iChip-Inspired Isolation, Bioactivities and Dereplication of Actinomycetota from Portuguese Beach Sediments

Santos, José Diogo Neves dos; João, Susana Afonso; Martín, Jesús; Vicente, Francisca; Reyes, Fernando; Lage, Olga Maria

doi:10.3390/microorganisms10071471

“…Isolation efforts inspired by the ichip were also performed using many kinds of sediments, such as marine sediments, mangrove sediment, and estuarine sediment, etc.. These studies have also helped us obtain many unculturable microorganisms, such as Actinomycetota resources and harmful substance degrading bacteria resources [39][40][41]. Generally speaking, this platform has been shown to increase microbial recovery from 5-to 300-fold, depending on the study [19].…”

Section: Discussionmentioning

confidence: 99%

Use of modified ichip for the cultivation of thermo-tolerant microorganisms from the hot spring

Zhao

¹

,

Shakir

²

,

Deng

³

et al. 2023

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Background Thermostable microorganisms are extremophiles. They have a special genetic background and metabolic pathway and can produce a variety of enzymes and other active substances with special functions. Most thermo-tolerant microorganisms from environmental samples have resisted cultivation on artificial growth media. Therefore, it is of great significance to isolate more thermo-tolerant microorganisms and study their characteristics to explore the origin of life and exploit more thermo-tolerant enzymes. Tengchong hot spring in Yunnan contains a lot of thermo-tolerant microbial resources because of its perennial high temperature. The ichip method was developed by D. Nichols in 2010 and can be used to isolate so-called “uncultivable” microorganisms from different environments. Here, we describe the first application of modified ichip to isolate thermo-tolerant bacteria from hot springs. Results In this study, 133 strains of bacteria belonging to 19 genera were obtained. 107 strains of bacteria in 17 genera were isolated by modified ichip, and 26 strains of bacteria in 6 genera were isolated by direct plating methods. 25 strains are previously uncultured, 20 of which can only be cultivated after being domesticated by ichip. Two strains of previously unculturable Lysobacter sp., which can withstand 85 °C, were isolated for the first time. Alkalihalobacillus, Lysobacter and Agromyces genera were first found to have 85 °C tolerance. Conclusion Our results indicate that the modified ichip approach can be successfully applied in a hot spring environment.

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“…For morphological characterization, the cultures were grown at 25 °C for 7 days in M600 medium [24]. Cellular structure and morphology of strain PMIC_1C1B T were assessed through SEM and TEM.…”

Section: Morphological and Physiological Characteristicsmentioning

confidence: 99%

“…Unless otherwise indicated, all physiological assays were performed at 25 °C for 7 days in M600 medium prepared with artificial sea water [24,51]. For the analysis of NaCl tolerance, M600 medium was prepared with artificial seawater with variable NaCl concentrations ranging from 0 to 10 % (w/v).…”

Section: Morphological and Physiological Characteristicsmentioning

confidence: 99%

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Microbacterium memoriense sp. nov., a member of the Actinomycetota from marine beach sediment of the north coast of Portugal

Santos,

Klimek,

Calusinska

et al. 2024

International Journal of Systematic and Evolutionary Microbiology

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The oceans harbour a myriad of unknown micro-organisms that remain unstudied because of a failure to establish the right growth conditions under laboratory conditions. To overcome this limitation, an isolation effort inspired by the iChip was performed using marine sediments from Memória beach, Portugal. A novel strain, PMIC_1C1BT, was obtained and subjected to a polyphasic study. Cells of strain PMIC_1C1BT were Gram-positive, rod-shaped, divided by binary fission and formed colonies that were shiny light-yellow. Based on its full 16S rRNA gene sequence, strain PMIC_1C1BT was phylogenetically associated to the genus Microbacterium and its closest relatives were Microbacterium aurum KACC 15219T (98.55 %), Microbacterium diaminobutyricum RZ63T (98.48 %) and Microbacterium hatanonis JCM 14558T (98.13 %). Strain PMIC_1C1BT had a genome size of 2 761 607 bp with 67.71 mol% of G+C content and 2582 coding sequences, which is lower than the genus average. Strain PMIC_1C1BT grew from 15 to 30 °C, optimally at 25 °C, at pH 6.0 to 11.0, optimally between pH 6.0 and 8.0, and from 0 to 5 % (w/v) NaCl, optimally between 2.0 and 3.0 %. It grew with casamino acids, glutamine, methionine, N-acetylglucosamine, sodium nitrate, tryptophan, urea and valine as sole nitrogen sources, and arabinose and cellobiose as sole carbon sources. The major cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C17 : 0. Genome mining revealed the presence of four biosynthetic gene clusters (BGCs) with low similarities to other known BCGs. Based on the polyphasic data, strain PMIC_1C1BT is proposed to represent a novel species, for which the name Microbacterium memoriense sp. nov. (=CECT 30366T=LMG 32350T) is proposed.

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“…The dried vial was weighted and the extract was then diluted to a concentration of 10 mg ml −1 in 20 % (v/v) dimethylsulphoxide. The antimicrobial screening of the pooled extract was performed against Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 29213 as described previously by dos Santos and collaborators [44].…”

Section: Antimicrobial Activitymentioning

confidence: 99%

Streptomyces meridianus sp. nov. isolated from brackish water of the Tagus estuary in Alcochete, Portugal

Santos

¹

,

Klimek

²

,

Całusińska

³

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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0

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An isolation effort focused on sporogenous Actinomycetota from the Tagus estuary in Alcochete, Portugal, yielded a novel actinomycetal strain, designated MTZ3.1T, which was subjected to a polyphasic taxonomic study. MTZ3.1T is characterised by morphology typical of members of the genus Streptomyces , with light beige coloured substrate mycelium, which does not release pigments to the culture medium and with helicoidal aerial hyphae that differentiate into spores with a light-grey colour. The phylogeny of MTZ3.1T, based on the full 16S rRNA gene sequence, indicated that its closest relatives were Streptomyces alkaliterrae OF1T (98.48 %), Streptomyces chumphonensis KK1-2T (98.41 %), Streptomyces albofaciens JCM 4342T (98.34 %), Streoptomyces paromomycinus NBRC 15454T (98.34 %) and Streptomyces chrestomyceticus NRBC 13444T (98.34 %). Moreover, average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA–DNA hybridisation (dDDH) are below the species cutoff values (ANI 67.70 and 68.35 %, AAI 77.06 and 76.71 % and dDDH 22.10 and 21.50 % for S. alkaliterrae OF1T and S. chumphonensis KK1-2T, respectively). Whole genome sequencing revealed that MTZ3.1T has a genome of 5 644 485 bp with a DNA G+C content of 71.29 mol% and 5044 coding sequences. Physiologically, MTZ3.1T is strictly aerobic, able to grow at 15–37 °C, optimally at 25 °C and between pH5 and 8 and showed high salinity tolerance, growing with 0–10 %(w/v) NaCl. Major cellular fatty acids are C15 : 0, iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. Furthermore, it was able to utilise a variety of nitrogen and carbon sources. Antimicrobial screening indicated that MTZ3.1T has potent anti- Staphylococcus aureus activity. On the basis of the polyphasic data, MTZ3.1T is proposed to represent a novel species, Streptomyces meridianus sp. nov. (= CECT 30416T = DSM 114037T=LMG 32463T).

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iChip-Inspired Isolation, Bioactivities and Dereplication of Actinomycetota from Portuguese Beach Sediments

Cited by 10 publications

References 119 publications

Use of modified ichip for the cultivation of thermo-tolerant microorganisms from the hot spring

Use of modified ichip for the cultivation of thermo-tolerant microorganisms from the hot spring

Microbacterium memoriense sp. nov., a member of the Actinomycetota from marine beach sediment of the north coast of Portugal

Streptomyces meridianus sp. nov. isolated from brackish water of the Tagus estuary in Alcochete, Portugal

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