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Sci China Life Sci. 2018 Dec;61(12):1451-1462. doi: 10.1007/s11427-018-9364-7. Epub 2018 Aug 13.

QMEC: a tool for high-throughput quantitative assessment of microbial functional potential in C, N, P, and S biogeochemical cycling.

Zheng B1,2,3,4, Zhu Y1,5, Sardans J3,4, Peñuelas J6,7, Su J8.

Author information

1
Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
2
University of Chinese Academy of Sciences, Beijing, 100049, China.
3
Consejo Superior de Investigaciones Científicas (CSIC), Global Ecology Unit, Centre for Ecological Research and Forestry Applications (CREAF)-CSIC-Universitat Autonoma de Barcelona (UAB), Bellaterra, 08193, Spain.
4
CREAF, Cerdanyola del Vallès, Barcelona, 08193, Spain.
5
State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
6
Consejo Superior de Investigaciones Científicas (CSIC), Global Ecology Unit, Centre for Ecological Research and Forestry Applications (CREAF)-CSIC-Universitat Autonoma de Barcelona (UAB), Bellaterra, 08193, Spain. josep.penuelas@uab.cat.
7
CREAF, Cerdanyola del Vallès, Barcelona, 08193, Spain. josep.penuelas@uab.cat.
8
Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China. jqsu@iue.ac.cn.

Abstract

Microorganisms are major drivers of elemental cycling in the biosphere. Determining the abundance of microbial functional traits involved in the transformation of nutrients, including carbon (C), nitrogen (N), phosphorus (P) and sulfur (S), is critical for assessing microbial functionality in elemental cycling. We developed a high-throughput quantitative-PCR-based chip, Quantitative microbial element cycling (QMEC), for assessing and quantifying the genetic potential of microbiota to mineralize soil organic matter and to release C, N, P and S. QMEC contains 72 primer pairs targeting 64 microbial functional genes for C, N, P, S and methane metabolism. These primer pairs were characterized by high coverage (average of 18-20 phyla covered per gene) and sufficient specificity (>70% match rate) with a relatively low detection limit (7-102 copies per run). QMEC was successfully applied to soil and sediment samples, identifying significantly different structures, abundances and diversities of the functional genes (P<0.05). QMEC was also able to determine absolute gene abundance. QMEC enabled the simultaneous qualitative and quantitative determination of 72 genes from 72 samples in one run, which is promising for comprehensively investigating microbially mediated ecological processes and biogeochemical cycles in various environmental contexts including those of the current global change.

KEYWORDS:

biogeochemical cycle; ecological process; elemental cycling; functional potential; high-throughput qPCR; microbial genes

PMID:
30136056
DOI:
10.1007/s11427-018-9364-7
[Indexed for MEDLINE]

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