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Microbe-Mediated Processes in Soils

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Front. Environ. Sci. | doi: 10.3389/fenvs.2018.00145

Microfluidic qPCR enables high throughput quantification of microbial functional genes but requires strict curation of primers

  • 1School of Biotechnology and Biomolecular Sciences, University of New South Wales, Australia
  • 2Department of Biological Sciences, Faculty of Science and Engineering, Macquarie University, Australia
  • 3Antarctic Conservation and Management, Australian Antarctic Division, Australia

Quantification of microbial functional genes enhances predictions of soil biogeochemical process rates, but reliance on low-throughput quantitative PCR (qPCR) limits the scope of ecological studies to a handful of targets. Here, we explore whether microfluidic qPCR (MFQPCR) is a viable high-throughput alternative for functional gene quantification, by evaluating the efficiency, specificity and sensitivity of 29 established and 12 newly designed primer pairs targeting taxonomic, nitrogen-cycling and hydrocarbon degradation genes in gDNA soil extracts, under three different sets of MFQPCR assay conditions. Without curation, commonly-used qPCR primer pairs yielded an extreme range of reaction efficiencies (25.9% - 100.1%), but when conditions were optimized, MFQPCR produced copy-number estimates comparable to traditional qPCR. To guide microbial soil ecologists considering adoption of MFQPCR, we present suggestions for primer selection, including omission of inosines, degeneracy scores of < 9, amplicon sizes of ≤ 211 bp, and GC content of 32-61%. We conclude that, while the nanoliter reaction volumes, rapid thermocycling and one-size-fits-all reaction conditions of MFQPCR necessitates more stringent primer selection criteria than is commonly applied in soil microbial ecology, the ability to quantify up to 96 targets in 96 samples makes MFQPCR a valuable tool for monitoring shifts in functional community abundances. MFQPCR will particularly suit studies targeting multiple clade-specific functional genes, or when primer design is informed by previous knowledge of the environment.

Keywords: Microfluidic qPCR, Quantitative PCR (qPCR), Nitrogen Cycle, functional genes, hydrocarbon degradation, microbial community, terrestrial ecology, biogeochemical cycles

Received: 19 Jul 2018; Accepted: 08 Nov 2018.

Edited by:

Luiz Fernando W. Roesch, Federal University of Pampa, Brazil

Reviewed by:

Roberta Fulthorpe, University of Toronto Scarborough, Canada
Satoshi Ishii, University of Minnesota Twin Cities, United States  

Copyright: © 2018 Crane, van Dorst, Hose, King and Ferrari. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Belinda C. Ferrari, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2033, Australia, b.ferrari@unsw.edu.au