Background

Leguminous crops could fix atmospheric nitrogen through their symbiotic and non-symbiotic associations with different microbes to survive and maintain nutrient in soils that are deficient in nitrogen. Only limited number of lateral roots of the legume prefers to formulate nodules. So far, it is unclear whether microbial communities in lateral roots with/without nodules are different, and whether the selection of microbiome among different types of lateral roots of a plant is a random process or is strictly controlled by the host plant.

Methods

We investigated the diversity and community structure of prokaryotic and eukaryotic microorganisms inhabiting in lateral roots with and without nodules of soybean via high-throughput 16S rDNA and 18S rDNA amplicon sequencing. In addition, quantitative microbial element cycling method was applied to estimate the functional genes that are related to carbon, nitrogen, phosphorus, sulfur cycling and methane metabolism.

Results

Microbiome in rhizosphere of lateral roots with nodules had significantly lower α-diversity and higher co-occurrence network complexity, compared to those of lateral roots without nodules. The neutral model analysis demonstrated that microbial community of lateral roots with nodules in rhizosphere soil were less affected by neutral process than that of lateral roots without nodules. In addition, we identified a keystone ecological cluster (Module #1) of the rhizosphere cross-kingdom network that positively correlated with multiple functional gene copies, suggesting that the microbial taxa in Module #1 could play important roles in nutrient cycling of rhizosphere microenvironment.

Conclusions

Overall, our study revealed the differences in microbial communities in the lateral roots with/without the nodule of root systems and identified a keystone ecological cluster positively linking with multiple functional cycling.

中文翻译：

---

大豆根系相关微生物组在有和没有根瘤的侧根之间的变化

背景

豆科作物可以通过与不同微生物的共生和非共生结合来固定大气中的氮，从而在缺氮的土壤中生存和维持养分。只有有限数量的豆科植物侧根更喜欢形成根瘤。到目前为止，尚不清楚有/无根瘤的侧根中微生物群落是否不同，以及植物不同类型侧根中微生物组的选择是随机过程还是受宿主植物严格控制。

方法

我们通过高通量 16S rDNA 和 18S rDNA 扩增子测序研究了栖息在有和没有根瘤的大豆侧根中的原核和真核微生物的多样性和群落结构。此外，还采用定量微生物元素循环方法估计了与碳、氮、磷、硫循环和甲烷代谢相关的功能基因。

结果

与没有根瘤的侧根相比，有根瘤的侧根根际微生物组具有显着降低的α多样性和更高的共现网络复杂性。中性模型分析表明，根际土壤中带瘤的侧根微生物群落受中性过程的影响小于无瘤侧根的微生物群落。此外，我们确定了与多个功能基因拷贝正相关的根际跨界网络的关键生态集群（模块#1），表明模块#1中的微生物类群可能在根际微环境的养分循环中发挥重要作用。

结论

总体而言，我们的研究揭示了具有/不具有根系根瘤的侧根中微生物群落的差异，并确定了与多种功能循环呈正相关的关键生态群。