Transcriptome analysis of Rhodobacter capsulatus grown on different nitrogen sources

Erkal, Nilüfer Afşar; Eser, Muazzez Gürgan; Özgür, Ebru; Gündüz, Ufuk; Eroğlu, İnci; Yücel, Meral

doi:10.1007/s00203-019-01635-x

Cited by 9 publications

(2 citation statements)

References 48 publications

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“…Moreover, 37 putative keystone taxa have higher average relative abundance (ranging from 0.01 to 0.38%) in the reducing high-As groundwater samples, namely, Pseudomonas (number of putative keystone taxa, 8), Sphingomonas (5), Rheinheimera (4), Vogesella (3), Acidovorax (2), Sphingopyxis (1), Novosphingobium (1), Erythrobacter (1), Sphingobium (1), Bacteriovorax (1), and unclassified genera from Planctomycetes (3), Sphingomonadales (1), Alphaproteobacteria (1), Sphingomonadales (1), Rhodobacteraceae (1), Nitrospirae (1), Micrococcaceae (1), and Caulobacterales (1) (Figure c). Members of the genera Pseudomonas, Sphingomonas , Enhydrobacter , and the family Rhodobacteraceae have been found to participate in ammonium oxidation, Fe(III) reduction, and/or As-related metabolism (As tolerance, As methylation, As(V) reduction, and As(III) oxidation). − Genera from the Planctomycetes are widely reported to be capable of anaerobic ammonium oxidation . Therefore, these putative keystone taxa may critically contribute to and/or respond to the groundwater As enrichment.…”

Section: Resultsmentioning

confidence: 99%

Genome-Resolved Metagenomic Analysis of Groundwater: Insights into Arsenic Mobilization in Biogeochemical Interaction Networks

Xiu

Nixon

et al. 2022

Environ. Sci. Technol.

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Section: Resultsmentioning

confidence: 99%

Genome-Resolved Metagenomic Analysis of Groundwater: Insights into Arsenic Mobilization in Biogeochemical Interaction Networks

Xiu

Nixon

et al. 2022

Environ. Sci. Technol.

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“…Regarding Cetobacterium and Rhodobacter , no reports in vinegar have been found for these microorganisms, but because they were present in most of the samples, mainly in those taken along the acetification process, they might play a prominent role in the microbial community. These genera have been associated with the use of diverse strategies for the production and assimilation of acetate, respectively ( Erkal et al, 2019 ; Bhute et al, 2020 ; Xie et al, 2022 ). Conversely, the presence of Bacillus (e.g., Bacillus amyloliquefaciens ) has been previously reported in vinegar, concretely, Zhang et al (2017) showed that they may contribute to the production of acetoin and tetramethylpyrazine, thus enhancing the organoleptic properties, mainly the flavor, of final Chinese vinegars.…”

Section: Discussionmentioning

confidence: 99%

Combining omics tools for the characterization of the microbiota of diverse vinegars obtained by submerged culture: 16S rRNA amplicon sequencing and MALDI-TOF MS

Román-Camacho

García-García²,

Santos-Dueñas³

et al. 2022

Front. Microbiol.

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Vinegars elaborated in southern Spain are highly valued all over the world because of their exceptional organoleptic properties and high quality. Among the factors which influence the characteristics of the final industrial products, the composition of the microbiota responsible for the process and the raw material used as acetification substrate have a crucial role. The current state of knowledge shows that few microbial groups are usually present throughout acetification, mainly acetic acid bacteria (AAB), although other microorganisms, present in smaller proportions, may also affect the overall activity and behavior of the microbial community. In the present work, the composition of a starter microbiota propagated on and subsequently developing three acetification profiles on different raw materials, an alcohol wine medium and two other natural substrates (a craft beer and fine wine), was characterized and compared. For this purpose, two different “omics” tools were combined for the first time to study submerged vinegar production: 16S rRNA amplicon sequencing, a culture-independent technique, and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), a culture-dependent method. Analysis of the metagenome revealed numerous taxa from 30 different phyla and highlighted the importance of the AAB genus Komagataeibacter, which was much more frequent than the other taxa, and Acetobacter; interestingly, also archaea from the Nitrososphaeraceae family were detected by 16S rRNA amplicon sequencing. MALDI-TOF MS confirmed the presence of Komagataeibacter by the identification of K. intermedius. These tools allowed for identifying some taxonomic groups such as the bacteria genera Cetobacterium and Rhodobacter, the bacteria species Lysinibacillus fusiformis, and even archaea, never to date found in this medium. Definitely, the effect of the combination of these techniques has allowed first, to confirm the composition of the predominant microbiota obtained in our previous metaproteomics approaches; second, to identify the microbial community and discriminate specific species that can be cultivated under laboratory conditions; and third, to obtain new insights on the characterization of the acetification raw materials used. These first findings may contribute to improving the understanding of the microbial communities’ role in the vinegar-making industry.

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NifA is the master regulator of both nitrogenase systems in Rhodobacter capsulatus

et al. 2019

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Rhodobacter capsulatus fixes atmospheric nitrogen (N2) by a molybdenum (Mo)‐nitrogenase and a Mo‐free iron (Fe)‐nitrogenase, whose production is induced or repressed by Mo, respectively. At low nanomolar Mo concentrations, both isoenzymes are synthesized and contribute to nitrogen fixation. Here we examined the regulatory interplay of the central transcriptional activators NifA and AnfA by proteome profiling. As expected from earlier studies, synthesis of the structural proteins of Mo‐nitrogenase (NifHDK) and Fe‐nitrogenase (AnfHDGK) required NifA and AnfA, respectively, both of which depend on the alternative sigma factor RpoN to activate expression of their target genes. Unexpectedly, NifA was found to be essential for the synthesis of Fe‐nitrogenase, electron supply to both nitrogenases, biosynthesis of their cofactors, and production of RpoN. Apparently, RpoN is the only NifA‐dependent factor required for target gene activation by AnfA, since plasmid‐borne rpoN restored anfH transcription in a NifA‐deficient strain. However, plasmid‐borne rpoN did not restore Fe‐nitrogenase activity in this strain. Taken together, NifA requirement for synthesis and activity of both nitrogenases suggests that Fe‐nitrogenase functions as a complementary nitrogenase rather than an alternative isoenzyme in R. capsulatus.

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Transcriptome analysis of Rhodobacter capsulatus grown on different nitrogen sources

Cited by 9 publications

References 48 publications

Genome-Resolved Metagenomic Analysis of Groundwater: Insights into Arsenic Mobilization in Biogeochemical Interaction Networks

Genome-Resolved Metagenomic Analysis of Groundwater: Insights into Arsenic Mobilization in Biogeochemical Interaction Networks

Combining omics tools for the characterization of the microbiota of diverse vinegars obtained by submerged culture: 16S rRNA amplicon sequencing and MALDI-TOF MS

NifA is the master regulator of both nitrogenase systems in Rhodobacter capsulatus

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