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Microorganisms are major drivers of elemental cycling in the biosphere substantially affecting carbon (C) and sulfur (S) metabolism, organic matter degradation, nitrogen (N) efflux and phosphorus (P) mobilization in the environment. Those processes may result in CO2 elevation, greenhouse gases release, nutrient loading and water consumption, which strongly influence ecosystems and humans. 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 biogeochemical processes and their current global changes.

In a new study in the journal Science China Life Sciences authors developed a high-throughput quantitative-PCR-based chip, Quantitative microbial element cycling (QMEC), for comprehensively profiling functional genes of the microbiota involved in C, N, P, S and methane cycling.

Biogeochemical nutrient cycling consists of numerous steps, each mediated by various functional genes. For example, N cycling is composed of several processes, including N fixation, nitrification, denitrification, ammonification, anaerobic ammonium oxidation, organic N mineralization and assimilatory and dissimilatory N reduction, with over 20 key microbial functional genes involved. “The comprehensive evaluation of microbial functional potential in CNPS biogeochemical cycling requires obtaining quantitative data for all these genes, which is extremely laborious when using conventional qPCR to process many environmental samples”, explains Dr. Bang-Xiao Zheng from CSIC-CREAF, Barcelona, now in University of Helsinki.


Figura 1. Global Ecology Unit.

To address these limitations, the authors of this study (i) designed a set of primer pairs targeting functional genes involved in C, N, P, and S cycling and (ii) developed a high-throughput qPCR-based functional-gene chip detection method, QMEC, for the simultaneous quantification of CNPS-cycling genes and further assessment of microbial potentials in CNPS biogeochemical dynamics and microbial responses to environmental changes. QMEC contains 36 reported and 36 novel primer pairs involved in C, N, P and S cycles, 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”, says Prof. Josep Peñuelas from CREAF-CSIC.