Microbial Community Composition, Diversity, and Function

Manter, Daniel K.; Moore, J. Michael; Lehman, R. Michael; Hamm, Alison

doi:10.1002/9780891189831.ch13

Cited by 2 publications

(2 citation statements)

References 119 publications

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“…The abundance of rRNA genes was used to estimate the relative biomass of bacteria and fungi and to calculate fungal/bacterial (F:B) ratios, a potential indicator of land management (Kuske et al., 2019; Manter et al., 2021). In support of the total DNA assay results, there were 37% greater bacterial ( p = 0.001) and 33% greater fungal ( p = 0.009) ribosomal gene copies under AMP compared to conventional management (Table 2).…”

Section: Resultsmentioning

confidence: 99%

“…Fluorescence readings were acquired using a Biotek FLx800TBI microplate reader (excitation: 485/20, emission: 528/20). Total DNA (ng g −1 dry soil) was used as a proxy for microbial biomass (Kuske et al., 2019) and supported by biomass estimates of bacteria and fungi using quantitative polymerase chain reaction (qPCR) of rRNA genes (Kuske et al., 2019; Manter et al., 2021) as described below.…”

Section: Methodsmentioning

confidence: 99%

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Soil microorganisms respond distinctively to adaptive multi‐paddock and conventional grazing in the southeastern United States

White

Yeater

Lehman

2023

Soil Science Soc of Amer J

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Variable results from studies of the associations between grazing management and soil microbiological properties in grasslands suggest the need for further investigation. We assessed the response of soil microbiological properties to conventional and adaptive multi‐paddock (AMP) grazing management practices at paired farms at five locations in the southeastern United States. We measured total DNA and abundances of fungi and bacteria by quantitative polymerase chain reaction (qPCR) as proxies for soil microbial biomass, potential carbon, nitrogen, and phosphorus cycling activities using qPCR of functional genes, and carbon mineralization activities by respiratory assays. Abundances of fungi (p = 0.009) and bacteria (p = 0.001) were greater under AMP management compared to conventional management; however, there was no difference in the fungal/bacterial ratios between management practices. Gene copies encoding for nitrification, denitrification, and phosphate hydrolysis were significantly greater (p < 0.05) under AMP compared to conventional management. Basal soil respiration was elevated (p = 0.004) under AMP compared to conventional management presumptively due to the greater abundance of microbes that were actively transforming plant exudates and residues. In contrast, labile carbon limitation of respiratory activities was greater (p ≤ 0.01) under conventional compared to AMP management indicating decreased processing of soil carbon and formation of microbial biomass. Using discriminant function analysis, the 19 biological response variables successfully classified 94% of the 180 soil samples according to grazing management. In summary, AMP grazing management influenced the numbers and key activities of soil microbes in a distinctive manner that is associated with the retention of soil organic carbon and nitrogen reported in these grazed grasslands.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Soil microorganisms respond distinctively to adaptive multi‐paddock and conventional grazing in the southeastern United States

White

Yeater

Lehman

2023

Soil Science Soc of Amer J

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Unveiling errors in soil microbial community sequencing: a case for reference soils and improved diagnostics for nanopore sequencing

Manter,

Reardon,

Ashworth

et al. 2024

Commun Biol

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The sequencing platform and workflow strongly influence microbial community analyses through potential errors at each step. Effective diagnostics and experimental controls are needed to validate data and improve reproducibility. This cross-laboratory study evaluates sources of variability and error at three main steps of a standardized amplicon sequencing workflow (DNA extraction, polymerase chain reaction [PCR], and sequencing) using Oxford Nanopore MinION to analyze agricultural soils and a simple mock community. Variability in sequence results occurs at each step in the workflow with PCR errors and differences in library size greatly influencing diversity estimates. Common bioinformatic diagnostics and the mock community are ineffective at detecting PCR abnormalities. This work outlines several diagnostic checks and techniques to account for sequencing depth and ensure accuracy and reproducibility in soil community analyses. These diagnostics and the inclusion of a reference soil can help ensure data validity and facilitate the comparison of multiple sequencing runs within and between laboratories.

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Microbial Community Composition, Diversity, and Function

Cited by 2 publications

References 119 publications

Soil microorganisms respond distinctively to adaptive multi‐paddock and conventional grazing in the southeastern United States

Soil microorganisms respond distinctively to adaptive multi‐paddock and conventional grazing in the southeastern United States

Unveiling errors in soil microbial community sequencing: a case for reference soils and improved diagnostics for nanopore sequencing

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