Publications by authors named "Boyke Bunk"

152 Publications

Genome and Methylome analysis of a phylogenetic novel cluster with introgression.

Microb Genom 2021 10;7(10)

Institut für Medizinische Mikrobiologie und Virologie, Universitätsmedizin Göttingen, Göttingen, Germany.

The intriguing recent discovery of strains, especially of clade 1, that (i) possess mosaic / alleles, (ii) demonstrate mixed multilocus sequence types (MLSTs) and (iii) have undergone genome-wide introgression has led to the speculation that these two species may be involved in an accelerated rate of horizontal gene transfer that is progressively leading to the merging of both species in a process coined 'despeciation'. In an MLST-based neighbour-joining tree of a number of and isolates of different clades, three prominent isolates formed a seemingly separate cluster besides the previously described and clades. In the light of the suspected, ongoing genetic introgression between the and species, this cluster of isolates is proposed to present one of the hybrid clonal complexes in the despeciation process of the genus. Specific DNA methylation as well as restriction modification systems are known to be involved in selective uptake of external DNA and their role in such genetic introgression remains to be further investigated. In this study, the phylogeny and DNA methylation of these putative / hybrid strains were explored, their genomic mosaic structure caused by introgression was demonstrated and basic phenotypic assays were used to characterize these isolates. The genomes of the three hybrid strains were sequenced using PacBio SMRT sequencing, followed by methylome analysis by Restriction-Modification Finder and genome analysis by Parsnp, Smash++ and blast. Additionally, the strains were phenotypically characterized with respect to growth behaviour, motility, eukaryotic cell invasion and adhesion, autoagglutination, biofilm formation, and water survival ability. Our analyses show that the three hybrid strains are clade 1 . strains, which have acquired between 8.1 and 9.1 % of their genome from . The genomic segments acquired are distributed over the entire genome and do not form a coherent cluster. Most of the genes originating from are involved in chemotaxis and motility, membrane transport, cell signalling, or the resistance to toxic compounds such as bile acids. Interspecies gene transfer from has contributed 8.1-9.1% to the genome of three isolates and initiated the despeciation between and . Based on their functional annotation, the genes originating from enable the adaptation of the three strains to an intra-intestinal habitat. The transfer of a fused type II restriction-modification system that recognizes the CAYNNNNNCTC/GAGNNNNNRTG motif seems to be the key for the recombination of the genetic material with genomes.
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http://dx.doi.org/10.1099/mgen.0.000679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8627207PMC
October 2021

Identification and Antibiotic Profiling of , an Underestimated Human Pathogen.

Front Microbiol 2021 22;12:712775. Epub 2021 Sep 22.

Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Dresden, Germany.

In the past 12 years, several case reports have clearly demonstrated that is capable of causing sepsis and bacteremia in humans. However, since most clinicians are not familiar with this species, little is known about its pathogenicity and treatment options while it is as rare but underestimated human pathogen. Therefore, a larger strain collection is required so that methods can be identified that are most suitable to obtain rapid and reliable identification. Moreover, the antimicrobial resistance profile needs to be elucidated in order to explore possible treatment options. Over a period of 6 years, we therefore have collected a total of 14 isolates in routine diagnostics, which now served as the basis for a comprehensive characterization with respect to identification and antibiotic profiling. We compared the accuracy and convenience of several identification techniques in which MALDI-TOF MS and sequencing of the 16S rRNA gene have proven to be suitable for identification of In addition, whole genome sequencing (WGS)-based digital DNA-DNA hybridization (dDDH) was used as a reference method for strain identification, and surprised with the detection of a novel subspecies. A combination of and analyses revealed a first insight into the antimicrobial resistance profile and the molecular basis of antimicrobial resistance. Based on our findings, trimethoprim/sulfamethoxazole, levofloxacin, and cephalosporins (e.g., ceftazidime) may be the best antibiotics to use in order to treat infections caused by , while resistance to fosfomycin, amikacin and tobramycin is observed.
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http://dx.doi.org/10.3389/fmicb.2021.712775DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8496446PMC
September 2021

Molecular basis of a bacterial-amphibian symbiosis revealed by comparative genomics, modeling, and functional testing.

ISME J 2021 Oct 2. Epub 2021 Oct 2.

Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany.

The molecular bases for the symbiosis of the amphibian skin microbiome with its host are poorly understood. Here, we used the odor-producer Pseudomonas sp. MPFS and the treefrog Boana prasina as a model to explore bacterial genome determinants and the resulting mechanisms facilitating symbiosis. Pseudomonas sp. MPFS and its closest relatives, within a new clade of the P. fluoresens Group, have large genomes and were isolated from fishes and plants, suggesting environmental plasticity. We annotated 16 biosynthetic gene clusters from the complete genome sequence of this strain, including those encoding the synthesis of compounds with known antifungal activity and of odorous methoxypyrazines that likely mediate sexual interactions in Boana prasina. Comparative genomics of Pseudomonas also revealed that Pseudomonas sp. MPFS and its closest relatives have acquired specific resistance mechanisms against host antimicrobial peptides (AMPs), specifically two extra copies of a multidrug efflux pump and the same two-component regulatory systems known to trigger adaptive resistance to AMPs in P. aeruginosa. Subsequent molecular modeling indicated that these regulatory systems interact with an AMP identified in Boana prasina through the highly acidic surfaces of the proteins comprising their sensory domains. In agreement with a symbiotic relationship and a highly selective antibacterial function, this AMP did not inhibit the growth of Pseudomonas sp. MPFS but inhibited the growth of another Pseudomonas species and Escherichia coli in laboratory tests. This study provides deeper insights into the molecular interaction of the bacteria-amphibian symbiosis and highlights the role of specific adaptive resistance toward AMPs of the hosts.
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http://dx.doi.org/10.1038/s41396-021-01121-7DOI Listing
October 2021

Complete Genome Sequencing of Isolates from Malaysia Reveals Massive Genome Rearrangement but High Conservation of Virulence-Associated Genes.

Pathogens 2021 Sep 15;10(9). Epub 2021 Sep 15.

Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany.

The ability of Leptospirae to persist in environments and animal hosts but to cause clinically highly variable disease in humans has made leptospirosis the most common zoonotic disease. Considering the paucity of data on variation in complete genomes of human pathogenic Leptospirae, we have used a combination of Single Molecule Real-Time (SMRT) and Illumina sequencing to obtain complete genome sequences of six human clinical isolates from Malaysia. All six contained the larger (4.28-4.56 Mb) and smaller (0.34-0.395 Mb) chromosome typical of human pathogenic Leptospirae and 0-7 plasmids. Only 24% of the plasmid sequences could be matched to databases. We identified a chromosomal core genome of 3318 coding sequences and strain-specific accessory genomes of 49-179 coding sequences. These sequences enabled detailed genomic strain typing (Genome BLAST Distance Phylogeny, DNA-DNA hybridization, and multi locus sequence typing) and phylogenetic classification (whole-genome SNP genotyping). Even though there was some shared synteny and collinearity across the six genomes, there was evidence of major genome rearrangement, likely driven by horizontal gene transfer and homologous recombination. Mobile genetic elements were identified in all strains in highly varying numbers, including in the locus, which defines serogroups and contributes to immune escape and pathogenesis. On the other hand, there was high conservation of virulence-associated genes including those relating to sialic acid, alginate, and lipid A biosynthesis. These findings suggest (i) that the antigenic variation, adaption to various host environments, and broad spectrum of virulence of are in part due to a high degree of genomic plasticity and (ii) that human pathogenic strains maintain a core set of genes required for virulence.
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http://dx.doi.org/10.3390/pathogens10091198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8467490PMC
September 2021

High Potential for Secondary Metabolite Production of CP157, Isolated From the Crustacean .

Front Microbiol 2021 28;12:688754. Epub 2021 Jun 28.

Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.

Secondary metabolites are key components in microbial ecology by mediating interactions between bacteria and their environment, neighboring species or host organisms. Bioactivities can be beneficial for both interaction partners or provide a competitive advantage only for the producer. Colonizers of confined habitats such as biofilms are known as prolific producers of a great number of bioactive secondary metabolites and are a potential source for novel compounds. We investigated the strain CP157, which originates from the biofilm on the carapace of a shell disease-affected specimen, for its potential to produce bioactive secondary metabolites. Its closed genome contains 22 extrachromosomal elements and several gene clusters potentially involved in biosynthesis of bioactive polyketides, bacteriocins, and non-ribosomal peptides. Culture extracts of CP157 showed antagonistic activities against bacteria from different phyla, but also against microalgae and crustacean larvae. Different HPLC-fractions of CP157 culture extracts had antibacterial properties, indicating that several bioactive compounds are produced by CP157. The bioactive extract contains several small, antibacterial compounds that partially withstand elevated temperatures, extreme pH values and exposure to proteolytic enzymes, providing high stability toward environmental conditions in the natural habitat of CP157. Further, screening of 17 spp. revealed that antimicrobial activity, hemolysis and production of -acyl homoserine lactones are common features within the genus. Taking into account the large habitat diversity and phylogenetic distance of the tested strains, we hypothesize that bioactive secondary metabolites play a central role in the ecology of spp. in their natural environments.
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http://dx.doi.org/10.3389/fmicb.2021.688754DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8273931PMC
June 2021

gen. nov., sp. nov, a haloalkaliphilic actinobacterium from a soda solonchak soil.

Int J Syst Evol Microbiol 2021 May;71(5)

All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia.

A haloalkaliphilic hydrolytic actinobacterium, strain ACPA22, was enriched and isolated in pure culture from saline alkaline soil (soda solonchak) in northeastern Mongolia. The isolate was facultatively alkaliphilic, growing at pH 6.5-10.5 (optimum at 7.3-9.0) and highly salt-tolerant, tolerating up to 3 M total Na as carbonates. The hydrolytic nature of ACPA22 was confirmed by two different growth-dependent methods and by the presence of multiple glycosidase-encoding genes in the genome. The 16S rRNA gene-based phylogenetic analysis demonstrated that strain ACPA22 formed a deep-branching lineage within the family with the highest sequence similarity value to 18 (92.1 %) and Miq-4 (91.8 %). The average amino acid identity values (56.1-61.5 %) between ACPA22 and other members with available genomes did not exceed the threshold reported for different genera. The cell wall of ACPA22 contained -diaminopimelic acid, glycine, glutamic acid and alanine in a molar ratio, characteristic of the peptidoglycan type A1γ'. The whole-cell sugars included mannose, galactose, arabinose, ribose and xylose. The major menaquinones were MK-10(Н) and MK-11(Н). The identified polar lipids were represented by phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. In addition, the strain had a few unidentified characteristic polar lipids, including an amine-containing phospholipid with chromatographic mobility similar to that of phosphatidylinositol. The polar lipid fatty acids were dominated by anteiso-C and iso-C. The genome included a chromosome of 3.94 Mbp (G+C content 61.5 mol%) encoding 3285 proteins and two plasmids of 59.8 and 14.8 kBp. Based on the data obtained in this study, a new genus and species, gen. nov., sp. nov, is proposed with the type strain ACPA22 (=DSM 106290=VKM Ac-2771).
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http://dx.doi.org/10.1099/ijsem.0.004804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8289206PMC
May 2021

sp. nov., a Novel Hyperthermophilic Starch-Degrading Archaeon.

Biology (Basel) 2021 Apr 29;10(5). Epub 2021 Apr 29.

Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, D-24118 Kiel, Germany.

A novel hyperthermophilic archaeon, termed strain T7324, was isolated from a mixed sulfate-reducing consortium recovered from hot water produced from a deep North Sea oil reservoir. The isolate is a strict anaerobic chemo-organotroph able to utilize yeast extract or starch as a carbon source. The genes for a number of sugar degradation enzymes and glutamate dehydrogenase previously attributed to the sulfate reducing strain of the consortium ( strain 7324) were identified in the nearly completed genome sequence. Sequence analysis of the 16S rRNA gene placed the strain in the genus, but with an average nucleotide identity that is less than 90% to its closest relatives. Phylogenomic treeing reconstructions placed the strain on a distinct lineage clearly separated from other spp. The results indicate that the strain T7324 represents a novel species, for which the name sp. nov. is proposed. The type strain is T7324 (=DSM 27149 = KCTC 15808).
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http://dx.doi.org/10.3390/biology10050387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8146568PMC
April 2021

Genomic and proteomic profiles of biofilms on microplastics are decoupled from artificial surface properties.

Environ Microbiol 2021 06 6;23(6):3099-3115. Epub 2021 May 6.

Institute of Pharmacy, University of Greifswald, Greifswald, Germany.

Microplastics in marine ecosystems are colonized by diverse prokaryotic and eukaryotic communities. How these communities and their functional profiles are shaped by the artificial surfaces remains broadly unknown. In order to close this knowledge gap, we set up an in situ experiment with pellets of the polyolefin polymer polyethylene (PE), the aromatic hydrocarbon polymer polystyrene (PS), and wooden beads along a coastal to estuarine gradient in the Baltic Sea, Germany. We used an integrated metagenomics/metaproteomics approach to evaluate the genomic potential as well as protein expression levels of aquatic plastic biofilms. Our results suggest that material properties had a minor influence on the plastic-associated assemblages, as genomic and proteomic profiles of communities associated with the structurally different polymers PE and PS were highly similar, hence polymer-unspecific. Instead, it seemed that these communities were shaped by biogeographic factors. Wood, on the other hand, induced the formation of substrate-specific biofilms and served as nutrient source itself. Our study indicates that, while PE and PS microplastics may be relevant in the photic zone as opportunistic colonization grounds for phototrophic microorganisms, they appear not to be subject to biodegradation or serve as vectors for pathogenic microorganisms in marine habitats.
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http://dx.doi.org/10.1111/1462-2920.15531DOI Listing
June 2021

Detection of a New Resistance-Mediating Plasmid Chimera in a -Positive Strain at a German University Hospital.

Microorganisms 2021 Mar 31;9(4). Epub 2021 Mar 31.

Institute for Medical Microbiology, University Medical Center Göttingen, 37075 Göttingen, Germany.

Mobile genetic elements, such as plasmids, facilitate the spread of antibiotic resistance genes in Enterobacterales. In line with this, we investigated the plasmid-resistome of seven gene-carrying isolates, which were isolated between 2013 and 2014 at the University Medical Center in Göttingen, Germany. All isolates were subjected to complete genome sequencing including the reconstruction of entire plasmid sequences. In addition, phenotypic resistance testing was conducted. The seven isolates comprised both disease-associated isolates and colonizers isolated from five patients. They fell into two clusters of three sequence type (ST)101 and two ST11 isolates, respectively; and ST15 and ST23 singletons. The seven isolates harbored various plasmids of the incompatibility (Inc) groups IncF, IncL/M, IncN, IncR, and a novel plasmid chimera. All genes were encoded on the IncL/M plasmids. Of note, distinct phenotypical resistance patterns associated with different sets of resistance genes encoded by IncL/M and IncR plasmids were observed among isolates of the ST101 cluster in spite of high phylogenetic relatedness of the bacterial chromosomes, suggesting nosocomial transmission. This highlights the importance of plasmid uptake and plasmid recombination events for the fast generation of resistance variability after clonal transmission. In conclusion, this study contributes a piece in the puzzle of molecular epidemiology of resistance gene-carrying plasmids in in Germany.
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http://dx.doi.org/10.3390/microorganisms9040720DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8066831PMC
March 2021

Filling the Gaps in the Cyanobacterial Tree of Life-Metagenome Analysis of DSM 106950, SAG 13.99 and DSM 107014.

Genes (Basel) 2021 03 9;12(3). Epub 2021 Mar 9.

Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, 38124 Braunschweig, Germany.

Cyanobacteria represent one of the most important and diverse lineages of prokaryotes with an unparalleled morphological diversity ranging from unicellular cocci and characteristic colony-formers to multicellular filamentous strains with different cell types. Sequencing of more than 1200 available reference genomes was mainly driven by their ecological relevance (, ), toxicity () and the availability of axenic strains. In the current study three slowly growing non-axenic cyanobacteria with a distant phylogenetic positioning were selected for metagenome sequencing in order to (i) investigate their genomes and to (ii) uncover the diversity of associated heterotrophs. High-throughput Illumina sequencing, metagenomic assembly and binning allowed us to establish nearly complete high-quality draft genomes of all three cyanobacteria and to determine their phylogenetic position. The cyanosphere of the limnic isolates comprises up to 40 heterotrophic bacteria that likely coexisted for several decades, and it is dominated by and . The diagnostic marker protein RpoB ensured in combination with our novel taxonomic assessment via BLASTN-dependent text-mining a reliable classification of the metagenome assembled genomes (MAGs). The detection of one new family and more than a dozen genera of uncultivated heterotrophic bacteria illustrates that non-axenic cyanobacteria are treasure troves of hidden microbial diversity.
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http://dx.doi.org/10.3390/genes12030389DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8001431PMC
March 2021

Streptomyces bathyalis sp. nov., an actinobacterium isolated from the sponge in a deep sea.

Antonie Van Leeuwenhoek 2021 Apr 17;114(4):425-435. Epub 2021 Feb 17.

Microbial Strain Collection (MISG), Helmholtz Centre for Infection Research (HZI), 38124, Braunschweig, Germany.

A novel actinobacterium, designated ASO4wet, was isolated from the unidentified sponge (SO4) in the deep sea collected of the North Atlantic Ocean. Study of 16S rRNA gene sequences indicated that strain ASO4wet is a member of the genus Streptomyces and showed the closest similarities to Streptomyces karpasiensis K413 (98.87 %), Streptomyces glycovorans YIM M 10366 (98.38 %), and Streptomyces abyssalis YIM M 10400 (97.53 %). Strain ASO4wet contained MK-9(H8) as the predominant menaquinone and the major fatty acids are iso-C, anteiso-C, and iso-C. Polyphasic taxonomy was carried out between strain ASO4wet and its phylogenetically closely related Streptomyces strains, which further elucidated their relatedness and revealed that strain ASO4wet could be distinguished from currently known Streptomyces species. Strain ASO4wet clearly represents a novel species in genus Streptomyces. We propose the name Streptomyces bathyalis sp. nov., with the type strain ASO4wet (= DSM 106605 = NCCB 100657). Analysis of the whole-genome sequence of S. bathyalis revealed that genome size is 7,377,472 bp with 6332 coding sequences.
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http://dx.doi.org/10.1007/s10482-021-01528-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7979654PMC
April 2021

Complete Genome Sequences of Streptococcus suis Pig-Pathogenic Strains 10, 13-00283-02, and 16085/3b.

Microbiol Resour Announc 2021 Jan 14;10(2). Epub 2021 Jan 14.

Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany

is an important pathogen of pigs that, as a zoonotic agent, can also cause severe disease in humans, including meningitis, endocarditis, and septicemia. We report complete and annotated genomes of strains 10, 13-00283-02, and 16085/3b, which represent the highly prevalent serotypes , , and , respectively.
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http://dx.doi.org/10.1128/MRA.01137-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7849699PMC
January 2021

Angucycline-like Aromatic Polyketide from a Novel Species Reveals Freshwater Snail as Underexplored Reservoir for Antibiotic-Producing Actinomycetes.

Antibiotics (Basel) 2020 Dec 29;10(1). Epub 2020 Dec 29.

Helmholtz Centre for Infection Research, Department of microbial Strain Collection, Inhoffenstrasse 7, D-38124 Braunschweig, Germany.

Antibiotic producers have mainly been isolated from soil, which often has led to the rediscovery of known compounds. In this study, we identified the freshwater snail as an unexplored source for new antibiotic producers. The bacterial diversity associated with the snail was characterized by a metagenomic approach using cultivation-independent high-throughput sequencing. Although Actinobacteria represented only 2% of the bacterial community, the focus was laid on the isolation of the genus due to its potential to produce antibiotics. Three strains (7NS1, 7NS2 and 7NS3) were isolated from , and the antimicrobial activity of the crude extracts were tested against a selection of Gram-positive and Gram-negative bacteria and fungi. 7NS3 showed the strongest activity against Gram-positive bacteria and, thus, was selected for genome sequencing and a phylogenomic analysis. 7NS3 represents a novel species, which was deposited as sp. DSM 110735 at the Leibniz Institute-German Collection of Microorganisms and Cell Cultures (DSMZ). Bioassay-guided high-performance liquid chromatography (HPLC) and high-resolution electrospray ionization-mass spectrometry (HR-ESI-MS) analyses of crude extract fractions resulted in the detection of four compounds, one of which matched the compound characteristics of emycin A, an angucycline-like aromatic polyketide. Genome mining studies based on the whole-genome sequence of 7NS3 resulted in the identification of a gene cluster potentially coding for emycin A biosynthesis. Our study demonstrates that freshwater snails like can represent promising reservoirs for the isolation of new antibiotic-producing actinobacterial species.
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http://dx.doi.org/10.3390/antibiotics10010022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7823578PMC
December 2020

Simultaneous Presence of Bacteriochlorophyll and Xanthorhodopsin Genes in a Freshwater Bacterium.

mSystems 2020 Dec 22;5(6). Epub 2020 Dec 22.

Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia

Photoheterotrophic bacteria represent an important part of aquatic microbial communities. There exist two fundamentally different light-harvesting systems: bacteriochlorophyll-containing reaction centers or rhodopsins. Here, we report a photoheterotrophic strain isolated from an oligotrophic lake, which contains complete sets of genes for both rhodopsin-based and bacteriochlorophyll-based phototrophy. Interestingly, the identified genes were not expressed when cultured in liquid organic media. Using reverse transcription quantitative PCR (RT-qPCR), RNA sequencing, and bacteriochlorophyll quantification, we document that bacteriochlorophyll synthesis was repressed by high concentrations of glucose or galactose in the medium. Coactivation of photosynthesis genes together with genes for TonB-dependent transporters suggests the utilization of light energy for nutrient import. The photosynthetic units were formed by ring-shaped light-harvesting complex 1 and reaction centers with bacteriochlorophyll and spirilloxanthin as the main light-harvesting pigments. The identified rhodopsin gene belonged to the xanthorhodopsin family, but it lacks salinixanthin antenna. In contrast to bacteriochlorophyll, the expression of xanthorhodopsin remained minimal under all experimental conditions tested. Since the gene was found in the same operon as a histidine kinase, we propose that it might serve as a light sensor. Our results document that photoheterotrophic bacteria use the energy of light under carbon-limited conditions, while under carbon-replete conditions, they cover all their metabolic needs through oxidative phosphorylation. Phototrophic organisms are key components of many natural environments. There exist two main phototrophic groups: species that collect light energy using various kinds of (bacterio)chlorophylls and species that utilize rhodopsins. Here, we present a freshwater bacterium sp. strain AAP5 which contains genes for both light-harvesting systems. We show that bacteriochlorophyll-based reaction centers are repressed by light and/or glucose. On the other hand, the rhodopsin gene was not expressed significantly under any of the experimental conditions. This may indicate that rhodopsin in may have other functions not linked to bioenergetics.
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http://dx.doi.org/10.1128/mSystems.01044-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7762795PMC
December 2020

The Role of ING2-E5A in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses.

Microorganisms 2020 Dec 17;8(12). Epub 2020 Dec 17.

Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany.

Members of the genera and were speculated to represent indicators reflecting process instability within anaerobic digestion (AD) microbiomes. Therefore, ING2-E5A was isolated from a biogas reactor sample and sequenced on the PacBio and Illumina MiSeq sequencers. Phylogenetic classification positioned the strain ING2-E5A in close proximity to and species (family Dysgonomonadaceae). ING2-E5A encodes a number of genes for glycosyl-hydrolyses (GH) which are organized in Polysaccharide Utilization Loci (PUL) comprising tandem CD-like genes for a TonB-dependent outer-membrane transporter and a cell surface glycan-binding protein. Different GHs encoded in PUL are involved in pectin degradation, reflecting a pronounced specialization of the ING2-E5A PUL systems regarding the decomposition of this polysaccharide. Genes encoding enzymes participating in amino acids fermentation were also identified. Fragment recruitments with the ING2-E5A genome as a template and publicly available metagenomes of AD microbiomes revealed that species are present in 146 out of 257 datasets supporting their importance in AD microbiomes. Metatranscriptome analyses of AD microbiomes uncovered active sugar and amino acid fermentation pathways for species. Likewise, screening of metaproteome datasets demonstrated expression of the PUL-specific component SusC providing further evidence that PUL play a central role for the lifestyle of species.
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http://dx.doi.org/10.3390/microorganisms8122024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7768429PMC
December 2020

Plant Species-Dependent Increased Abundance and Diversity of IncP-1 Plasmids in the Rhizosphere: New Insights Into Their Role and Ecology.

Front Microbiol 2020 27;11:590776. Epub 2020 Nov 27.

Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany.

IncP-1 plasmids, first isolated from clinical specimens (R751, RP4), are recognized as important vectors spreading antibiotic resistance genes. The abundance of IncP-1 plasmids in the environment, previously reported, suggested a correlation with anthropogenic pollution. Unexpectedly, qPCR-based detection of IncP-1 plasmids revealed also an increased relative abundance of IncP-1 plasmids in total community DNA from the rhizosphere of lettuce and tomato plants grown in non-polluted soil along with plant age. Here we report the successful isolation of IncP-1 plasmids by exploiting their ability to mobilize plasmid pSM1890. IncP-1 plasmids were captured from the rhizosphere but not from bulk soil, and a high diversity was revealed by sequencing 14 different plasmids that were assigned to IncP-1β, δ, and ε subgroups. Although backbone genes were highly conserved and mobile elements or remnants as Tn, IS, Tn, or class 1 integron were carried by 13 of the sequenced IncP-1 plasmids, no antibiotic resistance genes were found. Instead, seven plasmids had a operon with Tn-like transposon and five plasmids contained putative metabolic gene clusters linked to these mobile elements. In-depth sequence comparisons with previously known plasmids indicate that the IncP-1 plasmids captured from the rhizosphere are archetypes of those found in clinical isolates. Our findings that IncP-1 plasmids do not always carry accessory genes in unpolluted rhizospheres are important to understand the ecology and role of the IncP-1 plasmids in the natural environment.
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http://dx.doi.org/10.3389/fmicb.2020.590776DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7728920PMC
November 2020

A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity.

Nat Commun 2020 12 15;11(1):6389. Epub 2020 Dec 15.

ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany.

Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called 'Pig intestinal bacterial collection' (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota.
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http://dx.doi.org/10.1038/s41467-020-19929-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7738495PMC
December 2020

Wound infection caused by Photobacterium damselae in a 32-year-old woman: case report and review of the literature.

GMS Infect Dis 2020 17;8:Doc23. Epub 2020 Nov 17.

Leibniz-Institut DSMZ - Deutsche Sammlung für Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany.

The case of a 32-year-old woman is reported, who was affected by a persisting wound infection caused by after an accident in the Mediterranean Sea. Besides the clinical case, microbiological characteristics based on the phenotypic and genotypic description of the isolate (including whole genome data) are presented and discussed.
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http://dx.doi.org/10.3205/id000067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7705356PMC
November 2020

Candidatus Sulfurimonas marisnigri sp. nov. and Candidatus Sulfurimonas baltica sp. nov., thiotrophic manganese oxide reducing chemolithoautotrophs of the class Campylobacteria isolated from the pelagic redoxclines of the Black Sea and the Baltic Sea.

Syst Appl Microbiol 2021 Jan 20;44(1):126155. Epub 2020 Nov 20.

Leibniz Institute for Baltic Sea Research Warnemünde, 18119 Rostock, Germany.

Species of the genus Sulfurimonas are reported and isolated from terrestrial habitats and marine sediments and water columns with steep redox gradients. Here we report on the isolation of strains SoZ1 and GD2 from the pelagic redoxcline of the Black Sea and the Baltic Sea, respectively. Both strains are gram-stain-negative and appear as short and slightly curved motile rods. The autecological preferences for growth of strain SoZ1 were 0-25°C (optimum 20°C), pH 6.5-9.0 (optimum pH 7.5-8.0) and salinity 10-40gL (optimum 25gL). Preferences for growth of strain GD2 were 0-20°C (optimum 15°C), pH 7.0-8.0 (optimum pH 7.0-7.5) and salinity 5-40gL (optimum 21gL). Strain SoZ1 grew chemolithoautotrophically, while strain GD2 also showed heterotrophic growth with short chained fatty acids as carbon source. Both species utilized hydrogen (H), sulfide (HS here taken as the sum of HS, HS and S), elemental sulfur (S) and thiosulfate (SO) as electron donors and nitrate (NO), oxygen (O) and particulate manganese oxide (MnO) as electron acceptors. Based on 16S rRNA gene sequence similarity, both strains cluster within the genus Sulfurimonas with Sulfurimonas gotlandica GD1 as the closest cultured relative species with a sequence similarity of 96.74% and 96.41% for strain SoZ1 and strain GD2, respectively. Strains SoZ1 and GD2 share a ribosomal 16S sequence similarity of 99.27% and were demarcated based on average nucleotide identity and average amino acid identity of the whole genome sequence. These calculations have been applied to the whole genus. We propose the names Candidatus Sulfurimonas marisnigri sp. nov. and Candidatus Sulfurimonas baltica sp. nov. for the thiotrophic manganese reducing culture isolates from the Black Sea and Baltic Sea, respectively.
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http://dx.doi.org/10.1016/j.syapm.2020.126155DOI Listing
January 2021

Dilution-to-Stimulation/Extinction Method: a Combination Enrichment Strategy To Develop a Minimal and Versatile Lignocellulolytic Bacterial Consortium.

Appl Environ Microbiol 2021 01 4;87(2). Epub 2021 Jan 4.

Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia

The engineering of complex communities can be a successful path to understand the ecology of microbial systems and improve biotechnological processes. Here, we developed a strategy to assemble a minimal and effective lignocellulolytic microbial consortium (MELMC) using a sequential combination of dilution-to-stimulation and dilution-to-extinction approaches. The consortium was retrieved from Andean forest soil and selected through incubation in liquid medium with a mixture of three types of agricultural plant residues. After the dilution-to-stimulation phase, approximately 50 bacterial sequence types, mostly belonging to the , , , and , were significantly enriched. The dilution-to-extinction method demonstrated that only eight of the bacterial sequence types were necessary to maintain microbial growth and plant biomass consumption. After subsequent stabilization, only two bacterial species ( sp. and sp.) became highly abundant (>99%) within the MELMC, indicating that these are the key players in degradation. Differences in the composition of bacterial communities between biological replicates indicated that selection, sampling, and/or priority effects could shape the consortium structure. The MELMC can degrade up to ∼13% of corn stover, consuming mostly its (hemi)cellulosic fraction. Tests with chromogenic substrates showed that the MELMC secretes an array of endoenzymes able to degrade xylan, arabinoxylan, carboxymethyl cellulose, and wheat straw. Additionally, the metagenomic profile inferred from the phylogenetic composition along with an analysis of carbohydrate-active enzymes of 20 bacterial genomes support the potential of the MELMC to deconstruct plant polysaccharides. This capacity was mainly attributed to the presence of sp. The significance of our study mainly lies in the development of a combined top-down enrichment strategy (i.e., dilution to stimulation coupled to dilution to extinction) to build a minimal and versatile lignocellulolytic microbial consortium. We demonstrated that mainly two selectively enriched bacterial species ( sp. and sp.) are required to drive the effective degradation of plant polymers. Our findings can guide the design of a synthetic bacterial consortium that could improve saccharification (i.e., the release of sugars from agricultural plant residues) processes in biorefineries. In addition, they can help to expand our ecological understanding of plant biomass degradation in enriched bacterial systems.
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http://dx.doi.org/10.1128/AEM.02427-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7783344PMC
January 2021

Desulfolutivibrio sulfoxidireducens gen. nov., sp. nov., isolated from a pyrite-forming enrichment culture and reclassification of Desulfovibrio sulfodismutans as Desulfolutivibrio sulfodismutans comb. nov.

Syst Appl Microbiol 2020 Sep 21;43(5):126105. Epub 2020 Jun 21.

Department of Microorganisms, Leibniz Institute DSMZ-German Culture Collection for Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; Institute for Microbiology, Technical University of Braunschweig, 38106 Braunschweig, Germany. Electronic address:

Two strains of sulfate-reducing bacteria (J.5.4.2-L4.2.8 and J.3.6.1-H7) were isolated from a pyrite-forming enrichment culture and were compared phylogenetically and physiologically to the closest related type strain Desulfovibrio sulfodismutans DSM 3696. The isolated strains were vibrio-shaped, motile rods that stained Gram-negative. Growth occurred from 15 to 37°C and within a pH range of 6.5-8.5. Both strains used sulfate, thiosulfate, sulfite, and dimethyl sulfoxide (DMSO) as electron acceptor when grown with lactate. Lactate was incompletely oxidized to acetate. Formate and H were used as electron donor in the presence of acetate. Dismutation of thiosulfate and pyrosulfite was observed. The two new isolates differed from D. sulfodismutans by the utilization of DMSO as electron acceptor, 82% genome-wide average nucleotide identity (ANI) and 32% digital DNA-DNA hybridization (dDDH), thus representing a novel species. The type strain of the type species Desulfovibrio desulfuricans Essex6 revealed merely 88% 16S rRNA gene identity and 49% genome-wide average amino acid identity (AAI) to the new isolates as well as to D. sulfodismutans. Furthermore, the dominance of menaquinone MK-7 over MK-6 and the dominance of ai-C fatty acids were observed not only in the two new isolated strains but also in D. sulfodismutans. Therefore, the definition of a new genus is indicated for which the name Desulfolutivibrio is proposed. We propose for strains J.5.4.2-L4.2.8 and J.3.6.1-H7 the name Desulfolutivibrio sulfoxidireducens gen. nov. sp. nov. with strain J.5.4.2-L4.2.8 defined as type strain. In addition, we propose the reclassification of Desulfovibrio sulfodismutans as Desulfolutivibrio sulfodismutans comb. nov.
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http://dx.doi.org/10.1016/j.syapm.2020.126105DOI Listing
September 2020

Genome and Methylome Adaptation of -Negative Helicobacter pylori during Experimental Human Infection.

mBio 2020 08 25;11(4). Epub 2020 Aug 25.

Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany

Multiple studies have demonstrated rapid bacterial genome evolution during chronic infection with In contrast, little was known about genetic changes during the first stages of infection, when selective pressure is likely to be highest. Using single-molecule, real-time (SMRT) and Illumina sequencing technologies, we analyzed genome and methylome evolution during the first 10 weeks of infection by comparing the pathogenicity island (PAI)-negative challenge strain BCS 100 with pairs of reisolates from gastric antrum and corpus biopsy specimens of 10 human volunteers who had been infected with this strain as part of a vaccine trial. Most genetic changes detected in the reisolates affected genes with a surface-related role or a predicted function in peptide uptake. Apart from phenotypic changes of the bacterial envelope, a duplication of the catalase gene was observed in one reisolate, which resulted in higher catalase activity and improved survival under oxidative stress conditions. The methylomes also varied in some of the reisolates, mostly by activity switching of phase-variable methyltransferase (MTase) genes. The observed mutation spectrum was remarkable for a very high proportion of nonsynonymous mutations. Although the data showed substantial within-strain genome diversity in the challenge strain, most antrum and corpus reisolates from the same volunteers were highly similar to each other, indicating that the challenge infection represents a major selective bottleneck shaping the transmitted population. Our findings suggest rapid election of during early-phase infection providing adaptation to different individuals by common mechanisms of genetic and epigenetic alterations. Exceptional genetic diversity and variability are hallmarks of , but the biological role of this plasticity remains incompletely understood. Here, we had the rare opportunity to investigate the molecular evolution during the first weeks of infection by comparing the genomes and epigenomes of strain BCS 100 used to challenge human volunteers in a vaccine trial with those of bacteria reisolated from the volunteers 10 weeks after the challenge. The data provide molecular insights into the process of establishment of this highly versatile pathogen in 10 different human individual hosts, showing, for example, selection for changes in host-interaction molecules as well as changes in epigenetic methylation patterns. The data provide important clues to the early adaptation of to new host niches after transmission, which we believe is vital to understand its success as a chronic pathogen and develop more efficient treatments and vaccines.
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http://dx.doi.org/10.1128/mBio.01803-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7448279PMC
August 2020

Complete Genome Sequence and Manual Reannotation of Mycobacterium avium subsp. Strain DSM 44135.

Microbiol Resour Announc 2020 Aug 13;9(33). Epub 2020 Aug 13.

Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.

Here, we report the complete genome sequence of the subsp. reference strain DSM 44135, amended with a manual genome reannotation. The strain was originally described as strain 6783. It was isolated from feces from a dairy cow in northern Germany.
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http://dx.doi.org/10.1128/MRA.00711-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7427190PMC
August 2020

Streptomyces marianii sp. nov., a novel marine actinomycete from southern coast of India.

J Antibiot (Tokyo) 2021 01 13;74(1):59-69. Epub 2020 Aug 13.

Centre for Marine Science and Technology (CMST), Manonmaniam Sundaranar University, Rajakkamangalam, Kanyakumari District, Tamil Nadu, 629502, India.

A novel marine actinomycete strain designated ICN19 was isolated from the subtidal sediment of Chinnamuttam coast of Kanyakumari, India and subjected to polyphasic taxonomic analysis. Neighbour-joining tree based on 16S rRNA gene sequences of validly described type strains had revealed the strain ICN19 formed distinct cluster with Streptomyces wuyuanensis CGMCC 4.7042, Streptomyces tirandamycinicus HNM0039 and Streptomyces spongiicola HNM0071. Morphological, physiological and chemotaxonomic characteristics were consistent with those of members of the genus Streptomyces. The strain possessed LL-diaminopimelic acid as the diagnostic diamino acid. The predominant isoprenoid quinone was identified as MK-9(H8) (70%), MK-9(H6) (20%) and MK-9(H2) (2%), with the major cellular fatty acids (>10%) being anteiso-C, C and iso-C. The main polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannosides and three unidentified phospholipids. The dendrogram generated on the basis of MALDI-TOF mass spectra supports the strain differentiated from its neigbours. The genome sequence of strain ICN19 was 9,010,366 bp in size with a total of 7420 protein-coding genes and 98 RNA genes. The genomic G+C content of the novel strain was 71.27 mol%. The DNA-DNA relatedness between strain ICN19 and the reference strains with S. wuyuanensis CGMCC 4.7042, S. tirandamycinicus HNM0039 and S. spongiicola HNM0071 were 42.8%, 39.5% and 38%, respectively. Based on differences in physiological, biochemical, chemotaxonomic differences and whole-genome characteristics the isolated strain represents a novel species of the genus Streptomyces, for which the name Streptomyces marianii sp. nov. is proposed. Type strain is ICN19 (=MCC 3599 = KCTC 39749).
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http://dx.doi.org/10.1038/s41429-020-0360-zDOI Listing
January 2021

A publicly accessible database for genome sequences supports tracing of transmission chains and epidemics.

Microb Genom 2020 08 29;6(8). Epub 2020 Jul 29.

Braunschweig Integrated Center of Systems Biology (BRICS), Technical University, Braunschweig, Germany.

is the primary infectious cause of antibiotic-associated diarrhea. Local transmissions and international outbreaks of this pathogen have been previously elucidated by bacterial whole-genome sequencing, but comparative genomic analyses at the global scale were hampered by the lack of specific bioinformatic tools. Here we introduce a publicly accessible database within EnteroBase (http://enterobase.warwick.ac.uk) that automatically retrieves and assembles short-reads from the public domain, and calls alleles for core-genome multilocus sequence typing (cgMLST). We demonstrate that comparable levels of resolution and precision are attained by EnteroBase cgMLST and single-nucleotide polymorphism analysis. EnteroBase currently contains 18 254 quality-controlled genomes, which have been assigned to hierarchical sets of single-linkage clusters by cgMLST distances. This hierarchical clustering is used to identify and name populations of at all epidemiological levels, from recent transmission chains through to epidemic and endemic strains. Moreover, it puts newly collected isolates into phylogenetic and epidemiological context by identifying related strains among all previously published genome data. For example, HC2 clusters (i.e. chains of genomes with pairwise distances of up to two cgMLST alleles) were statistically associated with specific hospitals (<10) or single wards (=0.01) within hospitals, indicating they represented local transmission clusters. We also detected several HC2 clusters spanning more than one hospital that by retrospective epidemiological analysis were confirmed to be associated with inter-hospital patient transfers. In contrast, clustering at level HC150 correlated with -mer-based classification and was largely compatible with PCR ribotyping, thus enabling comparisons to earlier surveillance data. EnteroBase enables contextual interpretation of a growing collection of assembled, quality-controlled genome sequences and their associated metadata. Hierarchical clustering rapidly identifies database entries that are related at multiple levels of genetic distance, facilitating communication among researchers, clinicians and public-health officials who are combatting disease caused by .
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http://dx.doi.org/10.1099/mgen.0.000410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7641423PMC
August 2020

The transcription factor WRKY22 is required during cryo-stress acclimation in Arabidopsis shoot tips.

J Exp Bot 2020 08;71(16):4993-5009

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.

Storage of meristematic tissue at ultra-low temperatures offers a mean to maintain valuable genetic resources from vegetatively reproduced plants. To reveal the biology underlying cryo-stress, shoot tips of the model plant Arabidopsis thaliana were subjected to a standard preservation procedure. A transcriptomic approach was taken to describe the subsequent cellular events which occurred. The cryoprotectant treatment induced the changes in the transcript levels of genes associated with RNA processing and primary metabolism. Explants of a mutant lacking a functional copy of the transcription factor WRKY22 were compromised for recovery. A number of putative downstream targets of WRKY22 were identified, some related to phytohormone-mediated defense, to the osmotic stress response, and to development. There were also alterations in the abundance of transcript produced by genes encoding photosynthesis-related proteins. The wrky22 mutant plants developed an open stomata phenotype in response to their exposure to the cryoprotectant solution. WRKY22 probably regulates a transcriptional network during cryo-stress, linking the explant's defense and osmotic stress responses to changes in its primary metabolism. A model is proposed linking WRKY53 and WRKY70 downstream of the action of WRKY22.
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http://dx.doi.org/10.1093/jxb/eraa224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7475261PMC
August 2020

Stochastic Dispersal Rather Than Deterministic Selection Explains the Spatio-Temporal Distribution of Soil Bacteria in a Temperate Grassland.

Front Microbiol 2020 30;11:1391. Epub 2020 Jun 30.

Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.

Spatial and temporal processes shaping microbial communities are inseparably linked but rarely studied together. By Illumina 16S rRNA sequencing, we monitored soil bacteria in 360 stations on a 100 square meter plot distributed across six intra-annual samplings in a rarely managed, temperate grassland. Using a multi-tiered approach, we tested the extent to which stochastic or deterministic processes influenced the composition of local communities. A combination of phylogenetic turnover analysis and null modeling demonstrated that either homogenization by unlimited stochastic dispersal or scenarios, in which neither stochastic processes nor deterministic forces dominated, explained local assembly processes. Thus, the majority of all sampled communities (82%) was rather homogeneous with no significant changes in abundance-weighted composition. However, we detected strong and uniform taxonomic shifts within just nine samples in early summer. Thus, community snapshots sampled from single points in time or space do not necessarily reflect a representative community state. The potential for change despite the overall homogeneity was further demonstrated when the focus shifted to the rare biosphere. Rare OTU turnover, rather than nestedness, characterized abundance-independent β-diversity. Accordingly, boosted generalized additive models encompassing spatial, temporal and environmental variables revealed strong and highly diverse effects of space on OTU abundance, even within the same genus. This pure spatial effect increased with decreasing OTU abundance and frequency, whereas soil moisture - the most important environmental variable - had an opposite effect by impacting abundant OTUs more than the rare ones. These results indicate that - despite considerable oscillation in space and time - the abundant and resident OTUs provide a community backbone that supports much higher β-diversity of a dynamic rare biosphere. Our findings reveal complex interactions among space, time, and environmental filters within bacterial communities in a long-established temperate grassland.
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http://dx.doi.org/10.3389/fmicb.2020.01391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7338559PMC
June 2020

ClbR Is the Key Transcriptional Activator of Colibactin Gene Expression in Escherichia coli.

mSphere 2020 07 15;5(4). Epub 2020 Jul 15.

Institute of Hygiene, University of Münster, Münster, Germany

Colibactin is a nonribosomal peptide/polyketide hybrid natural product expressed by different members of the which can be correlated with induction of DNA double-strand breaks and interference with cell cycle progression in eukaryotes. Regulatory features of colibactin expression are only incompletely understood. We used strain M1/5 as a model to investigate regulation of expression of the colibactin determinant at the transcriptional level and to characterize regulatory elements located within the colibactin pathogenicity island itself. We measured transcription and observed that cultivation in defined minimal media led to increased colibactin expression relative to rich media. Transcription of directly responds to iron availability. We also characterized structural DNA elements inside the colibactin determinant involved in ClbR-dependent regulation, i.e., ClbR binding sites and a variable number of tandem repeats located upstream of We investigated the impact of overexpression or deletion at the transcriptome and proteome levels. Moreover, we compared global gene regulation under these conditions with that occurring upon overexpression or deletion of , which affects the flux of colibactin production. Combining the results of the transcriptome and proteome analyses with indirect measurements of colibactin levels by cell culture assays and an approximate quantification of colibactin via the second product of colibactin cleavage from precolibactin, N-myristoyl-d-asparagine, we demonstrate that the variable number of tandem repeats plays a significant regulatory role in colibactin expression. We identify ClbR as the only transcriptional activator known so far that is specific and essential for efficient regulation of colibactin production. The nonribosomal peptide/polyketide hybrid colibactin can be considered a bacterial virulence factor involved in extraintestinal infection and also a procarcinogen. Nevertheless, and despite its genotoxic effect, colibactin expression can also inhibit bacterial or tumor growth and correlates with probiotic anti-inflammatory and analgesic properties. Although the biological function of this natural compound has been studied extensively, our understanding of the regulation of colibactin expression is still far from complete. We investigated in detail the role of regulatory elements involved in colibactin expression and in the growth conditions that promote colibactin expression. In this way, our data shed light on the regulatory mechanisms involved in colibactin expression and may support the expression and purification of this interesting nonribosomal peptide/polyketide hybrid for further molecular characterization.
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http://dx.doi.org/10.1128/mSphere.00591-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7364221PMC
July 2020

Comparative Genomics Suggests Mechanisms of Genetic Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax.

Genome Biol Evol 2020 06;12(6):827-841

Division of Soil and Water Management, KU Leuven, Belgium.

Biodegradation of the phenylurea herbicide linuron appears a specialization within a specific clade of the Variovorax genus. The linuron catabolic ability is likely acquired by horizontal gene transfer but the mechanisms involved are not known. The full-genome sequences of six linuron-degrading Variovorax strains isolated from geographically distant locations were analyzed to acquire insight into the mechanisms of genetic adaptation toward linuron metabolism. Whole-genome sequence analysis confirmed the phylogenetic position of the linuron degraders in a separate clade within Variovorax and indicated that they unlikely originate from a common ancestral linuron degrader. The linuron degraders differentiated from Variovorax strains that do not degrade linuron by the presence of multiple plasmids of 20-839 kb, including plasmids of unknown plasmid groups. The linuron catabolic gene clusters showed 1) high conservation and synteny and 2) strain-dependent distribution among the different plasmids. Most of them were bordered by IS1071 elements forming composite transposon structures, often in a multimeric array configuration, appointing IS1071 as a key element in the recruitment of linuron catabolic genes in Variovorax. Most of the strains carried at least one (catabolic) broad host range plasmid that might have been a second instrument for catabolic gene acquisition. We conclude that clade 1 Variovorax strains, despite their different geographical origin, made use of a limited genetic repertoire regarding both catabolic functions and vehicles to acquire linuron biodegradation.
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http://dx.doi.org/10.1093/gbe/evaa085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7313664PMC
June 2020
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