Phylogenetic diversity of acidophilic actinomycetes from Malaysia

Muramatsu, Hideyuki; Murakami, Ryuji; Ibrahim, Zool Hilmi; Murakami, Kiyoshi; Shahab, Neelam; Nagai, Koji

doi:10.1038/ja.2011.57

Cited by 8 publications

(7 citation statements)

References 19 publications

(23 reference statements)

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“…However, after a few days of incubation, most isolation plates were covered with fungal mycelium, which overgrew the small colonies of actinomycetes. As Muramatsu et al 43 observed, the isolation of acidophilic actinomycetes is difficult due to fungal contamination, which grow well under acidic conditions. In addition, most antifungal agents such as nystatin are unstable at low pH.…”

Section: Resultsmentioning

confidence: 99%

Acidophilic actinomycetes from rhizosphere soil: diversity and properties beneficial to plants

2014

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Three hundred and fifty-one isolates of actinomycetes were recovered from 21 rhizospheric soil samples using acidified media of pH 5.5. They were evaluated for their antifungal, siderophore production and phosphate solubilization activities. The total count of actinomycetes growing on acidified starch casein agar and Gause no. 1 agar were below 2.48 × 10(4) CFU g(-1) soil. Two hundred and twelve isolates were assigned to acidophiles and the remaining 139 isolates were neutrophiles. Of these actinomycetes, 57.8, 32.5 and 50.4%, showed antagonistic activity against three rice pathogenic fungi; Fusarium moniliforme, Helminthosporium oryzae and Rhizoctonia solani, respectively. More than half of the isolates (68.1%) inhibited at least one tested pathogenic fungus, whereas 25.9% exhibited antifungal activities against all tested fungi. Three hundred and thirty-eight isolates (96.3%) produced siderophore and 266 isolates (75.8%) solubilized phosphate. A greater proportion of the acidophilic actinomycetes exhibited antifungal, siderophore production and phosphate solubilization activity compared with the neutrophiles. Three hundred and twenty-five isolates (92.6%) were classified as streptomycetes based on their morphological characteristics and the presence of the LL-isomeric form of diaminopimelic acid in whole-cell hydrolysates. The 16S ribosomal RNA (rRNA) gene analysis of representative non-streptomycete strains showed that the isolates belonged to seven genera, that is, Allokutzneria, Amycolatopsis, Mycobacterium, Nocardia, Nonomuraea, Saccharopolyspora and Verrucosispora. The potential antifungal acidophilic isolates, R9-4, R14-1, R14-5 and R20-5, showed close similarity to Streptomyces misionensis NBRC 13063(T) (AB184285) in terms of morphological characteristics and 16S rRNA gene sequences.

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Section: Resultsmentioning

confidence: 99%

Acidophilic actinomycetes from rhizosphere soil: diversity and properties beneficial to plants

2014

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“…Such high diversity of culturable actinomycetes from acidic environments reflected the use of several pretreatment methods and a range of selective media. In comparison, Muramatsu et al (17) isolated 122 actinomycetes from Malaysian acid soils (pH 4.2 to 5.9) and assigned them to six genera, while Suela et al (49) examined 2,152 actinobacterial strains from native Cerrado soils (pH 4.1 to 5.5) and classified them into nine genera. In this and the earlier studies, Streptomyces strains were the most frequently isolated and widely distributed among all samples investigated, although Actinoallomurus, Amycolatopsis, Nocardia, and Streptacidiphilus strains were also isolated.…”

Section: Discussionmentioning

confidence: 99%

“…Since the isolation of acidophilic streptomycetes from acidic soil samples by Williams and colleagues (15,16), studies of acidophilic actinomycetes have been focused mainly on the description of novel taxa and on their phylogenetic diversity (17)(18)(19)(20)(21)(22). Acidophilic actinomycetes can be assigned to two groups, namely, a group of moderately acidophilic actinomycetes with an optimal pH of around 6.0 and a group of obligately acidophilic actinomycetes with an optimal pH of no more than 4.0 (23).…”

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confidence: 99%

Red Soils Harbor Diverse Culturable Actinomycetes That Are Promising Sources of Novel Secondary Metabolites

Guo

Ning

et al. 2015

Appl Environ Microbiol

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Red soils, which are widely distributed in tropical and subtropical regions of southern China, are characterized by low organic carbon, high content of iron oxides, and acidity and, hence, are likely to be ideal habitats for acidophilic actinomycetes. However, the diversity and biosynthetic potential of actinomycetes in such habitats are underexplored. Here, a total of 600 actinomycete strains were isolated from red soils collected in Jiangxi Province in southeast China. 16S rRNA gene sequence analysis revealed a high diversity of the isolates, which were distributed into 26 genera, 10 families, and 7 orders within the class Actinobacteria; these taxa contained at least 49 phylotypes that are likely to represent new species within 15 genera. The isolates showed good physiological potentials for biosynthesis and biocontrol. Chemical screening of 107 semirandomly selected isolates spanning 20 genera revealed the presence of at least 193 secondary metabolites from 52 isolates, of which 125 compounds from 39 isolates of 12 genera were putatively novel. Macrolides, polyethers, diketopiperazines, and siderophores accounted for most of the known compounds. The structures of six novel compounds were elucidated, two of which had a unique skeleton and represented characteristic secondary metabolites of a putative novel Streptomyces phylotype. These results demonstrate that red soils are rich reservoirs for diverse culturable actinomycetes, notably members of the families Streptomycetaceae, Pseudonocardiaceae, and Streptosporangiaceae, with the capacity to synthesize novel bioactive compounds. While high-throughput sequencing methods expand our understanding of species diversity in microbial communities and reveal the presence of many new groups that were previously undetected in cultivation studies, the availability of pure cultures is still essential in order to discover new or useful bioactive compounds from microorganisms. As the most prolific secondary metabolite producers, actinomycetes account for approximately 41% of the bioactive microbial metabolites that have been discovered (1). In recent years, with the emergence of antibiotic-resistant microbial pathogens and rediscovery of known bioactive compounds, special habitats in the ocean (2, 3), sponges (4), plants (5, 6), and insects (7) have been found to be potentially important in the search and discovery of bioactive compound-producing strains. Nevertheless, soil is still the predominant source of secondary metabolite-producing actinomycetes. Unexplored and underexplored soil habitats have been found to be a rich source of actinomycetes that produce novel bioactive metabolites (8-10). Acidic soils in China, mostly red soils, are one such habitat.Red soils are generated by abundant rainfall and high temperature and are widespread in tropical and subtropical regions of southern China, covering about 1.13 million km 2 (11). These soils have been subjected to intensive weathering, and mineral nutrients (including Ca, Mg, P, and K) in the soil are mostly eluted, form...

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“…For example, the genera Streptomyces and Streptacidiphilus accounted for the majority (57.8 %) of 23 OTUs in a red soil in China, with pH between 2.6 and 6.6 [9]. Streptomyces and Streptacidiphilus also comprised 63.6 % of 33 Actinobacteria OTUs isolated from an acidic soil in Malaysia, with pH 4.15 to 5.89 [48]. Meanwhile, regarding the proportion of Actinobateria OTUs obtained from the current research in extremely acidic soil from a coal mine, the proportion of Actinobacteria OTUs having a close relationship to Streptomyces and Streptacidiphilus was 47.1 % of the whole detected phylum Actinobacteria.…”

Section: Diversity Of Rare Actinobacteria In Coal Minementioning

confidence: 99%

“…645 152, and Actinoallomurus sp. 645150 from acid soils in Malaysia [48], as well as Actinoallomurus sp. FXJ1.503 from a red soil in China [9].…”

Section: Phylogenetic Relationshipsmentioning

confidence: 99%

Diversity Analysis of an Extremely Acidic Soil in a Layer of Coal Mine Detected the Occurrence of Rare Actinobacteria

Pikoli

Sugoro

Suharti

2020

Walailak J Sci & Tech

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Studies that explore the diversity of microorganisms in unusual (extreme) environments have become more common. Our research aims to predict the diversity of bacteria that inhabit an extreme environment, a coal mine’s soil with pH of 2.93. Soil samples were collected from the soil at a depth of 12 meters from the surface, which is a clay layer adjacent to a coal seam in Tanjung Enim, South Sumatera, Indonesia. A culture-independent method, the polymerase chain reaction based denaturing gradient gel electrophoresis, was used to amplify the 16S rRNA gene to detect the viable-but-unculturable bacteria. Results showed that some OTUs that have never been found in the coal environment and which have phylogenetic relationships to the rare actinobacteria Actinomadura, Actinoallomurus, Actinospica, Streptacidiphilus, Aciditerrimonas, and Ferrimicrobium. Accordingly, the highly acidic soil in the coal mine is a source of rare actinobacteria that can be explored further to obtain bioactive compounds for the benefit of biotechnology.

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Phylogenetic diversity of acidophilic actinomycetes from Malaysia

Cited by 8 publications

References 19 publications

Acidophilic actinomycetes from rhizosphere soil: diversity and properties beneficial to plants

Acidophilic actinomycetes from rhizosphere soil: diversity and properties beneficial to plants

Red Soils Harbor Diverse Culturable Actinomycetes That Are Promising Sources of Novel Secondary Metabolites

Diversity Analysis of an Extremely Acidic Soil in a Layer of Coal Mine Detected the Occurrence of Rare Actinobacteria

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