Is the Juice Worth the Squeeze? Evaluating Peptide Nucleic Acid (PNA) Blockers for Reducing Plant DNA Contamination in 16S rRNA Gene Sequencing DOI Creative Commons
Lena Flörl, Nicholas A. Bokulich

PhytoFrontiers™, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 4, 2024

Next-generation sequencing of microbial communities frequently results in off-target amplification the host or environmental DNA, which can lead to substantial data loss. This challenge is particularly pronounced plant-associated microbiome studies, commonly used 16S rRNA primers co-amplify mitochondrial and chloroplast DNA. To mitigate this, peptide nucleic acid (PNA) blockers have been applied reduce nonbacterial However, actual concentrations vary significantly across it not clear whether this affects retrieved bacterial diversity. In study, we evaluated efficacy universal PNA a range estimated their impact on alpha beta We found that at low (0.25 µM) efficiently reduced DNA contamination. Further, they did significant effect diversity no clades appeared be co-inhibited by addition blockers. Although implementing polymerase chain reaction protocols requires further optimization, our findings demonstrate “juice” (enhanced depth) indeed “worth squeeze” (additional effort), as are powerful tool for improving outcomes. [Formula: see text] Copyright © 2025 The Author(s). an open access article distributed under CC BY-NC-ND 4.0 International license .

Language: Английский

Forest top canopy bacterial communities are influenced by elevation and host tree traits DOI Creative Commons
Yiwei Duan, Andjin Siegenthaler, Andrew K. Skidmore

et al.

Environmental Microbiome, Journal Year: 2024, Volume and Issue: 19(1)

Published: April 5, 2024

Abstract Background The phyllosphere microbiome is crucial for plant health and ecosystem functioning. While host species play a determining role in shaping the microbiome, trees of same that are subjected to different environmental conditions can still exhibit large degrees variation their diversity composition. Whether these intra-specific variations composition be observed over broader expanse forest landscapes remains unclear. In this study, we aim assess top canopy bacterial communities between within tree temperate European forests, focusing on Fagus sylvatica (European beech) Picea abies (Norway spruce). Results We profiled diversity, composition, driving factors, discriminant taxa 211 two Veluwe National Parks, Netherlands Bavarian Forest Park, Germany. found were primarily shaped by species, existed beech spruce. showed there was core all examined, community varied with elevation, diameter at breast height, leaf-specific traits (e.g., chlorophyll P content). These factors also correlated relative abundance specific families. Conclusions our results underscored importance demonstrated substantial range species. Drivers have implications both individual level, where differed based traits, landscape drivers like certain highly plastic leaf potentially link processes. eventually close associations exist, consistent patterns emerging from critical

Language: Английский

Citations

5
Tree vitality predicts plant-pathogenic fungal communities in beech forest canopies DOI Creative Commons
Yiwei Duan, Andjin Siegenthaler, Andrew K. Skidmore

et al.

Forest Ecology and Management, Journal Year: 2025, Volume and Issue: 585, P. 122588 - 122588

Published: March 18, 2025

Language: Английский

Citations

0
eDNA biodiversity from space: predicting soil bacteria and fungi alpha diversity in forests using DESIS satellite remote sensing DOI Creative Commons
Andrew K. Skidmore, Haidi Abdullah, Andjin Siegenthaler

et al.

International Journal of Remote Sensing, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 31

Published: March 20, 2025

Language: Английский

Citations

0
A diverse and distinct microbiome inside living trees DOI Open Access
Wyatt Arnold, Jonathan Gewirtzman, Peter A. Raymond

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 2, 2024

Abstract Despite significant advances in microbiome research across various environments 1 , the of Earth’s largest biomass reservoir– wood living trees 2 – remains largely unexplored. This oversight neglects a critical aspect global biodiversity and potentially key players tree health forest ecosystem functions. Here we illuminate inhabiting adapted to wood, further specialized individual host species. We demonstrate that single can approximately trillion microbes its aboveground internal tissues, with microbial communities partitioned between heartwood sapwood, each maintaining distinct minimal similarity other plant tissues or nearby components. Notably, emerges as unique ecological niche, distinguished part by endemic archaea anaerobic bacteria drive consequential biogeochemical processes. Our supports emerging idea “holobiont” 3,4 —a unit comprising associated microorganisms—and parallels human implications for health, disease, functionality 5 . By mapping structure, composition, potential sources functions microbiome, our findings pave way novel insights into physiology ecology, establish new frontier environmental microbiology.

Language: Английский

Citations

2
Further reduction in soil bacterial diversity under severe acidification in European temperate forests DOI Creative Commons
Mélody Rousseau, Andjin Siegenthaler, Andrew K. Skidmore

et al.

European Journal of Soil Science, Journal Year: 2024, Volume and Issue: 75(6)

Published: Sept. 1, 2024

Despite a decrease in industrial nitrogen and sulfur deposition over recent decades, soil acidification remains persistent challenge to European forest health, especially regions of intense agriculture urbanisation. Using topsoil eDNA metabarcoding functional annotations from sample 49 plots (each 30 × m) located The Netherlands Germany, we investigated the effect severe on bacterial taxonomic diversity under different types explored potential implications for nutrient cycling. Furthermore, assessed which parameters known influence communities affect these acidophilic communities. Here, are first demonstrate natural conditions that extremely acidic soils (pH <4.5) continues decline similarly across as pH further decreases intensifying human activity. Our results confirmed key driver communities, even soils. Ongoing reduce favouring taxa adapted extreme acidity primarily involved recalcitrant carbon-degradation compounds (e.g. cellulolysis = 0.78%-9.99%) while simultaneously diminishing associated with cycling fixation 6.72%-0.00%). Altogether, our findings indicate already soils, likely disrupting through changes immobilisation mineralisation processes. study highlights continuous temperate forests low levels, ecosystem functioning. significant reduction such gradient, demonstrated here, underscores necessity include severely acidified conservation programmes monitoring prevent degradation beyond repair.

Language: Английский

Citations

2
Rhizosphere-xylem sap connections in the olive tree microbiome: implications for biostimulation approaches DOI

Mónica Marques,

Isabel N. Sierra-García, Frederico Leitão

et al.

Journal of Applied Microbiology, Journal Year: 2024, Volume and Issue: 135(7)

Published: June 20, 2024

Climate change is endangering olive groves. Farmers are adapting by exploring new varieties of trees and examining the role microbiomes in plant health.The main objectives this work were to determine primary factors that influence microbiome analyze connection between rhizosphere endosphere compartments.

Language: Английский

Citations

0
Microbial community diversity analysis of kiwifruit pollen and identification of potential pathogens DOI

Jiaqi Yang,

Manli Yao,

Dan Zhang

et al.

Antonie van Leeuwenhoek, Journal Year: 2024, Volume and Issue: 117(1)

Published: Aug. 20, 2024

Language: Английский

Citations

0
Is the Juice Worth the Squeeze? Evaluating Peptide Nucleic Acid (PNA) Blockers for Reducing Plant DNA Contamination in 16S rRNA Gene Sequencing DOI Creative Commons
Lena Flörl, Nicholas A. Bokulich

PhytoFrontiers™, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 4, 2024

Next-generation sequencing of microbial communities frequently results in off-target amplification the host or environmental DNA, which can lead to substantial data loss. This challenge is particularly pronounced plant-associated microbiome studies, commonly used 16S rRNA primers co-amplify mitochondrial and chloroplast DNA. To mitigate this, peptide nucleic acid (PNA) blockers have been applied reduce nonbacterial However, actual concentrations vary significantly across it not clear whether this affects retrieved bacterial diversity. In study, we evaluated efficacy universal PNA a range estimated their impact on alpha beta We found that at low (0.25 µM) efficiently reduced DNA contamination. Further, they did significant effect diversity no clades appeared be co-inhibited by addition blockers. Although implementing polymerase chain reaction protocols requires further optimization, our findings demonstrate “juice” (enhanced depth) indeed “worth squeeze” (additional effort), as are powerful tool for improving outcomes. [Formula: see text] Copyright © 2025 The Author(s). an open access article distributed under CC BY-NC-ND 4.0 International license .

Language: Английский

Citations

0