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Lacroix EM, Gomes A, Heitmann GB, Schuler D, Dekas AE, Liptzin D, Aberle E, Watts DB, Nelson KA, Culman S, Fendorf S. Microbial Proxies for Anoxic Microsites Vary with Management and Partially Explain Soil Carbon Concentration. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:11459-11469. [PMID: 38875507 PMCID: PMC11223465 DOI: 10.1021/acs.est.4c01882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/26/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024]
Abstract
Anoxic microsites are potentially important but unresolved contributors to soil organic carbon (C) storage. How anoxic microsites vary with soil management and the degree to which anoxic microsites contribute to soil C stabilization remain unknown. Sampling from four long-term agricultural experiments in the central United States, we examined how anoxic microsites varied with management (e.g., cultivation, tillage, and manure amendments) and whether anoxic microsites determine soil C concentration in surface (0-15 cm) soils. We used a novel approach to track anaerobe habitat space and, hence, anoxic microsites using DNA copies of anaerobic functional genes over a confined volume of soil. No-till practices inconsistently increased anoxic microsite extent compared to conventionally tilled soils, and within one site organic matter amendments increased anaerobe abundance in no-till soils. Across all long-term tillage trials, uncultivated soils had ∼2-4 times more copies of anaerobic functional genes than their cropland counterparts. Finally, anaerobe abundance was positively correlated to soil C concentration. Even when accounting for other soil C protection mechanisms, anaerobe abundance, our proxy for anoxic microsites, explained 41% of the variance and 5% of the unique variance in soil C concentration in cropland soils, making anoxic microsites the strongest management-responsive predictor of soil C concentration. Our results suggest that careful management of anoxic microsites may be a promising strategy to increase soil C storage within agricultural soils.
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Affiliation(s)
- Emily M. Lacroix
- Department
of Earth System Science, Stanford University, Stanford, California 94305, United States
- Institut
des Dynamiques de la Surface Terrestre (IDYST), Université de Lausanne, Lausanne 1015, Switzerland
| | - Anna Gomes
- Department
of Earth System Science, Stanford University, Stanford, California 94305, United States
| | | | - Dylan Schuler
- Department
of Earth System Science, Stanford University, Stanford, California 94305, United States
| | - Anne E. Dekas
- Department
of Earth System Science, Stanford University, Stanford, California 94305, United States
| | - Daniel Liptzin
- Soil
Health Institute, Morrisville, North Carolina 27560, United States
| | - Ezra Aberle
- Carrington
Research Extension Center, North Dakota
State University, Carrington, North Dakota 58421, United States
| | - Dexter B. Watts
- National
Soils Dynamics Lab, Agricultural Research
Service, U.S. Department of Agriculture, Auburn, Alabama 36830, United States
| | - Kelly A. Nelson
- Lee
Greenley
Jr. Memorial Research Center, University
of Missouri, Novelty, Missouri 63460, United States
| | - Steven Culman
- Department
of Crop and Soil Science, Washington State
University, Pullman, Washington 99164, United States
| | - Scott Fendorf
- Department
of Earth System Science, Stanford University, Stanford, California 94305, United States
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Shinjo R, Oe F, Nakagawa K, Murase J, Asakawa S, Watanabe T. Type-specific quantification of particulate methane monooxygenase gene of methane-oxidizing bacteria at the oxic-anoxic interface of a surface paddy soil by digital PCR. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:392-403. [PMID: 37078408 PMCID: PMC10472520 DOI: 10.1111/1758-2229.13155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/10/2023] [Indexed: 05/03/2023]
Abstract
Aerobic methane-oxidizing bacteria (MOB) play an important role in mitigating methane emissions from paddy fields. In this study, we developed a differential quantification method for the copy number of pmoA genes of type Ia, Ib, and IIa MOB in paddy field soil using chip-based digital PCR. Three probes specific to the pmoA of type Ia, Ib, and IIa MOB worked well in digital PCR quantification when genomic DNA of MOB isolates and PCR-amplified DNA fragments of pmoA were examined as templates. When pmoA genes in the surface soil layer of a flooded paddy were quantified by digital PCR, the copy numbers of type Ia, Ib, and IIa MOB were 105 -106 , 105 -106 , and 107 copies g-1 dry soil, respectively, with the highest values in the top 0-2-mm soil layer. Especially, the copy numbers of type Ia and Ib MOB increased by 240% and 380% at the top layer after soil flooding, suggesting that the soil circumstances at the oxic-anoxic interfaces were more preferential for growth of type I MOB than type II MOB. Thus, type I MOB likely play an important role in the methane consumption at the surface paddy soil.
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Affiliation(s)
- Rina Shinjo
- Graduate School of Bioagricultural SciencesNagoya University, ChikusaNagoya464‐8601Japan
| | - Fumika Oe
- Graduate School of Bioagricultural SciencesNagoya University, ChikusaNagoya464‐8601Japan
| | - Koki Nakagawa
- School of Agricultural SciencesNagoya University, ChikusaNagoya464‐8601Japan
| | - Jun Murase
- Graduate School of Bioagricultural SciencesNagoya University, ChikusaNagoya464‐8601Japan
| | - Susumu Asakawa
- Graduate School of Bioagricultural SciencesNagoya University, ChikusaNagoya464‐8601Japan
| | - Takeshi Watanabe
- Graduate School of Bioagricultural SciencesNagoya University, ChikusaNagoya464‐8601Japan
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Lacroix EM, Aeppli M, Boye K, Brodie E, Fendorf S, Keiluweit M, Naughton HR, Noël V, Sihi D. Consider the Anoxic Microsite: Acknowledging and Appreciating Spatiotemporal Redox Heterogeneity in Soils and Sediments. ACS EARTH & SPACE CHEMISTRY 2023; 7:1592-1609. [PMID: 37753209 PMCID: PMC10519444 DOI: 10.1021/acsearthspacechem.3c00032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/07/2023] [Accepted: 07/21/2023] [Indexed: 09/28/2023]
Abstract
Reduction-oxidation (redox) reactions underlie essentially all biogeochemical cycles. Like most soil properties and processes, redox is spatiotemporally heterogeneous. However, unlike other soil features, redox heterogeneity has yet to be incorporated into mainstream conceptualizations of soil biogeochemistry. Anoxic microsites, the defining feature of redox heterogeneity in bulk oxic soils and sediments, are zones of oxygen depletion in otherwise oxic environments. In this review, we suggest that anoxic microsites represent a critical component of soil function and that appreciating anoxic microsites promises to advance our understanding of soil and sediment biogeochemistry. In sections 1 and 2, we define anoxic microsites and highlight their dynamic properties, specifically anoxic microsite distribution, redox gradient magnitude, and temporality. In section 3, we describe the influence of anoxic microsites on several key elemental cycles, organic carbon, nitrogen, iron, manganese, and sulfur. In section 4, we evaluate methods for identifying and characterizing anoxic microsites, and in section 5, we highlight past and current approaches to modeling anoxic microsites. Finally, in section 6, we suggest steps for incorporating anoxic microsites and redox heterogeneities more broadly into our understanding of soils and sediments.
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Affiliation(s)
- Emily M. Lacroix
- Institut
des Dynamiques de la Surface Terrestre (IDYST), Université de Lausanne, 1015 Lausanne, Switzerland
- Department
of Earth System Science, Stanford University, Stanford, California 94305, United States
| | - Meret Aeppli
- Institut
d’ingénierie de l’environnement (IIE), École Polytechnique Fédérale
de Lausanne, 1015 Lausanne, Switzerland
| | - Kristin Boye
- Environmental
Geochemistry Group, SLAC National Accelerator
Laboratory, Menlo Park, California 94025, United States
| | - Eoin Brodie
- Lawrence
Berkeley Laboratory, Earth and Environmental
Sciences Area, Berkeley, California 94720, United States
| | - Scott Fendorf
- Department
of Earth System Science, Stanford University, Stanford, California 94305, United States
| | - Marco Keiluweit
- Institut
des Dynamiques de la Surface Terrestre (IDYST), Université de Lausanne, 1015 Lausanne, Switzerland
| | - Hannah R. Naughton
- Lawrence
Berkeley Laboratory, Earth and Environmental
Sciences Area, Berkeley, California 94720, United States
| | - Vincent Noël
- Environmental
Geochemistry Group, SLAC National Accelerator
Laboratory, Menlo Park, California 94025, United States
| | - Debjani Sihi
- Department
of Environmental Sciences, Emory University, Atlanta, Georgia 30322, United States
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Competitiveness of Quantitative Polymerase Chain Reaction (qPCR) and Droplet Digital Polymerase Chain Reaction (ddPCR) Technologies, with a Particular Focus on Detection of Antibiotic Resistance Genes (ARGs). Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1030028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
With fast-growing polymerase chain reaction (PCR) technologies and various application methods, the technique has benefited science and medical fields. While having strengths and limitations on each technology, there are not many studies comparing the efficiency and specificity of PCR technologies. The objective of this review is to summarize a large amount of scattered information on PCR technologies focused on the two majorly used technologies: qPCR (quantitative polymerase chain reaction) and ddPCR (droplet-digital polymerase chain reaction). Here we analyze and compare the two methods for (1) efficiency, (2) range of detection and limitations under different disciplines and gene targets, (3) optimization, and (4) status on antibiotic resistance genes (ARGs) analysis. It has been identified that the range of detection and quantification limit varies depending on the PCR method and the type of sample. Careful optimization of target gene analysis is essential for building robust analysis for both qPCR and ddPCR. In our era where mutation of genes may lead to a pandemic of viral infectious disease or antibiotic resistance-induced health threats, this study hopes to set guidelines for meticulous detection, quantification, and analysis to help future prevention and protection of global health, the economy, and ecosystems.
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Phillips L, Nelson L. Introduction to Special Issue from Rhizosphere 5. Can J Microbiol 2021; 67:iii. [PMID: 34296952 DOI: 10.1139/cjm-2021-0117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Lori Phillips
- Research scientist, Agriculture and Agri-Food Canada
| | - Louise Nelson
- Professor Emerita, Dept. of Biology, The University of British Columbia, Okanagan Campus
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