Genome Sequence of Mushroom Soft-Rot Pathogen Janthinobacterium agaricidamnosum

Graupner, Katharina; Lackner, Gerald; Hertweck, Christian

doi:10.1128/genomea.00277-15

Cited by 14 publications

(10 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Comparative genomic study was performed to reveal the genomic diversity across the genus Janthinobacterium . Genome data included J. agaricidamnosum DSM9628 (HG322949, [ 36 ]); J. psychotolerans S3–2 (LOCQ00000000, [ 35 ]) and J. lividum with multiple strains of Marseille (CP000269; [ 37 ]); Ant5–2 (LNCE00000000, [ 38 ]); PAMC 25724 (AHHB00000000, [ 2 ]; CG3 (APFF00000000, [ 39 ]); HH01 (NZ_AMWD00000000, [ 40 ]); RIT308 (JFYR00000000, [ 41 ]); MTR (JRRH00000000, [ 42 ]);RA13 (JQNP01000001, [ 43 ]); KBS0711 (LBCO00000000, [ 44 ]); CG23_2 (CYSS00000000, [ 45 ]); DSM1522 (LRHW00000000), MP5059B (LRHX00000000), HH100 (LRHY00000000), HH102 (LRHZ00000000), HH103 (LRIA00000000), HH104 (LRIB00000000), HH106 (LRIC00000000), and HH107 (LRID00000000) [ 4 ]. Few other genome sequence were retrieved from Gold database or IMG [ 22 , 23 ]: J. lividum strain NFR18 (FPKH00000000); Janthinobacterium sp.…”

Section: Insights From the Genome Sequence And Comparative Genomicsmentioning

confidence: 99%

Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01

Kumar

Acharya

Singh

et al. 2018

Stand in Genomic Sci

View full text Add to dashboard Cite

A light pink coloured bacterial strain ERGS5:01 isolated from glacial stream water of Sikkim Himalaya was affiliated to Janthinobacterium lividum based on 16S rRNA gene sequence identity and phylogenetic clustering. Whole genome sequencing was performed for the strain to confirm its taxonomy as it lacked the typical violet pigmentation of the genus and also to decipher its survival strategy at the aquatic ecosystem of high elevation. The PacBio RSII sequencing generated genome of 5,168,928 bp with 4575 protein-coding genes and 118 RNA genes. Whole genome-based multilocus sequence analysis clustering, in silico DDH similarity value of 95.1% and, the ANI value of 99.25% established the identity of the strain ERGS5:01 (MCC 2953) as a non-violacein producing J. lividum. The genome comparisons across genus Janthinobacterium revealed an open pan-genome with the scope of the addition of new orthologous cluster to complete the genomic inventory. The genomic insight provided the genetic basis of freezing and frequent freeze-thaw cycle tolerance and, for industrially important enzymes. Extended insight into the genome provided clues of crucial genes associated with adaptation in the harsh aquatic ecosystem of high altitude.Electronic supplementary materialThe online version of this article (10.1186/s40793-018-0313-3) contains supplementary material, which is available to authorized users.

show abstract

Section: Insights From the Genome Sequence And Comparative Genomicsmentioning

confidence: 99%

Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01

Kumar

Acharya

Singh

et al. 2018

Stand in Genomic Sci

View full text Add to dashboard Cite

show abstract

“…While Janthinobacterium as well as Duganella appear to be non-pathogenic to humans, animals, and plants, they are well-known for their antifungal effects. For example, J. livium suppresses fungal growth on human and amphibian skin or J. agaricidamnsoum causes the soft rot disease on the mushroom Agaricus bisporus (Becker et al, 2009; Harris et al, 2009; Wiggins et al, 2011; Graupner et al, 2015; Ramsey et al, 2015). The antifungal activities within this Oxalobacteraceae family are most likely induced through a regulatory network in response to chitin or degradation products (Cretoiu et al, 2013; Kielak et al, 2013) and the involvement of the secondary metabolite violacein is hypothesized (Brucker et al, 2008; Ramsey et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Molecular Keys to the Janthinobacterium and Duganella spp. Interaction with the Plant Pathogen Fusarium graminearum

et al. 2016

View full text Add to dashboard Cite

Janthinobacterium and Duganella are well-known for their antifungal effects. Surprisingly, almost nothing is known on molecular aspects involved in the close bacterium-fungus interaction. To better understand this interaction, we established the genomes of 11 Janthinobacterium and Duganella isolates in combination with phylogenetic and functional analyses of all publicly available genomes. Thereby, we identified a core and pan genome of 1058 and 23,628 genes. All strains encoded secondary metabolite gene clusters and chitinases, both possibly involved in fungal growth suppression. All but one strain carried a single gene cluster involved in the biosynthesis of alpha-hydroxyketone-like autoinducer molecules, designated JAI-1. Genome-wide RNA-seq studies employing the background of two isolates and the corresponding JAI-1 deficient strains identified a set of 45 QS-regulated genes in both isolates. Most regulated genes are characterized by a conserved sequence motif within the promoter region. Among the most strongly regulated genes were secondary metabolite and type VI secretion system gene clusters. Most intriguing, co-incubation studies of J. sp. HH102 or its corresponding JAI-1 synthase deletion mutant with the plant pathogen Fusarium graminearum provided first evidence of a QS-dependent interaction with this pathogen.

show abstract

“…Chitinibacteraceae, the dominant bacterial family on D0, (with relative abundance 32.3%), was detected iñ 50x lower relative abundance (≤ 0.6%) in the rest of the samples. At D35F and D65F, the dominant OTUs (OTU0017 and OTU0070, classi ed as Pseudomonas viridi ava and Janthinobacterium agaricidamnosum, respectively), are described as plant [55][56][57][58] and mushroom pathogens [59][60].…”

Section: Discussionmentioning

confidence: 99%

Early Life Bacterial Succession Under Different Diet Regime Atlantic Salmon (Salmo salar L.)

Nikouli

Kormas

Yang

et al. 2020

Preprint

View full text Add to dashboard Cite

Backgound: The present study investigated the effect of different lipid source in the feed on the colonization and the bacterial succession in early life stages (fertilized eggs until 93 days post first feeding) of S. salar. The two diets used in this study, FD (fish oil based diet) and VD (vegetable oil based diet), were formulated to cover the fish nutritional requirements and except the lipid source the components were identical between them. Hindgut samples collected at 0, 35, 65 and 93 days post first feeding (dpff). Moreover, fertilized eggs, yolk sac larvae, rearing water and feed were also sampled in order to assess a possible contribution of their microbiota to the colonization of the gut. To analyze the composition of the bacterial communities, the Illumina MiSeq platform was used.Results: S. salar growth variables (mean wet weight and total length) did not differ significantly during the experiment (p> 0.05) across replicate tanks and between dietary treatments. The analysis of the 16S rDNA sequencing data revealed a total of 4548 unique OTUs, affiliated in 21 bacterial phyla. Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes were the dominant bacterial phyla. 13 OTUs were shared among all S. salar samples independent of life stage and diet treatment. Similarity percentages analysis (SIMPER) based on Bray–Curtis distance, showed that the average dissimilarity among the groups of the same life stages was 76.0%, whereas the average dissimilarity within groups of the same dietary treatment was 78.5% (FD) and 83.6% (VD).Conclusion: Feeding on either fish oil or vegetable oil-based diets, did not result in significant differences in the intestinal microbiota. The composition of gut microbiota did not differ significantly between the two dietary treatments, but changed with age, and each stage was characterized by different dominant bacteria. These OTUs are related to species that provide different functions and have been isolated from a variety of environments. Finally, this study revealed the occurrence of a core microbiota independent of the studied life stages and diet during the early life stages of Atlantic salmon.

show abstract

Genome Sequence of Mushroom Soft-Rot Pathogen Janthinobacterium agaricidamnosum

Cited by 14 publications

References 10 publications

Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01

Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01

Molecular Keys to the Janthinobacterium and Duganella spp. Interaction with the Plant Pathogen Fusarium graminearum

Early Life Bacterial Succession Under Different Diet Regime Atlantic Salmon (Salmo salar L.)

Contact Info

Product

Resources

About