Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer
Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer
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DOI：
10.1038/s41598-019-53679-0
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发表时间：
2019-11
影响因子：
4.6
通讯作者：
Luis H. Orellana;J. Hatt;Ramsunder Iyer;K. Chourey;R. Hettich;J. Spain;Wendy H. Yang;J. Chee-Sanford;R. Sanford;F. Löffler;K. Konstantinidis
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文献类型：
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作者：
Luis H. Orellana;J. Hatt;Ramsunder Iyer;K. Chourey;R. Hettich;J. Spain;Wendy H. Yang;J. Chee-Sanford;R. Sanford;F. Löffler;K. Konstantinidis
多组学技术在多大程度上可以反映situmicrobial过程速率仍不清楚，特别是对于高度多样化的栖息地，如土壤。在这里，我们使用中西部美国农业用地的桑迪土壤进行了微宇宙培养。用同位素标记的铵和尿素模拟施肥过程的微生态系统在培养192小时后显示出硝化作用（高达4.1 ± 0.87 µ g N-NO3 − g − 1干土d − 1）和N2O积累。硝化活性（NH4 + → NH2OH → NO → NO2-→ NO3 −）伴随着氨氧化细菌亚硝化单胞菌和亚硝化螺旋菌在孵育10至192小时之间16S rRNA基因（RNA/DNA）相对表达的6倍增加，而不像古细菌和comammox细菌那样显示稳定的基因表达。硝化活性和betaproteobacteria氨单加氧酶和亚硝酸盐氧化还原酶的转录丰度之间的密切关系表明，mRNA定量反映测得的活性，一般比DNA在这些条件下更敏感。虽然检测到与来自亚硝酸盐氧化微生物的管家蛋白相关的肽，但它们的丰度与活性并不显著相关，这表明元蛋白质组学仅提供了对活性的定性评估。总之，这些发现强调了多组学方法评估土壤中不同微生物群落的优势和局限性，并为硝化作用提供了新的见解。
To what extent multi-omic techniques could reflectin situmicrobial process rates remains unclear, especially for highly diverse habitats like soils. Here, we performed microcosm incubations using sandy soil from an agricultural site in Midwest USA. Microcosms amended with isotopically labeled ammonium and urea to simulate a fertilization event showed nitrification (up to 4.1 ± 0.87 µg N-NO3−g−1dry soil d−1) and accumulation of N2O after 192 hours of incubation. Nitrification activity (NH4+→ NH2OH → NO → NO2-→ NO3−) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteriaNitrosomonasandNitrosospira, unlike archaea and comammox bacteria, which showed stable gene expression. A strong relationship between nitrification activity and betaproteobacterial ammonia monooxygenase and nitrite oxidoreductase transcript abundances revealed that mRNA quantitatively reflected measured activity and was generally more sensitive than DNA under these conditions. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing diverse microbial communities in soils and provide new insights into nitrification.