A total of 38,481 Operational taxonomic units (OTUs) were identified and assigned to 27 phyla, 71 classes, 178 orders, 382 families, and 955 genera. The rarefaction plot lines showed the trend of the behavior of the curves, indicating that they tended to level off where the slope approached zero (Figure S1).
Diversity was determined via Shannon and Observed features indices, showing changes related to soil depth where the high values of both indices were found in samples near the surface.
In the ANOVA test, significant difference was found for Shannon and Observed features indexes with respect to the depth level but not at type of tree. Subsequently, with the post hoc Tukey's Honest Significant Difference (HSD) test, significant differences were found (p < 0.05) for the combinations of cherimoya 3 cm vs 30 cm in Shannon diversity index (Fig. 1a). Regarding the results of the Observed features test, a significant difference was found for the combinations of lucuma samples at a depth of 3 cm vs 30 cm (Fig. 1b).
Taxonomic Distribution in Bacterial Communities
Across all the samples, the relative abundance of bacteria phyla Proteobacteria, Acidobacteria, Planctomycetes, Actinobacteria, Firmicutes, and Gemmatimonadetes was 32, 21, 13, 11, 8 and 7%, respectively. The phyla with an abundance of less than 1% were Armatimonadetes, Candidatus Tectomicrobiota, Cyanobacteria, Deinococcus-Thermus, Fibrobacteres, and Verrucomicrobia. We evaluated 15 phyla and the 20 most abundant families and genera by each tree species. ANOVA and Tukey HSD statistical tests were performed to determine the significantly different samples (Fig. 3a).
In the case of lucuma, we found Proteobacteria, Acidobacteria, Plantomycetes, Actinobacteria, and Firmicutes as the most abundant phyla (Fig. 3b). The ANOVA test indicated that the abundance of the phylum Acidobacteria is high at a depth of 3 cm and decreases as depth increases; while the phylum Actinobacteria and Planctomycetes increase in abundance at 30 cm depth. The most common families evaluated were: Alcaligenaceae, Bacillaceae, Gemmataceae, Gemmatimonadacea, Nitrospiraceae, and Pyrinomonadaceae, but significant differences were found for the following four taxonomic categories: (i) Thermoanaerobaculaceae is the most abundant in shallow soils from 3 to 12 cm, while (ii) Burkholderiales, (iii) Hyphomicrobiaceae and (iv) Pirellulaceae are the most abundant in deep soils. The most abundant genera were Derxia, Bacillus, Gemmata, Gemmatimonas, and Nitrospira. However, Pirellula and Thiobacter were significantly more abundant at a depth of 30 cm, while Thermoanaerobaculum had a predilection for growing in shallow areas (Table S1). For cherimoya, significant differences were observed in near-surface soils. We observed that in soils 3 cm deep there was a higher abundance of Armatimonadetes and the genus Holophaga (Table S2).
Soil Physicochemical Parameters Related to Diversity
Between lucuma and cherimoya trees, significant differences were found in the parameters such as total nitrogen, available potassium, potassium exchangeable cation, calcium exchangeable cation, CEC, available Pphosphorus, B, Al, V, Cr, Cu, Zn, As, Mo, Ag, Cd, Sb, Ba, Pb, Na, Mg, K content (Table S4).
The pH was neutral to basic, the lucuma soil was saline for the three depths; although, for the cherimoya soil, up to the first 3 cm it was saline, and for the other two depths slightly saline. The P content was high for all three depths for both tree soils. The K content was medium for the lucuma soil at the depths of 3 and 12 cm, and low for the 30 cm depth, however, for the cherimoya soil it was high for 3 and 12 cm depths, and medium for 30 cm. The organic matter content was very low at all three depths for both tree soils, therefore, low amounts of carbon and nitrogen were found. The CEC was high for the lucuma soil at all depths for cherimoya soil at the depth of 3 cm, and medium for depths of 12 and 30 cm.
In the lucuma rhizospheric soil, only differences in calcium exchangeable cation were found. No differences were found in the contents of important parameters like total carbon, organic carbon, and total nitrogen content (Table S3). Pearson's correlation analysis on lucuma showed that alpha diversity indices were significantly correlated with some of the soil physicochemical properties (Fig. 4). The indexes of chao1, Se.ACE, and Shannon index were negatively correlated with several metals such as Ni, K, Al, Co, Fe, Na, Hg, Mg, Ba, Ti, Mn, Zn, and Be and with sodium exchangeable cation, total organic carbon and total carbon (Fig. 4a). The content of metals such as B, Zn, As, and Pb is above the maximum allowable limit according to Canadian Environmental Quality Guidelines (CEQGs). In the case of copper and cadmium, this was only higher in the cherimoya soil (Table S4).
On the other hand, in the cherimoya soil, significant differences were found in the total carbon, organic carbon, and available potassium contents, between at 3 cm content and that found at 12 and 30 cm. Besides, significant differences were found in potassium exchangeable cation, calcium exchangeable cation, and CEC between the content at 3 cm and that found at 30 cm. However, the total nitrogen content did not vary between the evaluated depths (Table S3). In the rhizospheric soil of the cherimoya crop, notable distinctions were noted. A negative correlation emerged between the total organic carbon (TOC) content and the SE.ACE functional diversity index, whereas a positive correlation was evident between TOC and the Shannon and Inverse Simpson diversity indices. Conversely, a positive correlation was established between the total carbon (TC) content and the Shannon diversity index. Additionally, there was a negative correlation between Ka and SE.ACE. Moreover, the Inverse Simpson index displayed a positive correlation with Ti and a negative correlation with Ni (Fig. 4a). On the other hand, on lucuma soil, total carbon (TC) demonstrated negative correlations with diversity indices, Observed, Chao1, ACE, and Fisher. Additionally, total organic carbon (TOC) exhibited negative correlations with Observed, Shannon, and Fisher indices. Total nitrogen (TN) showed a positive correlation with Simpson index. Furthermore, phosphorus (Pa) displayed positive correlations with Simpson and Inverse Simpson indices. Beryllium (Be) exhibited negative correlations with Chao1, ACE, and Shannon indices. Moreover, Chao1 index showed negative correlations with Mg2, K, Na, Ba, Ni, Ti, and Zn. Shannon index displayed negative correlations with Ba, Cd, Cr, Cu, Pb, and Zn (Fig. 4b).
LEfSe Analysis
The LEfSeapproach was employed to detect microorganisms that might display varying correlations concerning soil depth. In lucuma soil, at 3 cm of depth exhibited a greater abundance of significant bacterial taxa compared to 30 cm level of depth soil type. It was contrasting with the cherimoya soils. In cherimoya, in 3 cm of depth soil, LEfSe identified a bacteria enrichment of 2 phyla, 3 classes, 5 orders, 5 families, 8 genera, and 17 species, on the other hand, in 30 cm of depth soil 1 phylum, 1 class, 2 orders, 3 families, 6 genera, and 8 species were identified (Fig. 5a). In lucuma, in 3 cm of depth soil (log2 fold change > 0), LEfSe identified a bacteria enrichment of 2 phyla, 2 classes, 5 orders, 10 families, 11 genera, and 10 species. On the other hand, in 30 cm of depth soil (log2 fold change < 0) 1 phylum, 1 class, 3 orders, 4 families, 6 genera, and 7 species were identified (Fig. 5b).