The Experts below are selected from a list of 30348 Experts worldwide ranked by ideXlab platform
Jihong Jiang - One of the best experts on this subject based on the ideXlab platform.
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carbonate mineral formation under the influence of limestone colonizing Actinobacteria morphology and polymorphism
Frontiers in Microbiology, 2016Co-Authors: Jihong Jiang, Ying Huang, Bin LianAbstract:Microorganisms and their biomineralisation processes are widespread in almost every environment on earth. In this work, Streptomyces luteogriseus DHS C014, a dominant lithophilous Actinobacteria isolated from microbial mats on limestone rocks, was used to investigate its potential biomineralisation to allow a better understanding of bacterial contributions to carbonate mineralisation in nature. The ammonium carbonate free-drift method was used with mycelium pellets, culture supernatant, and spent culture of the strain. Mineralogical analyses showed that hexagonal prism calcite was only observed in the sub-surfaces of the mycelium pellets, which is a novel morphology mediated by microbes. Hemispheroidal vaterite appeared in the presence of spent culture, mainly because of the effects of soluble microbial products (SMP) during mineralisation. When using the liquid culture, doughnut-like vaterite was favoured by Actinobacterial mycelia, which has not yet been captured in previous studies. Our analyses suggested that the effects of mycelium pellets as a molecular template almost gained an advantage over SMP both in crystal nucleation and growth, having nothing to do with biological activity. It is thereby convinced that lithophilous Actinobacteria, S. luteogriseus DHS C014, owing to its advantageous genetic metabolism and filamentous structure, showed good biomineralisation abilities, maybe it would have geoactive potential for biogenic carbonate in local microenvironments.
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biodiversity and plant growth promoting traits of culturable endophytic Actinobacteria associated with jatropha curcas l growing in panxi dry hot valley soil
Applied Soil Ecology, 2015Co-Authors: Qian Miao, Weiwei Feng, Yu Wang, Ke Xing, Jihong JiangAbstract:Abstract One of the proposed mechanisms through which plant growth-promoting endophyte (PGPE) enhances plant growth is the production of 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD). However, information about the endophytic Actinobacteria with ACC deaminase activity associated with native plants is still very scarce. In this study, a total of 257 endophytic Actinobacterial isolates were obtained using Actinobacteria-selective media from surface sterilized roots, stems, leaves and seeds of the oil-seed plant Jatropha curcas L. collected from dry-hot valley soil. Morphological and the 16S rRNA sequence analysis showed that most of the isolates belong to the Streptomyces genus and other non-Streptomyces strains distributed onto 13 genera, with several new species. 19 strains were found to have ACC deaminase activity and they belong to the genera Streptomyces, Nonomuraea, Micrococcus and Kibdelosporangium. The functional ability of the ACC deaminase producing isolates to produce indole-3-acetic acid (IAA), siderophores, mineral phosphate solubilization and growth on nitrogen free semi-solid medium was also determined. Seven strains were selected to inoculate the axenically grown seedlings and they resulted in a significant increase in the seedling fresh weight, the seedling length, the root length and the leaf area of the endophytes-treated seedlings compared to the control. This is the first report on the diversity and characterization of endophytic Actinobacteria associated with important oil-seed plant J. curcas L. Our results demonstrate that some endophytic Actinobacterial strains have the promising PGP attributes to be developed as biofertilizers to enhance soil fertility and promote the plant growth.
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abundant and diverse endophytic Actinobacteria associated with medicinal plant maytenus austroyunnanensis in xishuangbanna tropical rainforest revealed by culture dependent and culture independent methods
Environmental Microbiology Reports, 2012Co-Authors: Huahong Chen, Wen-jun Li, Jihong Jiang, Guozhen Zhao, Jie Li, Lihua XuAbstract:Endophytes are now considered as an important component of biodiversity. However, the diversity of endophytic Actinobacteria associated with tropical rainforest native medicinal plants is essentially unknown. In this study, the diversity of endophytic Actinobacteria residing in root, stem and leaf tissues of medicinal plant Maytenus austroyunnanensis collected from tropical rainforest in Xishuangbanna, China was investigated with a combination of cultivation and culture-independent analysis on the basis of 16S rRNA gene sequencing. By using different selective isolation media and methods, a total of 312 Actinobacteria were obtained, and they were affiliated with the order Actinomycetales (distributed into 21 genera). Based on a protocol for endophytes enrichment, three 16S rRNA gene clone libraries were constructed and 84 distinct operational taxonomic units were identified and they distributed among the orders Actinomycetales and Acidimicrobiales, including eight suborders and at least 38 genera with a number of rare Actinobacteria genera. Phylogenetic analysis showed that 32% of the clones in the libraries had lower than 97% similarities with related type strains. Interestingly, six genera from the order Actinomycetales and uncultured clones from Acidimicrobiales have not, to our knowledge, been previously reported as endophytes. Our study confirms abundant endophytic Actinobacterial consortium in tropical rainforest native plant and suggests that this special habitat represents an underexplored reservoir of diverse and novel Actinobacteria of potential interest for bioactive compounds discovery.
Radhey S Gupta - One of the best experts on this subject based on the ideXlab platform.
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phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria
Microbiology and Molecular Biology Reviews, 2012Co-Authors: Radhey S GuptaAbstract:Summary: The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 Actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups of Actinobacteria as well as a number of their superageneric clades are resolved. We also describe large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades (viz., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylum Actinobacteria (excluding Coriobacteriia) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders of Actinobacteria. The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups of Actinobacteria in diverse environments. Genetic and biochemical studies on these Actinobacteria-specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria.
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signature proteins that are distinctive characteristics of Actinobacteria and their subgroups
Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2006Co-Authors: Ragi Paramanathan, Radhey S GuptaAbstract:The Actinobacteria constitute one of the main phyla of Bacteria. Presently, no morphological and very few molecular characteristics are known which can distinguish species of this highly diverse group. In this work, we have analyzed the genomes of four Actinobacteria (viz. Mycobacterium leprae TN, Leifsonia xyli subsp. xyli str. CTCB07, Bifidobacterium longum NCC2705 and Thermobifida fusca YX) to search for proteins that are unique to Actinobacteria. Our analyses have identified 233 Actinobacteria-specific proteins, homologues of which are generally not present in any other bacteria. These proteins can be grouped as follows: (i) 29 proteins uniquely present in most sequenced Actinobacterial genomes; (ii) 6 proteins present in almost all Actinobacteria except Bifidobacterium longum and another 37 proteins absent in B. longum and few other species; (iii) 11 proteins which are mainly present in Corynebacterium, Mycobacterium and Nocardia (CMN) subgroup as well as Streptomyces, T. fusca and Frankia sp., but they are not found in Bifidobacterium and Micrococcineae; (iv) 8 proteins that are specific for T. fusca and Streptomyces species, plus 2 proteins also present in the Frankia species; (v) 13 proteins that are specific for the Corynebacterineae or the CMN group; (vi) 14 proteins only found in Mycobacterium and Nocardia; (vii) 24 proteins unique to different Mycobacterium species; (viii) 8 proteins specific to the Micrococcineae; (ix) 85 proteins which are distributed sporadically in Actinobacterial species. Additionally, many examples of lateral gene transfer from Actinobacteria to Magnetospirillum magnetotacticum have also been identified. The identified proteins provide novel molecular means for defining and circumscribing the Actinobacteria phylum and a number of subgroups within it. The distribution of these proteins also provides useful information regarding interrelationships among the Actinobacterial subgroups. Most of these proteins are of unknown function and studies aimed at understanding their cellular functions should reveal common biochemical and physiological characteristics unique to either all Actinobacteria or particular subgroups of them. The identified proteins also provide potential targets for development of drugs that are specific for Actinobacteria.
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conserved indels in protein sequences that are characteristic of the phylum Actinobacteria
International Journal of Systematic and Evolutionary Microbiology, 2005Co-Authors: Radhey S GuptaAbstract:Gram-positive bacteria with a high G+C content are currently recognized as a distinct phylum, Actinobacteria, on the basis of their branching in 16S rRNA trees. Except for an insert in the 23S rRNA, there are no unique biochemical or molecular characteristics known at present that can distinguish this group from all other bacteria. In this work, three conserved indels (i.e. inserts or deletions) are described in three widely distributed proteins that are distinctive characteristics of the Actinobacteria and are not found in any other groups of bacteria. The identified signatures are a 2 aa deletion in cytochrome-c oxidase subunit 1 (Cox1), a 4 aa insert in CTP synthetase and a 5 aa insert in glutamyl-tRNA synthetase (GluRS). Additionally, the Actinobacterial specificity of the large insert in the 23S rRNA was also tested. Using primers designed for conserved regions flanking these signatures, fragments of most of these genes were amplified from 23 Actinobacterial species, covering many different families and orders, for which no sequence information was previously available. All the 61 sequenced fragments, except two in GluRS, were found to contain the indicated signatures. The presence of these signatures in various species from 20 families within this phylum provides evidence that they are likely distinctive characteristics of the entire phylum, which were introduced in a common ancestor of this group. The absence of all four of these signatures in Symbiobacterium thermophilum suggests that this species, which is distantly related to other Actinobacteria in 16S rRNA and CTP synthetase trees, may not be a part of the phylum Actinobacteria. The identified signatures provide novel molecular means for defining and circumscribing the phylum Actinobacteria. Functional studies on them should prove helpful in understanding novel biochemical and physiological characteristics of this group of bacteria.
Christopher M. M. Franco - One of the best experts on this subject based on the ideXlab platform.
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Biogeography and emerging significance of Actinobacteria in Australia and Northern Antarctica soils
Soil Biology & Biochemistry, 2020Co-Authors: Ricardo Araujo, Andrew Bissett, Pauline M. Mele, Frank Reith, Vadakattu V. S. R. Gupta, Christopher M. M. FrancoAbstract:Abstract Actinobacteria play key roles in terrestrial ecosystem functioning. They contribute to global carbon cycling through the decomposition of soil organic matter, they increase plant productivity and are widely known as prolific producers of bioactive compounds essential for human and animal health. The almost century-old search for new members of the Actinobacteria has so far proceeded without a compass directing researchers towards regions of Actinobacterial abundance and novel diversity. We show that such regions are found in Australia, a dry and warm continent with highly weathered soils. Here, Actinobacteria are highly abundant suggesting they may play an increasingly important role as climate becomes warmer and drier. Australian continental Actinobacterial diversity is associated with physicochemical factors, especially soil pHwater, exchangeable calcium and the regional climate. Patterns of their biogeography suggest that only a small fraction of Actinobacteria have the capability of dispersing throughout the Southern Hemisphere, especially across oceans. We identified a core soil Actinobacterial community across mainland Australia of 2211 OTUs which reduced to 490 OTUs when Tasmania, King Island, Christmas Island and Northern Antarctica were included. These 490 OTUs mapped to three families, i.e., Gaiellaceae, Micromonosporaceae and Nocardiaceae. This study also implicates disturbance regimes associated with agriculture in the reduction of Actinobacterial diversity, highlighting undisturbed soils as reservoirs for enriching adjacent agricultural soils. Interestingly, high OTU similarities between King Island and areas in Antarctica suggest a shared evolutionary history that persists to this day. In conclusion, Actinobacteria are highly abundant in Australian soils, suggesting they could play increasingly important roles in soils globally under future climate scenarios.
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Symbiosis and Pathogenicity of Actinobacteria
Biology and Biotechnology of Actinobacteria, 2017Co-Authors: Yitayal S. Anteneh, Christopher M. M. FrancoAbstract:Actinobacteia are known to interact with a number of macro and microorganisms. Symbiotic interaction between Actinobacteria and its host observed in insects, human, animals and plants, where the bacteria provide protection of the host against pathogen, produce essential nutrients, enzymes and facilitate digestion of food particles. In the other hand, Actinobacteria also responsible in causing of diseases like actinomycetoma and tuberculosis in human, nocardiosis and dermatophilosis in animals, and scab in plants. This chapter covers the literature which describes the symbiotic interaction of Actinobacteria with different vertebrates and invertebrates, as well as common Actinobacteria associated diseases in human, animals and plants.
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Endophytic Actinobacteria: Beneficial Partners for Sustainable Agriculture
Endophytes: Biology and Biotechnology, 2017Co-Authors: Ricardo Araujo, Onuma Kaewkla, Christopher M. M. FrancoAbstract:Endophytic Actinobacteria have been proven to be effective partners that have beneficial functions with a number of crop plants. A large number of studies have been carried out, showing these positive effects in laboratories and glasshouses, but with fewer reports of their effectiveness in the field. This chapter highlights the results of field trials of Actinobacterial endophytes conducted with cereals, vegetables such as tomato, cucumber, or cabbage, legumes such as chickpea or pea, fruits such as melon or grapes, peanuts, and woody plants.
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Endophytic Actinobacteria: Diversity and Ecology
Advances in Endophytic Research, 2013Co-Authors: Venkadasamy Govindasamy, Christopher M. M. Franco, Vadakattu V. S. R. GuptaAbstract:Actinobacteria are a group of Gram-positive microorganisms with a high G+C content in their DNA and belong to the phylum Actinobacteria, one of the largest phyla within bacteria. Some of these Actinobacteria have an endophytic lifestyle which occurs abundantly in most plants. The abundance and diversity of endophytic Actinobacterial colonisation depend on plant species, type of soils and other associated environmental conditions. Streptomyces spp. were reported as the most predominant species, and Microbispora, Micromonospora, Nocardioides, Nocardia and Streptosporangium are other common genera of endophytic Actinobacteria isolated from a diverse range of plant species, including those found in estuarine/mangrove ecosystems and algae and seaweeds of marine ecosystems. Over the years, isolation media have been devised and numerous methods have been standardised for the isolation, identification and characterisation of these endophytic Actinobacteria. Recent advances in molecular tools have revealed the ‘not yet cultured’ diversity within this group. Therefore, a combination of both culture-based and molecular techniques is essential to describe the diversity and ecology of endophytic Actinobacteria. The quest for Actinobacteria and their metabolic capabilities is ongoing, as they represent the largest ecological resource for secondary metabolites (plant hormones, antibiotics and other bioactive compounds), with potential biotechnological applications in agriculture, industry and medicine.
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rational approaches to improving the isolation of endophytic Actinobacteria from australian native trees
Microbial Ecology, 2013Co-Authors: Onuma Kaewkla, Christopher M. M. FrancoAbstract:In recent years, new Actinobacterial species have been isolated as endophytes of plants and shrubs and are sought after both for their role as potential producers of new drug candidates for the pharmaceutical industry and as biocontrol inoculants for sustainable agriculture. Molecular-based approaches to the study of microbial ecology generally reveal a broader microbial diversity than can be obtained by cultivation methods. This study aimed to improve the success of isolating individual members of the Actinobacterial population as pure cultures as well as improving the ability to characterise the large numbers obtained in pure culture. To achieve this objective, our study successfully employed rational and holistic approaches including the use of isolation media with low concentrations of nutrients normally available to the microorganism in the plant, plating larger quantities of plant sample, incubating isolation plates for up to 16 weeks, excising colonies when they are visible and choosing Australian endemic trees as the source of the Actinobacteria. A hierarchy of polyphasic methods based on culture morphology, amplified 16S rRNA gene restriction analysis and limited sequencing was used to classify all 576 Actinobacterial isolates from leaf, stem and root samples of two eucalypts: a Grey Box and Red Gum, a native apricot tree and a native pine tree. The classification revealed that, in addition to 413 Streptomyces spp., isolates belonged to 16 other Actinobacterial genera: Actinomadura (two strains), Actinomycetospora (six), Actinopolymorpha (two), Amycolatopsis (six), Gordonia (one), Kribbella (25), Micromonospora (six), Nocardia (ten), Nocardioides (11), Nocardiopsis (one), Nonomuraea (one), Polymorphospora (two), Promicromonospora (51), Pseudonocardia (36), Williamsia (two) and a novel genus Flindersiella (one). In order to prove novelty, 12 strains were characterised fully to the species level based on polyphasic taxonomy. One strain represented a novel genus in the family Nocardioides, and the other 11 strains were accepted as novel species. In summary, the holistic isolation strategies were successful in obtaining significant culturable Actinobacterial diversity within Australian native trees that includes rare and novel species.
Rohit Ghai - One of the best experts on this subject based on the ideXlab platform.
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Metagenomic recovery of phage genomes of uncultured freshwater Actinobacteria
The ISME Journal, 2017Co-Authors: Rohit Ghai, Maliheh Mehrshad, Carolina Megumi Mizuno, Francisco Rodriguez-valeraAbstract:Low-GC Actinobacteria are among the most abundant and widespread microbes in freshwaters and have largely resisted all cultivation efforts. Consequently, their phages have remained totally unknown. In this work, we have used deep metagenomic sequencing to assemble eight complete genomes of the first tailed phages that infect freshwater Actinobacteria. Their genomes encode the Actinobacterial-specific transcription factor whiB, frequently found in mycobacteriophages and also in phages infecting marine pelagic Actinobacteria. Its presence suggests a common and widespread strategy of modulation of host transcriptional machinery upon infection via this transcriptional switch. We present evidence that some whiB-carrying phages infect the acI lineage of Actinobacteria. At least one of them encodes the ADP-ribosylating component of the widespread bacterial AB toxins family (for example, clostridial toxin). We posit that the presence of this toxin reflects a ‘trojan horse’ strategy, providing protection at the population level to the abundant host microbes against eukaryotic predators.
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key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing
Molecular Ecology, 2014Co-Authors: Rohit Ghai, Carolina Megumi Mizuno, Antonio Picazo, Antonio Camacho, Francisco RodriguezvaleraAbstract:Freshwater ecosystems are critical but fragile environments directly affecting society and its welfare. However, our understanding of genuinely freshwater microbial communities, constrained by our capacity to manipulate its prokaryotic participants in axenic cultures, remains very rudimentary. Even the most abundant components, freshwater Actinobacteria, remain largely unknown. Here, applying deep metagenomic sequencing to the microbial community of a freshwater reservoir, we were able to circumvent this traditional bottleneck and reconstruct de novo seven distinct streamlined Actinobacterial genomes. These genomes represent three new groups of photoheterotrophic, planktonic Actinobacteria. We describe for the first time genomes of two novel clades, acMicro (Micrococcineae, related to Luna2,) and acAMD (Actinomycetales, related to acTH1). Besides, an aggregate of contigs belonged to a new branch of the Acidimicrobiales. All are estimated to have small genomes (approximately 1.2 Mb), and their GC content varied from 40 to 61%. One of the Micrococcineae genomes encodes a proteorhodopsin, a rhodopsin type reported for the first time in Actinobacteria. The remarkable potential capacity of some of these genomes to transform recalcitrant plant detrital material, particularly lignin-derived compounds, suggests close linkages between the terrestrial and aquatic realms. Moreover, abundances of Actinobacteria correlate inversely to those of Cyanobacteria that are responsible for prolonged and frequently irretrievable damage to freshwater ecosystems. This suggests that they might serve as sentinels of impending ecological catastrophes.
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breaking a paradigm cosmopolitan and abundant freshwater Actinobacteria are low gc
Environmental Microbiology Reports, 2012Co-Authors: Rohit Ghai, Katherine D Mcmahon, Francisco RodriguezvaleraAbstract:Summary Free-living Actinobacteria are universally recognized as high-GC organisms. Freshwater Actinobacteria have been identified as abundant and prevalent members of freshwater microbial communities, but the two most common lineages (acI and acIV) have remained impossible to culture to date. We have analysed metagenomic data from lakes and estuaries, and show that members of acI and acIV are indeed abundant. We then show that the majority of Actinobacterial reads from metagenomic datasets (both lakes and estuaries) are consistently low GC. Analysis of assembled scaffolds from these datasets also confirms that Actinobacterial scaffolds are primarily low GC, although high-GC scaffolds were also observed, indicating both types of Actinobacteria coinhabit. Phylogenetic analysis of 16S rRNA gene sequences, both from PCR-based clone libraries and metagenomic reads, and the discovery of a low-GC scaffold containing a partial 16S rRNA gene, points to the abundance of the well-known acI and acIV lineages of freshwater in these habitats, both of which appear to be low GC.
Qian Miao - One of the best experts on this subject based on the ideXlab platform.
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biodiversity and plant growth promoting traits of culturable endophytic Actinobacteria associated with jatropha curcas l growing in panxi dry hot valley soil
Applied Soil Ecology, 2015Co-Authors: Qian Miao, Weiwei Feng, Yu Wang, Ke Xing, Jihong JiangAbstract:Abstract One of the proposed mechanisms through which plant growth-promoting endophyte (PGPE) enhances plant growth is the production of 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD). However, information about the endophytic Actinobacteria with ACC deaminase activity associated with native plants is still very scarce. In this study, a total of 257 endophytic Actinobacterial isolates were obtained using Actinobacteria-selective media from surface sterilized roots, stems, leaves and seeds of the oil-seed plant Jatropha curcas L. collected from dry-hot valley soil. Morphological and the 16S rRNA sequence analysis showed that most of the isolates belong to the Streptomyces genus and other non-Streptomyces strains distributed onto 13 genera, with several new species. 19 strains were found to have ACC deaminase activity and they belong to the genera Streptomyces, Nonomuraea, Micrococcus and Kibdelosporangium. The functional ability of the ACC deaminase producing isolates to produce indole-3-acetic acid (IAA), siderophores, mineral phosphate solubilization and growth on nitrogen free semi-solid medium was also determined. Seven strains were selected to inoculate the axenically grown seedlings and they resulted in a significant increase in the seedling fresh weight, the seedling length, the root length and the leaf area of the endophytes-treated seedlings compared to the control. This is the first report on the diversity and characterization of endophytic Actinobacteria associated with important oil-seed plant J. curcas L. Our results demonstrate that some endophytic Actinobacterial strains have the promising PGP attributes to be developed as biofertilizers to enhance soil fertility and promote the plant growth.
