The OTU table gives an overall microbial community present in the given samples. From the generated OTU, the stacked bar charts are pivoted based on taxonomic levels from Phylum to Species. More than 30 phyla, 70 classes, 170 orders, 190 families, 240 genera of bacteria were identified across all the samples.
3.3.1. At the phylum level
About Twenty-one phyla were identified across all the samples (Supplementary Fig. S1). The most abundant ten phyla cover about 97 to 98% of all the phyla identified (Supplementary Fig. S2 and S3). These phyla were further classified into more than Classes, Orders, Families, Genera, and Species (Supplementary Fig. S4, S5, S6, S7, and S8). The most abundant bacterial phyla identified across all the soil samples were Proteobacteria, Planctomycetes, Actinobacteria, Firmicutes, Chloroflexi, Acidobacteria, Bacteroidetes, Verrucomicrobia, Gemmatimonadetes, Armatimonadetes, Cyanobacteria, Euryarchaeota, Nitrospirae, and Chlamydiae (Table 4).). The counts of Proteobacteria showed a reduction in the post-harvest soils compared to pre-plantation soils, except in the leaf waste compost amended soil, where there was an increase of 98.30% (YD = 23532; YDRAH = 46664). The maximum reduction was seen in the vermicompost amended soil, about 66.87% (YV = 30021; YVRAH = 9946), followed by fertiliser-amended soil in which there was a reduction of approximately 49.34% (YF = 81283; YFRAH = 47197). Proteobacteria counts were seen highest in the fertilizer amended soils sample in both pre-plantation and post-harvest of the river bank soil. While its count was highest in the kitchen waste compost amended post-harvest soil among the residential soil samples.
Table 4
Bacterial Phyla identified in different soil samples.
Phylum | Pre-plantation soils with OTUsPost-harvest soils with OTUs |
| YC | YD | YK | YM | YV | YF | YCR AH | YDR AH | YKR AH | YMR AH | YVR AH | YFR AH | NCR AH | NDR AH | NKR AH | NFR AH |
Proteobacteria | 17403 | 23532 | 45575 | 57753 | 30021 | 81283 | 13684 | 46664 | 41494 | 30138 | 9946 | 47197 | 32289 | 30254 | 53374 | 44137 |
Planctomycetes | 6594 | 10578 | 6847 | 22498 | 14486 | 40131 | 8924 | 29308 | 21839 | 19215 | 8423 | 27764 | 11065 | 7779 | 11093 | 12821 |
Actinobacteria | 2611 | 3335 | 6736 | 10980 | 4899 | 18452 | 3343 | 10878 | 10580 | 7538 | 2881 | 12448 | 9355 | 8916 | 12758 | 13700 |
Firmicutes | 9680 | 5363 | 12733 | 13258 | 6278 | 37115 | 4644 | 6546 | 18054 | 6025 | 3239 | 7337 | 1086 | 1178 | 3344 | 939 |
Chloroflexi | 23657 | 11493 | 15112 | 36788 | 17529 | 55091 | 10729 | 16782 | 13700 | 14137 | 4361 | 18677 | 10665 | 6764 | 13415 | 9568 |
Acidobacteria | 2611 | 3335 | 6736 | 10980 | 4899 | 18452 | 3343 | 10878 | 10580 | 7538 | 2881 | 12448 | 9355 | 8916 | 12758 | 13700 |
Bacteroidetes | 8044 | 5106 | 16476 | 21780 | 10242 | 20104 | 3013 | 7846 | 7375 | 5141 | 1288 | 9725 | 15190 | 15305 | 21034 | 20170 |
Verrucomicrobia | 638 | 1189 | 1224 | 2364 | 1800 | 5121 | 1293 | 4074 | 3912 | 2651 | 737 | 5303 | 3892 | 4316 | 7368 | 6008 |
Gemmatimonadetes | 83 | 188 | 254 | 365 | 266 | 952 | 277 | 1069 | 509 | 587 | 149 | 1358 | 424 | 171 | 972 | 332 |
Armatimonadetes | 63 | 84 | 249 | 326 | 206 | 585 | 85 | 337 | 327 | 202 | 56 | 541 | 278 | 525 | 638 | 854 |
Cyanobacteria | 576 | 892 | 508 | 1117 | 1755 | 9142 | 101 | 288 | 433 | 259 | 87 | 480 | 365 | 411 | 641 | 514 |
Euryarchaeota | 931 | 473 | 442 | 1771 | 1353 | 2755 | 184 | 133 | 127 | 101 | 36 | 184 | 369 | 337 | 369 | 429 |
[Thermi] | 341 | 439 | 649 | 4310 | 296 | 1198 | 107 | 71 | 273 | 269 | 30 | 112 | 243 | 119 | 207 | 121 |
Nitrospirae | 212 | 273 | 398 | 980 | 491 | 2627 | 235 | 810 | 642 | 442 | 283 | 1114 | 338 | 217 | 361 | 412 |
Chlamydiae | 200 | 296 | 342 | 546 | 416 | 1613 | 377 | 1186 | 989 | 862 | 161 | 1672 | 64 | 88 | 89 | 154 |
Total OTU | 73644 | 66576 | 114281 | 185816 | 94937 | 294621 | 50339 | 136870 | 130834 | 95105 | 34558 | 146360 | 94978 | 85296 | 138421 | 123859 |
This table shows the bacterial Phyla identified in the pre-plantation and post-harvest soil samples amended with different bio-compost. The level of bacterial phyla varied depending on the types of bio-compost used for soil amendment. There was a reduction of the bacterial phyla in the post-harvest soil samples, except in the leaf waste compost amended soil, where there was a significant increase in the bacterial phyla. |
Planctomycetes increased in the post-harvest soils amended with cow dung manure, leaf waste compost, and kitchen waste compost. At the same time, there was a decrease in its counts in the municipal organic waste compost, vermicompost, and fertilisers amended post-harvest soils as compared to pre-plantation soils. The highest increase of about 218% was observed in the kitchen waste compost amended soil, followed by the leaf waste compost amended soil, with a 177% increase in the post-harvest soil. The fertiliser-amended soil (YF) had the highest counts of Planctomycetes among the pre-plantation soil samples. At the same time, the leaf waste compost amended soil sample (YDRAH) had the highest counts of this phylum in the post-harvest soil samples.
Actinobacteria counts were increased in the post-harvest soil samples amended with cow dung manure, leaf waste compost, and kitchen waste compost. In contrast, there was a decrease in its counts in the soils amended with municipal organic waste compost, vermicompost, and fertilisers. The highest increase of Actinobacteria was seen in the leaf waste compost amended post-harvest soil with an increase of about 226% and in kitchen waste compost amended soil of about 57%. In comparison, the maximum decrease of about 41% was seen in the vermicompost amended soil, followed by the fertiliser-amended soil with a reduction of about 32%. Generally, the fertiliser-amended soil samples had the highest counts of Actinobacteria among all the soil samples. The fertiliser-amended soil (YF) had the highest count of Firmicutes in the pre-plantation soil samples, but its count was drastically reduced in the post-harvest soil sample, with a decrease of about 80%. The decline was also seen in the soil amended with vermicompost, municipal organic waste compost, and cow dung manure. But there was an increase in the Firmicutes counts in the post-harvest soil samples amended with leaf and kitchen waste compost. The kitchen waste compost-amended soil sample had the highest count of Firmicutes amongst all the post-harvest soil samples.
Chloroflexi and Bacteroidetes counts were increased in the post-harvest soil sample amended with leaf waste compost. Whereas there was a decrease in the fertiliser and other bio-composts amended post-harvest soil samples. The bacterial Phyla, such as Acidobacteria, Armatimonadetes, and Nitrospirae, were observed with increased counts in the post-harvest soil samples. These Phyla were reduced in the post-harvest soils amended with chemical fertilisers, municipal organic waste compost, and vermicompost. Gemmatimonadetes were relatively increased in all the post-harvest soil samples compared to pre-plantation soil samples. The other bacterial phyla, such as Cyanobacteria, Euryarchaeota, and Thermi, were also reduced in all the post-harvest soils. Generally, the beneficial phyla increased in the post-harvest soils, which were amended with leaf waste compost and kitchen waste compos. In contrast, there was a reduction in these phyla in the soils amended with chemical fertilisers, cow dung manure, municipal organic waste compost, and vermicompost. The most significant decrease was in the soil amended with vermicompost and chemical fertilisers, about 63% and 50%, respectively. Chlamydiae, which is a pathogenic bacterial phylum, was seen to increase in all the post-harvest soil samples. The highest counts were seen in the chemical fertiliser-amended soil, both in the pre-plantation and post-harvest soil samples.
3.3.2. At the genus and species level
The bacterial genera identified varied across the samples of pre-plantation and post-harvest soils, amended with chemical fertiliser and different types of bio-composts. About 30 bacterial genera constitute the core microbiome, detected above a threshold level across the samples. The levels of these core microbiome varied in different soil samples depending on the types of composts used as soil amendment (Fig. 6). In general, the significant beneficial genera seen across the soils samples with different proportions were Achromobacter, Agromyces, Bacillus, Clostridium, Nitrospira, Planctomyces, Pseudomonas, Steroidobacter, Streptomyces, Alicyclobacillus, Bdellovibrio, and others (Table 5; Fig. 7; and Supplementary Fig. S9). Achromobacter counts were found to be highest in the leaf waste compost amended soils, both in the pre-plantation and post-harvest samples. However, the counts were reduced in all the post-harvest soil samples except in the fertiliser-amended soil, where the count was slightly increased.
Table 5
Beneficial bacterial genera identified in different soil samples.
Bacterial Genera | Pre-plantation soil samples with OTUs | Post-harvest soil samples with OTUs |
| YC | YD | YK | YM | YV | YF | YCR AH | YDR AH | YKR AH | YMR AH | YVR AH | YFR AH | NCR AH | NDR AH | NKR AH | NFR AH |
Achromobacter | 69 | 238 | 19 | 25 | 46 | 38 | 36 | 140 | 7 | 17 | 13 | 48 | 55 | 13 | 27 | 70 |
Actinomadura | 34 | 1 | 670 | 426 | 9 | 3 | 27 | 9 | 259 | 73 | 27 | 2 | 11 | 16 | 740 | 6 |
Agromyces | 203 | 441 | 358 | 470 | 267 | 1056 | 74 | 348 | 208 | 148 | 90 | 331 | 21 | 23 | 4 | 10 |
Alcanivorax | 7 | 8 | 740 | 229 | 36 | 10 | 1 | 3 | 18 | 1 | 1 | 0 | 0 | 1 | 0 | 0 |
Brevibacterium | 566 | 18 | 3330 | 339 | 8 | 75 | 0 | 0 | 3 | 1 | 1 | 1 | 0 | 0 | 1 | 1 |
Bacillus | 261 | 69 | 554 | 514 | 80 | 658 | 417 | 137 | 1052 | 430 | 58 | 78 | 40 | 34 | 276 | 38 |
Clostridium | 20 | 22 | 19 | 59 | 25 | 63 | 128 | 53 | 114 | 43 | 32 | 40 | 1 | 2 | 25 | 2 |
Myxococcus | 114 | 300 | 510 | 1196 | 226 | 692 | 74 | 573 | 353 | 428 | 75 | 384 | 53 | 65 | 42 | 254 |
Halomonas | 2223 | 2 | 2038 | 63 | 13 | 2 | 0 | 0 | 1 | 0 | 1 | 0 | 1 | 2 | 6 | 2 |
Kaistobacter | 134 | 151 | 516 | 367 | 102 | 921 | 68 | 168 | 208 | 140 | 163 | 414 | 693 | 1026 | 1225 | 1479 |
Methanobacterium | 43 | 186 | 98 | 354 | 51 | 890 | 4 | 23 | 29 | 16 | 1 | 29 | 2 | 0 | 0 | 0 |
Methanosarcina | 632 | 1 | 12 | 90 | 67 | 35 | 90 | 1 | 4 | 3 | 5 | 0 | 14 | 0 | 9 | 2 |
Microbulbifer | 73 | 1 | 678 | 9 | 2 | 14 | 9 | 0 | 1008 | 4 | 2 | 1 | 10 | 7 | 33 | 2 |
Nitrospira | 156 | 254 | 346 | 831 | 349 | 1976 | 214 | 770 | 618 | 412 | 226 | 970 | 286 | 197 | 336 | 363 |
Planctomyces | 1144 | 1395 | 1221 | 4689 | 2407 | 5981 | 1208 | 3609 | 2779 | 2631 | 1323 | 3325 | 1492 | 856 | 1338 | 1356 |
Pseudomonas | 120 | 116 | 524 | 234 | 259 | 541 | 73 | 33 | 57 | 27 | 29 | 290 | 24 | 21 | 41 | 62 |
Rhodoplanes | 136 | 202 | 333 | 553 | 186 | 675 | 123 | 510 | 485 | 322 | 125 | 485 | 203 | 153 | 263 | 275 |
Sphingobacterium | 31 | 44 | 1162 | 83 | 56 | 183 | 0 | 0 | 4 | 1 | 1 | 8 | 11 | 6 | 7 | 11 |
Streptomyces | 2005 | 292 | 467 | 5423 | 245 | 2236 | 15 | 39 | 114 | 37 | 8 | 24 | 42 | 43 | 36 | 36 |
Steroidobacter | 276 | 292 | 416 | 883 | 327 | 670 | 343 | 1894 | 1559 | 1090 | 263 | 1000 | 1927 | 1025 | 2802 | 1275 |
Lactobacillus | 20 | 16 | 94 | 16 | 132 | 59 | 20 | 21 | 70 | 27 | 11 | 26 | 37 | 82 | 67 | 76 |
Xiphinematobacter | 46 | 220 | 21 | 107 | 42 | 231 | 72 | 242 | 427 | 133 | 29 | 347 | 18 | 126 | 187 | 88 |
Alicyclobacillus | 100 | 416 | 611 | 867 | 528 | 1811 | 161 | 824 | 532 | 356 | 130 | 1095 | 2 | 3 | 1 | 7 |
Truepera | 116 | 227 | 43 | 123 | 30 | 354 | 10 | 50 | 27 | 34 | 14 | 69 | 2 | 5 | 3 | 4 |
Gemmata | 206 | 438 | 347 | 1107 | 543 | 2334 | 790 | 2680 | 1498 | 2175 | 781 | 2687 | 334 | 287 | 471 | 506 |
Beneficial OTU | 9301 | 5368 | 18457 | 19396 | 6044 | 21583 | 3957 | 12127 | 11437 | 8550 | 3410 | 11655 | 5279 | 3993 | 7941 | 5926 |
Total OTU | 15220 | 12272 | 31931 | 42295 | 18333 | 49024 | 7928 | 23066 | 24704 | 19800 | 6352 | 24131 | 15722 | 14134 | 23460 | 21711 |
Percentage | 61% | 44% | 58% | 46% | 33% | 34% | 50% | 53% | 46% | 43% | 54% | 48% | 34% | 28% | 34% | 27% |
This table shows the beneficial genera identified in the soil samples amended with different bio-compost. The level of each bacterial genera varied depending on the types of bio-composts used as soil amendments. Generally, there was a reduction in the level of the beneficial bacteria in the post-harvest soil samples, except in the leaf waste compost amended soil, where there was an increase in the beneficial genera. |
Agromyces level was highest in the fertiliser-amended soil among the pre-plantation soil sample. Still, leaf waste compost amended soil became highest in its count in the post-harvest soil samples. There was a reduction in Agromyces counts in the post-harvest soil samples. The most significant decrease was seen in the fertiliser-amended soil at about 68%. While the leaf waste compost-amended soil saw the least reduction in Agromyces, about 21%. Bacillus count was highest in the fertiliser-amended soil (YF = 658) among the pre-plantation soil samples, but its count was reduced drastically, about 88%, in the post-harvest sample (YFRAH = 80).
The Bacillus levels were increased in the post-harvest soil samples amended with cow dung manure, leaf waste compost, and kitchen waste compost. The greatest increment of about 98% was seen in the leaf waste compost amended soil sample in the post-harvest soil samples. Among the post-harvest soil samples, the kitchen waste compost amended soil sample had the highest level of Bacillus in both the river bank soil and residential soil. Clostridium was detected with relatively lower counts in the pre-plantation soil samples, but its level was increased in the post-harvest soil samples. The Clostridium level was highest in the cow dung manure and kitchen waste compost-amended post-harvest soils. Nitrospira was identified with the highest count in fertiliser-amended soil, followed by municipal organic waste compost-amended soil among the pre-plantation soil samples. Though, its count was reduced to half in the post-harvest soil samples. While there was an increase in the Nitrospira counts in the post-harvest soil samples amended with cow dung manure, leaf waste compost, and kitchen waste compost. The count of Nitrospira was relatively higher in the fertiliser, cow dung manure and leaf waste compost-amended soil samples compared to municipal organic waste compost and vermicompost-amended soil samples amongst the post-harvest soil. Planctomyces counts were relatively high in all the soil samples. The highest counts were seen in the fertiliser and municipal organic waste compost-amended soil in the pre-plantation soil samples. Nonetheless, its count was reduced to almost half in the post-harvest soil samples. At the same time, there was an increase in the counts of Planctomyces in the post-harvest soils amended with cow dung manure, leaf waste compost, and kitchen waste compost. The leaf waste compost-amended soil sample had the highest level of Planctomycetes among the post-harvest soil samples. Steroidobacter was identified with relatively higher counts in the post-harvest soil samples than in the pre-plantation soils. The municipal organic waste compost-amended soil had the highest level in the pre-plantation soil samples. While, the Steroidobacter counts became highest in the leaf waste compost and kitchen waste compost-amended soil samples among the post-harvest soil samples.
Pseudomonas was higher in the pre-plantation soil samples than the post-harvest soil samples. In the pre-plantation soil samples, the kitchen waste compost and chemical fertiliser-amended soils had relatively higher counts of Bacillus, but the post-harvest soils had relatively similar levels of this genus, though slightly higher in the chemical fertiliser-amended sample. Streptomyces was observed with a relatively high count in the pre-plantation soils, but its count was reduced drastically in the post-harvest soil samples. The pre-plantation soil samples amended with municipal organic waste compost, chemical fertiliser, and cow dung manure were seen with relatively higher Streptomyces among the pre-plantation soil samples. Alicyclobacillus was seen with relatively higher levels in the pre-plantation soil samples amended with chemical fertiliser, municipal organic waste compost, kitchen waste compost, and vermicompost. But the count of Alicyclobacillus was reduced in the post-harvest soil samples. On the other hand, the soil samples amended with leaf waste compost and cow dung manure showed an increase in Alicyclobacillus in the post-harvest soil samples. Kaistobacter was also observed at a relatively higher level in the pre-plantation soil samples in all the amendments, but its counts were reduced in the post-harvest samples. This genus is the only bacterial genus that was observed to be higher in the residential soil than in the Yamuna floodplain soil samples. Kaistobacter was seen with relatively higher level in the fertilizer-amended soil sample in both the pre-plantation and post-harvest soils.
The other bacterial genera such as Brevibacterium, Halomonas, Methanobacterium, and Sphingobacterium, were observed to be relatively higher in the pre-plantation soil samples of all amendments, but their counts were reduced drastically in the post-harvest soil samples. The counts of such genera were highest in the kitchen waste compost-amended soil samples, except for the Methanobacterium, where the count was higher in the chemical fertiliser-amended soil sample. Microbulbifer was also observed to be relatively high only in the kitchen waste compost-amended soil samples, both in the pre-plantation and post-harvest.
There was a reduction in the overall OTUs of the beneficial genera in all the post-harvest soil samples compared to the pre-plantation soils, except in the leaf waste compost-amended soil. The leaf waste compost amended soil had the lowest beneficial OTU amongst the pre-plantation soils but the highest beneficial OTU among the post-harvest soil samples. There was an increase of about 125% in the OTU of the beneficial genera in the post-harvest soil amended with leaf waste compost. While, a reduction of about 46% was observed in the fertiliser-amended soil. The most significant reduction of the beneficial OTU was seen in the soil sample amended with cow dung manure, which was about a 57% reduction. The vermicompost and cow dung manure amended-soil samples had the lowest counts of beneficial OTUs among the post-harvest soil samples.
The pathogenic genera identified across the samples were Agrobacterium, Flavobacterium, Leptolyngbya, Geobacter, Nocardia, Mycobacterium, and others (Table 6). The pre-plantation soil samples had negligible levels of Agrobacterium, except in the leaf waste compost amended soil. While the counts of Agrobacterium were increased in all the post-harvest soil samples. Flavobacterium counts were higher in the pre-plantation soils than the post-harvest soils in all the samples. The fertiliser-amended soil samples had the highest counts of the Flavobacterium in both the pre-plantation and post-harvest soil samples. Whereas the cow dung-amended soils had the lowest counts of the genus in all the samples. Leptolyngbya was also detected across the samples, but its counts were relatively higher in the pre-plantation soil. The highest count of Leptolyngbya was seen in the fertiliser-amended soil samples, whereas the vermicompost-amended soil samples had the lowest counts in the pre-plantation as well as the post-harvest soil samples.
Table 6
Pathogenic bacterial genera identified in different soil samples.
Bacterial Genera | Pre-plantation soils with OTUs | Post-harvest soils with OTUs |
| YC | YD | YK | YM | YV | YF | YCR AH | YDR AH | YKR AH | YMR AH | YVR AH | YFR AH | NCR AH | NDR AH | NKR AH | NFR AH |
Agrobacterium | 1 | 131 | 5 | 0 | 9 | 3 | 18 | 376 | 6 | 142 | 16 | 24 | 40 | 68 | 31 | 43 |
Flavobacterium | 110 | 224 | 409 | 482 | 683 | 1442 | 35 | 48 | 95 | 37 | 63 | 103 | 78 | 67 | 88 | 195 |
Cupriavidus | 0 | 3 | 1 | 1 | 4 | 4 | 4 | 4 | 1 | 3 | 4 | 18 | 65 | 122 | 43 | 220 |
Prevotella | 6 | 4 | 17 | 10 | 21 | 20 | 0 | 1 | 6 | 6 | 3 | 5 | 9 | 18 | 27 | 20 |
Leptolyngbya | 159 | 157 | 166 | 204 | 127 | 1222 | 7 | 27 | 30 | 19 | 7 | 77 | 1 | 0 | 21 | 0 |
Balneimonas | 26 | 33 | 100 | 113 | 23 | 121 | 25 | 53 | 52 | 69 | 47 | 107 | 125 | 54 | 81 | 113 |
Protochlamydia | 2 | 7 | 24 | 20 | 5 | 57 | 10 | 38 | 52 | 59 | 5 | 75 | 0 | 12 | 3 | 12 |
Saccharothrix | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 7 | 0 | 21 | 405 |
Rhabdochlamydia | 3 | 14 | 18 | 29 | 10 | 42 | 2 | 26 | 10 | 14 | 7 | 30 | 2 | 26 | 7 | 52 |
Phaeospirillum | 20 | 48 | 57 | 136 | 38 | 202 | 55 | 110 | 106 | 80 | 24 | 132 | 83 | 137 | 174 | 266 |
Saprospira | 4 | 1 | 0 | 0 | 6 | 8 | 1 | 18 | 33 | 3 | 3 | 23 | 0 | 0 | 1 | 0 |
Aeromicrobium | 3 | 15 | 20 | 23 | 10 | 21 | 6 | 34 | 31 | 42 | 8 | 85 | 2 | 1 | 1 | 6 |
Legionella | 5 | 7 | 9 | 18 | 6 | 25 | 12 | 20 | 54 | 39 | 8 | 53 | 1 | 2 | 1 | 7 |
Geobacter | 11 | 4 | 29 | 40 | 13 | 146 | 20 | 159 | 99 | 93 | 22 | 248 | 38 | 45 | 225 | 17 |
Nocardia | 28 | 198 | 80 | 191 | 9 | 18 | 7 | 82 | 34 | 25 | 23 | 129 | 9 | 28 | 15 | 5 |
Mycobacterium | 409 | 579 | 1436 | 928 | 286 | 800 | 174 | 634 | 573 | 500 | 137 | 483 | 90 | 158 | 166 | 74 |
C.Solibacter | 63 | 82 | 129 | 295 | 105 | 467 | 88 | 182 | 167 | 149 | 41 | 258 | 217 | 150 | 366 | 213 |
Pathogenic OTU | 850 | 1507 | 2500 | 2490 | 1355 | 4598 | 464 | 1812 | 1349 | 1280 | 421 | 1850 | 767 | 888 | 1271 | 1648 |
Total OTU | 15220 | 12272 | 31931 | 42295 | 18333 | 49024 | 7928 | 23066 | 24704 | 19800 | 6352 | 24131 | 15722 | 14134 | 23460 | 21711 |
Percentage | 6% | 12% | 8% | 6% | 7% | 9% | 6% | 8% | 5% | 6% | 7% | 8% | 5% | 6% | 5% | 8% |
This table shows the pathogenic genera identified in the soil samples amended with different bio-compost. The level of each pathogenic bacterial genera varied depending on the types of bio-composts used as soil amendments. Generally, there was a reduction in the level of the beneficial bacteria in the post-harvest soil samples. |
The other bacterial genera such as Balneimonas, Protochlamydia, Rhabdochlamydia, and Phaeospirillum, were also found to be present across all the samples, but the number of counts varied across the samples. The fertiliser-amended soil samples had the highest level of all these pathogenic genera amongst the pre-plantation as well as the post-harvest soil samples. The level of Balneimonas, Protochlamydia, and Rhabdochlamydia remain almost the same in the post-harvest soils corresponding to the pre-plantation soils. While there was a slight increase in the counts of Phaeospirillum in the post-harvest soils concerning the pre-plantation soils. The vermicompost and cow dung manure-amended soil samples had the lowest counts of these pathogenic genera. Mycobacterium was detected with a relatively high concentration in all the samples. The kitchen waste and municipal organic waste compost-amended soils had the highest counts of Mycobacterium amongst the pre-plantation soils, while the leaf waste compost-amended soil had the highest count in the post-harvest soil samples. Geobacter was also detected with a relatively higher level in the post-harvest soil samples compared to the pre-plantation soils. The fertilizer-amended soil had the highest count of the genus amongst all the samples. The leaf waste compost-amended soil had the lowest count of the genus amongst the pre-plantation soils, whereas the cow dung manure and vermicompost-amended soils had the lowest counts in the post-harvest soil samples.
The overall sum of OTUs of pathogenic genera was observed to be highest in the fertiliser-amended soil samples in the pre-plantation soil as well as in the post-harvest soil. The cow dung manure and vermicompost amended soil samples had the lowest counts of pathogenic OTUs. In general, there was a reduction in the total pathogenic OTUs in the post-harvest soil samples at the genus level.
The resolution of the 16S rRNA metagenomic profiling of the bacterial microbiome became vaguer at the species level. But there was detection of some beneficial and pathogenic bacterial species in the soil samples. The type of bacterial species and its proportion present in the pre-plantation soil samples were different from the post-harvest soils and also varied amongst the soil samples amended with different types of bio-composts (Supplementary Fig. S10 and S11).
The major beneficial species identified across the samples were bacteriovorus, cellulosum, clausii, copri, debontii, diminuta, endophyticus, hirsuta, multivorum, ochraceum, vinacea, and others (Supplementary Table S1). The fertiliser-amended soil had the highest count of bacteriovorus amongst all the pre-plantation soil samples. In contrast, the leaf waste compost-amended soil sample had the highest level of the species in the post-harvest soil samples. The residential soil samples had a relatively higher bacteriovorus level than the riverbank soil samples. Cellulosum was found to be highest in the fertiliser and municipal organic waste compost-amended soil samples in the pre-plantation soils, while the leaf waste compost-amended soil had the highest counts of the species after the harvest. The abundance of copri was reduced in the post-harvest soil samples compared to the pre-plantation soils. The fertiliser and municipal organic waste compost-amended soils had the highest counts of copri before plantation, but the kitchen and leaf waste compost-amended soils had the higher counts of the species in the post-harvest samples. The counts of debontii were relatively higher in the post-harvest soil samples than the pre-plantation soils. Also, the residential soil samples had higher species counts than the Yamuna floodplain soil samples. The counts of diminuta and hirsuta were lower in the post-harvest soil samples compared to the pre-plantation soils samples. The fertiliser and municipal organic waste compost-amended soil samples had relatively higher diminuta. While the leaf waste compost and cow dung manure amended soils had the higher counts of hirsuta in both pre-plantation and post-harvest soil samples. The level of bacterial species, endophyticus, were also reduced in all the post-harvest soil samples, except in the soil sample amended with leaf waste compost in which there was an increase in its count. The level of ochraceum was observed to be higher in the post-harvest soil samples than the pre-plantation soil samples. The leaf waste compost and kitchen waste compost-amended soil samples had a relatively higher level of ochraceum in the post-harvest soil samples. The total counts of vinacea were observed to be lower in the post-harvest soils. The kitchen waste compost and municipal organic waste compost-amended soil samples were seen with a relatively higher level of the vinacea species, among all the soil samples, both in pre-plantation as well as post-harvest soils. Generally, the pre-plantation soils had a relatively higher counts of the beneficial species as compared to the post-harvest soils, except in the leaf waste compost-amended soil in which there was a slight increase in the count of the beneficial species.
The presence of some pathogenic species was also detected across the soil samples. The major pathogenic bacterial species identified were campisalis, fulvum, intestinale, parahaemolyticus, parainfluenza stationis, and stercorea(Supplementary Table S2).Campisalis was detected only in the pre-plantation soil which was amended with the kitchen waste compost. while, there was a complete absence of this bacterial species in all the post-harvest soil samples. The relative level of fulvum tend to increase in the post-harvest soil samples amended with cow dung manure, leaf waste compost, and kitchen waste compos. The counts of fulvum were highest in the fertilizer-amended soil in both pre-plantation and post-harvest soil samples. The count of parahaemolyticus was relatively high only in the pre-plantation soil which was amended with municipal organic waste compost, while the other soil samples had negligible level of this bacterial species. The level of stercorea was observed to be relatively higher in the pre-plantation soils compared to the post-harvest soils. The fertiliser-amended soil had the higher level of this bacterial species in all the soil samples. In general, the counts of pathogenic bacterial OTU at the species level were relatively higher in the fertiliser-amended soil samples in both the pre-plantation and post-harvest soil samples.