Use of polyvalent phage for reduction of streptomycetes on soil dilution plates

The 1-aminocyclopropane-1-carboxylic acid deaminase-producing Streptomyces violaceoruber UAE1 can provide protection from sudden decline syndrome on date palm

In the United Arab Emirates (UAE), sudden decline syndrome (SDS) is one of the major fungal diseases caused by Fusarium solani affecting date palm plantations. To minimize the impact of the causal agent of SDS on date palm, native actinobacterial strains isolated from rhizosphere soils of healthy date palm plants were characterized according to their antifungal activities against F. solani DSM 106836 (Fs). Based on their in vitro abilities, two promising biocontrol agents (BCAs), namely Streptomyces tendae UAE1 (St) andStreptomyces violaceoruber UAE1 (Sv), were selected for the production of antifungal compounds and cell wall degrading enzymes (CWDEs), albeit their variations in synthesizing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase (ACCD). Although both isolates showed antagonism when applied 7 days before the pathogen in the greenhouse experiments, the ACCD-producing Sv was relatively superior in its efficacy against SDS over the non-ACCD-producing St. This was evident from the symptoms of SDS in diseased date palm seedlings which were greatly reduced by Sv compared to St. On a scale of 5.0, the estimated disease severity indices in Fs-diseased seedlings were significantly (P < 0.05) reduced from 4.8 to 1.5 and 0.5 by St and Sv, respectively. Thus, the number of conidia of Fs recovered from plants pre-treated with both BCAs was comparable, but significantly (P < 0.05) reduced compared to plants without any BCA treatment. In addition, a significant (P < 0.05) decrease in ACC levels of both the root and shoot tissues was detected inSv + Fs seedlings to almost similar levels of healthy seedlings. However, in planta ACC levels highly increased in seedlings grown in soils infested with the pathogen alone or amended with St prior to F. solani infestation (St + Fs). This suggests a major role of ACCD production in relieving the stress of date palm seedlings infected with F. solani, thus supporting the integrated preventive disease management programs against this pathogen. This is the first report of effective rhizosphere actinobacterial BCAs to provide protection against SDS on date palm, and to help increase agricultural productivity in a more sustainable manner in the UAE and the other arid regions.

Effectiveness of Augmentative Biological Control of Streptomyces griseorubens UAE2 Depends on 1-Aminocyclopropane-1-Carboxylic Acid Deaminase Activity against Neoscytalidium dimidiatum

To manage stem canker disease on royal poinciana, actinobacterial isolates were used as biological control agents (BCAs) based on their strong in vitro inhibitory effects against Neoscytalidiumdimidiatum. Streptomyces griseorubens UAE2 and Streptomyces wuyuanensis UAE1 had the ability to produce antifungal compounds and cell-wall-degrading enzymes (CWDEs). Only S. griseorubens, however, restored the activity of 1-aminocyclopropane-1-carboxylate (ACC) deaminase (ACCD). In vivo apple fruit bioassay showed that lesion development was successfully constrained by either isolates on fruits inoculated with N. dimidiatum. In our greenhouse and container nursery experiments, S. griseorubens showed almost complete suppression of disease symptoms. This was evident when the preventive treatment of S. griseorubens significantly (p < 0.05) reduced the numbers of conidia of N. dimidiatum and defoliated leaves of royal poinciana seedlings to lesser levels than when S. wuyuanensis was applied, but comparable to control treatments (no pathogen). The disease management of stem canker was also associated with significant (p < 0.05) decreases in ACC levels in royal poinciana stems when S. griseorubens was applied compared to the non-ACCD-producing S. wuyuanensis. This study is the first to report the superiority of antagonistic actinobacteria to enhance their effectiveness as BCAs not only for producing antifungal metabolites and CWDEs but also for secreting ACCD.

Biological Control of Mango Dieback Disease Caused by Lasiodiplodia theobromae Using Streptomycete and Non-streptomycete Actinobacteria in the United Arab Emirates

Dieback caused by the fungus Lasiodiplodia theobromae is an important disease on mango plantations in the United Arab Emirates (UAE). In this study, 53 actinobacterial isolates were obtained from mango rhizosphere soil in the UAE, of which 35 (66%) were classified as streptomycetes (SA) and 18 (34%) as non-streptomycetes (NSA). Among these isolates, 19 (12 SA and 7 NSA) showed antagonistic activities against L. theobromae associated with either the production of diffusible antifungal metabolites, extracellular cell-wall-degrading enzymes (CWDEs), or both. Using a "novel" mango fruit bioassay, all isolates were screened in vivo for their abilities to reduce lesion severity on fruits inoculated with L. theobromae. Three isolates, two belonging to Streptomyces and one to Micromonospora spp., showed the strongest inhibitory effect against this pathogen in vitro and were therefore selected for tests on mango seedlings. Our results revealed that the antifungal action of S. samsunensis UAE1 was related to antibiosis, and the production of CWDEs (i.e., chitinase) and siderophores; whilst S. cavourensis UAE1 and M. tulbaghiae UAE1 were considered to be associated with antibiotic- and CWDE-production, respectively. Pre-inoculation in greenhouse experiments with the most promising actinobacterial isolates resulted in very high levels of disease protection in mango seedlings subsequently inoculated with the pathogen. This was evident by the dramatic reduction in the estimated disease severity indices of the mango dieback of individual biocontrol agent (BCA) applications compared with the pathogen alone, confirming their potential in the management of mango dieback disease. L. theobromae-infected mango seedlings treated with S. samsunensis showed significantly reduced number of defoliated leaves and conidia counts of L. theobromae by 2- and 4-fold, respectively, in comparison to the other two BCA applications. This indicates that the synergistic antifungal effects of S. samsunensis using multiple modes of action retarded the in planta invasion of L. theobromae. This is the first report of BCA effects against L. theobromae on mango seedlings by microbial antagonists. It is also the first report of actinobacteria naturally existing in the soils of the UAE or elsewhere that show the ability to suppress the mango dieback disease.

Streptophage-mediated control of off-flavour taint producing streptomycetes isolated from barramundi ponds

Off-flavour taint of aquaculture products is a global issue reducing consumer confidence in the farmed produce as they are taken up via the gills of fish, and deposited in the lipids of the animal. If the fish are not purged, resulting undesirable muddy earthy flavour taint can be tasted by consumers. These undesirable flavour and odour is caused by the terpenoid compounds namely geosmin and 2-methylisoborneol, produced as secondary metabolites by certain bacteria including the cyanobacteria and actinomycetes. Current strategies to remediate the problem rely on treating the symptoms not the cause and involve the use of time consuming purging methods and costly chemicals. Biological control using bacteriophages, specific to the problem causing bacteria, offers a natural alternative to chemical control, which might reduce further complications of copper based algaecides and its subsequent implications on water quality. In an adaptation of such biological control approach streptomycetes isolated from barramundi ponds were tested for their susceptibility to streptophages to understand whether host destruction via phage lysis would subsequently eliminate off-flavour taint productions by these isolates. Following the determination of the streptophage susceptibility of the isolates one of the most odourous streptomycete species (USC-14510) was selected to be tested further using different pond simulations resembling real-life applications. Geosmin was tested as the indicator of off-flavour taint production and as it has been previously reported that the cyanobacteria-actinomycete interactions occurring in ponds result in even greater levels of geosmin and 2-methylisoborneol, the geosmin levels for the isolate in the presence of cyanobacteria and streptophages were also tested. Findings indicated that the highly odourous Streptomyces species (USC-14510) once infected with streptophages, can lose its capacity to produce off-flavour taints. Pond simulation studies also revealed geosmin production was significantly reduced when streptophages were introduced into the pond water where streptomycete species were grown. The bacteriophage control method developed in the presented study might again confirm significant potential for the bacteriophage-mediated remediation strategy to be adapted by the aquaculture industry.

Isolation, Screening, and Identification of Novel Isolates of Actinomycetes from India for Antimicrobial Applications

The search for novel bioactive compounds from the natural environment has rapidly been gaining momentum with the increase in multi-drug resistant (MDR) pathogens. In the present study, the antimicrobial potential of novel actinomycetes has been evaluated by initial screening of six soil samples. Primary and secondary screening was performed against Bacillus subtilis, Staphylococcus aureus, Escherichia coli, Candida albicans, Candida tropicalis, Trichophyton rubrum, and other MDR bacterial and fungal test strains, thirteen active isolates were selected for further study. Microbial strains were identified on the basis of growth conditions and other biochemical characters. Five most active microbial strains were identified using 16S rRNA sequence homology and designated as Streptomyces xanthophaeus MTCC 11938, Streptomyces variabilis MTCC 12266, Streptomyces xanthochromogenes MTCC 11937, Streptomyces levis EU 124569, and Streptomyces sp. NCIM 5500. Four antibacterial and three antifungal compounds isolated from the above five isolates were purified and partially characterized using UV absorption and IR spectra. Two antibacterial metabolites, belong to chromone and peptide antibiotic, respectively. The antifungal compounds were found to be of non-polyene nature. In conclusion, we study the isolation of novel bacterial strains of actinomycetes for producing novel compounds having antibacterial and antifungal activities from the unexplored agro-ecological niches of India. Also, this study paves the way for further characterization of these isolates of Streptomyces sp. for their optimum utilization for antimicrobial purposes.

Evaluación de la producción de ácidos orgánicos por Streptomyces spp. y solubilización de tres fuentes de fósforo por la cepa T3A

<p class="MsoNormal" style="text-align: justify;"> </p><p><strong>Título en ingles: Evaluation of organic acid production by <em>Streptomyces</em> spp. and solubilization of three phosphorus sources by strain T3A</strong></p><p class="MsoNormal" style="text-align: justify;"> </p><p><strong>Título corto: </strong><strong>Producción de ácidos orgánicos por <em>Streptomyces</em> spp.  y solubilización de fosfatos por la cepa T3A.</strong></p><p class="MsoNormal" style="text-align: justify;"> </p><p><strong>Título corto en ingles: Organic acid production by <em>Streptomyces</em> spp. and solubilization by strain T3A</strong></p><p><strong>Resumen: </strong>Quince aislamientos de actinobacterias solubilizadoras de fósforo obtenidas a partir de suelos de los andes orientales colombianos fueron identificadas por sus características morfológicas y por la secuenciación del gen 16S ADNr. El análisis BLASTN de las 15 secuencias obtenidas mostró que los aislamientos pertenecían al género <em>Streptomyces. </em>Paralelamente, los aislamientos fueron sometidos a la detección de ácidos orgánicos, durante el proceso de solubilización de fósforo con la presencia mayoritaria de los ácidos oxálico, cítrico y glucónico. Dentro de las cepas evaluadas <em>Streptomyces </em>sp. T3A fue seleccionada para ser evaluada bajo diferentes fuentes de fósforo inorgánico debido a los resultados de evaluaciones cualitativas y cuantitativas realizadas previamente, en las cuales mostró una actividad solubilizadora de fósforo significativamente alta. Los resultados evidenciaron la capacidad de ésta actinobacteria para solubilizar diferentes fuentes de fosfatos insolubles con valores de 122 mgP·L^-1paraCa₃(PO₄)₂, 14 mgP·L^-1para AlPO₄ y 19,6 mgP·L^-1 para roca fosfórica. También los ensayos revelaron que la actividad se mantiene en un rango de pH de 5 a 8 con las mismas fuentes de fosfatos evaluadas. Los resultados presentados contribuyen al avance en la caracterización de estas bacterias como promotoras de crecimiento vegetal con el fin de presentarlos como un recurso clave a nivel de biotecnología agrícola.</p><p class="MsoNormal" style="text-align: justify;"> </p><p><strong>Palabras clave:</strong> <em>Streptomyces</em>, Solubilización de fósforo, ácidos orgánicos, actinobacteria, HPLC.</p><p class="MsoNormal" style="text-align: justify;"> </p><p><strong>Abstrac: </strong>Fifteen isolates of Eastern Cordillera of the Colombian Andes were identified by morphological characteristics and 16S rDNA gene sequence. The BLAST analysis of 15 sequences shows that isolates belong to <em>Streptomyes</em>. Also we detected the organic acids in the solubilization process mainly oxalic acid, citric acid and gluconic acid.  <em>Streptomyces </em>sp. (T3A) was selected in preliminary qualitative and quantitative assays by the high phosphorus solubilizing activity; in this work we evaluate this strain with different forms of inorganic phosphate. The results evidenced the capacity of this actinobacteria to solubilize phosphorous showed 122 mgP•L^-1 Ca₃(PO₄)₂, 14 mgP•L^-1 AlPO₄ and 19,6 mgP•L^-1 for rock phosphate. Also the assays revealed that the activity was maintained between a pH range of 5 to 8 with the same sources of insoluble phosphates evaluated. These results contribute to characterize these strains as plant growth promotion bacteria and as key source in agricultural biotech.</p><p class="MsoNormal" style="text-align: justify;"> </p><p><strong>Key words: </strong><em>Streptomyces, </em>phosphate solubilization, organic acids, actinobacteria, HPLC.</p><p class="MsoNormal" style="text-align: justify;"> </p><p><strong>Recibido: </strong>octubre 10 de 2014<strong>  Aprobado:</strong> abril 28 de 2015</p>

Natural solution to antibiotic resistance: bacteriophages 'The Living Drugs'

Antibiotics have been a panacea in animal husbandry as well as in human therapy for decades. The huge amount of antibiotics used to induce the growth and protect the health of farm animals has lead to the evolution of bacteria that are resistant to the drug’s effects. Today, many researchers are working with bacteriophages (phages) as an alternative to antibiotics in the control of pathogens for human therapy as well as prevention, biocontrol, and therapy in animal agriculture. Phage therapy and biocontrol have yet to fulfill their promise or potential, largely due to several key obstacles to their performance. Several suggestions are shared in order to point a direction for overcoming common obstacles in applied phage technology. The key to successful use of phages in modern scientific, farm, food processing and clinical applications is to understand the common obstacles as well as best practices and to develop answers that work in harmony with nature.

Exploitation of phage battery in the search for bioactive actinomycetes

Screening of microbial natural products continues to represent an important route to the discovery of novel bioactive compounds for the development of new therapeutic agents, and actinomycetes are still the major producers of biopharmaceuticals. Selective isolation of bioactive actinomycete species, in particular the rare ones, has thus become a target for industrial microbiologists. In this context, bacteriophages have proven to be useful tools as (1) naturally present indicators of under-represented or rare actinomycete taxa in environmental samples, (2) indicators of the relatedness of bioactive taxa in target-directed search and discovery, (3) de-selection agents of unwanted taxa on isolation plates in target-specific search for rare actinomycete taxa, (4) tools in screening assays for specific targets. Against this background, a number of case studies are presented to illustrate the use of bacteriophages as tools in actinomycete-origin bioactive compound search and discovery programs.

Use of phage battery to investigate the actinofloral layers of termite gut microflora

AIMS

The termite gut microbiota can include a variety of micro-organisms from the three domains: Bacteria, Archaea and Eucarya. The bacterial groups from the gut systems are mainly affiliated to the proteobacteria, the Gram-positive groups Bacterioiodes/Flavobacterium branch and the spirochetes, Firmicutes and Actinobacteria. However, culture independent molecular studies have revealed that the majority of these microbial gut symbionts have not yet been cultured, including actinobacterial clusters associated with termite guts. Accordingly, the aim of this study was to selectively isolate the actinofloral layers of gut associated microflora of the Coptotermes lacteus (Froggatt) species located at the Sunshine Coast Region of Queensland, Australia to increase our knowledge on the diversity of actinobacterial taxa present in the termite guts.

METHODS AND RESULTS

Actinofloral layers associated with the guts of the wood-eating subterranean termite C. lacteus were investigated by exploiting the phage susceptibility of different gut associated bacteria which impede the growth of actinomycetes on isolation plates. These unwanted microbial taxa were removed by exposing the gut contents to polyvalent bacteriophages specifically targeting different background bacterial taxa and after their removal from the isolation plates previously undetected and novel actinomycetes were successfully cultured from the gut samples.

CONCLUSIONS

Use of bacteriophages as a means of selective pressure successfully revealed the presence of novel actinomycete species within the guts of C. lacteus.

SIGNIFICANCE AND IMPACT OF THE STUDY

Molecular ecology has undoubtedly revealed the fascinating diversity of micro-organisms, which cannot be cultured. However, these advances in the field still have not provided the ability to detect and isolate micro-organisms effectively from their ecological niches. Accordingly, studies like the one described here have importance in increasing the chances of uncultured taxa to be isolated to complement molecular microbial ecological efforts towards the establishment of an understanding on the diversity of termite gut microflora.

Rhizosphere-competent isolates of streptomycete and non-streptomycete actinomycetes capable of producing cell-wall-degrading enzymes to controlPythium aphanidermatumdamping-off disease of cucumber

Fifty-eight streptomycete and 35 non-streptomycete actinomycetes were isolated from cucumber rhizosphere soil. These isolates were screened for the production of cell-wall-degrading enzymes using mycelial ( Pythium aphanidermatum (Edson) Fitzp.) fragment agar. Eighteen promising isolates were screened for their competence as root colonizers. Eight isolates showing exceptional rhizosphere competence significantly inhibited, in vitro, P. aphanidermatum, the causal agent of postemergence damping-off of cucumber ( Cucumis sativus L.) seedlings. The four most inhibitory isolates ( Actinoplanes philippinensis Couch, Microbispora rosea Nonomura and Ohara, Micromonospora chalcea (Foulerton) Ørskov, and Streptomyces griseoloalbus (Kudrina) Pridham et al.) produced in vitro β-1,3-, β-1,4-, and β-1,6-glucanases and caused lysis of P. aphanidermatum hyphae. None of these produced volatile inhibitors or siderophores. Only S. griseoloalbus produced diffusible inhibitory metabolites, whilst A. philippinensis and Micromonospora chalcea parasitized the oospores of P. aphanidermatum. These four isolates were subsequently tested in the greenhouse, individually or as a mixture, for their ability to suppress damping-off of cucumber seedlings in soil with or without cellulose amendment. The treatment, which included all four isolates in soil amended with cellulose, was significantly superior to all other treatments in suppressing damping-off and was nearly as good as the metalaxyl treatment. Results show that there is a potential to use a mixture of antagonistic rhizosphere-competent actinomycetes along with cellulose amendment rather than fungicides for the field management of this disease. This is the first study that has involved the screening of rhizosphere-competent non-streptomycete actinomycetes capable of producing cell-wall-degrading enzymes, for the management of Pythium diseases.

Actinophages as indicators of actinomycete taxa in marine environments

It is necessary to continue to screen for new metabolites and evaluate the potential of less known and new bacterial taxa so that new and improved compounds for future use against drug-resistant bacteria or for chemical modification may be developed. There has been considerable interest in the detection and identification of marine microorganisms since they have been reported to produce bioactive compounds ranging from antitumour to antibacterial and antiviral agents. In this study, an improved technique that involves the exploitation of marine actinophages as indicators of the marine actinomycete taxa and uses marine bacteriophages as tools to reduce the numbers of common marine bacteria, which impedes the growth of rare actinomycetes on isolation plates, has been applied. This technique reduced the numbers of colony forming units of unwanted bacteria on isolation plates and hence increased the chances of detecting novel marine actinomycete genera for isolation and subsequent screening for antiviral activity.

Selective isolation of bioactive soil actinomycetes belonging to the Streptomyces violaceusniger phenotypic cluster

AIMS

To devise and evaluate a strategy for isolating members of the Streptomyces violaceusniger phenotypic cluster, which are known to be a promising source of bioactive metabolites.

METHODS AND RESULTS

The treatment of four soil samples with 1.5% phenol (30 degrees C, 30 min) prior to inoculation on humic acid-vitamin (HV) agar eliminated most of the streptomycetes and other bacterial populations. The surviving streptomycetes on the HV isolation plates were subcultured, and species-group identification was made according to the probabilistic identification system of Williams et al. (1989). Of the 133 streptomycetes subcultured, 102 (77%), were assigned to the S. violaceusniger cluster. A test with an overlay technique revealed that all of these S. violaceusniger-cluster isolates had broad antimicrobial spectra, as they inhibited the growth of all test Gram-positive bacteria, yeasts and filamentous fungi. Antitumour activity against colon carcinoma cells was found among 68 or 67%, of these S. violaceusniger-cluster isolates, following growth in submerged culture.

CONCLUSIONS

Chemical pretreatment of soil samples with phenol reduces the growth of ubiquitous Streptomyces species, thereby facilitating the recovery of less-abundant S. violaceusniger-cluster strains that are characterized by high antimicrobial and antitumour activities.

SIGNIFICANCE AND IMPACT OF THE STUDY

The development and application of new methodologies with which to selectively isolate rare, bioactive streptomycete groups is important for discovering novel secondary metabolites with bioactive properties.

Application of sucrose-gradient centrifugation for selective isolation of Nocardia spp. from soil

AIMS

To devise and evaluate a method for selective isolation of the less abundant actinomycetes, Nocardia spp. in soil.

METHODS AND RESULTS

This newly developed method is based on differentiating Nocardia from other actinomycete taxa by centrifugation. A water suspension of air-dried soil is centrifuged through a gradient consisting of 10, 20, 30, 40 and 50% sucrose at 240 x g for 30 min. The 20% sucrose layer, which is enriched with Nocardia spp., is then diluted and plated on humic acid-vitamin agar supplemented with antibacterial agents. The proposed method consistently achieved selective isolation of Nocardia spp. in all 14 soil samples tested, which accounted for 5-89% of the total microbial population recovered. Tentative taxonomic characterization based on a restriction fragment length polymorphism (RFLP) analysis of the 16S ribosomal DNA suggested that many of the soil isolates could belong to N. asteroides, N. salmonicida or N. uniformis.

CONCLUSIONS

Differential centrifugation can successfully and efficiently isolate soil Nocardia populations that are suppressed by conventional dilution plating approaches.

SIGNIFICANCE AND IMPACT OF THE STUDY

The development and application of new methodologies with which to isolate less-explored actinomycete taxa is important for improving our knowledge about their taxonomy, ecology and industrial applications.

Application of actinomycetes to soil to ameliorate water repellency

AIMS

The aim of this study was to develop a novel isolation technique using a mixture of Bacillus and Streptomyces phages to selectively isolate wax-utilizing non-streptomycete actinomycetes effective in ameliorating water repellency in a problem soil.

METHODS AND RESULTS

Phages added to a soil suspension reduced the dominance of Bacillus and Streptomyces isolates and significantly increased the number of non-streptomycete actinomycetes on isolation plates. Promising isolates, grown on a medium containing beeswax as sole carbon source, were selected for application to water repellent soil. Their addition significantly reduced water repellency.

CONCLUSIONS

Phage application significantly increased the isolation of non-streptomycete actinomycetes. Wax-utilizing isolates were found to significantly reduce water repellency in a problem soil.

SIGNIFICANCE AND IMPACT OF THE STUDY

The phage technique can be used for the routine isolation of non-streptomycete actinomycetes. Beeswax medium can be used to selectively isolate wax-utilizing micro-organisms with the potential to ameliorate water repellency in soil.

Isolation of Dermatophilus congolensis phage from the 'lumpy wool' of sheep in Western Australia

A lytic phage with species-specific activity was isolated from wool samples infected with the actinomycete Dermatophilus congolensis, the agent of 'lumpy wool', collected from properties in Western Australia. The physiochemical properties, plaque morphology, host range and particle morphology of the phage isolated were characterized. The isolated phage reduced the cell numbers of Dermatophilus congolensis on infected wool samples in vitro. It may therefore have potential as a biocontrol agent of dermatophilosis.