scholarly journals Streptomyces tardus sp. nov.: A Slow-Growing Actinobacterium Producing Candicidin, Isolated From Sediments of the Trondheim Fjord

2021 ◽  
Vol 12 ◽  
Author(s):  
Stanislava Králová ◽  
Megan Sandoval-Powers ◽  
Dorelle V. Fawwal ◽  
Kristin F. Degnes ◽  
Anna Sofia Lewin ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Gene Clusters ◽  
Diaminopimelic Acid ◽  
Antifungal Compound ◽  
Marine Actinobacteria ◽  
Pathogenic Yeast ◽  
Taxonomic Novelty ◽  
Slow Growing

Marine environments are home to an extensive number of microorganisms, many of which remain unexplored for taxonomic novelty and functional capabilities. In this study, a slow-growing Streptomyces strain expressing unique genomic and phenotypic characteristics, P38-E01T, was described using a polyphasic taxonomic approach. This strain is part of a collection of over 8,000 marine Actinobacteria isolates collected in the Trondheim fjord of Norway by SINTEF Industry (Trondheim, Norway) and the Norwegian University of Science and Technology (NTNU, Trondheim, Norway). Strain P38-E01T was isolated from the sediments of the Trondheim fjord, and phylogenetic analyses affiliated this strain with the genus Streptomyces, but it was not closely affiliated with other described species. The closest related type strains were Streptomyces daliensis YIM 31724T (98.6%), Streptomyces rimosus subsp. rimosus ATCC 10970T (98.4%), and Streptomyces sclerotialus NRRL ISP-5269T (98.3%). Predominant fatty acids were C16:0 iso, C16:0, and Summed Feature 3, and the predominant respiratory quinones were MK-10(H6), MK-10(H4), and MK9(H4). The main polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphoglycolipid. The whole-cell sugars were glucose, ribose, and in minor amounts, mannose. The cell wall peptidoglycan contained LL-diaminopimelic acid. The draft genome has a size of 6.16 Mb, with a %G + C content of 71.4% and is predicted to contain at least 19 biosynthetic gene clusters encoding diverse secondary metabolites. Strain P38-E01T was found to inhibit the growth of the pathogenic yeast Candida albicans ATCC 90028 and a number of Gram-positive bacterial human and plant pathogens. Metabolites extracted from cultures of P38-E01T were analyzed by mass spectrometry, and it was found that the isolate produced the antifungal compound candicidin. Phenotypic and chemotaxonomic signatures, along with phylogenetic analyses, distinguished isolate P38-E01T from its closest neighbors; thus, this isolate represents a novel species of the genus Streptomyces for which the name Streptomyces tardus sp. nov. (P38-E01T = CCM 9049T = DSM 111582T) is proposed.

scholarly journals Genome-based Classification of Streptomyces Pinistramenti sp. nov., a Novel Actinomycete Isolated From a Pine Forest Soil in Poland With a Focus on Its Biotechnological and Ecological Properties

2022 ◽  
Author(s):  
Magdalena Śwecimska ◽  
Patrycja Golinska ◽  
Michael Goodfellow
Keyword(s):  
Phylogenetic Trees ◽  
Plant Pathogens ◽  
Draft Genome ◽  
Morphological Characteristics ◽  
Taxonomic Status ◽  
Housekeeping Genes ◽  
Gene Clusters ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Fungal Plant Pathogens

Abstract A genomic-based polyphasic study was undertaken to establish the taxonomic status and biotechnological and ecological potential of a Streptomyces strain, isolate SF28T, that was recovered from the litter layer in a polish Pinus sylvestris forest. The isolate had morphological characteristics and chemotaxonomic properties consistent with its classification in the genus Streptomyces. It formed long straight chains of spores with smooth surfaces, contained LL-diaminopimelic acid and glucose and ribose in whole-organism hydrolysates, produced major proportions of straight, iso- and anteiso- fatty acids, hexa- and octa-hydrogenated menaquinones with nine isoprenoid units and had a polar lipid pattern composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, glycophospholipids and three uncharacterized components. Phylogenetic trees prepared using 16S rRNA gene and multilocus gene sequences of conserved housekeeping genes showed that the isolate formed a branch that was loosely associated with the type strains of several validly published Streptomyces species. A draft genome generated for the isolate was rich in natural product-biosynthetic gene clusters with the potential to produce new specialised metabolites, notably antibiotics, and stress related genes which provide an insight into how they may have adapted to the harsh conditions that prevail in acidic forest soils. A phylogenomic tree based on the genomes of the isolate and its phylogenetic neighbours confirmed that it formed a distinct lineage well separated from its closest evolutionary relatives. The isolate shared low average nucleotide index and digital DNA:DNA hybridization values with its phylogenomic neighbours and was also distinguished from them using a combination of cultural and micromorphological properties. Given this wealth of taxonomic data it is proposed that isolate SF28T (=DSM 113360T=PCM 3163T) be classified in the genus Streptomyces as Streptomyces pinistramenti sp. nov. The isolate showed pronounced antimicrobial activity, especially against fungal plant pathogens.

scholarly journals Bacillus acidinfaciens sp. nov., isolated from farmland soil

2019 ◽  
Vol 69 (4) ◽  
pp. 1075-1080 ◽  
Author(s):  
Leni Sun ◽  
Yan Chen ◽  
Wei Tian ◽  
Lunguang Yao ◽  
Zhaojin Chen ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Farmland Soil

A Gram-stain-positive, rod-shaped, motile bacterial strain, designated 3-2-2T, was isolated from field topsoil collected from a western suburb of Nanyang city, Henan province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 3-2-2T was a member of the genus Bacillus and most closely related to Bacillus fortis R-6514T (98.9 % similarity), Bacillus terrae RA9T (98.0 %) and Bacillus fordii R-7190T (97.7 %). A draft genome sequence determined for strain 3-2-2T revealed a DNA G+C content of 42.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between 3-2-2T and the closely related Bacillus species ranged 79.4–84.2 % and 23.4–24.6 %. The major fatty acids of strain 3-2-2T were iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The major isoprenoid quinone was MK-7. meso-Diaminopimelic acid was detected in the peptidoglycan. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. The results of phylogenetic analyses, in silico genomic comparisons, and chemotaxonomic and phenotypic analyses clearly indicated that strain 3-2-2T represents a novel species within the genus Bacillus , for which the name Bacillus acidinfaciens sp. nov. is proposed. The type strain is 3-2-2T (=CGMCC 1.13685T=LMG 30839T).

scholarly journals Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp. plantarum is a later heterotypic synonym of Bacillus methylotrophicus

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2104-2109 ◽  
Author(s):  
Christopher A. Dunlap ◽  
Soo-Jin Kim ◽  
Soon-Wo Kwon ◽  
Alejandro P. Rooney
Keyword(s):  
Bacillus Amyloliquefaciens ◽  
Type Strain ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Growth Promoters ◽  
Bacillus Methylotrophicus

The rhizosphere-isolated bacteria belonging to the Bacillus amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus clades are an important group of strains that are used as plant growth promoters and antagonists of plant pathogens. These properties have made these strains the focus of commercial interest. Here, we present the draft genome sequence of B. methylotrophicus KACC 13105T ( = CBMB205T). Comparative genomic analysis showed only minor differences between this strain and the genome of the B. amyloliquefaciens subsp. plantarum type strain, with the genomes sharing approximately 95 % of the same genes. The results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar. In fact, our results show that the type strain of B. amyloliquefaciens subsp. plantarum FZB42T ( = DSM 23117T = BGSC 10A6T) does not cluster with other members of the B. amyloliquefaciens taxon. Instead, it clusters well within a clade of strains that are assigned to B. methylotrophicus, including the type strain of that species. Therefore, we propose that the subspecies B. amyloliquefaciens subsp. plantarum should be reclassified as a later heterotypic synonym of B. methylotrophicus.

scholarly journals Nakamurella Leprariae Sp. Nov., Isolated From a Lichen Sample

2021 ◽  
Author(s):  
De-Feng An ◽  
Shao-Juan Yang ◽  
Long-Qian Jiang ◽  
Xin-Yu Wang ◽  
Xiao-Yu Huang ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Pr China ◽  
Diamino Acid ◽  
Taxonomic Approach ◽  
High Level ◽  
Reference Strains ◽  
The 16S Rrna Gene

Abstract A novel actinobacterium, YIM 132084T, was isolated from Lepraria sp. lichen collected from Yunnan province, south-west PR China and identified by a polyphasic taxonomic approach. The strain was Gram-stain-positive, aerobic, catalase-positive, oxidase-negative, non-motile and coccus-shaped. Colonies were round, convex, smooth and light orange yellow in colour. It grew at 10–40 ℃ (optimum 28 ℃), at pH 6.0–11.0 (optimum pH 7.0) and in the presence of 0–4 % NaCl (optimum 0 %). Strain YIM 132084T comprised diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as the major polar lipids, MK-8(H4) as the predominant menaquinone, and anteiso-C15:0, anteiso-C17:0, iso-C15:0 and iso-C16:0 as major fatty acids. Strain YIM 132084T had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, and mannose, ribose, glucose and rhamnose as whole-cell sugars. The 16S rRNA gene sequence showed high level of similarity with Nakamurella flavida KCTC 19127T (97. 7%) and Nakamurella flava CGMCC 4.7524T (97.7%). The G + C content of the genomic DNA was 72.4 mol%. Strain YIM 132084T showed an average nucleotide identity value of 76.1 % and 74.9 %, a digital DNA-DNA hybridizations value of 20.9 % and 20.6 % with the reference strains Nakamurella flavida and Nakamurella flava based on draft genome sequences, respectively. The results of the phenotypic, chemotaxonomic and phylogenetic analyses, showed that strain YIM 132084T represents a novel species of the genus Nakamurella, for which the name Nakamurella leprariae sp. nov. is proposed. The type strain is YIM 132084T (= CGMCC 4.7667T = NBRC 114280T = KCTC 49367T).

scholarly journals Gene cluster conservation identifies melanin and perylenequinone biosynthesis pathways in multiple plant pathogenic fungi

2018 ◽  
Author(s):  
Malaika K. Ebert ◽  
Rebecca E. Spanner ◽  
Ronnie de Jonge ◽  
David J. Smith ◽  
Jason Holthusen ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Pathogenic Fungi ◽  
Gene Clusters ◽  
Host Cells ◽  
Plant Pathogenic Fungi ◽  
Biosynthetic Pathways ◽  
Biosynthetic Gene ◽  
Melanin Production

SummaryPerylenequinones are a family of structurally related polyketide fungal toxins with nearly universal toxicity. These photosensitizing compounds absorb light energy which enables them to generate reactive oxygen species that damage host cells. This potent mechanism serves as an effective weapon for plant pathogens in disease establishment. The sugar beet pathogenCercospora beticolasecretes the perylenequinone cercosporin during infection. We have shown recently that the cercosporin toxin biosynthesis(CTB)gene cluster is present in several other phytopathogenic fungi, prompting the search for biosynthetic gene clusters (BGCs) of structurally similar perylenequinones in other fungi. Here, we report the identification of the elsinochrome and phleichrome BGCs ofElsinoё fawcettiiandCladosporium phlei,respectively, based on gene cluster conservation with theCTBand hypocrellin BGCs. Furthermore, we show that previously reported BGCs for elsinochrome and phleichrome are involved in melanin production. Phylogenetic analysis of the corresponding melanin polyketide synthases (PKSs) and alignment of melanin BGCs revealed high conservation between the established and newly identifiedC. beticola, E. fawcettii,andC. phleimelanin BGCs. Mutagenesis of the identified perylenequinone and melanin PKSs inC. beticolaandE. fawcettiicoupled with mass spectrometric metabolite analyses confirmed their roles in toxin and melanin production.Originality and significance statementGenes involved in secondary metabolite (SM) production are often clustered together to form biosynthetic pathways. These pathways frequently have highly conserved keystone enzymes which can complicate allocation of a biosynthetic gene cluster (BGC) to the cognate SM. In our study, we utilized a combination of comparative genomics, phylogenetic analyses and biochemical approaches to reliably identify BGCs for perylenequinone toxins and DHN-melanin in multiple plant pathogenic fungi. Furthermore, we show that earlier studies that aimed to identify these perylenequinone pathways were misdirected and actually reported DHN-melanin biosynthetic pathways. Our study outlines a reliable approach to successfully identify fungal SM pathways.

scholarly journals Draft Genome Sequences of Six Bacillus Strains and One Brevibacillus Strain Isolated from the Rhizosphere of Perennial Ryegrass (Lolium perenne)

2019 ◽  
Vol 8 (4) ◽  
Author(s):  
Zhibo Li ◽  
Chunxu Song ◽  
Anne de Jong ◽  
Oscar P. Kuipers
Keyword(s):  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
Plant Pathogens ◽  
Draft Genome ◽  
Gene Clusters ◽  
Antagonistic Activity ◽  
Genome Sequences ◽  
Modes Of Action ◽  
Bacillus Strains

Seven strains of endospore-forming bacteria with antagonistic activity against a series of plant pathogens were sequenced in order to investigate their antimicrobial gene clusters and antimicrobial modes of action. The selected strains include six Bacillus strains and one Brevibacillus strain.

scholarly journals Draft Genome Sequences of Endophytic Pseudomonas spp. Isolated from Grapevine Tissue and Antagonistic to Grapevine Trunk Disease Pathogens

2019 ◽  
Vol 8 (26) ◽  
Author(s):  
Jennifer Niem ◽  
Regina Billones-Baaijens ◽  
Sandra Savocchia ◽  
Benjamin Stodart
Keyword(s):  
Plant Pathogens ◽  
Draft Genome ◽  
Gene Clusters ◽  
Antagonistic Activity ◽  
Genome Sequences ◽  
Putative Gene ◽  
Content Type ◽  
Trunk Disease ◽  
Grapevine Trunk Disease ◽  
Biocontrol Activity

Endophytic strains of Pseudomonas were isolated from grapevine tissues and exhibited antagonistic activity against several grapevine trunk disease pathogens. The draft genome sequences of the four strains revealed the presence of putative gene clusters that may impart biocontrol activity against plant pathogens.

scholarly journals Bacillus salacetis sp. nov., a slightly halophilic bacterium from Thai shrimp paste (Ka-pi)

2019 ◽  
Vol 69 (4) ◽  
pp. 1162-1168 ◽  
Author(s):  
Rungsima Daroonpunt ◽  
Supalurk Yiamsombut ◽  
Jaruwan Sitdhipol ◽  
Somboon Tanasupawat
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Halophilic Bacterium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Slightly Halophilic Bacterium

A Gram-stain-positive, slightly halophilic, endospore-forming, strictly aerobic, rod-shaped bacterium, designated SKP7-4T, was isolated from shrimp paste collected from Samut Sakhon province, Thailand. Strain SKP7-4T grew at pH 6.0–9.0 (optimum, 7.5), at 20–40 °C (37 °C) and in 0–15 % (w/v) NaCl (1–3 %). The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Menaquinone with seven isoprene units was the major isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unidentified phospholipids were detected as polar lipids. It contained iso-C15 : 0 and anteiso-C15 : 0 as major cellular fatty acids. On the basis of 16S rRNA gene sequence analysis, strain SKP7-4T belonged to the genus Bacillus and was closely related to Bacillus vietnamensis JCM 11124T, Bacillus marisflavi JCM 11544T, Bacillus aquimaris JCM 11545T and B acillus oryzaecorticis JCM 19602T, with 98.7, 97.9, 97.8 and 97.8 % similarity, respectively. The draft genome of SKP7-4T was 4.68 Mb with 5208 coding sequences with an average G+C content of 43.2 mol%. The ANIb and ANIm values of strain SKP7-4T were 70.0 and 84.3 %, respectively, and the digital DNA–DNA hybridization value was 20 % in comparison with the draft genome of B. vietnamensis JCM 11124T. On the basis of the results of phenotypic, chemotaxonomic and phylogenetic analyses, the strain should represent a novel species of the genus Bacillus and the name Bacillus salacetis sp. nov. is proposed. The type strain is SKP7-4T (=JCM 33205T=KCTC 43014T=TISTR 2596T).

scholarly journals Draft Genome Sequences of Fungus Aspergillus calidoustus

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Fabian Horn ◽  
Jörg Linde ◽  
Derek J. Mattern ◽  
Grit Walther ◽  
Reinhard Guthke ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Genome Sequence ◽  
Functional Annotation ◽  
Draft Genome ◽  
Genome Mining ◽  
Gene Clusters ◽  
Draft Genome Sequence ◽  
Genome Sequences

Here, we report the draft genome sequence of Aspergillus calidoustus (strain SF006504) . The functional annotation of A. calidoustus predicts a relatively large number of secondary metabolite gene clusters. The presented genome sequence builds the basis for further genome mining.

scholarly journals Rubritalea halochordaticola sp. nov., a carotenoid-producing verrucomicrobial species isolated from a marine chordate

2011 ◽  
Vol 61 (7) ◽  
pp. 1515-1520 ◽  
Author(s):  
Jaewoo Yoon ◽  
Satoru Matsuda ◽  
Kyoko Adachi ◽  
Hiroaki Kasai ◽  
Akira Yokota
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Sea Squirt ◽  
Cell Biomass ◽  
Taxonomic Approach

A Gram-negative-staining, obligately aerobic, non-motile, rod-shaped and chemoheterotrophic bacterium, designated strain MN1-1006T, was isolated from an ascidian (sea squirt) sample, and was studied using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the new isolate shared approximately 93–99% sequence similarity with recognized species of the genus Rubritalea within the phylum ‘Verrucomicrobia’. DNA–DNA hybridization values between strain MN1-1006T and Rubritalea squalenifaciens HOact23T and Rubritalea sabuli YM29-052T were 57% and 14.5%, respectively. Strain MN1-1006T produced carotenoid compounds that rendered the cell biomass a reddish pink colour. The strain also contained squalene. The cell-wall peptidoglycan of the novel strain contained muramic acid and meso-diaminopimelic acid. The DNA G+C content of strain MN1-1006T was 51.4 mol%. The major cellular fatty acids were iso-C14:0, iso-C16:0 and anteiso-C15:0. The major isoprenoid quinone was MK-9. On the basis of these data, it was concluded that strain MN1-1006T represents a novel species of the genus Rubritalea, for which the name Rubritalea halochordaticola sp. nov. is proposed. The type strain is MN1-1006T ( = KCTC 23186T = NBRC 107102T).

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