Publications by authors named "Jörg Overmann"

200 Publications

Contrasting responses of above- and belowground diversity to multiple components of land-use intensity.

Nat Commun 2021 06 24;12(1):3918. Epub 2021 Jun 24.

Institute of Zoology, Terrestrial Ecology, University of Cologne, Köln, Germany.

Land-use intensification is a major driver of biodiversity loss. However, understanding how different components of land use drive biodiversity loss requires the investigation of multiple trophic levels across spatial scales. Using data from 150 agricultural grasslands in central Europe, we assess the influence of multiple components of local- and landscape-level land use on more than 4,000 above- and belowground taxa, spanning 20 trophic groups. Plot-level land-use intensity is strongly and negatively associated with aboveground trophic groups, but positively or not associated with belowground trophic groups. Meanwhile, both above- and belowground trophic groups respond to landscape-level land use, but to different drivers: aboveground diversity of grasslands is promoted by diverse surrounding land-cover, while belowground diversity is positively related to a high permanent forest cover in the surrounding landscape. These results highlight a role of landscape-level land use in shaping belowground communities, and suggest that revised agroecosystem management strategies are needed to conserve whole-ecosystem biodiversity.
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http://dx.doi.org/10.1038/s41467-021-23931-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8225671PMC
June 2021

Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria.

mSystems 2021 May 18;6(3). Epub 2021 May 18.

Functional Microbiome Research Group, RWTH University Hospital, Aachen, Germany

The gut microbiome is crucial for both maturation of the immune system and colonization resistance against enteric pathogens. Although chicken are important domesticated animals, the impact of their gut microbiome on the immune system is understudied. Therefore, we investigated the effect of microbiome-based interventions on host mucosal immune responses. Increased levels of IgA and IgY were observed in chickens exposed to maternal feces after hatching compared with strict hygienic conditions. This was accompanied by increased gut bacterial diversity as assessed by 16S rRNA gene amplicon sequencing. Cultivation work allowed the establishment of a collection of 43 bacterial species spanning 4 phyla and 19 families, including the first cultured members of 3 novel genera and 4 novel species that were taxonomically described. This resource is available at www.dsmz.de/chibac A synthetic community consisting of nine phylogenetically diverse and dominant species from this collection was designed and found to be moderately efficient in boosting immunoglobulin levels when provided to chickens early in life. The immune system plays a crucial role in sustaining animal health. Its development is markedly influenced by early microbial colonization of the gastrointestinal tract. As chicken are fully dependent on environmental microbes after hatching, extensive hygienic measures in production facilities are detrimental to the microbiota, resulting in low colonization resistance against pathogens. To combat enteric infections, antibiotics are frequently used, which aggravates the issue by altering gut microbiota colonization. Intervention strategies based on cultured gut bacteria are proposed to influence immune responses in chicken.
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http://dx.doi.org/10.1128/mSystems.01300-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8269260PMC
May 2021

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

Environ Microbiol 2021 Jun 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

Recent advances in culture-based gut microbiome research.

Int J Med Microbiol 2021 Apr 25;311(3):151485. Epub 2021 Feb 25.

Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany; ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany. Electronic address:

Gut microbes affect the physiology of their hosts. Studying their diversity and functions is thus of utmost importance as it will open new avenues towards the discovery of new biomolecules and the treatment of diseases. Gut microbiome research is currently boosted by the unification of metagenomics, which has dominated the field in the last two decades, and cultivation, which is experiencing a renaissance. Each of these approaches has advantages and drawbacks that can be overcome if used synergistically. In this brief article, we summarize recent literature and own studies on the cultivation of gut microbes, provide a succinct status quo of cultured fractions and collections of isolates, and give short opinions on challenges and next steps to take.
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http://dx.doi.org/10.1016/j.ijmm.2021.151485DOI Listing
April 2021

Dinoroseobacter shibae Outer Membrane Vesicles Are Enriched for the Chromosome Dimer Resolution Site .

mSystems 2021 Jan 12;6(1). Epub 2021 Jan 12.

Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany

Outer membrane vesicles (OMVs) are universally produced by prokaryotes and play important roles in symbiotic and pathogenic interactions. They often contain DNA, but a mechanism for its incorporation is lacking. Here, we show that , a dinoflagellate symbiont, constitutively secretes OMVs containing DNA. Time-lapse microscopy captured instances of multiple OMV production at the septum during cell division. DNA from the vesicle lumen was up to 22-fold enriched for the region around the terminus of replication (). The peak of coverage was located at a conserved 28-bp palindromic sequence required for binding of the site-specific tyrosine recombinases XerC/XerD. These enzymes are activated at the last stage of cell division immediately prior to septum formation when they are bound by the divisome protein FtsK. We suggest that overreplicated regions around the terminus have been repaired by the FtsK-XerC/XerD molecular machinery. The vesicle proteome was clearly dominated by outer membrane and periplasmic proteins. Some of the most abundant vesicle membrane proteins were predicted to be required for direct interaction with peptidoglycan during cell division (LysM, Tol-Pal, Spol, lytic murein transglycosylase). OMVs were 15-fold enriched for the saturated fatty acid 16:00. We hypothesize that constitutive OMV secretion in is coupled to cell division. The footprint of the FtsK--XerC/XerD molecular machinery suggests a novel potentially highly conserved route for incorporation of DNA into OMVs. Clearing the division site from small DNA fragments might be an important function of vesicles produced during exponential growth under optimal conditions. Gram-negative bacteria continually form vesicles from their outer membrane (outer membrane vesicles [OMVs]) during normal growth. OMVs frequently contain DNA, and it is unclear how DNA can be shuffled from the cytoplasm to the OMVs. We studied OMV cargo in , a symbiont of dinoflagellates, using microscopy and a multi-omics approach. We found that vesicles formed during undisturbed exponential growth contain DNA which is enriched for genes around the replication terminus, specifically, the binding site for an enzyme complex that is activated at the last stage of cell division. We suggest that the enriched genes are the result of overreplication which is repaired by their excision and excretion via membrane vesicles to clear the divisome from waste DNA.
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http://dx.doi.org/10.1128/mSystems.00693-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7901474PMC
January 2021

gen. nov., sp. nov. and sp. nov., novel members of fam. nov. within the order isolated from soil.

Int J Syst Evol Microbiol 2021 Feb;71(2)

Braunschweig University of Technology, Spielmanstraße 7, 38106 Braunschweig, Germany.

Members of the metabolically diverse order inhabit a wide range of environments. Two strains affiliated with this order were isolated from soils in Germany and characterized by a polyphasic approach. Cells of strains 0125_3 and Swamp67 are Gram-negative rods, non-motile, non-spore-forming, non-capsulated and divide by binary fission. They tested catalase-negative, but positive for cytochrome -oxidase. Both strains form small white colonies on agar plates and grow aerobically and chemoorganotrophically on SSE/HD 1 : 10 medium, preferably utilizing organic acids and proteinaceous substrates. Strains 0125_3 and Swamp67 are mesophilic and grow optimally without NaCl addition at slightly alkaline conditions. Major fatty acids are C  7, C and C. The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyglycerol. The predominant respiratory quinone is Q-8. The G+C content for 0125_3 and Swamp67 was 67 and 66.1 %, respectively. The 16S rRNA gene analysis indicated that the closest relatives (<91 % sequence similarity) of strain 0125_3 were ATCC 25196, FAM5 and AcBE2-1, while ATCC 25196, Nv1 and APG3 were closest to strain Swamp67. The two novel strains shared 97.4 % 16S rRNA gene sequence similarity with one another and show low average nucleotide identity of their genomes (83.8 %). Based on the phenotypic, chemotaxonomic, genomic and phylogenetic analysis, we propose the two novel species sp. nov (type strain 0125_3=DSM 104443=LMG 29998=CECT 9241) and sp. nov. (type strain Swamp67=DSM 104440=LMG 29997=CECT 9242) of the novel genus gen. nov., within the novel family fam. nov.
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http://dx.doi.org/10.1099/ijsem.0.004631DOI Listing
February 2021

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

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

Cryo-EM structure of a Ca-bound photosynthetic LH1-RC complex containing multiple αβ-polypeptides.

Nat Commun 2020 10 2;11(1):4955. Epub 2020 Oct 2.

Faculty of Science, Ibaraki University, Mito, 310-8512, Japan.

The light-harvesting-reaction center complex (LH1-RC) from the purple phototrophic bacterium Thiorhodovibrio strain 970 exhibits an LH1 absorption maximum at 960 nm, the most red-shifted absorption for any bacteriochlorophyll (BChl) a-containing species. Here we present a cryo-EM structure of the strain 970 LH1-RC complex at 2.82 Å resolution. The LH1 forms a closed ring structure composed of sixteen pairs of the αβ-polypeptides. Sixteen Ca ions are present in the LH1 C-terminal domain and are coordinated by residues from the αβ-polypeptides that are hydrogen-bonded to BChl a. The Ca-facilitated hydrogen-bonding network forms the structural basis of the unusual LH1 redshift. The structure also revealed the arrangement of multiple forms of α- and β-polypeptides in an individual LH1 ring. Such organization indicates a mechanism of interplay between the expression and assembly of the LH1 complex that is regulated through interactions with the RC subunits inside.
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http://dx.doi.org/10.1038/s41467-020-18748-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7532537PMC
October 2020

Global Response of Phaeobacter inhibens DSM 17395 to Deletion of Its 262-kb Chromid Encoding Antibiotic Synthesis.

Microb Physiol 2020 24;30(1-6):9-24. Epub 2020 Jul 24.

General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany,

The marine alphaproteobacterium Phaeobacter inhibens DSM 17395, a member of the Roseobacter group, was recently shown to markedly enhance growth upon deletion of its 262-kb chromid encoding biosynthesis of tropodithietic acid (TDA). To scrutinize the metabolic/regulatory adaptations that underlie enhanced growth of the Δ262 mutant, its transcriptome and proteome compared to the wild type were investigated in process-controlled bioreactors with Casamino Acids as growth substrate. Genome resequencing revealed only few additional genetic changes (a heterogenic insertion, prophage activation, and several point mutations) between wild type and Δ262 mutant, albeit with no conceivable effect on the studied growth physiology. The abundances of the vast majority of transcripts and proteins involved in the catabolic network for complete substrate oxidation to CO2 were found to be unchanged, suggesting that the enhanced amino acid utilization of the Δ262 mutant did not require elevated synthesis of most enzymes of the catabolic network. Similarly, constituents of genetic information processing and cellular processes remained mostly unchanged. In contrast, 426 genes displayed differential expression, of which 410 were localized on the 3.2-Mb chromosome, 5 on the 65-kb chromid, and 11 on the 78-kb chromid. Notably, the branched-chain amino transferase IlvE acting on rapidly utilized Val, Ile, and Leu was upregulated. Moreover, the transportome was reconfigured, as evidenced from increased abundances of transcripts and proteins of several uptake systems for amino acids and inorganic nutrients (e.g., phosphate). Some components of the respiratory chain were also upregulated, which correlates with the higher respiration rates of the Δ262 mutant. Furthermore, chromosomally encoded transcripts and proteins that are peripherally related to TDA biosynthesis (e.g., the serine acyl transferase CysE) were strongly downregulated in the Δ262 mutant. Taken together, these observations reflect adaptations to enhanced growth as well as the functional interconnectivity of the replicons of P. inhibens DSM 17395.
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http://dx.doi.org/10.1159/000508591DOI Listing
July 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

Bacterial mock communities as standards for reproducible cytometric microbiome analysis.

Nat Protoc 2020 09 7;15(9):2788-2812. Epub 2020 Aug 7.

Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.

Flow cytometry has recently established itself as a tool to track short-term dynamics in microbial community assembly and link those dynamics with ecological parameters. However, instrumental configurations of commercial cytometers and variability introduced through differential handling of the cells and instruments frequently cause data set variability at the single-cell level. This is especially pronounced with microorganisms, which are in the lower range of optical resolution. Although alignment beads are valuable to generally minimize instrumental noise and align overall machine settings, an artificial microbial cytometric mock community (mCMC) is mandatory for validating lab workflows and enabling comparison of data between experiments, thus representing a necessary reference standard for the reproducible cytometric characterization of microbial communities, especially in long-term studies. In this study, the mock community consisted of two Gram-positive and two Gram-negative bacterial strains, which can be assembled with respective subsets of cells, including spores, in any selected ratio or concentration. The preparation of the four strains takes a maximum of 5 d, and the stains are storable with either PFA/ethanol fixation at -20 °C or drying at 4 °C for at least 6 months. Starting from this stock, an mCMC can be assembled within 1 h. Fluorescence staining methods are presented and representatively applied with two high-resolution cell sorters and three benchtop flow cytometers. Benchmarked data sets allow the use of bioinformatic evaluation procedures to decode community behavior or convey qualified cell sorting decisions for subsequent high-resolution sequencing or proteomic routines.
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http://dx.doi.org/10.1038/s41596-020-0362-0DOI Listing
September 2020

gen. nov., sp. nov., a novel prosthecate, budding member of the family isolated from forest soil.

Int J Syst Evol Microbiol 2020 Sep 7;70(9):4966-4977. Epub 2020 Aug 7.

Braunschweig University of Technology, Spielmanstraße 7, 38106 Braunschweig, Germany.

The family comprises prosthecate bacteria with a dimorphic cell cycle and also non-prosthecate bacteria. Cells of all described species divide by binary fission. Strain 0127_4 was isolated from forest soil in Baden Württemberg (Germany) and determined to be the first representative of the family which divided by budding. Cells of strain 0127_4 were Gram-negative, rod-shaped, prosthecate, motile by means of a polar flagellum, non-spore-forming and non-capsulated. The strain formed small white colonies and grew aerobically and chemo-organotrophically utilizing organic acids, amino acids and proteinaceous substrates. 16S rRNA gene sequence analysis indicated that this bacterium was related to TH1-2 and DRW22-8 with 91.3 and 89.7% sequence similarity, respectively. Four unidentified glycolipids were detected as the major polar lipids and, unlike all described members of the family , phosphatidylglycerol was absent. The major fatty acids were summed feature 8 (Cω7/Cω6), summed feature 9 (iso-Cω9/C 10-methyl), C and summed feature 3 (C 6/C 7). The major respiratory quinone was Q-10. The G+C content of the genomic DNA was 63.5 %. Based on the present taxonomic characterization, strain 0127_4 represents a novel species of a new genus, gen. nov., sp. nov. The type strain of is 0127_4 (=DSM 104635=CECT 9243).
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http://dx.doi.org/10.1099/ijsem.0.004367DOI Listing
September 2020

Blind spots in global soil biodiversity and ecosystem function research.

Nat Commun 2020 08 3;11(1):3870. Epub 2020 Aug 3.

German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.

Soils harbor a substantial fraction of the world's biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil taxa and ecosystem functioning data across soil macroecological studies and 17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research.
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http://dx.doi.org/10.1038/s41467-020-17688-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7400591PMC
August 2020

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

2-Hydroxysorangiadenosine: Structure and Biosynthesis of a Myxobacterial Sesquiterpene-Nucleoside.

Molecules 2020 Jun 9;25(11). Epub 2020 Jun 9.

Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany.

Myxobacteria represent an under-investigated source for biologically active natural products featuring intriguing structural moieties with potential applications, e.g., in the pharmaceutical industry. Sorangiadenosine and the here-discovered 2-hydroxysorangiadenosine are myxobacterial sesquiterpene-nucleosides with an unusual structural moiety, a bicyclic eudesmane-type sesquiterpene. As the biosynthesis of these rare terpene-nucleoside hybrid natural products remains elusive, we investigated secondary metabolomes and genomes of several 2-hydroxysorangiadenosine-producing myxobacteria. We report the isolation and full structure elucidation of 2-hydroxysorangiadenosine and its cytotoxic and antibiotic activities and propose a biosynthetic pathway in the myxobacterium MCy10943.
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http://dx.doi.org/10.3390/molecules25112676DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7321100PMC
June 2020

Characterization of Clostridioides difficile DSM 101085 with A-B-CDT+ Phenotype from a Late Recurrent Colonization.

Genome Biol Evol 2020 05;12(5):566-577

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

During the last decades, hypervirulent strains of Clostridioides difficile with frequent disease recurrence and increased mortality appeared. Clostridioides difficile DSM 101085 was isolated from a patient who suffered from several recurrent infections and colonizations, likely contributing to a fatal outcome. Analysis of the toxin repertoire revealed the presence of a complete binary toxin locus and an atypical pathogenicity locus consisting of only a tcdA pseudogene and a disrupted tcdC gene sequence. The pathogenicity locus shows upstream a transposon and has been subject to homologous recombination or lateral gene transfer events. Matching the results of the genome analysis, neither TcdA nor TcdB production but the expression of cdtA and cdtB was detected. This highlights a potential role of the binary toxin C. difficile toxin in this recurrent colonization and possibly further in a host-dependent virulence. Compared with the C. difficile metabolic model strains DSM 28645 (630Δerm) and DSM 27147 (R20291), strain DSM 101085 showed a specific metabolic profile, featuring changes in the threonine degradation pathways and alterations in the central carbon metabolism. Moreover, products originating from Stickland pathways processing leucine, aromatic amino acids, and methionine were more abundant in strain DSM 101085, indicating a more efficient use of these substrates. The particular characteristics of strain C. difficile DSM 101085 may represent an adaptation to a low-protein diet in a patient with recurrent infections.
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http://dx.doi.org/10.1093/gbe/evaa072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7250501PMC
May 2020

New ECCO model documents for Material Deposit and Transfer Agreements in compliance with the Nagoya Protocol.

FEMS Microbiol Lett 2020 03;367(5)

Micoteca da Universidade do Minho (MUM), CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.

The European Culture Collections' Organisation presents two new model documents for Material Deposit Agreement (MDA) and Material Transfer Agreement (MTA) designed to enable microbial culture collection leaders to draft appropriate agreement documents for, respectively, deposit and supply of materials from a public collection. These tools provide guidance to collections seeking to draft an MDA and MTA, and are available in open access to be used, modified, and shared. The MDA model consists of a set of core fields typically included in a 'deposit form' to collect relevant information to facilitate assessment of the status of the material under access and benefit sharing (ABS) legislation. It also includes a set of exemplary clauses to be included in 'terms and conditions of use' for culture collection management and third parties. The MTA model addresses key issues including intellectual property rights, quality, safety, security and traceability. Reference is made to other important tools such as best practices and code of conduct related to ABS issues. Besides public collections, the MDA and MTA model documents can also be useful for individual researchers and microbial laboratories that collect or receive microbial cultures, keep a working collection, and wish to share their material with others.
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http://dx.doi.org/10.1093/femsle/fnaa044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164777PMC
March 2020

Delineation of a Subgroup of the Genus Paraburkholderia, Including P. terrae DSM 17804T, P. hospita DSM 17164T, and Four Soil-Isolated Fungiphiles, Reveals Remarkable Genomic and Ecological Features-Proposal for the Definition of a P. hospita Species Cluster.

Genome Biol Evol 2020 04;12(4):325-344

Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands.

The fungal-interactive (fungiphilic) strains BS001, BS007, BS110, and BS437 have previously been preliminarily assigned to the species Paraburkholderia terrae. However, in the (novel) genus Paraburkholderia, an as-yet unresolved subgroup exists, that clusters around Paraburkholderia hospita (containing the species P. terrae, P. hospita, and Paraburkholderia caribensis). To shed light on the precise relationships across the respective type strains and the novel fungiphiles, we here compare their genomic and ecophysiological features. To reach this goal, the genomes of the three type strains, with sizes ranging from 9.0 to 11.5 Mb, were de novo sequenced and the high-quality genomes analyzed. Using whole-genome, ribosomal RNA and marker-gene-concatenate analyses, close relationships between P. hospita DSM 17164T and P. terrae DSM 17804T, versus more remote relationships to P. caribensis DSM 13236T, were found. All four fungiphilic strains clustered closely to the two-species cluster. Analyses of average nucleotide identities (ANIm) and tetranucleotide frequencies (TETRA) confirmed the close relationships between P. hospita DSM 17164T and P. terrae DSM 17804T (ANIm = 95.42; TETRA = 0.99784), as compared with the similarities of each one of these strains to P. caribensis DSM 13236T. A species cluster was thus proposed. Furthermore, high similarities of the fungiphilic strains BS001, BS007, BS110, and BS437 with this cluster were found, indicating that these strains also make part of it, being closely linked to P. hospita DSM 17164T (ANIm = 99%; TETRA = 0.99). We propose to coin this cluster the P. hospita species cluster (containing P. hospita DSM 17164T, P. terrae DSM 17804T, and strains BS001, BS007, BS110, and BS437), being clearly divergent from the closely related species P. caribensis (type strain DSM 13236T). Moreover, given their close relatedness to P. hospita DSM 17164T within the cluster, we propose to rename the four fungiphilic strains as members of P. hospita. Analysis of migratory behavior along with fungal growth through soil revealed both P. terrae DSM 17804T and P. hospita DSM 17164T (next to the four fungiphilic strains) to be migration-proficient, whereas P. caribensis DSM 13236T was a relatively poor migrator. Examination of predicted functions across the genomes of the seven investigated strains, next to several selected additional ones, revealed the common presence of features in the P. hospita cluster strains that are potentially important in interactions with soil fungi. Thus, genes encoding specific metabolic functions, biofilm formation (pelABCDEFG, pgaABCD, alginate-related genes), motility/chemotaxis, type-4 pili, and diverse secretion systems were found.
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http://dx.doi.org/10.1093/gbe/evaa031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186790PMC
April 2020

First Report of Kosakonia radicincitans Bacteraemia from Europe (Austria) - Identification and Whole-Genome Sequencing of Strain DSM 107547.

Sci Rep 2020 02 6;10(1):1948. Epub 2020 Feb 6.

Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria.

Kosakonia radicincitans is a species within the new genus Kosakonia. Many strains of this genus have been isolated from plants, but some strains are assumed to act as facultative human pathogens. In this study, an in-depth analysis of a Kosakonia isolate from human blood was performed. The strain was originally isolated from blood and identified as a member of the Enterobacter cloacae complex, exhibiting an atypical result in susceptibility testing. Therefore, the genetic background was examined, including phylogenetic classification and screening for virulence factors. Using whole-genome sequencing, the isolate was identified as a K. radicincitans strain, revealing a virulence gene cluster for yersiniabactin biosynthesis in contrast to all other strains of the species. Whole-genome sequencing was the perfect method for identifying putative virulence factors of a particular Kosakonia strain and will help distinguish beneficial strains from pathogenic strains in the future. To our knowledge, this is the first report of Kosakonia-related bacteraemia from Europe.
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http://dx.doi.org/10.1038/s41598-020-58689-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7005327PMC
February 2020

Genomic, metabolic and phenotypic variability shapes ecological differentiation and intraspecies interactions of Alteromonas macleodii.

Sci Rep 2020 01 21;10(1):809. Epub 2020 Jan 21.

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

Ecological differentiation between strains of bacterial species is shaped by genomic and metabolic variability. However, connecting genotypes to ecological niches remains a major challenge. Here, we linked bacterial geno- and phenotypes by contextualizing pangenomic, exometabolomic and physiological evidence in twelve strains of the marine bacterium Alteromonas macleodii, illuminating adaptive strategies of carbon metabolism, microbial interactions, cellular communication and iron acquisition. In A. macleodii strain MIT1002, secretion of amino acids and the unique capacity for phenol degradation may promote associations with Prochlorococcus cyanobacteria. Strain 83-1 and three novel Pacific isolates, featuring clonal genomes despite originating from distant locations, have profound abilities for algal polysaccharide utilization but without detrimental implications for Ecklonia macroalgae. Degradation of toluene and xylene, mediated via a plasmid syntenic to terrestrial Pseudomonas, was unique to strain EZ55. Benzoate degradation by strain EC673 related to a chromosomal gene cluster shared with the plasmid of A. mediterranea EC615, underlining that mobile genetic elements drive adaptations. Furthermore, we revealed strain-specific production of siderophores and homoserine lactones, with implications for nutrient acquisition and cellular communication. Phenotypic variability corresponded to different competitiveness in co-culture and geographic distribution, indicating linkages between intraspecific diversity, microbial interactions and biogeography. The finding of "ecological microdiversity" helps understanding the widespread occurrence of A. macleodii and contributes to the interpretation of bacterial niche specialization, population ecology and biogeochemical roles.
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http://dx.doi.org/10.1038/s41598-020-57526-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6972757PMC
January 2020

gen. nov., sp. nov. and sp. nov., two new members of the family isolated from the rhizosphere of .

Int J Syst Evol Microbiol 2020 Mar;70(3):1850-1860

Braunschweig University of Technology, Universitätsplatz 2, 38106, Braunschweig, Germany.

Two strains of the family were isolated from the rhizosphere of the medicinal plant . Cells of both strains were Gram-stain-negative, motile by means of a single polar flagellum, non-spore-forming, non-capsulated, short rods that divided by binary fission. Colonies were small and white. Strains R5913 and R5959 were oxidase-positive, mesophilic, neutrophilic and grew optimally without NaCl. Both grew under aerobic and microaerophilic conditions and on a limited range of substrates with best results on yeast extract. Major fatty acids were C cyclo 8 and C; in addition, Cω7 was also found as a predominant fatty acid in strain R5913. The major respiratory quinone was ubiquinone 10 (Q-10). The DNA G+C contents of strains R5913 and R5959 were 66.0 and 67.4 mol%, respectively. 16S rRNA gene sequence comparison revealed that the closest relatives (<92 % similarity) of the strains are MCCC 1A02656, CGMCC 1.7660, D78 and 04SU4-P. The two novel strains shared 98.6 % sequence similarity and represent different species on the basis of low average nucleotide identity of their genomes (83.8 %). Based on the combined phenotypic, genomic and phylogenetic investigations, the two strains represent two novel species of a new genus in the family , for which the name gen. nov. is proposed, comprising the type species sp. nov. (type strain R5913=DSM 109816=CECT 9472) and sp. nov. (type strain R5959=DSM 109817=CECT 9620).
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http://dx.doi.org/10.1099/ijsem.0.003983DOI Listing
March 2020

Direct and indirect effects of forest management on tree-hole inhabiting aquatic organisms and their functional traits.

Sci Total Environ 2020 Feb 22;704:135418. Epub 2019 Nov 22.

Forest Entomology, Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland.

Ecological communities in forests have been shown to be strongly affected by forest management but a detailed understanding of how different components of management affect insect communities directly and indirectly via environmental variables, how management influences functional trait diversity and composition, and whether these results can be transferred to other functional groups besides insects (e.g. bacteria or nematodes) is still missing. To address these questions we used water-filled tree holes, which provide habitats for insect larvae and other aquatic organisms in forests, as a model system. We mapped all water-filled tree holes in 75 forest plots (1 ha) under different management intensity in three regions of Germany. We measured structural and climatic conditions at different spatial scales, sampled insect communities in 123 tree holes and bacterial and nematode communities in a subset of these. We found that forest management in terms of harvesting intensity and the proportion of non-natural tree species (species not part of the natural vegetation at the sites) negatively affected tree-hole abundance. An increased proportion of non-natural tree species had a positive direct effect on insect richness and functional diversity in the tree holes. However, a structural equation model showed that increasing management intensity had negative indirect effects on insect abundance and richness, operating via environmental variables at stand and tree-hole scale. Functional diversity and trait composition of insect communities similarly responded to changes in management-related variables. In contrast to insects, bacterial and nematode richness were not directly impacted by forest management but by other environmental variables. Our results suggest that forest management may strongly alter insect communities of tree holes, while nematodes and bacteria seem less affected. Most effects in our study were indirect and negative, indicating that management has often complex consequences for forest communities that should be taken into account in forest management schemes.
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http://dx.doi.org/10.1016/j.scitotenv.2019.135418DOI Listing
February 2020

Corrigendum: A Metataxonomic Tool to Investigate the Diversity of .

Front Microbiol 2019;10:2581. Epub 2019 Nov 8.

Neglected Tropical Diseases Work Group, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.

[This corrects the article DOI: 10.3389/fmicb.2019.02094.].
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http://dx.doi.org/10.3389/fmicb.2019.02581DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856545PMC
November 2019
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