The state of rhizospheric science in the era of multi-omics: A practical guide to omics technologies

White, Richard Allen; Rivas‐Ubach, Albert; Borkum, Mark; Köberl, Martina; Pena, Aivett Bilbao; Colby, Sean; Hoyt, David; Bingol, Kerem; Kim, Young-Mo; Wendler, Jason P.; Hixson, Kim; Jansson, Christer

doi:10.1016/j.rhisph.2017.05.003

Cited by 76 publications

(38 citation statements)

References 101 publications

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“…One key challenge in biology is to translate this information to determine the phenotype of an organism by combining genome, transcriptome, proteome, metabolome, structural, and physiological information. Organisms perform many of the functions through the use of small molecules and metabolites; therefore, small biological molecules, metabolites provide unique piece of information to help in shedding the light on phenotypic characteristics of genome sequence [ 3 , 4 , 5 , 6 , 7 ].…”

Section: Introductionmentioning

confidence: 99%

Recent Advances in Targeted and Untargeted Metabolomics by NMR and MS/NMR Methods

2018

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Metabolomics has made significant progress in multiple fronts in the last 18 months. This minireview aimed to give an overview of these advancements in the light of their contribution to targeted and untargeted metabolomics. New computational approaches have emerged to overcome the manual absolute quantitation step of metabolites in one-dimensional (1D) 1H nuclear magnetic resonance (NMR) spectra. This provides more consistency between inter-laboratory comparisons. Integration of two-dimensional (2D) NMR metabolomics databases under a unified web server allowed for very accurate identification of the metabolites that have been catalogued in these databases. For the remaining uncatalogued and unknown metabolites, new cheminformatics approaches have been developed by combining NMR and mass spectrometry (MS). These hybrid MS/NMR approaches accelerated the identification of unknowns in untargeted studies, and now they are allowing for profiling ever larger number of metabolites in application studies.

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Section: Introductionmentioning

confidence: 99%

Recent Advances in Targeted and Untargeted Metabolomics by NMR and MS/NMR Methods

2018

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“…Root associated rhizosphere microbiome is a highly dynamic interface containing >30,000 bacterial species (1)(2)(3). Rhizobium are symbiotic nitrogen-fixing bacteria that form plant-accessory structures with leguminous plants (e.g., Trifolium) known as nodules, which biological nitrogen fixation the process of transforming molecular nitrogen (N2) into ammonium (NH3) occurs (4).…”

Section: Discussionmentioning

confidence: 99%

Unraveling the Draft Genome Sequence of Paenibacillus sp. tmac-D7 a Non-Rhizobial Endophyte from Trifolium macraei Located in Bodega Bay, California

White¹,

Mclachlan²,

Dunham³

et al. 2019

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Paenibacillus sp. tmac-D7 was isolated from coastline growing Trifolium macraei (double-head clover) root nodules from Bodega Bay, California. The draft genome is 5,567,337 bp with a G+C% of 52.4%, an N50 of 114,261 bp, and 5,282 predicted protein-coding genes. Paenibacillus, while found in many other environments, is frequently isolated from root nodules, with many acting as plant pathogen antagonists. Paenibacillus sp. tmac-D7 is the first genome of a non-rhizobial endophyte isolate from wild Trifolium macraei (double-head clover).

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“…Rhizosphere soils represent one of the most microbially diverse ecosystems on the planet (1)(2)(3). Understanding microbes that fix atmospheric nitrogen (i.e., diazotrophs) within the rhizosphere interface is critical for soil health and crop production.…”

Section: Discussionmentioning

confidence: 99%

Elucidation of the Draft Genome Sequence of Ideonella azotifigens DSMZ21438 A Novel Aerobic Diazotroph of the Betaproteobacteria Isolated from Grass Rhizosphere Soil

White¹,

Norman²,

Mclachlan³

et al. 2019

Preprint

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Here, we report the draft genome sequence of the type strain of Ideonella azotifigens DSMZ21438T (formally 1a22T = JCM15503T). Ideonella azotifigens DSMZ21438T a novel betaproteobacterial non-symbiotic nitrogen-fixing grass rhizosphere dwelling microbe. The 891,561 paired-end shotgun reads were quality filtered and decontaminated with the ATLAS pipeline, then assembled with Unicycler. The genome size is 6,257,981 bp, an N50 size of 7,849 bp, with a G+C content of 66.71%, and with 5,882 predicted protein-coding genes. I. azotifigens DSMZ21438T represents the first member of the genus isolated from rhizosphere soil, providing a framework for further study into non-alphaproteobacterial nitrogen fixation and synthetic biology applications.

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The state of rhizospheric science in the era of multi-omics: A practical guide to omics technologies

Cited by 76 publications

References 101 publications

Recent Advances in Targeted and Untargeted Metabolomics by NMR and MS/NMR Methods

Recent Advances in Targeted and Untargeted Metabolomics by NMR and MS/NMR Methods

Unraveling the Draft Genome Sequence of <i>Paenibacillus </i>sp. tmac-D7 a Non-Rhizobial Endophyte from <i>Trifolium macraei</i> Located in Bodega Bay, California <strong> </strong>

Elucidation of the Draft Genome Sequence of <em>Ideonella azotifigens</em> DSMZ21438 A Novel Aerobic Diazotroph of the Betaproteobacteria Isolated from Grass Rhizosphere Soil

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