An Improved Method for Soil DNA Extraction to Study the Microbial Assortment within Rhizospheric Region

<table class="table-group" id="tab2"><tr><td><table class="table"><tr><td class="thead-hr" colspan="4"><hr/></td></tr><tr class="thead"><td align="left">DNA extraction protocol</td><td align="center">Amount of DNA (<i>µ</i>g/mL)</td><td align="center"><span style="width: 41.8936ptpx;"><svg height="13.995pt" id="M1" style="vertical-align:-4.87466pt" version="1.1" viewbox="-0.0498162 -9.12034 41.8936 13.995" width="41.8936pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g transform="matrix(.0135,0,0,-0.0135,0,0)"><path d="M673 0V28C608 34 594 43 563 129C499 303 432 494 370 665L339 656L132 132C98 43 84 37 20 28V0H238V28C162 35 154 45 175 108C188 150 203 192 219 237H432C454 176 474 122 487 83S491 36 428 28V0H673ZM418 280H234C265 362 296 450 328 535H330L418 280Z" id="g190-66"></path><glyph.data ascent="989" descent="-360" horiz-adv-x="691" vert-adv-y="691"></glyph.data></g><g transform="matrix(.0095,0,0,-0.0095,9.397,3.264)"><path d="M414 144C384 79 371 75 317 75H135L276 221C367 316 408 376 408 465C408 570 327 635 237 635C179 635 131 609 100 575L42 494L67 471C94 510 138 565 205 565C277 565 321 517 321 435C321 348 258 270 195 195C146 137 88 81 33 26V0H411C423 44 433 88 446 135L414 144Z" id="g50-51"></path><glyph.data ascent="3443" descent="-2856" horiz-adv-x="487" vert-adv-y="487"></glyph.data></g><g transform="matrix(.0095,0,0,-0.0095,14.016,3.264)"><path d="M141 347C171 480 264 541 327 570C364 587 403 599 436 605L429 641C389 634 339 622 300 609C191 570 37 458 37 239C37 86 126 -12 245 -12C367 -12 454 89 454 210C454 314 380 397 272 397C252 397 230 390 208 380L141 347ZM231 338C323 338 366 257 366 174C366 108 340 27 263 27C180 27 129 123 129 244C129 268 130 292 135 310C158 323 193 338 231 338Z" id="g50-55"></path><glyph.data ascent="3443" descent="-2856" horiz-adv-x="487" vert-adv-y="487"></glyph.data></g><g transform="matrix(.0095,0,0,-0.0095,18.634,3.264)"><path d="M245 635C92 635 37 457 37 312C37 149 91 -12 244 -12C395 -12 449 166 449 312C449 469 395 635 245 635ZM243 598C332 598 358 454 358 312C358 173 334 26 245 26C158 26 128 174 128 313S152 598 243 598Z" id="g50-49"></path><glyph.data ascent="3443" descent="-2856" horiz-adv-x="487" vert-adv-y="487"></glyph.data></g><g transform="matrix(.0095,0,0,-0.0095,23.253,3.264)"><path d="M381 704H317L48 -163H112L381 704Z" id="g50-48"></path><glyph.data ascent="3443" descent="-2856" horiz-adv-x="429" vert-adv-y="429"></glyph.data></g><g transform="matrix(.0095,0,0,-0.0095,27.325,3.264)"><path d="M414 144C384 79 371 75 317 75H135L276 221C367 316 408 376 408 465C408 570 327 635 237 635C179 635 131 609 100 575L42 494L67 471C94 510 138 565 205 565C277 565 321 517 321 435C321 348 258 270 195 195C146 137 88 81 33 26V0H411C423 44 433 88 446 135L414 144Z" id="g50-51"></path><glyph.data ascent="3443" descent="-2856" horiz-adv-x="487" vert-adv-y="487"></glyph.data></g><g transform="matrix(.0095,0,0,-0.0095,31.944,3.264)"><path d="M290 377C321 398 342 415 358 430C378 450 389 473 389 502C389 578 329 635 238 635H237C184 635 137 610 109 578L64 515L88 493C112 529 154 573 208 573S303 542 303 482C303 409 233 370 141 341L149 308C165 313 190 319 215 319C272 319 341 283 341 193C342 98 292 43 222 43C163 43 122 72 96 94C88 101 79 100 70 94C61 87 47 73 46 60C44 47 48 37 62 23C76 10 118 -12 165 -12C238 -12 430 62 430 223C430 297 379 359 290 375V377Z" id="g50-52"></path><glyph.data ascent="3443" descent="-2856" horiz-adv-x="487" vert-adv-y="487"></glyph.data></g><g transform="matrix(.0095,0,0,-0.0095,36.562,3.264)"><path d="M245 635C92 635 37 457 37 312C37 149 91 -12 244 -12C395 -12 449 166 449 312C449 469 395 635 245 635ZM243 598C332 598 358 454 358 312C358 173 334 26 245 26C158 26 128 174 128 313S152 598 243 598Z" id="g50-49"></path><glyph.data ascent="3443" descent="-2856" horiz-adv-x="487" vert-adv-y="487"></glyph.data></g></svg></span></td><td align="center"><span style="width: 41.8936ptpx;"><svg height="13.995pt" id="M2" style="vertical-align:-4.87466pt" version="1.1" viewbox="-0.0498162 -9.12034 41.8936 13.995" width="41.8936pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g transform="matrix(.0135,0,0,-0.0135,0,0)"><path d="M673 0V28C608 34 594 43 563 129C499 303 432 494 370 665L339 656L132 132C98 43 84 37 20 28V0H238V28C162 35 154 45 175 108C188 150 203 192 219 237H432C454 176 474 122 487 83S491 36 428 28V0H673ZM418 280H234C265 362 296 450 328 535H330L418 280Z" id="g190-66"></path><glyph.data ascent="989" descent="-360" horiz-adv-x="691" vert-adv-y="691"></glyph.data></g><g transform="matrix(.0095,0,0,-0.0095,9.397,3.264)"><path d="M414 144C384 79 371 75 317 75H135L276 221C367 316 408 376 408 465C408 570 327 635 237 635C179 635 131 609 100 575L42 494L67 471C94 510 138 565 205 565C277 565 321 517 321 435C321 348 258 270 195 195C146 137 88 81 33 26V0H411C423 44 433 88 446 135L414 144Z" id="g50-51"></path><glyph.data ascent="3443" descent="-2856" horiz-adv-x="487" vert-adv-y="487"></glyph.data></g><g transform="matrix(.0095,0,0,-0.0095,14.016,3.264)"><path d="M141 347C171 480 264 541 327 570C364 587 403 599 436 605L429 641C389 634 339 622 300 609C191 570 37 458 37 239C37 86 126 -12 245 -12C367 -12 454 89 454 210C454 314 380 397 272 397C252 397 230 390 208 380L141 347ZM231 338C323 338 366 257 366 174C366 108 340 27 263 27C180 27 129 123 129 244C129 268 130 292 135 310C158 323 193 338 231 338Z" id="g50-55"></path><glyph.data ascent="3443" descent="-2856" horiz-adv-x="487" vert-adv-y="487"></glyph.data></g><g transform="matrix(.0095,0,0,-0.0095,18.634,3.264)"><path d="M245 635C92 635 37 457 37 312C37 149 91 -12 244 -12C395 -12 449 166 449 312C449 469 395 635 245 635ZM243 598C332 598 358 454 358 312C358 173 334 26 245 26C158 26 128 174 128 313S152 598 243 598Z" id="g50-49"></path><glyph.data ascent="3443" descent="-2856" horiz-adv-x="487" vert-adv-y="487"></glyph.data></g><g transform="matrix(.0095,0,0,-0.0095,23.253,3.264)"><path d="M381 704H317L48 -163H112L381 704Z" id="g50-48"></path><glyph.data ascent="3443" descent="-2856" horiz-adv-x="429" vert-adv-y="429"></glyph.data></g><g transform="matrix(.0095,0,0,-0.0095,27.325,3.264)"><path d="M414 144C384 79 371 75 317 75H135L276 221C367 316 408 376 408 465C408 570 327 635 237 635C179 635 131 609 100 575L42 494L67 471C94 510 138 565 205 565C277 565 321 517 321 435C321 348 258 270 195 195C146 137 88 81 33 26V0H411C423 44 433 88 446 135L414 144Z" id="g50-51"></path><glyph.data ascent="3443" descent="-2856" horiz-adv-x="487" vert-adv-y="487"></glyph.data></g><g transform="matrix(.0095,0,0,-0.0095,31.944,3.264)"><path d="M253 635C142 635 71 555 71 471C71 401 113 353 178 316C144 294 106 267 91 252C70 231 46 202 46 157C46 51 132 -12 241 -12C328 -12 442 52 442 168C442 257 379 305 311 343C354 373 380 398 388 407C406 428 417 458 417 487C417 568 348 635 253 635ZM240 600C288 600 340 563 340 481C340 423 313 387 279 360C207 394 148 427 148 499C148 549 182 600 240 600ZM252 23C188 23 129 73 129 163C129 217 162 266 211 298C289 260 360 217 360 144C360 69 312 23 252 23Z" id="g50-57"></path><glyph.data ascent="3443" descent="-2856" horiz-adv-x="487" vert-adv-y="487"></glyph.data></g><g transform="matrix(.0095,0,0,-0.0095,36.562,3.264)"><path d="M245 635C92 635 37 457 37 312C37 149 91 -12 244 -12C395 -12 449 166 449 312C449 469 395 635 245 635ZM243 598C332 598 358 454 358 312C358 173 334 26 245 26C158 26 128 174 128 313S152 598 243 598Z" id="g50-49"></path><glyph.data ascent="3443" descent="-2856" horiz-adv-x="487" vert-adv-y="487"></glyph.data></g></svg></span></td></tr><tr><td class="thead-hr" colspan="4"><hr/></td></tr><tr><td align="left">DNA extraction using PEG/NaCl method [<a href="/journals/mbi/2014/518960/#B13">8</a>]</td><td align="center">0.73</td><td align="center">1.12</td><td align="center">1.26</td></tr><tr><td align="left">DNA extraction using commercial soil DNA extraction kit (<i>Soil Master</i> DNA extraction kit; EPICENTRE, Madison, WI, USA)</td><td align="center">0.79</td><td align="center">1.21</td><td align="center">1.32</td></tr><tr><td align="left">DNA extraction by mannitol-PBS-PEG/NaCl method</td><td align="center">2.20</td><td align="center">1.84</td><td align="center">1.81</td></tr><tr><td align="left">DNA extraction by mannitol-PBS-PCI method</td><td align="center">2.36</td><td align="center">1.93</td><td align="center">1.84</td></tr><tr><td align="left">DNA extraction by mannitol-PBS-CTAB method</td><td align="center">2.67</td><td align="center">2.07</td><td align="center">1.85</td></tr><tr class="table-tr"><td colspan="4"><hr class="tbody-hr"/></td></tr></table></td></tr></table>

Comparison of amount, purity of DNA, and humic acid contamination extracted from various isolation protocols.

Molecular Biology International

tab2

Table 2

Table 2: An Improved Method for Soil DNA Extraction to Study the Microbial Assortment within Rhizospheric Region 