Abstract
Understanding the role of soil microbes is critical to ecosystem processes, and more thorough comparisons of measurement proxies for soil microbial biomass could broaden the inclusion of explicit microbial parameterization in soil carbon cycling and earth system models. We measured physical, chemical, and biological data from eight soil orders representing 11 major biomes and four climate regions. Four prominent methods to measure microbial abundance—chloroform fumigation extraction (CFE), total DNA yield, gene copy number by quantitative polymerase chain reaction (GCN), and phospholipid fatty acids (PLFA)—were compared to assess their relationships with each other and with soil characteristics. Correlations were observed when comparing methods, with CFE correlating strongly with total DNA yield, GCN, and PLFA; CFE with bacterial GCN and bacterial PLFA; and to a lesser extent, total PLFA and total DNA yield. Correlations improved with the removal of organic soils (Histosols, Gelisols). Comparisons involving extracted DNA were improved by correcting for clay content, due to DNA extraction inefficiencies in clay-rich soils. Correlations involving fungi (PLFA or GCN) were always less significant. These methods could serve as reliable, inter-relatable proxies for the estimation of total soil microbial biomass while recognizing that the proxies are less effective at parsing differences between bacteria and fungi. We provide specific equations to relate measures of soil microbial biomass by these four different methods to enable microbial models to utilize a greater diversity of observed data sources in parameterizations and simulations. Caveats for the equations and their values are also discussed.
| Original language | English |
|---|---|
| Article number | 109844 |
| Journal | Soil Biology and Biochemistry |
| Volume | 208 |
| DOIs | |
| State | Published - Sep 2025 |
Funding
Copyright notice: This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan).The authors gratefully acknowledge the contribution of soils provided by researchers from around the globe, including Yuri Zinn of Universidade Federal de Lavras in Brazil and Sindhu Jagadamma of the University of Tennessee (Lavras soils); Melissa C. Schrock of The Reckoning International and Sindhu Jagadamma (Kakamega soils); Steve Sebestyen and Randy Kolka at the U.S. Department of Agriculture (USDA) Forest Service Northern Research Station (Marcell Experimental Forest (MEF) soils); Paul Hanson of Oak Ridge National Laboratory (ORNL) who manages the U.S. Department of Energy (DOE) Spruce and Peatland Response to Changing Environments (SPRUCE) experiment located in the MEF; Jeffrey S. Dukes of the Carnegie Institution for Science and Carol Goranson of the University of Massachusetts in Boston (BACE soils); Matthew D. Wallenstein of Colorado State University (PHACE soils); Steve Allison and Sarah Evans of the University of California at Irving (Loma Ridge soils); Julie Jastrow of the U.S. Department of Energy Argonne National Laboratory (Fermi soils); Jennifer Z. Williams of The Pennsylvania State University and Ashlee Dere of the University of Nebraska at Omaha (Critical Zone soils and Big Ridge soils); Anna M. Wagner of the U.S. Army Engineer Research and Development Center's Cold Regions Research and Engineering Laboratory (Barrow and Fairbanks soils); and Roger McCoy and Sarah Nicley of the Tennessee Department of Environment and Conservation and Brian Lester of UT-Battelle (Big Ridge soils). We also thank Carol Loopstra at the University of Minnesota Department of Soil, Water, and Climate for laboratory assistance. We also acknowledge two anonymous reviewers whose suggestions improved this manuscript. This work was partially financially supported by the U.S. DOE Office of Biological and Environmental Research through the Terrestrial Ecosystem Science Scientific Focus Area at ORNL. ORNL is managed by UT-Battelle, LLC, under contract DE-AC05-00OR22725 with the U.S. DOE. The USDA Forest Service supported the long-term research program at the MEF (FS#21-CR-11242307-051). This work was also supported by SeaGrant grant number CON000000070744-00085442. The authors gratefully acknowledge the contribution of soils provided by researchers from around the globe, including Yuri Zinn of Universidade Federal de Lavras in Brazil and Sindhu Jagadamma of the University of Tennessee (Lavras soils); Melissa C. Schrock of The Reckoning International and Sindhu Jagadamma (Kakamega soils); Steve Sebestyen and Randy Kolka at the U.S. Department of Agriculture (USDA) Forest Service Northern Research Station (Marcell Experimental Forest (MEF) soils); Paul Hanson of Oak Ridge National Laboratory (ORNL) who manages the U.S. Department of Energy (DOE) Spruce and Peatland Response to Changing Environments (SPRUCE) experiment located in the MEF; Jeffrey S. Dukes of the Carnegie Institution for Science and Carol Goranson of the University of Massachusetts in Boston (BACE soils); Matthew D. Wallenstein of Colorado State University (PHACE soils); Steve Allison and Sarah Evans of the University of California at Irving (Loma Ridge soils); Julie Jastrow of the U.S. Department of Energy Argonne National Laboratory (Fermi soils); Jennifer Z. Williams of The Pennsylvania State University and Ashlee Dere of the University of Nebraska at Omaha (Critical Zone soils and Big Ridge soils); Anna M. Wagner of the U.S. Army Engineer Research and Development Center's Cold Regions Research and Engineering Laboratory (Barrow and Fairbanks soils); and Roger McCoy and Sarah Nicley of the Tennessee Department of Environment and Conservation and Brian Lester of UT-Battelle (Big Ridge soils). We also thank Carol Loopstra at the University of Minnesota Department of Soil, Water, and Climate for laboratory assistance. We also acknowledge two anonymous reviewers whose suggestions improved this manuscript. This work was partially financially supported by the U.S. DOE Office of Biological and Environmental Research through the Terrestrial Ecosystem Science Scientific Focus Area at ORNL. ORNL is managed by UT-Battelle, LLC, under contract DE-AC05-00OR22725 with the U.S. DOE. The USDA Forest Service supported the long-term research program at the MEF (FS#21-CR-11242307-051). This work was also supported by SeaGrant grant number CON000000070744-00085442. Copyright notice: This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan ( http://energy.gov/downloads/doe-public-access-plan ).
Keywords
- Chloroform fumigation extraction
- DNA
- PLFA
- qPCR
- Soil carbon cycle modeling
- Soil microbial biomass