A novel Delftia plant symbiont capable of autotrophic methylotrophy

Agafonova, N. V.; Доронина, Н. В.; Капаруллина, Е. Н.; Федоров, Д. Н.; Гафаров, А. Б.; Сазонова, О. И.; Sokolov, S. L.; Trotsenko, Yu. A.

doi:10.1134/s0026261717010039

Cited by 20 publications

(18 citation statements)

References 25 publications

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“…In addition to methanol, ESM-1 grew on formic acid, a C1 compound, as a sole source of carbon and energy, highlighting the methylotrophic nature of this bacterium. These findings are in accordance with that reported recently by Agafonova et al (2017a) who provided the first comprehensive description of a facultative methylotrophic strain, Lp-1, within the genus Delftia . Lp-1 was isolated from root-nodules of Lupinus polyphyllus and exhibited a substantially high level of the 16S rRNA gene sequence similarity (99.9%) with D .…”

Section: Resultssupporting

confidence: 93%

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Polyphasic characterization of Delftia acidovorans ESM-1, a facultative methylotrophic bacterium isolated from rhizosphere of Eruca sativa

Khalifa

Almalki

2019

Saudi Journal of Biological Sciences

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In this study, one bacterial strain, ESM-1, was isolated from rhizosphere of Eruca sativa, growing in Al Hofouf, Saudia Arabia, after enrichment with methanol as a sole carbon and energy source in a batch culture. ESM-1 was characterized by a polyphasic approach. The strain was identified as Delftia acidovorans at similarity level of 99.9% of the 16S rRNA gene sequences. Results of the Biolog Gen III MicroPlate test system showed that strain ESM-1 reacted positively to 47 (50%) including the one-carbon compound formic acid, and partially positive to 6 (∼6.4%) out of the 94 different the traits examined. The total cellular fatty acids composition of the strain ESM-1 was (C16:1ω7c/C16:1ω6c) and C16:0) and matched that of Delftia acidovorans at a similarity index of 0.9, providing a robustness to the ESM-1 identification. Furthermore, ESM-1 displayed a complex polar lipid profile consisting of phosphatidylethanolamine, phosphatidylglycerol, glycolipid, aminolipid, in addition to uncharacterized lipids. The DNA G+C content of the strain was 66.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain ESM1-1 was clearly clustered within the Delftia clade and constructed a monophyletic subcluster with Delftia acidovorans NBRC14950. The results addressed that ESM-1 is a facultative methylotrophic bacterium indigenous to Al Hofouf region and opens the door for potential biotechnological applications (e.g., bioremediation) of this strain, in future. Additionally, these findings assure that the total cellular fatty acid analysis and 16S rRNA gene are reliable tool for bacterial characterization and identification.

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Section: Resultssupporting

confidence: 93%

“…These results were in general agreement with those determined with Delftia spp. (Agafonova et al, 2017a, Wen et al, 1999).…”

Section: Resultsmentioning

confidence: 99%

Polyphasic characterization of Delftia acidovorans ESM-1, a facultative methylotrophic bacterium isolated from rhizosphere of Eruca sativa

Khalifa

Almalki

2019

Saudi Journal of Biological Sciences

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“…Variovorax, Ramlibacter and Leptothrix genera within the Comamonadaceae were 13 C labelled in the rhizospheres of pea plants incubated with ambient and elevated 13 CO 2 . Strains from these genera have previously been found in rhizosphere environments [56][57][58][59]. The family Comamonadaceae contains bacteria that are metabolically versatile and can use a broad range of carbon substrates, enhance the cycling of sulfur in soil and suppress fungal pathogens [57,60].…”

Section: Phylogenetic Analysis Of the Exudate-utilising Community Of mentioning

confidence: 99%

“…The family Comamonadaceae contains bacteria that are metabolically versatile and can use a broad range of carbon substrates, enhance the cycling of sulfur in soil and suppress fungal pathogens [57,60]. Genera within this family include Variovorax and Delftia, which contain species known to grow on methanol [58,61]. An examination of all available genomes of members of the Comamonadaceae revealed that representatives of 28 out of 34 genera contain xoxF genes.…”

Section: Phylogenetic Analysis Of the Exudate-utilising Community Of mentioning

confidence: 99%

Impact of plants on the diversity and activity of methylotrophs in soil

et al. 2020

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Background: Methanol is the second most abundant volatile organic compound in the atmosphere, with the majority produced as a metabolic by-product during plant growth. There is a large disparity between the estimated amount of methanol produced by plants and the amount which escapes to the atmosphere. This may be due to utilisation of methanol by plant-associated methanol-consuming bacteria (methylotrophs). The use of molecular probes has previously been effective in characterising the diversity of methylotrophs within the environment. Here, we developed and applied molecular probes in combination with stable isotope probing to identify the diversity, abundance and activity of methylotrophs in bulk and in plant-associated soils. Results: Application of probes for methanol dehydrogenase genes (mxaF, xoxF, mdh2) in bulk and plant-associated soils revealed high levels of diversity of methylotrophic bacteria within the bulk soil, including Hyphomicrobium, Methylobacterium and members of the Comamonadaceae. The community of methylotrophic bacteria captured by this sequencing approach changed following plant growth. This shift in methylotrophic diversity was corroborated by identification of the active methylotrophs present in the soils by DNA stable isotope probing using 13 C-labelled methanol. Sequencing of the 16S rRNA genes and construction of metagenomes from the 13 C-labelled DNA revealed members of the Methylophilaceae as highly abundant and active in all soils examined. There was greater diversity of active members of the Methylophilaceae and Comamonadaceae and of the genus Methylobacterium in plant-associated soils compared to the bulk soil. Incubating growing pea plants in a 13 CO 2 atmosphere revealed that several genera of methylotrophs, as well as heterotrophic genera within the Actinomycetales, assimilated plant exudates in the pea rhizosphere. Conclusion: In this study, we show that plant growth has a major impact on both the diversity and the activity of methanol-utilising methylotrophs in the soil environment, and thus, the study contributes significantly to efforts to balance the terrestrial methanol and carbon cycle.

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“…The root endosphere of NahG/ACD plants were enriched for two taxa (ASVs 1 and 2) that were classified into genus Anaerobacillus (Phylum: Firmicutes) and Delftia (Phylum: Proteobacteria), respectively. Delftia is a highly diverse root-colonizer, and some isolates have been characterized for their biocontrol and plant growth promotion (PGP) properties (Morel, Cagide, Minteguiaga, Dardanelli & Castro-Sowinski 2015; Agafonova et al 2017).…”

Section: Discussionmentioning

confidence: 99%

Defense hormones modulate root microbiome diversity and composition in tomato

French

Ghaste

Widhalm

et al. 2019

Preprint

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Plant roots live closely associated with soil microbes. Understanding how roots defend against pathogenic microbes while associating with non-pathogenic microbes is critical to using root microbiomes for successful outcomes. The aim of this study was to determine the contribution of the plant defense hormones ethylene (ET), jasmonic acid (JA), and salicylic acid (SA) to the tomato root microbiome. We used 16S rRNA amplicon sequencing to examine the root microbiome of four tomato genotypes defective in three hormone pathways. We found that ET and SA pathways, but not JA, were critical for root endosphere microbial alpha (α)-diversity. Root endosphere communities of ACD, deficient in a precursor of ET, and the SA-deficient NahG transgenic, had significantly less α-diversity than wild-type tomatoes. NahG and ACD root endosphere enrichment profiles were similar and driven by two taxa. In NahG, ACD, and in a panel of 24 wild-type tomatoes, the abundance of these two taxa was correlated with lower root endosphere α-diversity. The abundance of these taxa was also moderately negatively correlated with the level of SA in roots. Our results suggest that SA and ET pathways contribute to tomato root endosphere diversity by modulating the abundance of specific bacterial taxa.

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A novel Delftia plant symbiont capable of autotrophic methylotrophy

Cited by 20 publications

References 25 publications

Polyphasic characterization of Delftia acidovorans ESM-1, a facultative methylotrophic bacterium isolated from rhizosphere of Eruca sativa

Polyphasic characterization of Delftia acidovorans ESM-1, a facultative methylotrophic bacterium isolated from rhizosphere of Eruca sativa

Impact of plants on the diversity and activity of methylotrophs in soil

Defense hormones modulate root microbiome diversity and composition in tomato

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