TY - GEN A1 - Friedrich, Ines A1 - Hollensteiner, Jacqueline A1 - Scherf, Janna A1 - Weyergraf, Judith A1 - Klassen, Anna A1 - Poehlein, Anja A1 - Hertel, Robert A1 - Daniel, Rolf T1 - Complete Genome Sequence of Stenotrophomonas indicatrix DAIF1 T2 - Microbiology Resource Announcements N2 - We present the complete genome of Stenotrophomonas indicatrix DAIF1, which was isolated from an oligotrophic pond in a water protection area. Whole-genome alignments indicated that strain DAIF1 belongs to the species Stenotrophomonas indicatrix. The whole genome (4,639,375 bp) harbors 4,108 protein-encoding genes, including 3,029 genes with assigned functions. Y1 - 2021 UR - https://mra.asm.org/content/10/6/e01484-20 U6 - https://doi.org/10.1128/MRA.01484-20 SN - 2576-098X VL - 10 IS - 6 SP - 1 EP - 3 ER - TY - GEN A1 - Hollensteiner, Jacqueline A1 - Friedrich, Ines A1 - Hollstein, Lucas A1 - Lamping, Jan-Philipp A1 - Wolf, Kalina A1 - Liesegang, Heiko A1 - Poehlein, Anja A1 - Hertel, Robert A1 - Daniel, Rolf T1 - Complete Genome Sequence of Kinneretia sp. Strain DAIF2, Isolated from a Freshwater Pond T2 - Microbiology Resource Announcements N2 - Kinneretia sp. strain DAIF2 was isolated from a eutrophic freshwater pond. The genome consists of a single chromosome (6,010,585 bp) with a GC content of 69.3%. The whole-genome-based phylogeny of DAIF2 revealed a closest relation to the genus Kinneretia. Y1 - 2021 UR - https://mra.asm.org/content/10/8/e00003-21 U6 - https://doi.org/10.1128/MRA.00003-21 SN - 2576-098X VL - 10 IS - 8 SP - 1 EP - 3 ER - TY - GEN A1 - Otte, Kolja A1 - Kühne, Nora A1 - Furrer, Alexandra A1 - Lozada, Lina A1 - Lutz, Veronika A1 - Schilling, Tobias A1 - Hertel, Robert T1 - A CRISPR-Cas9 tool to explore the genetics of Bacillus subtilis phages T2 - Letters in Applied Microbiology N2 - Here we present pRH030, a new CRISPR-Cas9 tool for the genetic engineering of Bacillus phages and beyond. It is based on the Streptococcus pyogenes cas9 with its native constitutive promoter, tracrRNA, and a gRNA precursor. The constitutive expression of Cas9 was conducive to the inactivation of viral attackers and enhanced phage mutagenesis efficiency up to 100%. The gRNA precursor can be built-up to an artificial CRISPR array with up to 5 spacers (target sequences) assembled from ordinary oligonucleotides and directly cloned into pRH030. Required time and resources remain comparable to a single gRNA cloning. These properties make pRH030 an attractive new system for the modification of Bacillus phages and qualify it for research beyond genetic construction. Y1 - 2020 UR - https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/lam.13349 U6 - https://doi.org/10.1111/lam.13349 SN - 1472-765X VL - 71 IS - 6 SP - 588 EP - 595 ER - TY - GEN A1 - Friedrich, Ines A1 - Hollensteiner, Jacqueline A1 - Schneider, Dominik A1 - Poehlein, Anja A1 - Hertel, Robert A1 - Daniel, Rolf T1 - First Complete Genome Sequences of Janthinobacterium lividum EIF1 and EIF2 and their Comparative Genome Analysis T2 - Genome Biology and Evolution N2 - We present the first two complete genomes of the Janthinobacterium lividum species, namely strains EIF1 and EIF2, which both possess the ability to synthesize violacein. The violet pigment violacein is a secondary metabolite with antibacterial, antifungal, antiviral, and antitumoral properties. Both strains were isolated from environmental oligotrophic water ponds in Göttingen. The strains were phylogenetically classified by ANI analysis and showed a species assignment to Janthinobacterium lividum with 97.72% (EIF1) and 97.66% (EIF2) identity. These are the first complete genome sequences of strains belonging to the species Janthinobacterium lividum. The genome of strain EIF1 consists of one circular chromosome (6,373,589 bp) with a GC-content of 61.98%. The genome contains 5,551 coding sequences, 122 rRNAs, 93 tRNAs, and 1 tm-RNA. The genome of EIF2 comprises one circular chromosome (6,399,352 bp) with a GC-content of 61.63% and a circular plasmid p356839 (356,839 bp) with a GC-content of 57.21%. The chromosome encodes 5,691 coding sequences, 122 rRNAs, 93 tRNAs, and 1 tm-RNA and the plasmid harbors 245 coding sequences. In addition to the highly conserved chromosomally encoded violacein operon, the plasmid comprises a non-ribosomal peptide synthetase cluster (NRPS) with similarity to xenoamicin, which is a bioactive compound effective against protozoan parasites. Y1 - 2020 UR - https://academic.oup.com/gbe/article/doi/10.1093/gbe/evaa148/5870831 U6 - https://doi.org/10.1093/gbe/evaa148 SN - 1759-6653 VL - 12 IS - 10 SP - 1782 EP - 1788 ER - TY - GEN A1 - Richts, Björn A1 - Hertel, Robert A1 - Potot, Sébastien A1 - Poehlein, Anja A1 - Daniel, Rolf A1 - Schyns, Ghislain A1 - Prágai, Zoltán A1 - Commichau, Fabian M. T1 - Complete Genome Sequence of the Prototrophic Bacillus subtilis subsp. subtilis Strain SP1 T2 - Microbiology Resource Announcements N2 - Here, we present the complete genome sequence of the Bacillus subtilis strain SP1. This strain is a descendant of the laboratory strain 168. The strain is suit- able for biotechnological applications because the prototrophy for tryptophan has been restored. Due to laboratory cultivation, the strain has acquired 24 additional sequence variations. Y1 - 2020 UR - https://mra.asm.org/content/9/32/e00825-20 U6 - https://doi.org/10.1128/MRA.00825-20 SN - 2576-098X VL - 9 IS - 32 ER - TY - GEN A1 - Lilge, Lars A1 - Hertel, Robert A1 - Morabbi Heravi, Kambiz A1 - Henkel, Marius A1 - Commichau, Fabian M. A1 - Hausmann, Rudolf T1 - Draft Genome Sequence of the Type Strain Bacillus subtilis subsp. subtilis DSM10 T2 - Microbiology Resource Announcements N2 - The Bacillus subtilis subsp. subtilis type strain DSM10 has been used as a reference in various studies. However, detailed information about the genome has not been available. Therefore, whole-genome sequencing was performed, and the sequence was compared with that of the related B. subtilis strain NCIB3610. Y1 - 2021 UR - https://mra.asm.org/content/10/10/e00158-21 U6 - https://doi.org/10.1128/MRA.00158-21 SN - 2576-098X VL - 10 IS - 10 SP - 1 EP - 3 ER - TY - GEN A1 - Riedel, Ramona A1 - Commichau, Fabian M. A1 - Benndorf, Dirk A1 - Hertel, Robert A1 - Holzer, Katharina A1 - Mardoukhi, Mohammad Saba Yousef A1 - Noack, Laura A1 - Martienssen, Marion T1 - Biodegradation of selected aminophosphonates by the bacterial isolate Ochrobactrum sp. BTU1 T2 - Microbial Research N2 - Aminophosphonates, like glyphosate (GS) or metal chelators such as ethylenediaminetetra(methylenephosphonic acid) (EDTMP), are released on a large scale worldwide. Here, we have characterized a bacterial strain capable of degrading synthetic aminophosphonates. The strain was isolated from LC/MS standard solution. Genome sequencing indicated that the strain belongs to the genus Ochrobactrum. Whole-genome classification using pyANI software to compute a pairwise ANI and other metrics between Brucella assemblies and Ochrobactrum contigs revealed that the bacterial strain is designated as Ochrobactrum sp. BTU1. Degradation batch tests with Ochrobactrum sp. BTU1 and the selected aminophosphonates GS, EDTMP, aminomethylphosphonic acid (AMPA), iminodi(methylene-phosphonic) (IDMP) and ethylaminobis(methylenephosphonic) acid (EABMP) showed that the strain can use all phosphonates as sole phosphorus source during phosphorus starvation. The highest growth rate was achieved with AMPA, while EDTMP and GS were least supportive for growth. Proteome analysis revealed that GS degradation is promoted by C-P lyase via the sarcosine pathway, i.e., initial cleavage at the C-P bond. We also identified C-P lyase to be responsible for degradation of EDTMP, EABMP, IDMP and AMPA. However, the identification of the metabolite ethylenediaminetri(methylenephosphonic acid) via LC/MS analysis in the test medium during EDTMP degradation indicates a different initial cleavage step as compared to GS. For EDTMP, it is evident that the initial cleavage occurs at the C-N bond. The detection of different key enzymes at regulated levels, form the bacterial proteoms during EDTMP exposure, further supports this finding. Y1 - 2024 U6 - https://doi.org/10.1016/j.micres.2024.127600 SN - 0944-5013 VL - 280 SP - 1 EP - 12 ER - TY - GEN A1 - Hertel, Robert A1 - Schöne, Kerstin A1 - Mittelstädt, Carolin A1 - Meißner, Janek A1 - Zschoche, Nick A1 - Collignon, Madeline A1 - Kohler, Christian A1 - Friedrich, Ines A1 - Schneider, Dominik A1 - Hoppert, Michael A1 - Kuhn, Ramona A1 - Schwedt, Inge A1 - Scholz, Patricia A1 - Poehlein, Anja A1 - Martienssen, Marion A1 - Ischebeck, Till A1 - Daniel, Rolf A1 - Commichau, Fabian M. T1 - Characterization of glyphosate-resistant Burkholderia anthina and Burkholderia cenocepacia isolates from a commercial Roundup® solution T2 - Environmental Microbiology Reports N2 - Roundup® is the brand name for herbicide solutions containing glyphosate, which specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase of the shikimate pathway. The inhibition of the EPSP synthase causes plant death because EPSP is required for biosynthesis of aromatic amino acids. Glyphosate also inhibits the growth of archaea, bacteria, Apicomplexa, algae and fungi possessing an EPSP synthase. Here, we have characterized two glyphosate-resistant bacteria from a Roundup solution. Taxonomic classification revealed that the isolates 1CH1 and 2CH1 are Burkholderia anthina and Burkholderia cenocepacia strains respectively. Both isolates cannot utilize glyphosate as a source of phosphorus and synthesize glyphosate-sensitive EPSP synthase variants. Burkholderia. anthina 1CH1 and B. cenocepacia 2CH1 tolerate high levels of glyphosate because the herbicide is not taken up by the bacteria. Previously, it has been observed that the exposure of soil bacteria to herbicides like glyphosate promotes the development of antibiotic resistances. Antibiotic sensitivity testing revealed that the only the B. cenocepacia 2CH1 isolate showed increased resistance to a variety of antibiotics. Thus, the adaptation of B. anthina 1CH1 and B. cenocepacia 2CH1 to glyphosate did not generally increase the antibiotic resistance of both bacteria. However, our study confirms the genomic adaptability of bacteria belonging to the genus Burkholderia. Y1 - 2022 U6 - https://doi.org/10.1111/1758-2229.13022 SN - 1758-2229 VL - 14 IS - 1 SP - 70 EP - 84 ER - TY - GEN A1 - Friedrich, Ines A1 - Bodenberger, Bernhard A1 - Neubauer, Hannes A1 - Hertel, Robert A1 - Daniel, Rolf T1 - Down in the pond: Isolation and characterization of a new Serratia marcescens strain (LVF3) from the surface water near frog's lettuce (Groenlandia densa) T2 - PLoS One N2 - Serratia marcescens is a species that belongs to the family of Yersiniaceae. This family comprises taxa representing opportunistic human- and phytopathogens but also plant growth-promoting rhizobacteria (PGPR). This study describes a novel Gram-negative strain (LVF3R) of the species Serratia marcescens. The strain was characterized genomically, morphologically, and physiologically. In addition, the potential of the isolate to act as a host strain to assess the diversity of Serratia associated phages in environmental samples was explored. Average nucleotide identity analysis revealed that LVF3R belongs to the species Serratia marcescens. In silico analysis and ProphageSeq data resulted in the identification of one prophage, which is capable of viral particle formation. Electron microscopy showed cells of a rod-shaped, flagellated morphotype. The cells revealed a length and width of 1-1.6 μm and 0.8 μm, respectively. LVF3R showed optimal growth at 30 C and in the presence of up to 2% (w/v) NaCl. It exhibited resistances to ampicillin, erythromycin, oxacillin, oxytetracycline, rifampicin, tetracycline, and vancomycin. Genome data indicate that strain S. marcescens LVF3R is a potential PGPR strain. It harbors genes coding for indole acetic acid (IAA) biosynthesis, siderophore production, plant polymer degradation enzymes, acetoin synthesis, flagellar proteins, type IV secretion system, chemotaxis, phosphorous solubilization, and biofilm formation. Y1 - 2021 UR - https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0259673 U6 - https://doi.org/10.1371/journal.pone.0259673 SN - 1932-6203 VL - 16 IS - 11 ER - TY - GEN A1 - Hertel, Robert A1 - Gibhardt, Johannes A1 - Martienssen, Marion A1 - Kuhn, Ramona A1 - Commichau, Fabian M. T1 - Molecular mechanisms underlying glyphosate resistance in bacteria T2 - Environmental Microbiology N2 - Glyphosate is a nonselective herbicide that kills weeds and other plants competing with crops. Glyphosate specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase, thereby depleting the cell of EPSP serving as a precursor for biosynthesis of aromatic amino acids. Glyphosate is considered to be toxicologically safe for animals and humans. Therefore, it became the most-important herbicide in agriculture. However, its intensive application in agriculture is a serious environmental issue because it may negatively affect the biodiversity. A few years after the discovery of the mode of action of glyphosate, it has been observed that bacteria evolve glyphosate resistance by acquiring mutations in the EPSP synthase gene, rendering the encoded enzyme less sensitive to the herbicide. The identification of glyphosate-resistant EPSP synthase variants paved the way for engineering crops tolerating increased amounts of the herbicide. This review intends to summarize the molecular mechanisms underlying glyphosate resistance in bacteria. Bacteria can evolve glyphosate resistance by (i) reducing glyphosate sensitivity or elevating production of the EPSP synthase, by (ii) degrading or (iii) detoxifying glyphosate and by (iv) decreasing the uptake or increasing the export of the herbicide. The variety of glyphosate resistance mechanisms illustrates the adaptability of bacteria to anthropogenic substances due to genomic alterations. Y1 - 2021 U6 - https://doi.org/10.1111/1462-2920.15534 SN - 1462-2920 SN - 1462-2912 VL - 23 IS - 6 SP - 2891 EP - 2905 ER -