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Comparison of Whole-Cell Fatty Acid (MIDI) or Phospholipid Fatty Acid (PLFA) Extractants as Biomarkers to Profile Soil Microbial Communities

  • Soil Microbiology
  • Published:
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Abstract

The whole-cell lipid extraction to profile microbial communities on soils using fatty acid (FA) biomarkers is commonly done with the two extractants associated with the phospholipid fatty acid (PLFA) or Microbial IDentification Inc. (MIDI) methods. These extractants have very different chemistry and lipid separation procedures, but often shown a similar ability to discriminate soils from various management and vegetation systems. However, the mechanism and the chemistry of the exact suite of FAs extracted by these two methods are poorly understood. Therefore, the objective was to qualitatively and quantitatively compare the MIDI and PLFA microbial profiling methods for detecting microbial community shifts due to soil type or management. Twenty-nine soil samples were collected from a wide range of soil types across Oregon and extracted FAs by each method were analyzed by gas chromatography (GC) and GC-mass spectrometry. Unlike PLFA profiles, which were highly related to microbial FAs, the overall MIDI-FA profiles were highly related to the plant-derived FAs. Plant-associated compounds were quantitatively related to particulate organic matter (POM) and qualitatively related to the standing vegetation at sampling. These FAs were negatively correlated to respiration rate normalized to POM (RespPOM), which increased in systems under more intensive management. A strong negative correlation was found between MIDI-FA to PLFA ratios and total organic carbon (TOC). When the reagents used in MIDI procedure were tested for the limited recovery of MIDI-FAs from soil with high organic matter, the recovery of MIDI-FA microbial signatures sharply decreased with increasing ratios of soil to extractant. Hence, the MIDI method should be used with great caution for interpreting changes in FA profiles due to shifts in microbial communities.

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Abbreviations

AMF:

Arbuscular mycorrhyzal fungi

ECL:

Equivalent chain lengths

IDV:

Indicator value provided to each FAME by ISA

ISA:

Indicator species analysis

MPEP:

MIDI-preferentially extracted peaks

POM:

Particulate organic matter

TOC:

Total organic carbon

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Acknowledgments

We thank Dr. Bernd R.T. Simoneit and Patricia M. Medeiros (College of Oceanic and Atmospheric Sciences – OSU, Corvallis, OR) for the GC-MS analysis and peak identification, Ms. Joan Sandeno for helping in the soil sampling, Renato Castelao for assisting with FAME data management. Guilherme Chaer, who provided thoughtful comments, which improved the interpretation and presentation of our results. M.F. Fernandes acknowledges fellowship support from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq-Brazil).

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Authors and Affiliations

  1. Embrapa Coastal Tablelands, Av. Beira Mar 3250, Aracaju, SE, 49025-040, Brazil

    Marcelo F. Fernandes

  2. School of Natural Resources, Ohio State University, Columbus, OH, 43210-1085, USA

    Jyotisna Saxena & Richard P. Dick

  3. 2015 Fyffe Road, 61A Parker Food Science & Technology Building, Columbus, OH, 43210, USA

    Richard P. Dick

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  1. Marcelo F. Fernandes
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  2. Jyotisna Saxena
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  3. Richard P. Dick
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Correspondence to Richard P. Dick.

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Fernandes, M.F., Saxena, J. & Dick, R.P. Comparison of Whole-Cell Fatty Acid (MIDI) or Phospholipid Fatty Acid (PLFA) Extractants as Biomarkers to Profile Soil Microbial Communities. Microb Ecol 66, 145–157 (2013). https://doi.org/10.1007/s00248-013-0195-2

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