Amycolatopsis granulosa sp nov., Amycolatopsis ruanii sp nov and Amycolatopsis thermalba sp nov., thermophilic actinomycetes isolated from arid soils

The taxonomic positions of three thermophilic actinomycetes isolated from arid soil samples were established by using a polyphasic approach. The organisms had chemical and morphological features that were consistent with their classification in the genus Amycolatopsis. 16S rRNA gene sequence data supported the classification of the isolates in the genus Amycolatopsis and showed that they formed distinct branches in the Amycolatopsis methanolica subclade. DNA-DNA relatedness studies between the isolates and their phylogenetic neighbours showed that they belonged to distinct genomic species. The three isolates were readily distinguished from one another and from the type strains of species classified in the A. methanolica subclade based on a combination of phenotypic properties and by genomic fingerprinting. Consequently, it is proposed that the three isolates be classified in the genus Amycolatopsis as representatives of Amycolatopsis granulosa sp. nov. (type strain GY307(T)=NCIMB 14709(T)=NRRL B-24844(T)), Amycolatopsis ruanii sp. nov. (type strain NMG112(T)=NCIMB 14711(T)=NRRL B-24848(T)) and Amycolatopsis thermalba sp. nov. (type strain SF45(T)=NCIMB 14705(T)=NRRL B-24845(T)).Conselho Nacional de Desenvolvimento Cientifico e Tecnologico [201066/2009-2

Effects of Open-Top Chamber on soil chemical properties and microbial growth

Global warming is the main concern in today’s century as it comes with numerous side effects to the natural environment. Open Top Chambers (OTC) consist of metal constructions with transparent vertical side-walls and a frustum on top. An opening in the middle of the frustum allows an air exchange to reduce temperature and humidity effects in the chamber. The size of the open top chamber which is located in Universiti Putra Malaysia is slanted 60o , 50cm tall, 2.08m basal diameter hexagon chamber. The Open Top Chamber experiments were carried out to determine how much global warming has affected and is still affecting the temperature, pH, the moisture and the growth of the microbes in the tropical soil. The aim of this study is to elucidate the effects of temperature increase on the soil microbes’ population and on the pH of the soil. The study was conducted to observe the effect of heat on the population of soil microbes and the pH of the soil which was collected on the same day for 6 consecutive months. The microbes from the samples were grown on agar plates. The population of microbes on the plates were used as values were for Colony Forming Unit (CFU) value calculations. The effects of OTCs on mean temperature showed a large range of CFU values throughout the 6 months but did not differ significantly between studies. Increases in mean monthly and diurnal temperature were strongly related, indicating that the presence of warming effect by the OTCs. Such predictive power allows a better mechanistic understanding of observed biotic response to experimental warming. This study will be useful for the understanding of the global warming effect on microbes. The Open Top Chamber experiment has proven to be one of the effective model for global warming research and data collected especially on the growth of soil microbial obtained would be of great use for further experiments

Amycolatopsis systematics A new beginning

SIGLEAvailable from British Library Document Supply Centre- DSC:DXN055301 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

Selective isolation and characterisation of novel members of the family Nocardiopsaceae and other actinobacteria from a marine sediment of Tioman Island

Tioman Island is one of many sources for underexplored actinobacterial diversity in Malaysia. Selective isolation, molecular profiling, 16S rRNA gene sequencing and phylogenetic analyses were carried out to highlight the diversity of the marine actinobacterial community in a sediment collected off Tioman Island. A high number of diverse actinobacteria were recovered using skim milk/HEPES pre-treatment on a mannitol-based medium. A total of 123 actinobacterial strains were isolated, including thirty obligate marine actinobacteria putatively identified as Salinispora spp. Molecular fingerprinting profiles obtained with a double digestion approach grouped the remaining non-Salinispora-like strains into 24 different clusters, with Streptomyces and Blastococcus as the major clusters. A total of 17 strains were identified as novel actinobacterial species within the genera Streptomyces (n = 6), Blastococcus (n = 5), Marinactinospora (n = 3), Nocardiopsis (n = 1), Agromyces (n = 1) and Nonomuraea (n = 1) based on 16S rRNA gene sequence analyses. Polyphasic data from three putative Marinactinospora spp. showed that the strains represent a new genus in the Nocardiopsaceae family. Crude extracts from the strains were also found to inhibit the growth of Gram-positive (Staphylococcus aureus, Bacillus subtilis) and Gram-negative (Providencia alcalifaciens) pathogens. Hierarchical clustering of the bioactivities of an active fraction revealed a unique profile, which is closely related that of fosfomycin

Identification of indigenous bacteria isolated from shrimp aquaculture wastewater with bioremediation application: total ammoniacal nitrogen (TAN) and nitrite removal

Deterioration of water quality mainly due to high total ammonia nitrogen (TAN) and nitrite will affect the productivity of shrimp culture. In this study, three indigenous strains assigned as VCM5, VCM8 and VCM12 were evaluated for their ability to degrade TAN and nitrite. These strains were inoculated into shrimp aquaculture wastewater to enhance the degradation of TAN and nitrite. All the strains reduced TAN and nitrite level from the shrimp aquaculture wastewater significantly (p<0.05). Strain VCM5 (GenBank accession number KJ700465) and VCM8 (GenBank accession number KJ700464) showed 99.71% sequence similarity with the 16S rRNA gene type species Bacillus vietnamensis 15-1T (ABO99708) and strain VCM12 (GenBank accession number KJ700463) showed 99.05% sequence similarity with 16S rRNA gene sequence type species Gordonia bronchialis DSM43247T (CP001802)

Amycolatopsis thermophila sp nov and Amycolatopsis viridis sp nov., thermophilic actinomycetes isolated from arid soil

The taxonomic positions of two thermophilic actinomycetes isolated from an arid Australian soil sample were established based on an investigation using a polyphasic taxonomic approach. The organisms had chemical and morphological properties typical of members of the genus Amycolatopsis and formed distinct phyletic lines in the Amycolatopsis methanolica 16S rRNA subclade. The two organisms were distinguished from one another and from the type strains of related species of the genus Amycolatopsis using a range of phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the two isolates be classified in the genus Amycolatopsis as Amycolatopsis thermophila sp. nov. (type strain GY088(T)=NCIMB 14699(T)=NRRL B-24836(T)) and Amycolatopsis viridis sp. nov. (type strain GY115(T)=NCIMB 14700(T)= NRRL B-24837(T)).Conselho Nacional de Desenvolvimento Cientifico e Tecnologico in the UK [201066/2009-2

In vitro and In vivo evaluation of streptomyces suppressions against anthracnose in chili caused by colletotrichum

The isolation of 66 streptomycetes from rhizosphere soil of chili plants was done for their inhibitory activities against three different dominant species of Colletotrichum namely C. acutatum, C. gloeosporioides and C. capsici. Twenty one streptomycetes strains were active against at least one of the Colletotrichum species. In addition, ten strains that inhibited the in vitro growth of Colletotrichum species showed chitinase activity. Strain P42, which displayed the highest inhibitory activity against all three anthracnose fungi species and high chitinase activity was tested as biological control agent in a greenhouse study. The strain successfully controlled chili anthracnose disease by significantly reducing the disease severity. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain P42 belongs to the Streptomyces rochei clade. The results of the current study showed that rhizosphere-derived soil of chili plants is an important source of bioactive streptomycetes which are antagonistic against Colletotrichum

Promoter effect of microbes in slope eco-engineering: Effects on plant growth, soil quality and erosion rate at different vegetation densities

Slope revegetation is claimed to be accelerated with the right choice of plants and effective planting techniques for the root establishment. In addition, microorganisms also promote plant growth via nutrient intensification and soil-root enhancement, hence may alleviate soil surface erosion. Thus, this study is aimed to identify the effects of microbial application on plant growth, soil properties and soil erosion rate at different vegetation densities. Six experimental plots were set up at the Guthrie Corridor Expressway, Selangor, Malaysia, with different amount of microbial application and vegetation density. Dense vegetation cover with microbial application (DM) plot exhibited the highest soil microbes abundance and fungal/bacteria (F/B) ratio after 24 months of observation. Meanwhile, photosynthetic rate and root length density of Lantana camara in the DM plot revealed the highest rate, followed by Melastoma malabathricum and Bauhinia purpurea. Moreover, the soil of DM plot had also increased in CEC, total N, and respiration rate, reflecting the soil quality. Consequently, erosion rate of DM plot exhibited the 52.6% of total decrement from the initial experiment. Thus, microbes are proven to be relatively good promoters for the improvement of plant growth performance, the soil quality and alleviate the soil erosion of the slope

Marinitenerispora sediminis gen. nov., sp. nov., a member of the family Nocardiopsaceae isolated from marine sediment

Three novel actinobacterial strains, designated as TPS16T, TPS81 and TPS83, were isolated from a sample of marine sediment collected from Tioman Island, Malaysia. The strains formed abundant branched substrate mycelia without fragmentation along with production of blue spores and blue diffusible pigment on soybean meal agar. The strains could grow at pH ranging from pH 6 to 12 and in 0-8% (w/v) NaCl. Cell-wall hydrolysis showed the presence of meso-diaminopimelic acid. The strains were closely related to Marinactinospora thermotolerans SCSIO 00652T (97.60 %) and Marinactinospora endophytica YIM 690053T (96.87%) based on phylogenetic analysis of 16S rRNA gene sequences. Multilocus sequence analysis including gyrB, recA and rpoB genes further confirmed that strain TPS16T represented a distinct branch within the family Nocardiopsaceae. The predominant menaquinones were MK-11(H2), MK-10(H2), MK-11(H4) and MK-10(H4), while the major fatty acids were found to be iso-C16:0, anteiso-C17:0, iso-C15:0 and C18:1ω9c. Genome sequencing revealed genome sizes of approximately 6 Mb and G+C contents of 73.8 mol%. A new genus, Marinitenerispora gen. nov., is proposed within the family Nocardiopsaceae based on polyphasic data and the type species is Marinitenerispora sediminis gen. nov., sp. nov. The type strain is TPS16T (=DSM 46825T=TBRC 5138T). © 2019 The Authors

Sponges of Tioman and their actinomycetes inhabitants

Actinomycetes were isolated from marine sponges of Tioman Island and taxonomically characterized up to genus level. Four hundred and seven putative actinomycetes were recovered from39 marine sponge samples collected from nine sites in Tioman Island using standard isolation protocols developed in the study. The actinomycetes population ranged from 2.72 x 102 to 0.6 x 102 colony forming unit (cfu)/g of dry sample. Isolates were then assigned into 11 color groups. Fifty three morphologically different representatives observed under the binocular light microscope were selected for chemotaxonomic, cultural, morphological and physiological characteristization. Chemotaxonomically, 21 (41%) isolates with L,L-diaminopimelic acid (DAP) and no diagnostic sugars pattern in the whole-cell wall hydrolysate were tentative streptomycetes (chemotype I), while 32 (59%) isolates with meso-DAP with observed three different sugars pattern were tentative non-streptomycetes (chemotype II/D, IV/A and III/B). Based on salt tolerance and carbon utilization test, forty five halo-groups and forty one carbo-groups were observed, indicating probable forty one to forty five different species or strains. The tentative genus diversity of rare actinomycetes in the marine sponges was Actinoplanes, Micromonospora, Sprilliplanes, Pseudonocardia, Nocardia, Rhodococcus, Saccharomonospora and Salinispora. Thirty eight crude extracts were tested against 13 bacterial strains and three fungal strains. Thirty four (64.2%) isolates exhibited antibacterial and antifungal activities, out of which eight (18.9%) isolates exhibited broad spectrum bioactivity