Malik Ashish A, Thomson Bruce C, Whiteley Andrew S, Bailey Mark, Griffiths Robert I
Centre for Ecology and Hydrology, Wallingford, United Kingdom
Centre for Ecology and Hydrology, Wallingford, United Kingdom.
mBio. 2017 Jul 5;8(4):e00799-17. doi: 10.1128/mBio.00799-17.
Environmental factors relating to soil pH are important regulators of bacterial taxonomic biodiversity, yet it remains unclear if such drivers affect community functional potential. To address this, we applied whole-genome metagenomics to eight geographically distributed soils at opposing ends of a landscape soil pH gradient (where "low-pH" is ~pH 4.3 and "high-pH" is ~pH 8.3) and evaluated functional differences with respect to functionally annotated genes. First, differences in taxonomic and functional diversity between the two pH categories were assessed with respect to alpha diversity (mean sample richness) and gamma diversity (total richness pooled for each pH category). Low-pH soils, also exhibiting higher organic matter and moisture, consistently had lower taxonomic alpha and gamma diversity, but this was not apparent in assessments of functional alpha and gamma diversity. However, coherent changes in the relative abundances of annotated genes between low- and high-pH soils were identified; with strong multivariate clustering of samples according to pH independent of geography. Assessment of indicator genes revealed that the acidic organic-rich soils possessed a greater abundance of cation efflux pumps, C and N direct fixation systems, and fermentation pathways, indicating adaptations to both acidity and anaerobiosis. Conversely, high-pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings highlight the distinctive physiological adaptations required for bacteria to survive in soils of various nutrient availability and edaphic conditions and more generally indicate that bacterial functional versatility with respect to functional gene annotations may not be constrained by taxonomy. Over a set of soil samples spanning Britain, the widely reported reductions in bacterial taxonomic richness at low pH were found not to be accompanied by significant reductions in the richness of functional genes. However, consistent changes in the abundance of related functional genes were observed, characteristic of differential ecological and nutrient acquisition strategies between high-pH mineral soils and low-pH organic anaerobic soils. Our assessment at opposing ends of a soil gradient encapsulates the limits of functional diversity in temperate climates and identifies key pathways that may serve as indicators for soil element cycling and C storage processes in other soil systems. To this end, we make available a data set identifying functional indicators of the different soils; as well as raw sequences, which given the geographic scale of our sampling should be of value in future studies assessing novel genetic diversity of a wide range of soil functional attributes.
与土壤pH值相关的环境因素是细菌分类生物多样性的重要调节因子，但这些驱动因素是否会影响群落功能潜力仍不清楚。为了解决这个问题，我们对景观土壤pH梯度两端地理分布的8种土壤应用了全基因组宏基因组学（其中“低pH值”约为pH 4.3，“高pH值”约为pH 8.3），并根据功能注释基因评估了功能差异。首先，针对α多样性（平均样本丰富度）和γ多样性（每个pH类别汇总的总丰富度）评估了两个pH类别之间的分类和功能多样性差异。低pH值土壤，同时也表现出较高的有机质和湿度，其分类α和γ多样性始终较低，但在功能α和γ多样性评估中并不明显。然而，在低pH值和高pH值土壤之间确定了注释基因相对丰度的连贯变化；样本根据pH值进行了强大的多变量聚类，与地理位置无关。对指示基因的评估表明，酸性富含有机质的土壤拥有更多的阳离子外排泵、碳和氮直接固定系统以及发酵途径，表明对酸性和厌氧环境都有适应性。相反，高pH值土壤拥有更多直接由转运蛋白介导的有机碳和氮底物获取机制。这些发现突出了细菌在不同养分可用性和土壤条件的土壤中生存所需的独特生理适应性，更普遍地表明，就功能基因注释而言，细菌的功能多功能性可能不受分类学的限制。在一组跨越英国的土壤样本中，广泛报道的低pH值下细菌分类丰富度的降低并未伴随着功能基因丰富度的显著降低。然而，观察到相关功能基因丰度的一致变化，这是高pH值矿质土壤和低pH值有机厌氧土壤之间不同生态和养分获取策略的特征。我们在土壤梯度两端的评估概括了温带气候下功能多样性的限度，并确定了可能作为其他土壤系统中土壤元素循环和碳储存过程指标的关键途径。为此，我们提供了一个数据集，用于识别不同土壤的功能指标；以及原始序列，鉴于我们采样的地理范围，这些序列在未来评估广泛土壤功能属性的新遗传多样性的研究中应该具有价值。
