Draft Genome Sequence of
            <i>Donghicola</i>
            sp. Strain KarMa, a Model Organism for Monomethylamine-Degrading Nonmethylotrophic Bacteria

Zecher, Karsten; Suleiman, Marcel; Wibberg, Daniel; Winkler, Anderson M.; Philipp, Bodo; Kalinowski, Jörn

doi:10.1128/genomea.01623-16

Cited by 5 publications

(3 citation statements)

References 8 publications

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“…The marine bacterium Donghicola sp. strain KarMa was isolated and characterized in a previous study regarding its physiology ( Suleiman et al, 2016 ) and its genome ( Zecher et al, 2017 ). The type strains Alteromonas macleodii DSM6062, Celeribacter halophilus DSM26270, Marinobacter adhaerens DSM23420, Roseobacter denitrificans DSM7001, Roseovarius indicus DSM26383, Ruegeria pomeroyi DSS-3 (DSM15171), Sulfitobacter noctilucicola DSM101015, and Sulfitobacter pseudonitzschiae DSM26824 were obtained from the DSMZ (Germany).…”

Section: Methodsmentioning

confidence: 99%

“…Genes for the degradation of MMA and GBT were identified previously in the genome of strain KarMa ( Zecher et al, 2017 ). Genes for the degradation of DMA and TMA were identified in the genome of strain KarMa by basic local alignment search tool (BLAST) analysis [National Center for Biotechnology Information (NCBI) BLASTp analysis with default settings; Altschul et al, 1990 ] using sequences of the TMA monooxygenase ( tmm ), the trimethylamine- N -oxide demethylase ( tdm ), and the DMA monooxygenase ( dmmCBAD ) from R. pomeroyi DSS-3 (DSM15171) as query sequences because the respective function of these genes had been verified experimentally in this bacterium ( Lidbury et al, 2015 ; Lidbury et al, 2017 ).…”

Section: Methodsmentioning

confidence: 99%

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Evidence of Interdomain Ammonium Cross-Feeding From Methylamine- and Glycine Betaine-Degrading Rhodobacteraceae to Diatoms as a Widespread Interaction in the Marine Phycosphere

2020

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Dissolved organic nitrogen (DON) compounds such as methylamines (MAs) and glycine betaine (GBT) occur at detectable concentrations in marine habitats and are also produced and released by microalgae. For many marine bacteria, these DON compounds can serve as carbon, energy, and nitrogen sources, but microalgae usually cannot metabolize them. Interestingly though, it was previously shown that Donghicola sp. strain KarMa—a member of the marine Rhodobacteraceae —can cross-feed ammonium such that the ammonium it produces upon degrading monomethylamine (MMA) then serves as nitrogen source for the diatom Phaeodactylum tricornutum ; thus, these organisms form a mutual metabolic interaction under photoautotrophic conditions. In the present study, we investigated whether this interaction plays a broader role in bacteria–diatom interactions in general. Results showed that cross-feeding between strain KarMa and P. tricornutum was also possible with di- and trimethylamine as well as with GBT. Further, cross-feeding of strain KarMa was also observed in cocultures with the diatoms Amphora coffeaeformis and Thalassiosira pseudonana with MMA as the sole nitrogen source. Regarding cross-feeding involving other Rhodobacteraceae strains, the in silico analysis of MA and GBT degradation pathways indicated that algae-associated Rhodobacteraceae -type strains likely interact with P. tricornutum in a similar manner as the strain KarMa does. For these types of strains (such as Celeribacter halophilus , Roseobacter denitrificans , Roseovarius indicus , Ruegeria pomeroyi , and Sulfitobacter noctilucicola ), ammonium cross-feeding after methylamine degradation showed species-specific patterns, whereas bacterial GBT degradation always led to diatom growth. Overall, the degradation of DON compounds by the Rhodobacteraceae family and the subsequent cross-feeding of ammonium may represent a widespread, organism-specific, and regulated metabolic interaction for establishing and stabilizing associations with photoautotrophic diatoms in the oceans.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Evidence of Interdomain Ammonium Cross-Feeding From Methylamine- and Glycine Betaine-Degrading Rhodobacteraceae to Diatoms as a Widespread Interaction in the Marine Phycosphere

2020

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“…( 33 ) and for strains Tü 2108 and A 4/2 as described in Zecher et al. ( 34 ). Genome sequence-specific information is listed in Supplementary Table S2 .…”

Section: Methodsmentioning

confidence: 99%

Ψ-Footprinting approach for the identification of protein synthesis inhibitor producers

Handel

Kulik

Wex

et al. 2022

NAR Genomics and Bioinformatics

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Today, one of the biggest challenges in antibiotic research is a targeted prioritization of natural compound producer strains and an efficient dereplication process to avoid undesired rediscovery of already known substances. Thereby, genome sequence-driven mining strategies are often superior to wet-lab experiments because they are generally faster and less resource-intensive. In the current study, we report on the development of a novel in silico screening approach to evaluate the genetic potential of bacterial strains to produce protein synthesis inhibitors (PSI), which was termed the protein synthesis inhibitor ('psi’) target gene footprinting approach = Ψ-footprinting. The strategy is based on the occurrence of protein synthesis associated self-resistance genes in genome sequences of natural compound producers. The screening approach was applied to 406 genome sequences of actinomycetes strains from the DSMZ strain collection, resulting in the prioritization of 15 potential PSI producer strains. For twelve of them, extract samples showed protein synthesis inhibitory properties in in vitro transcription/translation assays. For four strains, namely Saccharopolyspora flava DSM 44771, Micromonospora aurantiaca DSM 43813, Nocardioides albertanoniae DSM 25218, and Geodermatophilus nigrescens DSM 45408, the protein synthesis inhibitory substance amicoumacin was identified by HPLC-MS analysis, which proved the functionality of the in silico screening approach.

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Changes in the microbial community of Litopenaeus vannamei larvae and rearing water during different growth stages after disinfection treatment of hatchery water

et al. 2020

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Draft Genome Sequence of Donghicola sp. Strain KarMa, a Model Organism for Monomethylamine-Degrading Nonmethylotrophic Bacteria

Cited by 5 publications

References 8 publications

Evidence of Interdomain Ammonium Cross-Feeding From Methylamine- and Glycine Betaine-Degrading Rhodobacteraceae to Diatoms as a Widespread Interaction in the Marine Phycosphere

Evidence of Interdomain Ammonium Cross-Feeding From Methylamine- and Glycine Betaine-Degrading Rhodobacteraceae to Diatoms as a Widespread Interaction in the Marine Phycosphere

Ψ-Footprinting approach for the identification of protein synthesis inhibitor producers

Changes in the microbial community of Litopenaeus vannamei larvae and rearing water during different growth stages after disinfection treatment of hatchery water

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