Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná (UFPR), Curitiba, Brazil.
Department of Soils and Agricultural Engineer, UFPR, Curitiba, Brazil.
Microbiome. 2018 Jun 11;6(1):106. doi: 10.1186/s40168-018-0482-8.
pH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to "spillover effects" on other chemical parameters (e.g., availability of Al, Fe, Mn, Zn, and Cu) and plant growth, but these indirect effects on the microbial communities are rarely investigated. Usually, pH also co-varies with some confounding factors, such as land use, soil management (e.g., tillage and chemical inputs), plant cover, and/or edapho-climatic conditions. So, a more comprehensive analysis of the direct and indirect effects of pH brings a better understanding of the mechanisms driving prokaryotic (archaeal and bacterial) community structures.
We evaluated an agricultural soil pH gradient (from 4 to 6, the typical range for tropical farms), in a liming gradient with confounding factors minimized, investigating relationships between prokaryotic communities (16S rRNA) and physical-chemical parameters (indirect effects). Correlations, hierarchical modeling of species communities (HMSC), and random forest (RF) modeling indicated that both direct and indirect effects of the pH gradient affected the prokaryotic communities. Some OTUs were more affected by the pH changes (e.g., some Actinobacteria), while others were more affected by the indirect pH effects (e.g., some Proteobacteria). HMSC detected a phylogenetic signal related to the effects. Both HMSC and RF indicated that the main indirect effect was the pH changes on the availability of some elements (e.g., Al, Fe, and Cu), and secondarily, effects on plant growth and nutrient cycling also affected the OTUs. Additionally, we found that some of the OTUs that responded to pH also correlated with CO, CH, and NO greenhouse gas fluxes.
Our results indicate that there are two distinct pH-related mechanisms driving prokaryotic community structures, the direct effect and "spillover effects" of pH (indirect effects). Moreover, the indirect effects are highly relevant for some OTUs and consequently for the community structure; therefore, it is a mechanism that should be further investigated in microbial ecology.
pH 值常被报道为土壤中原核生物群落结构的主要驱动因素。然而，pH 值的变化也与其他化学参数（如 Al、Fe、Mn、Zn 和 Cu 的可用性）和植物生长的“溢出效应”有关，但这些对微生物群落的间接影响很少被研究。通常，pH 值也与一些混杂因素（如土地利用、土壤管理（如耕作和化学投入）、植被覆盖和/或土壤-气候条件）共同变化。因此，更全面地分析 pH 值的直接和间接效应可以更好地理解驱动原核生物（古菌和细菌）群落结构的机制。
我们在一个石灰梯度中评估了农业土壤 pH 值梯度（从 4 到 6，是热带农场的典型范围），同时最小化混杂因素的影响，调查了原核生物群落（16S rRNA）与物理化学参数（间接效应）之间的关系。相关性、物种群落层次建模（HMSC）和随机森林（RF）建模表明，pH 值梯度的直接和间接效应都影响了原核生物群落。一些 OTUs 受 pH 值变化的影响更大（例如，一些放线菌），而其他 OTUs 受间接 pH 值效应的影响更大（例如，一些变形菌）。HMSC 检测到与效应相关的系统发育信号。HMSC 和 RF 都表明，主要的间接效应是 pH 值变化对一些元素（如 Al、Fe 和 Cu）的可用性的影响，其次是对植物生长和养分循环的影响也影响了 OTUs。此外，我们发现，一些对 pH 值有响应的 OTUs也与 CO、CH 和 NO 等温室气体通量相关。
我们的结果表明，有两种不同的与 pH 值相关的机制驱动原核生物群落结构，即 pH 值的直接效应和“溢出效应”（间接效应）。此外，间接效应对一些 OTUs 及其群落结构具有重要意义；因此，这是一个在微生物生态学中应进一步研究的机制。
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