Unraveling the Complexity of Soil Microbiomes in a Large-Scale Study Subjected to Different Agricultural Management in Styria

Köberl, Martina; Wagner, Philipp; Müller, Henry; Matzer, Robert; Unterfrauner, Hans; Cernava, Tomislav; Berg, Gabriele

doi:10.3389/fmicb.2020.01052

Cited by 43 publications

(22 citation statements)

References 62 publications

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“…The soil microbiota is crucial for agricultural productivity due to their contributions to and effects on nutrient mineralization, disease suppression, water retention or degradation of harmful molecules. A loss of species diversity and reduced abundance in the soil can therefore result in a plant microbiota being less rich in species diversity, resulting in decreased growth, increased susceptibility to diseases, and finally in harvest losses (Korenblum et al, 2020;Köberl et al, 2020). Agricultural practices such as continued monocultures without fallow periods can have detrimental effects on the soil microorganisms, and these effects can be caused by the release of plant metabolites into the soil (Li et al, 2019).…”

Section: General Effects Of the Plant Metabolites On Soil Bacteriamentioning

confidence: 99%

Differential Impact of Plant Secondary Metabolites on the Soil Microbiota

Schütz¹,

Frindte²,

Cui³

et al. 2021

Front. Microbiol.

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Plant metabolites can shape the microbial community composition in the soil. Two indole metabolites, benzoxazolinone (BOA) and gramine, produced by different Gramineae species, and quercetin, a flavonoid synthesized by many dicot species, were studied for their impacts on the community structure of field soil bacteria. The three plant metabolites were directly added to agricultural soil over a period of 28 days. Alterations in bacterial composition were monitored by next generation sequencing of 16S rRNA gene PCR products and phospholipid fatty acid analysis. Treatment of the soil with the plant metabolites altered the community composition from phylum to amplicon sequence variant (ASV) level. Alpha diversity was significantly reduced by BOA or quercetin, but not by gramine. BOA treatment caused a decrease of the relative abundance of 11 ASVs, while only 10 ASVs were increased. Gramine or quercetin treatment resulted in the increase in relative abundance of many more ASVs (33 or 38, respectively), most of them belonging to the Proteobacteria. Isolation and characterization of cultivable bacteria indicated an enrichment in Pseudarthrobacter or Pseudomonas strains under BOA/quercetin or BOA/gramine treatments, respectively. Therefore, the effects of the treatments on soil bacteria were characteristic for each metabolite, with BOA exerting a predominantly inhibitory effect, with only few genera being able to proliferate, while gramine and quercetin caused the proliferation of many potentially beneficial strains. As a consequence, BOA or gramine biosynthesis, which have evolved in different barley species, is accompanied with the association of distinct bacterial communities in the soil, presumably after mutual adaptation during evolution.

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Section: General Effects Of the Plant Metabolites On Soil Bacteriamentioning

confidence: 99%

Differential Impact of Plant Secondary Metabolites on the Soil Microbiota

Schütz¹,

Frindte²,

Cui³

et al. 2021

Front. Microbiol.

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“…The effect of HAp on such taxa is summed in Figure 10 and Figure 11 . Flavobacterium genus, for example, is a plant growth promoter and phytopathogen antagonist [ 77 ], but HAp decreased the population of Flavobacterium from 3 to 1% of the total microbiome, although it did mildly increase the total number of discriminable species, from 15 to 17. Rhizobium and Devosia genera also correlated positively with plant growth [ 78 ], and HAp increased the relative presence of Rhizobium from 0.4 to 0.5% and reduced the number of distinct species from five to four, while it did not affect the Devosia genus (0.2%) nor the Rhizobiaceae family (1%) to which a number of positive root bacteria belong.…”

Section: Resultsmentioning

confidence: 99%

Altering Microbiomes with Hydroxyapatite Nanoparticles: A Metagenomic Analysis

Uskoković

Wu²

2022

Materials

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Hydroxyapatite (HAp), the most abundant biological material among mammals, has been recently demonstrated to possess moderate antibacterial properties. Metagenomics provides a series of tools for analyzing the simultaneous interaction of materials with larger communities of microbes, which may aid in optimizing the antibacterial activity of a material such as HAp. Here, a microbiome intrinsic to the sample of sandy soil collected from the base of an African Natal plum (Carissa macrocarpa) shrub surrounding the children’s sandbox at the Arrowhead Park in Irvine, California was challenged with HAp nanoparticles and analyzed with next-generation sequencing for hypervariable 16S ribosomal DNA base pair homologies. HAp nanoparticles overwhelmingly reduced the presence of Gram-negative phyla, classes, orders, families, genera and species, and consequently elevated the relative presence of their Gram-positive counterparts. Thermodynamic, electrostatic and chemical bonding arguments were combined in a model proposed to explain this selective affinity. The ability of amphiphilic surface protrusions of lipoteichoic acid in Gram-positive bacteria and mycolic acid in mycobacteria to increase the dispersibility of the bacterial cells and assist in their resistance to capture by the solid phase is highlighted. Within the Gram-negative group, the variability of the distal, O-antigen portion of the membrane lipopolysaccharide was shown to be excessive and the variability of its proximal, lipid A portion insufficient to explain the selectivity based on chemical sequence arguments. Instead, flagella-driven motility proves to be a factor favoring the evasion of binding to HAp. HAp displayed a preference toward binding to less pathogenic bacteria than those causative of disease in humans, while taxa having a positive agricultural effect were largely captured by HAp, indicating an evolutionary advantage this may have given it as a biological material. The capacity to selectively sequester Gram-negative microorganisms and correspondingly alter the composition of the microbiome may open up a new avenue in environmental and biomedical applications of HAp.

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“…A loss of species diversity and reduced abundance in the soil can therefore result in incomplete plant microbiota with reduced functions, resulting in decreased growth, increased susceptibility to diseases, and finally in harvest losses. Recently, Köberl et al identified edaphic conditions, including soil pH and herbicide usage as important factors for soil microbial community structures in vineyards, orchards and other crop soils (Köberl et al, 2020). Agricultural practices such as continued monocultures without fallow periods can have detrimental effects on the soil microorganisms, and these effects can be caused by the release of plant metabolites into the soil.…”

Section: Discussionmentioning

confidence: 99%

Differential impact of plant secondary metabolites on the soil microbiota

Schütz¹,

Frindte²,

Cui³

et al. 2021

Preprint

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Plant metabolites can shape the microbial community composition in the soil. Two indole metabolites, benzoxazolinone (BOA) and gramine, produced by different Gramineae species, and quercetin, a flavonoid synthesized by many dicot species, were studied for their impacts on the community structure of soil bacteria. The three plant metabolites were directly added to agricultural soil over a period of 28 days. Alterations in bacterial composition were monitored by next generation sequencing of 16S rRNA gene PCR products and phospholipid fatty acid analysis. Treatment of the soil with the plant metabolites altered the composition of bacterial taxa on the phylum and genus levels. Alpha diversity was significantly altered by BOA or quercetin, but not by gramine. BOA treatment caused an increase in the relative abundances of only four genera, three of them belonging to the Actinobacteriota. Gramine or quercetin treatment resulted in the increase in relative abundance of 13 or 14 genera, respectively, most of them belonging to the Proteobacteria. The relative abundance of 22 genera was decreased after BOA treatment, 16 of which were also decreased by gramine or quercetin. Isolation and characterization of cultivable bacterial indicated an enrichment in specific Arthrobacter or Pseudomonas strains. Therefore, the effects of the treatments on soil bacteria were characteristic for each metabolite, with BOA exerting a broad-spectrum inhibitory effect, with only few genera able to proliferate, while gramine and quercetin caused the proliferation of many potentially beneficial strains. As a consequence, benzoxazolinone or gramine biosynthesis which have evolved in different barley species, is accompanied with the association with distinct bacterial communities in the soil, presumably after mutual adaptation during evolution.

show abstract

Unraveling the Complexity of Soil Microbiomes in a Large-Scale Study Subjected to Different Agricultural Management in Styria

Cited by 43 publications

References 62 publications

Differential Impact of Plant Secondary Metabolites on the Soil Microbiota

Differential Impact of Plant Secondary Metabolites on the Soil Microbiota

Altering Microbiomes with Hydroxyapatite Nanoparticles: A Metagenomic Analysis

Differential impact of plant secondary metabolites on the soil microbiota

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