Effect of fabric mulch ground covers on lemon trees rhizosphere microbiome in Florida flatwood soils

Santiago, John M.; Fox, John-Paul; Guzmán, Sandra M.; Rossi, Lorenzo

doi:10.3389/fsoil.2023.1110370

Cited by 3 publications

(3 citation statements)

References 55 publications

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“…As a result we would expect these enzymes to perform well on other genomes irrespective of complexity and GC content, especially when using pure genomic DNA as used here. It should be noted that RepliQa is also reported to be tolerant to many known PCR inhibitors that can be present in crude extracts and has been shown to efficiently amplify targets from soil [ 27 ] and insects [ 28 ]. Given that these enzymes give efficient amplification of both high and low GC content loci, though not tested here, it is expected that they would be particularly suited for amplification of metagenomes and microbial communities containing many different species at different percentages and with widely varying GC content genomes.…”

Section: Discussionmentioning

confidence: 99%

Identifying the best PCR enzyme for library amplification in NGS

Quail,

Corton,

Uphill

et al. 2024

Microbial Genomics

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Background. PCR amplification is a necessary step in many next-generation sequencing (NGS) library preparation methods []. Whilst many PCR enzymes are developed to amplify single targets efficiently, accurately and with specificity, few are developed to meet the challenges imposed by NGS PCR, namely unbiased amplification of a wide range of different sizes and GC content. As a result PCR amplification during NGS library prep often results in bias toward GC neutral and smaller fragments. As NGS has matured, optimized NGS library prep kits and polymerase formulations have emerged and in this study we have tested a wide selection of available enzymes for both short-read Illumina library preparation and long fragment amplification ahead of long-read sequencing. We tested over 20 different hi-fidelity PCR enzymes/NGS amplification mixes on a range of Illumina library templates of varying GC content and composition, and find that both yield and genome coverage uniformity characteristics of the commercially available enzymes varied dramatically. Three enzymes Quantabio RepliQa Hifi Toughmix, Watchmaker Library Amplification Hot Start Master Mix (2X) ‘Equinox’ and Takara Ex Premier were found to give a consistent performance, over all genomes, that mirrored closely that observed for PCR-free datasets. We also test a range of enzymes for long-read sequencing by amplifying size fractionated S. cerevisiae DNA of average size 21.6 and 13.4 kb, respectively. The enzymes of choice for short-read (Illumina) library fragment amplification are Quantabio RepliQa Hifi Toughmix, Watchmaker Library Amplification Hot Start Master Mix (2X) ‘Equinox’ and Takara Ex Premier, with RepliQa also being the best performing enzyme from the enzymes tested for long fragment amplification prior to long-read sequencing.

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Section: Discussionmentioning

confidence: 99%

Identifying the best PCR enzyme for library amplification in NGS

Quail,

Corton,

Uphill

et al. 2024

Microbial Genomics

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show abstract

Section: Discussionmentioning

confidence: 99%

Identifying the best PCR enzyme for library amplification in NGS

Quail

Corton

Uphill

et al. 2022

Preprint

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Background PCR amplification is a necessary step in many next generation sequencing (NGS) library preparation methods[1] [2]. Whilst many PCR enzymes are developed to amplify single targets efficiently, accurately and with specificity, few are developed to meet the challenges imposed by NGS PCR, namely unbiased amplification of a wide range of different sizes and GC content. As a result PCR amplification during NGS library prep often results in bias toward GC neutral and smaller fragments. As NGS has matured, optimised NGS library prep kits and polymerase formulations have emerged and in this study we have tested a wide selection of available enzymes for both short read Illumina library preparation and long fragment amplification ahead of long-read sequencing. Results We tested over 20 different Hi-fidelity PCR enzymes/NGS amplification mixes on a range of Illumina library templates of varying GC content and composition, and find that both yield and genome coverage uniformity characteristics of the commercially available enzymes varied dramatically. Three enzymes Quantabio RepliQa Hifi Toughmix, Watchmaker Library Amplification Hot Start Master Mix (2X) Equinox and Takara Ex Premier were found to give a consistent performance, over all genomes, that mirrored closely that observed for PCR free datasets. We also test a range of enzymes for long read sequencing by amplifying size fractionated S. cerevisiae DNA of average size 21.6 and 13.4kb respectively. Conclusion The enzymes of choice for short read (Illumina) library fragment amplification are Quantabio RepliQa Hifi Toughmix, Watchmaker Library Amplification Hot Start Master Mix (2X) Equinox and Takara Ex Premier, with RepliQa also being the best performing enzyme from the enzymes tested for long fragment amplification prior to long read sequencing.

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“…The CS1_515F (5 -ACACTGAC-GACATGGTTCTACAGTGYCAGCMGCCGCGGTAA-3 ) and CS2_926R (5 -TACGGTAGC-AGAGACTTGGTCTCCGYCAATTYMTTTRAGTTT-3 ) primers were then used in the PCR amplification of the DNA, specifically, the V4-V5 variable regions' RNA genes. The Genomics and Microbiome Core Facility (GMCF) at Rush University (Chicago, IL, USA) executed both the library preparation and sequencing of the DNA samples according to the methods found in Santiago et al [31].…”

Section: Dna Quantification and Pcr Amplification Of Rhizophere Soil ...mentioning

confidence: 99%

Impacts of Oak Mulch Amendments on Rhizosphere Microbiome of Citrus Trees Grown in Florida Flatwood Soils

Santiago,

Hallman,

Fox

et al. 2023

Microorganisms

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Rhizosphere interactions are an understudied component of citrus production. This is even more important in Florida flatwood soils, which pose significant challenges in achieving sustainable and effective fruit production due to low natural fertility and organic matter. Citrus growers apply soil amendments, including oak mulch, to ameliorate their soil conditions. Thus, the aim of this research was to evaluate the effects of oak mulch on citrus nutrient uptake, soil characteristics, and rhizosphere composition. The plant material consisted of ‘Valencia’ sweet orange (Citrus × sinensis) trees grafted on ‘US-812’ (C. reticulata × C. trifoliata) rootstock. The experiment consisted of two treatments, which included trees treated with oak mulch (300 kg of mulch per plot) and a control. The soil and leaf nutrient contents, soil pH, cation exchange capacity, moisture, temperature, and rhizosphere bacterial compositions were examined over the course of one year (spring and fall 2021). During the spring samplings, the citrus trees treated with oak mulch resulted in significantly greater soil Zn and Mn contents, greater soil moisture, and greater rhizosphere bacterial diversity compared to the control, while during the fall samplings, only a greater soil moisture content was observed in the treated trees. The soil Zn and Mn content detected during the spring samplings correlated with the significant increases in the diversity of the rhizosphere bacterial community composition. Similarly, the reduced rates of leaching and evaporation (at the soil surface) of oak mulch applied to Florida sandy soils likely played a large role in the significant increase in moisture and nutrient retention.

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Effect of fabric mulch ground covers on lemon trees rhizosphere microbiome in Florida flatwood soils

Cited by 3 publications

References 55 publications

Identifying the best PCR enzyme for library amplification in NGS

Identifying the best PCR enzyme for library amplification in NGS

Identifying the best PCR enzyme for library amplification in NGS

Impacts of Oak Mulch Amendments on Rhizosphere Microbiome of Citrus Trees Grown in Florida Flatwood Soils

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