Alternative nitrogenase of Paenibacillus sonchi genomovar Riograndensis: An insight in the origin of Fe-nitrogenase in the Paenibacillaceae family

Ribeiro, Igor Daniel Alves; Bach, Evelise; Passaglia, Luciane Maria Pereira

doi:10.1016/j.ympev.2022.107624

Cited by 3 publications

(9 citation statements)

References 82 publications

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“…To gain insight into the evolution of the genus Paenibacillus on the genome level, the pangenome repertoire of P. sonchi was analyzed by using not only the complete genome sequence of the genomovar Riograndensis SBR5T ( Brito et al, 2015 ), but also those of the genomovars Oryzarum CAR114, Oryzarum CAS34 and Sonchi LMG_24727 ( Ribeiro et al 2022 ). The genomovars shared 39% of all genes (4,365 of 11,205 genes).…”

Section: P Sonchi Genomovar Riograndensis Sbr5t: Isolation (...mentioning

confidence: 99%

“…Next, a pangenome analysis of one of the five phylogenetically isolated clades of diazotrophic Paenibacillus genomes was performed since it comprised most Paenibacillus genomes harboring alternative nitrogenase genes (83 genomes passed the quality criteria) including that of P. sonchi genomovar Riograndensis SBR5T. About 1,100 genes make up this core pangenome ( Ribeiro et al 2022 ). The pangenome was determined to be open since an increasing tendency to expand the pangenome repertoire was observed if more genomes were incorporated, whereas the core pangenome was stabilized.…”

Section: P Sonchi Genomovar Riograndensis Sbr5t: Isolation (...mentioning

confidence: 99%

“…The pangenome was determined to be open since an increasing tendency to expand the pangenome repertoire was observed if more genomes were incorporated, whereas the core pangenome was stabilized. This is characteristic of bacteria living in multiple or complex niches, and complex communities with larger effective population sizes ( Ribeiro et al 2022 ). The pangenome analysis helped the characterization of the occurrence of different types of nitrogenases in P. sonchi genomomar Riograndensis (s. below).…”

Section: P Sonchi Genomovar Riograndensis Sbr5t: Isolation (...mentioning

confidence: 99%

“…The evolution of the alternative nitrogenase has been studied in some detail in the Paenibacillaceae family by bioinformatics analysis ( Ribeiro et al, 2022 ). Of 930 genomes in the Paenibacillaceae family, 160 were identified as putative diazotrophic genomes.…”

Section: P Sonchi Genomovar Riograndensis Sbr5t As a Pgprmentioning

confidence: 99%

“…Thus, 17% of these species are expected to fix nitrogen. Of these, only a subset making up 2.5% of all Paenibacillaceae genomes possess genes for the alternative Fe- or V- nitrogenase enzymes ( Ribeiro et al , 2022 ). Genomes encoding the Fe-only nitrogenase shared two operons, nifEN and anfHDGK , and belonged to the three genera Gorillibacterium, Fontibacillus, and Paenibacillus, in the latter there is the addition of the nifX in the operon that contains the nifEN genes.…”

Section: P Sonchi Genomovar Riograndensis Sbr5t As a Pgprmentioning

confidence: 99%

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Genome-based analyses to learn from and about Paenibacillus sonchi genomovar Riograndensis SBR5T

Wendisch,

Brito,

Passaglia

2023

Genet. Mol. Biol.

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Paenibacillus sonchi genomovar Riograndensis SBR5T is a plant growth-promoting rhizobacterium (PGPR) isolated in the Brazilian state of Rio Grande do Sul from the rhizosphere of Triticum aestivum. It fixes nitrogen, produces siderophores as well as the phytohormone indole-3-acetic acid, solubilizes phosphate and displays antagonist activity against Listeria monocytogenes and Pectobacterium carotovorum. Comprehensive omics analysis and the development of genetic tools are key to characterizing and engineering such non-model microorganisms. Therefore, the complete genome of SBR5T was sequenced, and shown to encode 6,705 proteins, 87 tRNAs, and 27 rRNAs and it enabled a landscape transcriptome analysis that unveiled conserved transcriptional and translational patterns and characterized operon structures and riboswitches. The pangenome of P. sonchi species is open with a stable core pangenome. At the same time, the analysis of genes coding for nitrogenases revealed that the trait of nitrogen fixation is sparse within the Paenibacillaceae family and the presence of Fe-only nitrogenase in the P. sonchi group was exclusive to SBR5T. The development of genetic tools for SBR5T enabled genetic transformation, plasmid construction for constitutive and inducible gene expression, and gene repression using the CRISPRi system. Altogether, the work with P. sonchi can guide the study of non-model bacteria with economic potential.

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Section: P Sonchi Genomovar Riograndensis Sbr5t: Isolation (...mentioning

confidence: 99%

Section: P Sonchi Genomovar Riograndensis Sbr5t: Isolation (...mentioning

confidence: 99%

Section: P Sonchi Genomovar Riograndensis Sbr5t: Isolation (...mentioning

confidence: 99%

Section: P Sonchi Genomovar Riograndensis Sbr5t As a Pgprmentioning

confidence: 99%

Section: P Sonchi Genomovar Riograndensis Sbr5t As a Pgprmentioning

confidence: 99%

See 3 more Smart Citations

Genome-based analyses to learn from and about Paenibacillus sonchi genomovar Riograndensis SBR5T

Wendisch,

Brito,

Passaglia

2023

Genet. Mol. Biol.

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Proteome profiling of Paenibacillus sonchi genomovar Riograndensis SBR5T under conventional and alternative nitrogen fixation

Ribeiro,

Paes,

Wendisch

et al. 2024

Journal of Proteomics

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Annual Weeds Suppression and Oat Forage Yield Responses to Crop Density Management in an Oat-Cultivated Grassland: A Case Study in Eastern China

Tang,

Li,

Guo

et al. 2024

Agronomy

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Although weeds can be inhibited by high planting densities, canopy shading, elemental balance and soil microbial recruitment are not yet adequately considered when measuring competitive effects on weed control. The effects of oat (Avena sativa) planting density (60 to 600 plants m−2) on the biomass and shoot element balance of oat and weeds were evaluated in a field experiment. The shift in the microbial community of the dominant weed species was examined in a pot experiment by growing the weed alone and in competition with 360 oat plants m−2 (recommended planting density) under greenhouse conditions. Increasing oat planting density beyond 360 plants m−2 did not improve oat forage yield or weed suppression. Compared to 60 plants m−2, the biomass of broadleaf and grass weeds decreased by 1122% and 111%, respectively, at a density of 360 plants m−2, while oat forage biomass increased by 60% and leaf area index by 24%. The improved canopy properties suppressed competing weeds through increased shading. Typically, the C:N and C:P ratios of shoots of Echinochloa crus-galli and Digitaria sanguinalis were higher than those of Portulaca oleracea and Chenopodium album. At high planting densities, E. crus-galli and D. sanguinalis exhibited high P contents and low N:P ratios, suggesting a limited supply of N nutrients for growth. Soil bacterial community assay showed that the composition of microbial communities of the two grass weeds were shaped by the presence of oat competition, which also considerably depleted several important functional microbes associated with nutrient cycling in the weeds’ rhizosphere. These results highlight that increased crop density significantly improves the crop competitive advantage over weeds through increased shading, reduced elemental balance, and beneficial microorganisms of weeds, thereby reducing the need for herbicides or physical weed control in oat cropping system.

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Alternative nitrogenase of Paenibacillus sonchi genomovar Riograndensis: An insight in the origin of Fe-nitrogenase in the Paenibacillaceae family

Cited by 3 publications

References 82 publications

Genome-based analyses to learn from and about Paenibacillus sonchi genomovar Riograndensis SBR5T

Genome-based analyses to learn from and about Paenibacillus sonchi genomovar Riograndensis SBR5T

Proteome profiling of Paenibacillus sonchi genomovar Riograndensis SBR5T under conventional and alternative nitrogen fixation

Annual Weeds Suppression and Oat Forage Yield Responses to Crop Density Management in an Oat-Cultivated Grassland: A Case Study in Eastern China

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