The number of reads, GC content, and total OTUs
The operational taxonomic units (OTU), generated from sequencing the V3–V4 region of the 16S rRNA gene, represented the individual microbial count and thus was a direct measure of the microbial richness. In general, the OTU was in the range of 10,000–20,000 in soil A produce, while soil B produce had much lesser OTU, in the range 800–10,000. Overall, the produce grown in soil A with cow dung manure had the highest number of reads, OTU, highest GC content of 55%, and had the highest library size indicating greatest microbial richness, followed by the leaf waste compost produce, which was at the second high level with respect to both the OTU number and the library size. Comparing the total OTUs of the conventional produce in both soils, it was observed that the total OTU of soil A fertilizer produce was much higher than the soil B fertilizer produce. The OTUs in both soils increase on addition of organic waste composts (Table 1).
Table 1 The number of reads, GC content, and the total number of OTUs (operational taxonomic units): this table shows the increment in the OTU among the compost produce compared to the fertilizer produce Microbiome diversity
Alpha and beta diversity
All samples were rarefied to even the sequencing depth based on the sample having lowest sequencing depth, and the analysis was visualized with the filtered data source. The alpha diversity was measured using four metrics, Chao1, Shannon, Simpson, and Fisher, with the statistical method of T-test/ANOVA. The Chao 1 index and Fisher index represents the species richness considering the species diversity. In contrast, Shannon and Simpson represent species richness and the evenness with which a species is distributed in a population. Simpson index gives more weightage to the species richness. The Chao 1 index computed for identifying the alpha diversity showed that the cow dung manure produces from both the soil types had the highest alpha diversity (soil A, Chao 1 index = 70; Shannon index = 2.71; Simpson index = 0.87; Fisher index = 13.3; soil B, Chao 1 index = 70.5; Shannon index = 2.90; Simpson index = 0.90; Fisher index = 15.6), while the municipal waste compost produce in soil A had the least alpha diversity and the most uneven species distribution (Chao 1 index = 39; Shannon index = 1.99; Simpson index = 0.75; Fisher index = 6.6). The p-value in Chao1, Shannon, Simpson, and Fisher alpha diversity index was measured to be 0.45803, 0.20568, 0.12833, and 0.81583 with the ANOVA F-value of − 0.78777, − 1.4653, − 1.732, and − 2.2041 (Fig. 1).
The rarefaction curve of both the soil produces showed that the species richness followed the same order in both soils A and B. The cow dung manure and the fertilizer produce had the highest species richness. In contrast, the soil A produces with municipal and vermicompost had relatively lower species richness than the conventional produces. Similarly, in the case of the produces from soil B, cow dung manure produce and fertilizer produce had the highest species richness followed by the NDRL and NKRL (Fig. 2a).
The beta diversity measured the species richness between two communities and was constructed at the taxonomic level of genus with the Bray–Curtis index distance method based on permutational MANOVA (PERMANOVA) statistical method with p < 0.127 and f-value of 1.7128. It was observed that YDR, YMR, YCR, NDRL1, and NKRL, the group of urban organic waste compost produces, clustered together. Also, the samples, viz., NCRL0 and YVR, were placed very close to this cluster group. While the conventional produce, YFR and NFR, of both the soils was placed distant from this cluster group. The dendrogram prepared on the Bray–Curtis index with the Ward clustering algorithm showed that the groups YDR and YMR were closely related but substantially different from the other groups, YCR, YFR, and YVR. Similarly, the groups NFRL1 and NCRL0 were closely related but substantially different from the other groups, NDRL and NKRL. NDRL was different from the other groups like the NFRL1 and NCRL0 but substantially close to other groups, YDR, YMR, NKRL, and YCR (Fig. 2b, c).
Taxonomic classification and identification of beneficial and pathogenic microbes
Phylum level
In total, 42 phyla were reported across all the produces. The top 10 phyla, which were found to cover almost 99.5–99.9% of the total identified phyla are presented in Figs. 3 and 4. Among all the produce, the common phyla that constitute maximum percentage of the top ten phyla included Proteobacteria, Firmicutes, Actinobacteria, Cyanobacteria, and Bacteroidetes. Proteobacteria formed the maximum abundance in leaf waste compost produce from soil A and followed by vermicompost produce. It was found to be lowest in the fertilizer produce of soil B. Firmicutes had the maximum abundance in fertilizer produce from soil A but the fertilizer produces from soil B had the lowest proportion. Actinobacteria was the major abundant phyla in cow dung manure produce grown in soil A. It was lowest in proportion in the fertilizer produce of soil B. Cyanobacteria was the most abundant phyla in cow dung manure produce grown in soil B. Its lowest proportion was observed in the municipal waste compost produce in soil A. Bacteroidetes was the major abundant phyla in the municipal waste compost produce grown in soil A, but the leaf waste compost produces from soil A had the lowest proportion. Few phyla like the Euryarchaeota, Acidobacteria, Planctomycetes, Verrucomicrobia, and Chloroflexi were present exclusively in abundance in cow dung manure produce of soil A. Tenericutes phyla were abundant in leaf waste compost produce grown in soil A. Fusobacteria and Thermi were the least abundant phyla (Figs. 3 and 4).
Genus’ level
At the genus level, 156 genera were detected, with only a tiny fraction (28 genera) constituting the core microbiome. The core microbiome refers to the set of taxa detected in a high fraction of the population above a given abundance threshold. The count data is transformed to the compositional (relative) abundance to perform such analysis. At a detection threshold of 0.010, the relative abundant genera that constituted the core microbiome included the Shingobacterium, Pseudomonas, Achromobacter, and Paenibacillus with a prevalence of 0.6–1.0 at the lowest detection threshold of 0.010–0.125. The genera such as Bacillus, Olivibacter, Haloferax, Prevotella, Streptomyces, Cellvibrio, Alkaliphilus, and Staphylococcus formed the second abundant group of genera with the prevalence of 0.4 detected at 0.010–0.082 of detection threshold. The genera Acinetobacter, Stenotrophomonas, Chryseobacterium, Coprococcus, Saccharopoluspora, Pediococcus, Coreynebacterium, Streptococcus, Rothia, Lactobacillus, Devosia, Cupriavidus, Sporosarcina, Planomicrobium, Arthrobacter, and Nocardioides were present at the lowest prevalence of 0.0–0.2 at detection threshold of 0.010–0.440. The data was visualized with a sample prevalence of 20% and a relative abundance of 0.1% (Supplementary Fig. S1).
The heat map (Supplementary Fig. S2) was constructed at genus taxonomic level with the detailed view mode of < 1500 features. The samples are clustered using the Ward cluster algorithm based on the Euclidean distance measure. The heat map displayed the generic diversity among different produces, such as the YFR had a unique genera representation that included Corynebacterium, Salmonella, Brachybacterium, and Sporosarcina. The genera like Clostridium, Brevundimonas, and Ochrobactrum were exclusive to the YDR. The YMR had Lysobacter, Lysinibacillus, Flavobacterium, Sphingobacterrium, and Paracoccus as unique genera. Arthrobacter, Enterobacter, Acinetobacter, and Bacillus were unique to the YVR. The genera like Saccharopolyspora, Truepera, Balneimonas, Prauserella, Gemmata, Luteimonas, Mycobacterium, Nitrospira, Alicyclobacillus, Flavisolibacter, Saccharomonospora, and Brevibacillus were exclusive to the YCR. The Halococcus, Leptotrichia, Streptococcus, Lactobacillus, Neisseria, Leuconostoc, Saccharothrix, Bifidobacterium, Rothia, Georgenia, Rhodococcus, Prevotella, Exeguobacterium, Dialister, Gluconobacter, Catenibacterium, Prevotella-1, Bacteroides, Haloferax, Pediococcus, Acetobacter, Actinomyces, Streptomyces, Fusobacterium, and Haloarcula were unique to the NFRL1. The genera like the Kocuria, Steotrophomonas, Coprococcus, Novispirillum, Azospirillum, Cupriavidus, and Olivibacter were unique to the NDR. The Plantomyces, Chryseobactrium, Amycolatopsis, Faecalibacterium, Nocardia, Halogeometricum, and Nocardiodes were exclusively present in the NKRL.
Out of the 156 identified genera, the top 20 genera that covered 76.5–99.9% of the total identified genera were presented in Figs. 5 and 6. Among all the produce, beneficial genera like the Sphingobacterium, Pseudomonas, Achromobacter, Paenibacillus, and Bacillus were common and constituted the maximum percentage abundance of the top 10 genera. Sphingobacterium constituted the maximum abundance in YDR and YMR, while the fertilizer produce of soil B had the lowest proportion of these genera. Pseudomonas was the major abundant genera in YCR and NKRL, whereas NFRL1 had its lowest proportion. Achromobacter was the major abundant genera in YCR and NKR, whereas NFRL1 had its lowest proportion. Paenibacillus constituted the maximum abundance in YDR and YMR, whereas NFRL1 had its lowest proportion. Bacillus constituted the maximum abundance in YDR and YMR, whereas NFRL1 had its lowest proportion. Thus, it was seen that the conventional produce had least amount of these beneficial genera (Table 2). The pathogenic genera like Corynebacterium, Acinetobacter, Cellvibrio, Chryseobacterium, Enterobacter, Streptococcus, and Streptomyces were comparatively abundant in YFR, YVR, YFR, NCRL0, YVR, YCR, and YCR respectively (Table 3).
Table 2 Beneficial bacterial genus identified in all produces with its corresponding OTUs: this table shows the top ten identified beneficial genera Table 3 Pathogenic genera present in all organic produces with its corresponding OTUs: this table shows the abundant identified pathogenic genera Species level
The detection resolution was low at the species level and only 108 species were detected. The top 10 abundant species covered 92.5–99.8% of the detected species (Supplementary Figs. S3 and S4). The species like the hirsuta, copri, and clausii constituted the major proportion of the beneficial species present in most of the produces. The hirsuta spp. was detected to be abundance in the YCR, while it was completely absent in the NFRL1, NDRL, and NKRL. The copri spp. was abundant in the YFR while absent in the YCR. The clausii spp. was found abundant in NKRL, whereas absent in the YMR. Interestingly some species, viz., stercorea, sphaeroids, and transvalensis, were common among the soil B compost produces, while they were generally absent in the soil A produces and in the soil B fertilizer produce. Few halotolerant species like the oncorhynchi and rugosa were present in soil A produce while absent in soil B produce.
The pathogenic species that were commonly abundant included stutzeri, mizutaii, and multivorum. The stutzeri spp. was found to have major proportion in the YDR, whereas the least abundance in the NCRL0. The mizutaii spp. was abundant in YMR, whereas least abundant in YCR. The multivorum spp. was abundant in NDRL, whereas least abundant was in the YFR.
Bacterial genera comparison
The microbiome detected at the genus level was analyzed and compared. Based on this assorted data, a Venn diagram which clearly showed that the produce of two different soil types had less bacterial genera that are unique to them, such as soil A produces had only 13.9% unique genera, whereas soil B had only 19.8% unique genera. About 43.1% of the bacterial genera were common across all the produces (Supplementary Fig. S5; Supplementary Table S1).
Analyzing the abundance of beneficial and pathogenic genera present across all the produces, it was observed that the YDR had comparatively maximum beneficial microbial genera. In contrast the NFR had the lowest beneficial microbial genera. The NCR was observed to have relatively maximum pathogenic microbial genera, whereas the YDR had the lowest pathogenic microbial genera. The ratio of the beneficial to the pathogenic genera was in the order YDR > NDRL > NKRL > YMR > YCR > YFR > YVR > NFRL1 > NCRL0 (Table 4).
Table 4 Comparative analysis of beneficial and pathogenic genera OTU: this table presents the percentage and ratio of beneficial to pathogenic genera in different organic and fertilizer produceYFR, soil A fertilizer produce; YDR, soil A leaf waste compost produce; YMR, soil A municipal waste compost produce; YCR, soil A cow dung manure produce; YVR, soil A vermicompost produce; NFRL1, soil B fertilizer produce; NDRL, soil B leaf waste compost produce; NCRL0, soil B cow dung compost; NKRL, soil B kitchen waste compost produce