Culture-dependent and culture-independent methods reveal diverse methylotrophic communities in terrestrial environments

Eyice, Özge; Schäfer, Hendrik

doi:10.1007/s00203-015-1160-x

Cited by 11 publications

(9 citation statements)

References 66 publications

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“…Performing the PCR with DNA extracted from samples that were shown or would be expected to contain bacteria capable of methanethiol degradation (based on their known degradation of DMS and DMSP for instance) also yielded bands of the correct size. These samples included DNA extracted from DMS enrichment cultures from Brassica rhizosphere soil, bulk agricultural soil (Eyice and Schäfer 2016), rhizosphere sediment of Spartina anglica (a DMSP-producing plant) obtained from Stiffkey salt marsh (Norfolk, UK) and surface sediments of Stiffkey saltmarsh. Saltmarshes are known to be environments with high turnover of DMSP, DMS and MT (e.g.…”

Section: Resultsmentioning

confidence: 99%

Bacterial SBP56 identified as a Cu-dependent methanethiol oxidase widely distributed in the biosphere

et al. 2017

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Oxidation of methanethiol (MT) is a significant step in the sulfur cycle. MT is an intermediate of metabolism of globally significant organosulfur compounds including dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS), which have key roles in marine carbon and sulfur cycling. In aerobic bacteria, MT is degraded by a MT oxidase (MTO). The enzymatic and genetic basis of MT oxidation have remained poorly characterized. Here, we identify for the first time the MTO enzyme and its encoding gene (mtoX) in the DMS-degrading bacterium Hyphomicrobium sp. VS. We show that MTO is a homotetrameric metalloenzyme that requires Cu for enzyme activity. MTO is predicted to be a soluble periplasmic enzyme and a member of a distinct clade of the Selenium-binding protein (SBP56) family for which no function has been reported. Genes orthologous to mtoX exist in many bacteria able to degrade DMS, other one-carbon compounds or DMSP, notably in the marine model organism Ruegeria pomeroyi DSS-3, a member of the Rhodobacteraceae family that is abundant in marine environments. Marker exchange mutagenesis of mtoX disrupted the ability of R. pomeroyi to metabolize MT confirming its function in this DMSP-degrading bacterium. In R. pomeroyi, transcription of mtoX was enhanced by DMSP, methylmercaptopropionate and MT. Rates of MT degradation increased after pre-incubation of the wild-type strain with MT. The detection of mtoX orthologs in diverse bacteria, environmental samples and its abundance in a range of metagenomic data sets point to this enzyme being widely distributed in the environment and having a key role in global sulfur cycling.

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Section: Resultsmentioning

confidence: 99%

Bacterial SBP56 identified as a Cu-dependent methanethiol oxidase widely distributed in the biosphere

et al. 2017

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“…Thiobacillus thioparus bacteria possess an enzyme that can breakdown thiocyanate – a common compound found in glucosinolates ( Katayama et al, 1998 ). Furthermore, their growth has been shown to increase in response to dimethylsulfide (DMS), which is a by-product of the decomposition of Brassica biomass ( Bending and Lincoln, 1999 ; Eyice and Schäfer, 2016 ). These observations may indicate that root-derived glucosinolates and decomposition derivatives play an important role in shaping the soil bacterial community of Brassica rhizospheres.…”

Section: Discussionmentioning

confidence: 99%

Rhizosphere Bacterial Communities Differ According to Fertilizer Regimes and Cabbage (Brassica oleracea var. capitata L.) Harvest Time, but Not Aphid Herbivory

et al. 2018

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Rhizosphere microbial communities are known to be highly diverse and strongly dependent on various attributes of the host plant, such as species, nutritional status, and growth stage. High-throughput 16S rRNA gene amplicon sequencing has been used to characterize the rhizosphere bacterial community of many important crop species, but this is the first study to date to characterize the bacterial and archaeal community of Brassica oleracea var. capitata. The study also tested the response of the bacterial community to fertilizer type (organic or synthetic) and N dosage (high or low), in addition to plant age (9 or 12 weeks) and aphid (Myzus persicae) herbivory (present/absent). The impact of aboveground herbivory on belowground microbial communities has received little attention in the literature, and since the type (organic or mineral) and amount of fertilizer applications are known to affect M. percicae populations, these treatments were applied at agricultural rates to test for synergistic effects on the soil bacterial community. Fertilizer type and plant growth were found to result in significantly different rhizosphere bacterial communities, while there was no effect of aphid herbivory. Several operational taxonomic units were identified as varying significantly in abundance between the treatment groups and age cohorts. These included members of the S-oxidizing genus Thiobacillus, which was significantly more abundant in organically fertilized 12-week-old cabbages, and the N-fixing cyanobacteria Phormidium, which appeared to decline in synthetically fertilized soils relative to controls. These responses may be an effect of accumulating root-derived glucosinolates in the B. oleracea rhizosphere and increased N-availability, respectively.

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“…Phyllosphere is a unique habitat that harbors PPFMs in a range 10 × 10 4 to 356 × 10 4 CFU g −1 of fresh leaf, however, population may vary between different crop species [12,29]. The most common inhabitants on phyllosphere are genera Hyphomicrobium, Methylobacterium, Pseudomonas, Hydrogenophaga, Rhodococcus, Flavobacterium, and Variovorax [1]. Phyllosphere is directly exposed to harsh environmental conditions such as temperature, relative humidity, and UV radiations that present a unique challenge in determining the microbial abundance.…”

Section: Mechanism Of Methanol Metabolismmentioning

confidence: 99%

Prospect of pink pigmented facultative methylotrophs in mitigating abiotic stress and climate change

et al. 2022

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Apparently, climate change is observed in form of increased greenhouse gases (CH 4 , CO 2 , N 2 O, CFC), temperature (0.5-1°C), and UV radiations (UV B and UV C). It is affecting every aspect of ecosystem functioning; however, terrestrial crops are the most vulnerable group and crop productivity largely remains a challenge. Due to climate change, seed yield and nutrient depletion are inevitable in future scenarios. To overcome this problem microbial groups that exhibit plant growth promoting attributes and provide protection against environmental stress should be studied. One such group is the pink pigmented facultative methylotrophs (PPFMs) that can induce overall fitness to plants.PPFMs are involved in phosphorous mineralization, siderophore, ACC deaminase, phytohormone production, and assimilation of greenhouse gases. Additionally, these organisms can also resist harmful UV radiations effectively as they possess polyketide synthases that could serve as source of novel bioactives that can protect plant from abiotic stress. The review article comprehensively highlights the multifunctional traits of PPFMs and their role in mitigating climate change with an aim to use this important organism as microbial inoculants for sustainable agriculture under climate-changing scenarios.climate change, greenhouse gases, phyllosphere, pink pigmented facultative methylotrophs, terrestrial crops | INTRODUCTIONMethylotrophs belong to diverse classes of α, β, and γ proteobacteria group, they are gram-negative, rodshaped, strict aerobic microbes. Methylotrophy is also exhibited by members of Verrucomicrobia, Firmicutes, Flavobacterium, and Actinobacteria [1]. A small group of methylotrophs encompassing 51 species appear pink in color due to carotenoid pigments and are often referred as pink pigmented facultative methylotrophs (PPFMs) (http://www.bacterio.net/methylobacterium.html). Methylorubrum extorquens is the best-studied member of

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Culture-dependent and culture-independent methods reveal diverse methylotrophic communities in terrestrial environments

Cited by 11 publications

References 66 publications

Bacterial SBP56 identified as a Cu-dependent methanethiol oxidase widely distributed in the biosphere

Bacterial SBP56 identified as a Cu-dependent methanethiol oxidase widely distributed in the biosphere

Rhizosphere Bacterial Communities Differ According to Fertilizer Regimes and Cabbage (Brassica oleracea var. capitata L.) Harvest Time, but Not Aphid Herbivory

Prospect of pink pigmented facultative methylotrophs in mitigating abiotic stress and climate change

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