Modestobacter altitudinis sp. nov., a novel actinobacterium isolated from Atacama Desert soil

Golińska, Patrycja; Świecimska, Magdalena; Montero‐Calasanz, Maria del Carmen; Yaramis, Adnan; Igual, José M.; Bull, Alan T.; Goodfellow, Michael

doi:10.1099/ijsem.0.004212

Cited by 13 publications

(7 citation statements)

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“…This complement of genes included cspC and cspE which express for cold shock proteins (Etchegaray and Inouye 1999) and chaperone genes such as clpB, clpC, clpX and hrcA which are involved in responses to heat shock(Li et al 2011). In turn, genes such as betA, betB and proU are involved in the uptake of betaine and choline, metabolites, which help in responses to osmotic stress(Boncompagni et al 1999;Nau-Wagner et al 2012), as do enzymes expressed by genes katE and soxR(Normand et al 2012;Golińska et al 2020), and the products of genes trx and trxR…”

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confidence: 99%

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

Świecimska

Golińska

Goodfellow

2022

Antonie van Leeuwenhoek

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A genomic-based polyphasic study was undertaken to establish the taxonomic status and biotechnological and ecological potential of a Streptomyces strain, isolate SF28 T , that was recovered from the litter layer in a polish Pinus sylvestris forest. The isolate had morphological characteristics and chemotaxonomic properties consistent with its classi cation 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, isoand anteisofatty 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 con rmed 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 SF28 T (=DSM 113360 T =PCM 3163 T ) be classi ed in the genus Streptomyces as Streptomyces pinistramenti sp. nov. The isolate showed pronounced antimicrobial activity, especially against fungal plant pathogens.

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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

Świecimska

Golińska

Goodfellow

2022

Antonie van Leeuwenhoek

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“…Furthermore, the strain has the capacity to produce carbonic anhydrase proteins which are required for fixation of carbon dioxide [ 65 , 68 ] thereby suggesting that its potential to grow as a lithoautotroph. This discovery provides further evidence that filamentous actinobacteria in carbon-limiting, extreme biomes are capable of adopting a lithoautotrophic lifestyle, as shown by the type strains of novel Blastococcus , Geodermatophilus and Modestobacter species [ 69 , 70 , 71 , 72 , 73 ].…”

Section: Resultsmentioning

confidence: 79%

Biotechnological and Ecological Potential of Micromonospora provocatoris sp. nov., a Gifted Strain Isolated from the Challenger Deep of the Mariana Trench

et al. 2021

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A Micromonospora strain, isolate MT25T, was recovered from a sediment collected from the Challenger Deep of the Mariana Trench using a selective isolation procedure. The isolate produced two major metabolites, n-acetylglutaminyl glutamine amide and desferrioxamine B, the chemical structures of which were determined using 1D and 2D-NMR, including 1H-15N HSQC and 1H-15N HMBC 2D-NMR, as well as high resolution MS. A whole genome sequence of the strain showed the presence of ten natural product-biosynthetic gene clusters, including one responsible for the biosynthesis of desferrioxamine B. Whilst 16S rRNA gene sequence analyses showed that the isolate was most closely related to the type strain of Micromonospora chalcea, a whole genome sequence analysis revealed it to be most closely related to Micromonospora tulbaghiae 45142T. The two strains were distinguished using a combination of genomic and phenotypic features. Based on these data, it is proposed that strain MT25T (NCIMB 15245T, TISTR 2834T) be classified as Micromonospora provocatoris sp. nov. Analysis of the genome sequence of strain MT25T (genome size 6.1 Mbp) revealed genes predicted to responsible for its adaptation to extreme environmental conditions that prevail in deep-sea sediments.

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“…Similarly 151 isolates from the litter and mineral layers of the pine forest soils comprised 65 and 86 strains from the northern and southern slopes of the inland dune system supporting pine, including pairs of strains classified as Catenulispora pinisilvae ( Świecimska et al, 2021a ) and Catenulispora pinistramenti ( Świecimska et al, 2021b ). The isolates from the desert soils included 6 classified as either Modestobacter altitudinis ( Golińska et al, 2020a ) or Modestobacter excelsi ( Golińska et al, 2020b ) and the type strain of Micromonosporra acroterricola ( Carro et al, 2019 ). Isolates were taken from the selective isolation plates based on characteristic colonial properties.…”

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confidence: 99%

Generation of a high quality library of bioactive filamentous actinomycetes from extreme biomes using a culture-based bioprospecting strategy

2023

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IntroductionFilamentous actinomycetes, notably members of the genus Streptomyces, remain a rich source of new specialized metabolites, especially antibiotics. In addition, they are also a valuable source of anticancer and biocontrol agents, biofertilizers, enzymes, immunosuppressive drugs and other biologically active compounds. The new natural products needed for such purposes are now being sought from extreme habitats where harsh environmental conditions select for novel strains with distinctive features, notably an ability to produce specialized metabolites of biotechnological value.MethodsA culture-based bioprospecting strategy was used to isolate and screen filamentous actinomycetes from three poorly studied extreme biomes. Actinomycetes representing different colony types growing on selective media inoculated with environmental suspensions prepared from high-altitude, hyper-arid Atacama Desert soils, a saline soil from India and from a Polish pine forest soil were assigned to taxonomically predictive groups based on characteristic pigments formed on oatmeal agar. One hundred and fifteen representatives of the colour-groups were identified based on 16S rRNA gene sequences to determine whether they belonged to validly named or to putatively novel species. The antimicrobial activity of these isolates was determined using a standard plate assay. They were also tested for their capacity to produce hydrolytic enzymes and compounds known to promote plant growth while representative strains from the pine forest sites were examined to determine their ability to inhibit the growth of fungal and oomycete plant pathogens.ResultsComparative 16S rRNA gene sequencing analyses on isolates representing the colour-groups and their immediate phylogenetic neighbours showed that most belonged to either rare or novel species that belong to twelve genera. Representative isolates from the three extreme biomes showed different patterns of taxonomic diversity and characteristic bioactivity profiles. Many of the isolates produced bioactive compounds that inhibited the growth of one or more strains from a panel of nine wild strains in standard antimicrobial assays and are known to promote plant growth. Actinomycetes from the litter and mineral horizons of the pine forest, including acidotolerant and acidophilic strains belonging to the genera Actinacidiphila,Streptacidiphilus and Streptomyces, showed a remarkable ability to inhibit the growth of diverse fungal and oomycete plant pathogens.DiscussionIt can be concluded that selective isolation and characterization of dereplicated filamentous actinomyctes from several extreme biomes is a practical way of generating high quality actinomycete strain libraries for agricultural, industrial and medical biotechnology.

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Modestobacter altitudinis sp. nov., a novel actinobacterium isolated from Atacama Desert soil

Abstract: Three presumptive Modestobacter strains isolated from a high altitude Atacama Desert soil were the subject of a polyphasic study. The isolates, strains 1G4T Show more

Cited by 13 publications

References 77 publications

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

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

Biotechnological and Ecological Potential of Micromonospora provocatoris sp. nov., a Gifted Strain Isolated from the Challenger Deep of the Mariana Trench

Generation of a high quality library of bioactive filamentous actinomycetes from extreme biomes using a culture-based bioprospecting strategy

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