Phosphorus mining activities alter endophytic bacterial communities and metabolic functions of surrounding vegetables and crops

Li, Qiang; Xiang, Peng; Li, Lijiao; Zhang, Ting; Wu, Qian; Bao, Zhijie; Tu, Wenying; Zhao, Changsong

doi:10.1007/s11104-023-05961-4

Cited by 16 publications

(8 citation statements)

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“…Mutations, natural selection, and genetic drift are all factors that contribute to the development of synonymous codons and thus have a considerable effect on genome evolution ( Li et al, 2018 ; Li B. et al, 2022 ). It has been proposed that interspecific differences in codon usage can be explained by a mutation mechanism in which codon bias is caused by the rate of repair of nucleotide bias or point mutations ( LaBella et al, 2019 ; Lamolle et al, 2022 ; Li et al, 2022c , 2023b ). Natural selection theory postulates that synonymous mutations that have an effect on an organism’s ability to adapt will be either favored or disfavored over the course of evolution, resulting in changes in codon usage in genomes or genes ( Dhindsa et al, 2020 ; Cope and Shah, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

Xiao

Luo

et al. 2023

Front. Microbiol.

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IntroductionCodon usage bias is a prevalent phenomenon observed across various species and genes. However, the specific attributes of codon usage in the mitochondrial genome of Ganoderma species remain unknown.MethodsIn this study, we investigated the codon bias of 12 mitochondrial core protein-coding genes (PCGs) in 9 Ganoderma species, including 13 Ganoderma strains.ResultsThe codons of all Ganoderma strains showed a preference for ending in A/T. Additionally, correlations between codon base composition and the codon adaptation index (CAI), codon bias index (CBI) and frequency of optimal codons (FOP) were identified, demonstrating the impact of base composition on codon bias. Various base bias indicators were found to vary between or within Ganoderma strains, including GC3s, the CAI, the CBI, and the FOP. The results also revealed that the mitochondrial core PCGs of Ganoderma have an average effective number of codons (ENC) lower than 35, indicating strong bias toward certain codons. Evidence from neutrality plot and PR2-bias plot analysis indicates that natural selection is a major factor affecting codon bias in Ganoderma. Additionally, 11 to 22 optimal codons (ΔRSCU>0.08 and RSCU>1) were identified in 13 Ganoderma strains, with GCA, AUC, and UUC being the most widely used optimal codons in Ganoderma. By analyzing the combined mitochondrial sequences and relative synonymous codon usage (RSCU) values, the genetic relationships between or within Ganoderma strains were determined, indicating variations between them. Nevertheless, RSCU-based analysis illustrated the intra- and interspecies relationships of certain Ganoderma species.DiscussionThis study deepens our insight into the synonymous codon usage characteristics, genetics, and evolution of this important fungal group.

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Section: Introductionmentioning

confidence: 99%

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

Xiao

Luo

et al. 2023

Front. Microbiol.

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“…Endophytes are ubiquitous in land–based plants (Lodewyckx et al., 2002; Mundt & Hinkle, 1976). While endophytes were traditionally thought to be only fungi, recent studies have shown that bacteria can also act as endophytes (Jayakumar et al., 2021; Li et al., 2023; Lodewyckx et al., 2002). To investigate the contribution of endophytes to in situ leaf N 2 O emissions, either a bactericide (streptomycin) or a fungicide (cycloheximide) solution was injected into the branches of the investigated plant taxa growing in situ (Experiment 6).…”

Section: Resultsmentioning

confidence: 99%

“…Endophytes are ubiquitous in land-based plants (Lodewyckx et al, 2002;Mundt & Hinkle, 1976). While endophytes were traditionally thought to be only fungi, recent studies have shown that bacteria can also act as endophytes (Jayakumar et al, 2021;Li et al, 2023;Lodewyckx et al, 2002). Note: The area data was obtained from Kirschbaum et al (2006) and House et al (2002); while dry biomass density and ratio of foliage to biomass (R) were sourced from Foley (1994).…”

Section: Epipremnum Aureummentioning

confidence: 99%

Foliar N₂O emissions constitute a significant source to atmosphere

Qin,

Pang,

et al. 2024

Global Change Biology

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Nitrous oxide (N2O) is a potent greenhouse gas and causes stratospheric ozone depletion. While the emissions of N2O from soil are widely recognized, recent research has shown that terrestrial plants may also emit N2O from their leaves under controlled laboratory conditions. However, it is unclear whether foliar N2O emissions are universal across varying plant taxa, what the global significance of foliar N2O emissions is, and how the foliage produces N2O in situ. Here we investigated the abilities of 25 common plant taxa, including trees, shrubs and herbs, to emit N2O under in situ conditions. Using 15N isotopic labeling, we demonstrated that the foliage‐emitted N2O was predominantly derived from nitrate. Moreover, by selectively injecting biocide in conjunction with the isolating and back‐inoculating of endophytes, we demonstrated that the foliar N2O emissions were driven by endophytic bacteria. The seasonal N2O emission rates ranged from 3.2 to 9.2 ng N2O–N g−1 dried foliage h−1. Extrapolating these emission rates to global foliar biomass and plant N uptake, we estimated global foliar N2O emission to be 1.21 and 1.01 Tg N2O–N year−1, respectively. These estimates account for 6%–7% of the current global annual N2O emission of 17 Tg N2O–N year−1, indicating that in situ foliar N2O emission is a universal process for terrestrial plants and contributes significantly to the global N2O inventory. This finding highlights the importance of measuring foliar N2O emissions in future studies to enable the accurate assigning of mechanisms and the development of effective mitigation.

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“…Sphingomonas paucimobilis was identified as a widespread nitrogen-fixing endophyte of wild and cultivated rice roots in Nepal ( Engelhard et al, 2000 ). Finally, Sphingomonas panii has been identified as a root endophyte of wheat, along with soybean and lettuce, and shown to have plant growth promoting activities ( Li et al, 2023 ).…”

Section: Discussionmentioning

confidence: 99%

Conservation and diversity of the pollen microbiome of Pan-American maize using PacBio and MiSeq

Khalaf,

Shrestha,

Reid

et al. 2023

Front. Microbiol.

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Pollen is a vector for diversification, fitness-selection, and transmission of plant genetic material. The extent to which the pollen microbiome may contribute to host diversification is largely unknown, because pollen microbiome diversity within a plant species has not been reported, and studies have been limited to conventional short-read 16S rRNA gene sequencing (e.g., V4-MiSeq) which suffers from poor taxonomic resolution. Here we report the pollen microbiomes of 16 primitive and traditional accessions of maize (corn) selected by indigenous peoples across the Americas, along with the modern U.S. inbred B73. The maize pollen microbiome has not previously been reported. The pollen microbiomes were identified using full-length (FL) 16S rRNA gene PacBio SMRT sequencing compared to V4-MiSeq. The Pan-American maize pollen microbiome encompasses 765 taxa spanning 39 genera and 46 species, including known plant growth promoters, insect-obligates, plant pathogens, nitrogen-fixers and biocontrol agents. Eleven genera and 13 species composed the core microbiome. Of 765 taxa, 63% belonged to only four genera: 28% were Pantoea, 15% were Lactococcus, 11% were Pseudomonas, and 10% were Erwinia. Interestingly, of the 215 Pantoea taxa, 180 belonged to a single species, P. ananatis. Surprisingly, the diversity within P. ananatis ranged nearly 10-fold amongst the maize accessions analyzed (those with ≥3 replicates), despite being grown in a common field. The highest diversity within P. ananatis occurred in accessions that originated near the center of diversity of domesticated maize, with reduced diversity associated with the north–south migration of maize. This sub-species diversity was revealed by FL-PacBio but missed by V4-MiSeq. V4-MiSeq also mis-identified some dominant genera captured by FL-PacBio. The study, though limited to a single season and common field, provides initial evidence that pollen microbiomes reflect evolutionary and migratory relationships of their host plants.

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Phosphorus mining activities alter endophytic bacterial communities and metabolic functions of surrounding vegetables and crops

Cited by 16 publications

References 75 publications

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

Foliar N₂O emissions constitute a significant source to atmosphere

Conservation and diversity of the pollen microbiome of Pan-American maize using PacBio and MiSeq

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Phosphorus mining activities alter endophytic bacterial communities and metabolic functions of surrounding vegetables and crops

Cited by 16 publications

References 75 publications

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

Foliar N2O emissions constitute a significant source to atmosphere

Conservation and diversity of the pollen microbiome of Pan-American maize using PacBio and MiSeq

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Product

Resources

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Foliar N₂O emissions constitute a significant source to atmosphere