DeAngelis Kristen M, Brodie Eoin L, DeSantis Todd Z, Andersen Gary L, Lindow Steven E, Firestone Mary K
Ecology Department, Lawrence Berkeley National Lab, Berkeley, CA, USA.
ISME J. 2009 Feb;3(2):168-78. doi: 10.1038/ismej.2008.103. Epub 2008 Nov 13.
Roots moving through soil induce physical and chemical changes that differentiate rhizosphere from bulk soil, and the effects of these changes on soil microorganisms have long been a topic of interest. The use of a high-density 16S rRNA microarray (PhyloChip) for bacterial and archaeal community analysis has allowed definition of the populations that respond to the root within the complex grassland soil community; this research accompanies compositional changes reported earlier, including increases in chitinase- and protease-specific activity, cell numbers and quorum sensing signal. PhyloChip results showed a significant change compared with bulk soil in relative abundance for 7% of the total rhizosphere microbial community (147 of 1917 taxa); the 7% response value was confirmed by16S rRNA terminal restriction fragment length polymorphism analysis. This PhyloChip-defined dynamic subset was comprised of taxa in 17 of the 44 phyla detected in all soil samples. Expected rhizosphere-competent phyla, such as Proteobacteria and Firmicutes, were well represented, as were less-well-documented rhizosphere colonizers including Actinobacteria, Verrucomicrobia and Nitrospira. Richness of Bacteroidetes and Actinobacteria decreased in soil near the root tip compared with bulk soil, but then increased in older root zones. Quantitative PCR revealed rhizosphere abundance of beta-Proteobacteria and Actinobacteria at about 10(8) copies of 16S rRNA genes per g soil, with Nitrospira having about 10(5) copies per g soil. This report demonstrates that changes in a relatively small subset of the soil microbial community are sufficient to produce substantial changes in functions observed earlier in progressively more mature rhizosphere zones.
根系在土壤中生长会引发物理和化学变化，从而使根际土壤有别于原土体土壤，而这些变化对土壤微生物的影响长期以来一直是人们感兴趣的话题。利用高密度16S rRNA微阵列（PhyloChip）对细菌和古菌群落进行分析，有助于明确复杂草地土壤群落中对根系产生响应的菌群；该研究伴随着此前报道的成分变化，包括几丁质酶和蛋白酶特异性活性、细胞数量以及群体感应信号的增加。PhyloChip分析结果显示，根际微生物群落中7%（1917个分类单元中的147个）的相对丰度与原土体土壤相比有显著变化；16S rRNA末端限制性片段长度多态性分析证实了这7%的响应值。这个由PhyloChip定义的动态亚群由所有土壤样本中检测到的44个门中的17个门的分类单元组成。预期的具有根际定殖能力的门，如变形菌门和厚壁菌门，有很好的代表性，一些在根际定殖方面记录较少的门类，包括放线菌门、疣微菌门和硝化螺旋菌门也是如此。与原土体土壤相比，根尖附近土壤中拟杆菌门和放线菌门的丰富度降低，但在较老的根区则增加。定量PCR显示根际中β-变形菌门和放线菌门的丰度约为每克土壤16S rRNA基因10⁸拷贝，而硝化螺旋菌门约为每克土壤10⁵拷贝。本报告表明土壤微生物群落中一个相对较小的亚群发生变化，就足以在逐渐成熟的根际区域中产生此前观察到的功能上的显著变化。
