@misc{RichtsHertelPototetal., author = {Richts, Bj{\"o}rn and Hertel, Robert and Potot, S{\´e}bastien and Poehlein, Anja and Daniel, Rolf and Schyns, Ghislain and Pr{\´a}gai, Zolt{\´a}n and Commichau, Fabian M.}, title = {Complete Genome Sequence of the Prototrophic Bacillus subtilis subsp. subtilis Strain SP1}, series = {Microbiology Resource Announcements}, volume = {9}, journal = {Microbiology Resource Announcements}, number = {32}, issn = {2576-098X}, doi = {10.1128/MRA.00825-20}, pages = {3}, abstract = {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.}, language = {en} } @misc{OtteKuehneFurreretal., author = {Otte, Kolja and K{\"u}hne, Nora and Furrer, Alexandra and Lozada, Lina and Lutz, Veronika and Schilling, Tobias and Hertel, Robert}, title = {A CRISPR-Cas9 tool to explore the genetics of Bacillus subtilis phages}, series = {Letters in Applied Microbiology}, volume = {71}, journal = {Letters in Applied Microbiology}, number = {6}, issn = {1472-765X}, doi = {10.1111/lam.13349}, pages = {588 -- 595}, abstract = {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.}, language = {en} } @misc{FriedrichHollensteinerSchneideretal., author = {Friedrich, Ines and Hollensteiner, Jacqueline and Schneider, Dominik and Poehlein, Anja and Hertel, Robert and Daniel, Rolf}, title = {First Complete Genome Sequences of Janthinobacterium lividum EIF1 and EIF2 and their Comparative Genome Analysis}, series = {Genome Biology and Evolution}, volume = {12}, journal = {Genome Biology and Evolution}, number = {10}, issn = {1759-6653}, doi = {10.1093/gbe/evaa148}, pages = {1782 -- 1788}, abstract = {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 G{\"o}ttingen. 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.}, language = {en} } @misc{LilgeHertelMorabbiHeravietal., author = {Lilge, Lars and Hertel, Robert and Morabbi Heravi, Kambiz and Henkel, Marius and Commichau, Fabian M. and Hausmann, Rudolf}, title = {Draft Genome Sequence of the Type Strain Bacillus subtilis subsp. subtilis DSM10}, series = {Microbiology Resource Announcements}, volume = {10}, journal = {Microbiology Resource Announcements}, number = {10}, issn = {2576-098X}, doi = {10.1128/MRA.00158-21}, pages = {1 -- 3}, abstract = {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.}, language = {en} } @misc{HollensteinerFriedrichHollsteinetal., author = {Hollensteiner, Jacqueline and Friedrich, Ines and Hollstein, Lucas and Lamping, Jan-Philipp and Wolf, Kalina and Liesegang, Heiko and Poehlein, Anja and Hertel, Robert and Daniel, Rolf}, title = {Complete Genome Sequence of Kinneretia sp. Strain DAIF2, Isolated from a Freshwater Pond}, series = {Microbiology Resource Announcements}, volume = {10}, journal = {Microbiology Resource Announcements}, number = {8}, issn = {2576-098X}, doi = {10.1128/MRA.00003-21}, pages = {1 -- 3}, abstract = {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.}, language = {en} } @misc{FriedrichHollensteinerScherfetal., author = {Friedrich, Ines and Hollensteiner, Jacqueline and Scherf, Janna and Weyergraf, Judith and Klassen, Anna and Poehlein, Anja and Hertel, Robert and Daniel, Rolf}, title = {Complete Genome Sequence of Stenotrophomonas indicatrix DAIF1}, series = {Microbiology Resource Announcements}, volume = {10}, journal = {Microbiology Resource Announcements}, number = {6}, issn = {2576-098X}, doi = {10.1128/MRA.01484-20}, pages = {1 -- 3}, abstract = {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.}, language = {en} } @misc{FriedrichKlassenNeubaueretal., author = {Friedrich, Ines and Klassen, Anna and Neubauer, Hannes and Schneider, Dominik and Hertel, Robert and Daniel, Rolf}, title = {Living in a Puddle of Mud: Isolation and Characterization of Two Novel Caulobacteraceae Strains Brevundimonas pondensis sp. nov. and Brevundimonas goettingensis sp. nov.}, series = {Applied Microbiology}, volume = {1}, journal = {Applied Microbiology}, number = {1}, issn = {2673-8007}, doi = {10.3390/applmicrobiol1010005}, pages = {38 -- 59}, abstract = {Brevundimonas is a genus of freshwater bacteria belonging to the family Caulobacteraceae. The present study describes two novel species of the genus Brevundimonas (LVF1 T and LVF2 T ). Both were genomically, morphologically, and physiologically characterized. Average nucleotide identity analysis revealed both are unique among known Brevundimonas strains. In silico and additional ProphageSeq analyses resulted in two prophages in the LVF1 T genome and a remnant prophage in the LVF2 T genome. Bacterial LVF1 T cells form an elliptical morphotype, in average 1 µ m in length and 0.46 µ m in width, with a single flagellum. LVF2 T revealed motile cells approximately 1.6 µ m in length and 0.6 µ m in width with a single flagellum, and sessile cell types 1.3 µ m in length and 0.6 µ m in width. Both are Gram-negative, aerobic, have optimal growth at 30 ◦ C (up to 0.5 to 1\% NaCl). Both are resistant towards erythromycin, meropenem, streptomycin, tetracycline and vancomycin. Anaerobic growth was observed after 14 days for LVF1 T only. For LVF1 T the name Brevundimonas pondensis sp. nov. and for LVF2 T the name Brevundimonas goettingensis sp. nov. are proposed. Type strains are LVF1 T (=DSM 112304 T = CCUG 74982 T = LMG 32096 T ) and LVF2 T (=DSM 112305 T = CCUG 74983 T = LMG 32097 T ).}, language = {en} } @misc{KohmHertel, author = {Kohm, Katharina and Hertel, Robert}, title = {The life cycle of SPβ and related phages}, series = {Archives of Virology}, volume = {166}, journal = {Archives of Virology}, number = {8}, issn = {1432-8798}, doi = {10.1007\%2Fs00705-021-05116-9}, pages = {2119 -- 2130}, abstract = {Phages are viruses of bacteria and are the smallest and most common biological entities in the environment. They can reproduce immediately after infection or integrate as a prophage into their host genome. SPβ is a prophage of the Gram-positive model organism Bacillus subtilis 168, and it has been known for more than 50 years. It is sensitive to dsDNA damage and is induced through exposure to mitomycin C or UV radiation. When induced from the prophage, SPβ requires 90 min to produce and release about 30 virions. Genomes of sequenced related strains range between 128 and 140 kb, and particle-packed dsDNA exhibits terminal redundancy. Formed particles are of the Siphoviridae morphotype. Related isolates are known to infect other B. subtilis clade members. When infecting a new host, SPβ presumably follows a two-step strategy, adsorbing primarily to teichoic acid and secondarily to a yet unknown factor. Once in the host, SPβ-related phages pass through complex lysis-lysogeny decisions and either enter a lytic cycle or integrate as a dormant prophage. As prophages, SPβ-related phages integrate at the host chromosome's replication terminus, and frequently into the spsM or kamA gene. As a prophage, it imparts additional properties to its host via phage-encoded proteins. The most notable of these functional proteins is sublancin 168, which is used as a molecular weapon by the host and ensures prophage maintenance. In this review, we summarise the existing knowledge about the biology of the phage regarding its life cycle and discuss its potential as a research object.}, language = {en} } @misc{FriedrichBodenbergerNeubaueretal., author = {Friedrich, Ines and Bodenberger, Bernhard and Neubauer, Hannes and Hertel, Robert and Daniel, Rolf}, title = {Down in the pond: Isolation and characterization of a new Serratia marcescens strain (LVF3) from the surface water near frog's lettuce (Groenlandia densa)}, series = {PLoS One}, volume = {16}, journal = {PLoS One}, number = {11}, issn = {1932-6203}, doi = {10.1371/journal.pone.0259673}, abstract = {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.}, language = {en} } @misc{KohmFloccariLutzetal., author = {Kohm, Katharina and Floccari, Valentina and Lutz, Veronika and Nordmann, Birthe and Mittelst{\"a}dt, Carolin and Poehlein, Anja and Dragos, Anna and Commichau, Fabian M. and Hertel, Robert}, title = {The Bacillus phage SPβ and its relatives: A temperate phage model system reveals new strains, species, prophage integration loci, conserved proteins and lysogeny management components}, series = {bioRxiv beta}, journal = {bioRxiv beta}, doi = {10.1101/2021.11.22.469490}, pages = {44}, abstract = {The Bacillus phage SPβ has been known for about 50 years, but only a few strains are avalible. We isolated four new wild type strains of the SPbeta species. Phage vB_BsuS-Goe14 introduces its prophage into the spoVK locus, previously not observed to be used by SPβ-like phages. We could also reveal the SPβ-like phage genome replication strategy, the genome packaging mode, and the phage genome opening point. We extracted 55 SPβ-like prophages from public Bacillus genomes, thereby discovering three more integration loci and one additional type of integrase. The identified prophages resembled four new species clusters and three species orphans in the genus Spbetavirus. The determined core proteome of all SPβ-like prophages consists of 38 proteins. The integration cassette proved to be not conserved even though present in all strains. It consists of distinct integrases. Analysis of SPβ transcriptomes revealed three conserved genes, yopQ, yopR, and yokI, to be transcribed from a dormant prophage. While yopQ and yokI could be deleted from the prophage without activating the prophage, damaging of yopR led to a clear-plaque phenotype. Under the applied laboratory conditions, the yokI mutant showed an elevated virion release implying the YokI protein being a component of the arbitrium system.}, language = {en} }