Background and aims

The plant root exhibits significant heterogeneity, which deeply affects the associated microbial communities, but the spatial heterogeneity of microbiome associated with root is often overlooked.

Methods

Using the mini-rhizobox approach, 16S rRNA profiling and bioinformatics analyses, we analyzed an extensive dataset of 2,185 samples to decipher the mechanisms governing the assembly of the bacterial community associated with pepper roots.

Results

Our results revealed high spatial variability in bacterial communities of individual pepper root. Stochastic processes were identified as the primary drivers of bacterial community assembly at adjacent points, particularly in secondary roots, whereas deterministic processes exerted more influence in main roots and their junctions with secondary roots. Correspondingly, only 22.3% of commonly occurring ASVs followed skewed Gaussian distributions along root depth. These findings highlight randomness in bacterial community along roots. Nonetheless, bacterial richness, as indicated by the log₁₀ transformation of detected ASVs, showed a strong negative correlation with the dominance rate (R² = 0.994), emphasizing the significance of community composition over richness for advancing sustainable agriculture. Additionally, a distance-decay relationship was observed, with increasing divergence between the main and secondary roots. Both cooperative and antagonistic interactions among microbial taxa are highly context-dependent, identifying Sphingomonas and Pseudomonas as the most cooperative and antagonistic genera, respectively.

Conclusions

Microbial communities associated with plant roots are assembled primarily by stochastic processes, involving a few commonly occurring and more rarely occurring species, and are governed by two new novel rules: species richness and dominance rates, as well as a medium-strength distance-decay relationship.

中文翻译：

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辣椒 （Capsicum annuum） 根相关微生物组随机性背后的两个生态学规则

 背景和目标

植物根系表现出显著的异质性，这深刻影响了相关的微生物群落，但与根相关的微生物组的空间异质性经常被忽视。

 方法

使用微型根茎盒方法、16S rRNA 分析和生物信息学分析，我们分析了包含 2,185 个样本的广泛数据集，以破译控制与辣椒根相关的细菌群落组装的机制。

 结果

我们的结果表明，辣椒单个根的细菌群落具有高度的空间变异性。随机过程被确定为细菌群落在相邻点组装的主要驱动因素，特别是在次生根中，而确定性过程在主根及其与次生根的连接处施加更大的影响。相应地，只有 22.3% 的常见 ASV 沿根深遵循偏高斯分布。这些发现突出了根系细菌群落的随机性。尽管如此，如检测到的 ASV 的 log₁₀ 转化所表明的那样，细菌丰富度与优势率呈很强的负相关 （R² = 0.994），强调了群落组成高于丰富度对推进可持续农业的重要性。此外，观察到距离-衰减关系，主根和次根之间的分歧越来越大。微生物类群之间的合作和拮抗相互作用都高度依赖于环境，分别将鞘氨醇单胞菌和假单胞菌确定为最合作和最拮抗的属。

 结论

与植物根相关的微生物群落主要通过随机过程组装，涉及一些常见和更罕见的物种，并受两个新规则的支配：物种丰富度和优势率，以及中等强度的距离-衰减关系。