Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
Appl Environ Microbiol. 2018 Jul 17;84(15). doi: 10.1128/AEM.00598-18. Print 2018 Aug 1.
Numerous studies have examined the long-term effect of experimental nitrogen (N) deposition in terrestrial ecosystems; however, N-specific mechanistic markers are difficult to disentangle from responses to other environmental changes. The strongest picture of N-responsive mechanistic markers is likely to arise from measurements over a short (hours to days) time scale immediately after inorganic N deposition. Therefore, we assessed the short-term (3-day) transcriptional response of microbial communities in two soil strata from a pine forest to a high dose of N fertilization (ca. 1 mg/g of soil material) in laboratory microcosms. We hypothesized that N fertilization would repress the expression of fungal and bacterial genes linked to N mining from plant litter. However, despite N suppression of microbial respiration, the most pronounced differences in functional gene expression were between strata rather than in response to the N addition. Overall, ∼4% of metabolic genes changed in expression with N addition, while three times as many (∼12%) were significantly different across the different soil strata in the microcosms. In particular, we found little evidence of N changing expression levels of metabolic genes associated with complex carbohydrate degradation (CAZymes) or inorganic N utilization. This suggests that direct N repression of microbial functional gene expression is not the principle mechanism for reduced soil respiration immediately after N deposition. Instead, changes in expression with N addition occurred primarily in general cell maintenance areas, for example, in ribosome-related transcripts. Transcriptional changes in functional gene abundance in response to N addition observed in longer-term field studies likely result from changes in microbial composition. Ecosystems are receiving increased nitrogen (N) from anthropogenic sources, including fertilizers and emissions from factories and automobiles. High levels of N change ecosystem functioning. For example, high inorganic N decreases the microbial decomposition of plant litter, potentially reducing nutrient recycling for plant growth. Understanding how N regulates microbial decomposition can improve the prediction of ecosystem functioning over extended time scales. We found little support for the conventional view that high N supply represses the expression of genes involved in decomposition or alters the expression of bacterial genes for inorganic N cycling. Instead, our study of pine forest soil 3 days after N addition showed changes in microbial gene expression related to cell maintenance and stress response. This highlights the challenge of establishing predictive links between microbial gene expression levels and measures of ecosystem function.
许多研究都考察了陆地生态系统中实验性氮（N）沉积的长期影响；然而，N 特定的机制标记物很难与对其他环境变化的反应区分开来。最能反映 N 响应机制标记物的情况可能是在无机 N 沉积后立即进行的短时间（数小时至数天）尺度上的测量。因此，我们在实验室微宇宙中评估了来自松林的两个土壤层中的微生物群落对高剂量 N 施肥（约 1mg/g 土壤物质）的短期（3 天）转录反应。我们假设 N 施肥会抑制与从植物凋落物中提取 N 相关的真菌和细菌基因的表达。然而，尽管 N 抑制了微生物呼吸，但功能基因表达的最显著差异是在层次之间，而不是对 N 添加的响应。总的来说，约有 4%的代谢基因的表达随 N 添加而改变，而在微宇宙中，跨越不同土壤层的基因有三倍（约 12%）的显著差异。特别是，我们几乎没有发现 N 改变与复杂碳水化合物降解（CAZymes）或无机 N 利用相关的代谢基因表达水平的证据。这表明，N 对微生物功能基因表达的直接抑制不是 N 沉积后立即降低土壤呼吸的主要机制。相反，N 添加引起的表达变化主要发生在核糖体相关转录物等一般细胞维持区域。对 N 添加的功能基因丰度的转录变化在长期野外研究中观察到，可能是由于微生物组成的变化。生态系统从人为来源（包括肥料和工厂和汽车的排放）中接收越来越多的氮（N）。高水平的 N 会改变生态系统的功能。例如，高无机 N 会降低微生物对植物凋落物的分解，从而可能减少植物生长的养分循环。了解 N 如何调节微生物分解可以提高对扩展时间尺度上生态系统功能的预测。我们几乎没有发现支持以下传统观点的证据，即高 N 供应会抑制分解相关基因的表达或改变细菌无机 N 循环基因的表达。相反，我们对 N 添加后 3 天的松林土壤的研究表明，与细胞维持和应激反应相关的微生物基因表达发生了变化。这凸显了在微生物基因表达水平与生态系统功能测量之间建立预测性联系的挑战。
