteobacteria and Firmicutes dominate organic farming systems in long-term field experiments, with plant growth-promoting genera also enriched , while Actinobacteria and Acidobacteria predominate in conventionally managed lands. In the present study, soil type, land use, crop rotation, crop variety, and climate/weather were all standardized in a short-term field experiment conducted on adjacent plots that share the same land use history, same soil edaphic properties, and same environmental stressors . In each plot, a synthetic chemical fertilizer and a natural fertilizer were applied, followed by planting with Solanum lycopersicum and Beta vulgaris.Previously, this system was used to demonstrate that short-term organic fertilizer application did influence the accumulation of essential and non-essential elements within these crops, but overall, there was little or no clear effect of the fertilizer type on the elemental accumulation in the fruits, suggesting that the plant nutritional value was neither improved nor reduced in the short-term.

Here, we employed 16S rRNA amplicon sequencing to characterize how the soil microbial community responded to these treatments and to determine to what extent the community shifts are comparable to the changes occurring in the long term. We identified biomarkers of fertilization type and correlated bacterial shifts with the accumulation of chemical elements in soil and tomato and Swiss chard roots. The proportional differences in predicted bacterial functional genes in response to the fertilizer amendment were also evaluated. Extending the duration of the experiment would help to resolve whether the microbial shifts observed here are persistent over time and determine if the treatments have an impact on soil quality in the long term, which is ultimately required for evaluating the sustainability of land-use regimes. A field experiment was conducted on adjacent plots to study the prokaryotes community diversity and composition of soils under different fertilization treatments, conventional versus organic. In each of the plots, two plant species and B. vulgaris were planted in two subplots . Soils samples were collected over 3 months after fertilization and crop planting.While most studies agree that farming practices impact soil microbiota and the accumulation of elements within the plant, obtaining generalizable conclusions has been difficult, as results are dependent on the applied management, the composition of the organic amendments, the time of harvesting, the time span studied, the rotation of crops planted, and so on.In the present study, which standardizes for differences in soil properties, crop type, and climate conditions, changes in soil microbial richness were observed over the duration of the experiment associated with the crops’ developmental stage. Interestingly, microbial richness was greatest in July and lowest in August for both conventional and organic soils, suggesting that while nutrient supplies start to decrease, there is a decrease in richness.

In addition, the combined effect of ‘sampling date’ and ‘farming system’ significantly correlated with bacterial richness, with the values being higher in organic soils. While the higher richness in organic systems might be in part due to the introduction of microorganisms present in the manure into the soil , Bacteroidetes, and Chloroflflexi,previous data suggest that organic farming systems promote habitat diversification, favoring a more heterogeneous species distribution, or by stimulating the growth of copiotrophic microorganisms.In conventional soils, lower diversity might be expected because of the elimination or growth inhibition of particular bacteria in response to chemical compounds coming from pesticides/fungicides. Predicted functional diversity, however, did not change according to the farming system. pH is known to influence microbial composition as well as the mobility of heavy metals, influencing micronutrients’ uptake. In the present study, while pH was a determinant factor explaining the bacterial community structure found in the soil samples, it did not correlate with the alpha diversity estimate. Despite both plots starting at the same pH values, conventional fertilizer resulted in a reduced pH over time, consistent with the observed impact of chemical fertilizers in longer-term experiments. pH variation influences Proteobacteria, Actinobacteria, and Acidobacteria abundances. For example, Lauber et al. found that the relative abundance of Acidobacteria decreased with pH, while Actinobacteria and Bacteroidetes positively correlated with soil pH. In our study, Bacteroidetes positively correlated with pH,raspberries in pots while Actinobacteria was negatively correlated. The different trends observed in this study might result from the soil having only been fertilized once, which would select for copiotrophic taxa, compared with other studies where multiple recurrent fertilizations were applied over years. In addition, titanium abundance was positively associated with the community structure found in organic soils, and negatively associated with that of conventional soils. In contrast, the abundances of Ag, Mn, As, Fe, Co, Cd, and Ni were mainly associated with conventional soils. Titanium is considered to be a beneficial element for plant growth, improving crop performance through stimulating the activity of certain enzymes, enhancing chlorophyll content and photosynthesis, promoting nutrient uptake, strengthening stress tolerance, and improving crop yield and quality. In agreement, organic soils in the present study shifted towards the enrichment of taxa involved in nutrient cycling as well as in disease suppression. When studying the accumulation of chemical elements within the plants, Liñero et al. documented a differential accumulation according to the fertilization practice. Higher concentrations of Mn, Co, Na, Mg, Cd, and Tl were observed in conventionally grown tomato plants, while Mo, Cu, Zn, K, and Ba abundances were higher in the organically grown ones. Similarly, Swiss chards under organic amendment were more concentrated in Ba and some nutrients. Interestingly, the soil bacterial community of the present study was a good predictor of Mo and Cu accumulation in organic tomato and Swiss chard roots, thus suggesting that those elements’ absorption is favored, in part, by means of the soil microbial activity.

For instance, because of the spraying of copper sulfate on plant aerial parts, a higher accumulation of Cu might be expected in organic roots. Besides, its higher concentration in organic agricultural practices has been previously associated with a higher presence of arbuscular mycorrhizal fungi, and their synergistic interactions with several bacteria, such as species belonging to Rhizobiales and Methylococcales, are already well known. The soil’s bacterial community composition was significantly influenced by the management practice in the 3 months of the experiment, as observed in previous long-term studies. However, the experiment conducted should be extended over time to assess whether the microbial shifts associated with the farming system and the differential uptake of elements by the crops under study persist, in order to evaluate the farming system’s impact on the quality and health of soil, and hence the sustenance of the system. In any case, in the present study, similar to Lupatini et al., but in contrast to Wang et al., organic samples tended to have greater beta diversity compared with conventional samples, suggesting a greater heterogeneity in the microbial composition of organic soils. Hartmann et al. found that ~10% of bacterial and fungal OTUs were specific to the farming system and Lupatini et al. reported that Proteobacteria and Acidobacteria were highly sensitive to the farming practice. In the current study, the abundances of most common bacterial phyla were not statistically different between farming systems, but few phyla were significantly associated with each of the farming systems. For instance, Chloroflflexi, Thermi, Spirochaetes, and Euryarchaeota had greater mean relative abundance in organic soils, while a higher abundance of Firmicutes was observed in conventional soils. Within Chloroflflexi, members of the class Anaerolineae were enriched, which are known for their role in nitrogen cycling and have been previously identified as a highly represented bacterial group in manure. Several other denitrifiers were also augmented compared with conventional soils, including genera Azoarcus and Thauera, Parvibaculum, and Saccharomonospora, while nitrifiers were depleted. Ding et al. observed a similar result when studying microbial community changes in a long-term organic greenhouse farming, where the relative abundances of ammonia oxidizing microorganisms and anaerobic ammonium oxidation bacteria decreased in the organic soil. Furthermore, an increase in methylotrophic bacteria, for instance, those belonging to families Methylophilaceae and Methylococcaceae , as well as the archaea Methanosarcina, was observed, likely associated with their capability to metabolize methane and its derivative compounds that accumulated after the decomposition of the introduced organic matter in organic farming. Taxa belonging to Myxoccocales, Alteromonodaceae, and various Rhizobiales OTUs, known to contribute to general nutrient cycling , were also more abundant in organic soils, similar to previous reports. Members of Ignavibacteria order, suggested to be involved in the degradation of organic matter, were higher in the soil under the organic farming, similar to the results observed in longer-term field and greenhouse studies. However, other groups known to be capable of degrading various complex organic materials coming from manure or compost, such as several genera within Firmicutes phyla, did not respond in that direction. While it could be speculated that they might need recurrent organic amendments to respond, a 12-year greenhouse study suggested that Firmicutes were the least affected phyla by farming system. Interestingly, previous studies report that organic farming systems tend to increase the abundance of microbial taxa associated with plant health promotion. Several members of Firmicutes and Actinobacteria have been associated with disease suppression and have been reported to be augmented in organic farming. However, this was not the case in this study after a one-time manure application, where, for instance, higher abundances of Bacillus, Nocardia, Mycobacterium, and Rhodococcus were observed in the conventional soils. Besides, the plant growth-promoting Myxococcales was ~3.5 times more abundant in organic compared with conventional soils. They are considered to be micropredators that can produce secondary metabolites with antibacterial and anti-fungal activities, killing other microorganisms, and as such, have been suggested to likely play a key role as potential disease-suppressing bacteria in organic farming soils. Interestingly, Myxococcales, unlike the mentioned Firmicutes and Actinobacteria members, have been consistently found to be enriched in organic soils in both short- and long-term experiments, thus suggesting a rapid and lasting response of this bacteria to the organic amendment. Thus, these organisms’ population distribution and functional genes deserve further investigation.