Habitats of rare actinobacteria.
Abstract
Actinobacteria have exceptional metabolic diversity and are a rich source of several useful bioactive natural products. Most of these have been derived from Streptomyces, the dominant genus of Actinobacteria. Hence, it is necessary to explore rare actinobacteria for the production of novel bioactive compounds. Amongst the novel metabolites, anti-quorum-sensing agents, which can curb infection without killing pathogens, are gaining importance. Not many studies are targeting anti-quorum-sensing agents from rare actinobacteria and this research area is still in its infancy. This field may lead to novel bioactive compounds that can act against bacterial quorum-sensing systems. These agents can attenuate the virulence of the pathogens without challenging their growth, thereby preventing the emergence of resistant strains and facilitating the elimination of pathogens by the host’s immune system. Therefore, this chapter describes the general characteristics and habitats of rare actinobacteria, isolation and cultivation methods, the methods of screening rare actinobacteria for anti-quorum sensing compounds, methods of evaluation of their properties, and future prospects in drug discovery.
Keywords
- rare actinobacteria
- quorum sensing
- anti-quorum-sensing compounds
- swarming
- biofilm
1. Introduction
Most of these antibiotics in clinical use today have been developed from compounds isolated from
Recent evidence has demonstrated that rare actinobacteria, might represent a unique source of novel biologically active compounds, and methods designed to isolate and identify a wide variety of such actinobacteria have been developed. These methods include a variety of pre-treatment techniques in combination with appropriately supplementing selective agar media with specific antimicrobial agents.
At present, not more than 50 rare actinobacterial taxa are reported to produce 2500 bioactive compounds [5]. Thus, it is crucial that new groups of rare actinobacteria be pursued as sources of novel pharmaceutically active metabolites. Amongst the novel metabolites, anti-quorum sensing (AQS) agents, which can curb infection without a killing action, are gaining importance. Bacterial cell–cell communication, dubbed quorum sensing, is intricately related to virulence. An associated phenomenon is bacterial swarming which allows the spread of disease and virulence.
The discovery that many pathogenic bacteria employ quorum sensing (QS) to regulate their pathogenicity and virulence factor production makes the QS system an attractive target for antimicrobial therapy. Targeting the pathogenesis instead of killing the organism may provide less selective pressure for the development of resistance. Therefore, it has been suggested that inactivating the QS system in bacteria using QS inhibitors holds great promise for the treatment of infectious diseases. These compounds can attenuate the virulence of the pathogens without challenging their growth, thereby preventing the emergence of resistant strains and facilitating the elimination of pathogens by the host’s immune system. Therefore, a search for anti-quorum-sensing agents as attractive alternatives to treat infection has become logical and gathered momentum [6].
Although antimicrobial properties of actinobacteria have been extensively studied, less is known about AQS activities of rare actinobacteria which may be a rich source of active compounds that can act against bacterial quorum-sensing systems.
2. Defining rare Actinobacteria
Rare Actinobacteria are defined as certain types of Actinobacteria which are abundant in various habitats but are difficult to isolate [7]. These include all non-
Members of the genus
3. Habitats of rare Actinobacteria
Actinobacteria inhabit a wide range of habitats with diverse climatic conditions, including those of extreme temperatures and pH as well as marine waters, deserts and soil [23]. However, they are mainly found in soil. It is also observed that even though actinobacteria are found in all layers of soil, their density decreases with increasing depth [24]. Environmental factors such as pH of the soil, humus content and soil type directly influence the population density and type of rare actinobacteria present [7]. Table 1 summarizes a few rare actinobacteria isolated from various habitats.
Habitat | Genus | Reference |
---|---|---|
Forest Soil | [25, 26, 27, 28, 29] | |
Desert Soil | [30, 31, 32, 33] | |
Garden Soil | [34] | |
Alkaline soil | [35, 36] | |
Soil sample from Oil springs | [37] | |
Sandy Soil | [38, 39, 40] | |
Farmland Soil | [41, 42] | |
Saline Soil | [43, 44, 45, 46, 47] | |
Soil from tropical rainforest | [48, 49, 50, 51, 52] | |
Soil sample from Paddy fields | [53, 54, 55] | |
Soil near wastewater Treatment facility/Activated Sludge | [56, 57, 58, 59] | |
Dried Seaweed | [60, 61, 62, 63] | |
Marine Water | [64, 65, 66, 67, 68] | |
Caves | [69, 70, 71] | |
Roots of Plants | [71, 72, 73, 74, 75, 76] | |
Leaves of Plants | [77, 78, 79] | |
Stems of Plants | [80, 81, 82, 83] | |
Glaciers | [84, 85, 86] | |
Volcanic rocks | [87, 88] |
4. Isolation of rare Actinobacteria
4.1 Pretreatment methods
Isolation of rare actinobacteria is a strenuous task, mainly because they are slow growing. After collection of samples, the type of pretreatment method used decides the viability and isolation of the species under study. While several types of pretreatment methods are available, the requirement of each organism is different. A few common methods include suspending samples in distilled water followed by incubation in a rotary shaker, air drying the samples, or heat treatment in oven at 45֯C–65֯C [89].
Pretreatment method | Type of Actinobacteria | Antibiotic for selective isolation | Suggested isolation media | Reference |
---|---|---|---|---|
| Thermophilic Actinobacteria | Cycloheximide, Kanamycin | Czapeck medium, glycerol asparagine medium, Oatmeal medium | [92, 93] |
Halophilic and Alkalophilic actinobacteria | Nalidixic acid | Starch-casein agar, glycerol asparagine medium, T3 medium, | [30, 94] | |
Acidophilic Actinobacteria | Cycloheximide, Nystatin | ISP4, ISP2, Acidified oatmeal agar and modified Bennett’s agar | [95, 96] | |
Actinobacteria from Plant origins | Pimaricin, penicillin G and polymyxin B | Sodium Propionate medium, Yeast extract medium, ISP2, ISP3, Potato dextrose agar | [97, 98] | |
Actinobacteria from Soil | Actidione, Nystatin | HV Agar, Glycerol-arginine medium, Medium supplied with superoxide dismutase, PDA | [30, 99, 100] | |
Marine Actinobacteria | Cycloheximide, Nystatin | Glycerol-asparagine, Glycerol-glycine, Chitin, Starch-Casein | [101, 102, 103] | |
Rare Actinobacteria | Nystatin | HV, HP, Trehalose-Proline agar, ISP5, B4, | [89, 104] |
4.2 Use of antibiotics for selective isolation
Pretreatments do reduce a fraction of unwanted predominant fast-growing organisms. However, use of antibiotics in isolation media along with pretreatment substantially increases the chances of selective isolation as it effectively eliminates fast growing and competitive bacteria. By virtue of this property, antibiotics like gentamicin and novobiocin were successfully used to isolate members of the genus
4.3 Use of specific isolation media
It is observed that the growth of rare actinobacteria is highly sensitive to contamination by some known fast-growing organisms such as fungus, other bacteria and a few common streptomyces. Hence conventional methods of isolation are ineffective in isolating rare actinobacteria and there is a need to find more advanced and highly selective isolation methods [24]. Studies have shown that in abundance of nutrients, Actinobacteria prefer exponential growth over the production of secondary metabolite [105]. It is also reported that enzymes for secondary metabolite production are inhibited in presence of glucose [106]. Factors such as the type of chemical or physical pre-treatment used [24], pH, temperature and duration of incubation as well as sources of essential nutrients used greatly affect the rate of growth of rare actinomycetes as well as metabolite production [107]. Effect of each of these factors should be considered while designing a culture medium.
A carbon source can thus either be suitable for growth or for metabolite production but not both. Generally, monosaccharides or sugars that are metabolized rapidly are found to be most suitable for growth while polysaccharides or sugars that metabolize slowly are more suitable for antibiotic production [107]. A comparison between inorganic and organic nitrogen sources used revealed that use of organic nitrogen source resulted in maximum growth as well as metabolite production [104]. Evidences have shown that antibiotic accumulation increases as soon as the nitrogen source used in medium is entirely utilized by the organism [108]. Addition of excess inorganic phosphates resulted in rapid growth since it aids the consumption of Carbon and Nitrogen sources as well as accelerates the rate of cellular respiration but it lowers the production of secondary metabolites [109].
Antibiotic production begins extensively in mid log and late log phase and is continuous in the stationary phase of bacterial growth curve [110]. Multiple studies done on various species of actinobacteria suggest that, antibiotic production is maximum at neutral pH [111] and temperature of 30°C [112, 113]. Further, requirement of other important constituents of growth medium such as trace metals and minerals vary with species and culture conditions.
Apart from all the above-mentioned common isolation media, the requirement of each bacterium is different and hence the selective media should be designed keeping in mind the nutritional requirements of target organism. In order to facilitate the process of designing selective isolation media, information from various taxonomic, phenotypic and antibiotic sensitivity databases can be used [97].
5. Anti-quorum sensing
Quorum sensing is a mechanism of cell-to-cell communication seen in bacteria which occurs by the means of certain autoinducer or chemical signal molecules. The concentration of these autoinducer molecules increases with increase in cell density. Once a certain threshold concentration is reached, these autoinducer molecules lead to alteration of gene expression in the population [114]. It is now known that quorum sensing is the underlying mechanism of a wide spectrum of bacterial physiological processes such as virulence [115, 116], bioluminescence [117], motility [118], sporulation [119], conjugation [120], development of genetic competence [121] as well as synthesis of antibiotics [122].
Considering the implications of quorum sensing in various aspects of bacterial life processes, it is evident that inhibiting quorum sensing could have potential therapeutic applications [123, 124]. There are various strategies in which the quorum sensing pathways can be inhibited. Together, they are called as quorum-quenching and the compounds or molecules used to do so are called as AQS compounds. Strategies used in quorum quenching include: Inhibition of synthesis of autoinducer molecule, designing analogues of autoinducer molecule or receptor analogues [125] and antibody or enzyme catalyzed hydrolysis of autoinducer molecule [126].
N-acyl homoserine lactones (AHLs) are an important class of signaling molecules produced by Gram negative bacteria which are known to govern the population density [127]. Lactonases are the enzymes which hydrolyse either the amide linkage between lactone and acyl side chain or affects the ester bond thereby inhibiting the signaling molecule [128]. Further, acylases [129] and oxidoreductases [130] are also found to have quorum quenching activities. Degradation of signaling molecules is also possible via antibody mediated catalysis.
6. Methods of screening and evaluation of anti-quorum sensing compounds isolated from rare Actinobacteria
While the method of preparation of bacterial extracts remains the same, various conventional and virtual screening methods are used to screen compounds for their AQS activity.
6.1 Pigment inhibition assays
Formation of violacein, a purple pigment in the reporter strain
6.2 Swarming motility and biofilm formation assays
Swarming and biofilm formation are other quorum sensing controlled processes seen in bacteria such as
6.3 Molecular and physiochemical methods
Genes encoding polyketide synthase I and II (PKS-I and PKS-II), and nonribosomal peptide synthetases (NRPS), are responsible for synthesis of novel AQS compounds in rare actinobacteria [138, 144]. PCR Screening of a given bacterium for these genes is helpful in detecting the presence of quorum quenching activity [145]. Purified compounds isolated from the broth cultures of such bacteria can be further subjected to Physiochemical screening methods such as UV–Vis spectrophotometry, TLC to determine the nature of compound which exhibits AQS activity [138]. Some strains of
6.4 In silico screening methods
Biosynthetic gene clusters in a given bacteria can be identified using genome mining studies. 20 biosynthetic gene clusters are reported in a single strain of
7. Conclusion
Though work on Rare actinobacteria and bioactive compounds from them is gathering momentum, not many studies are targeted towards isolation and identification of AQS compounds from rare actinobacteria and this research area is still in its infancy. These studies may lead to novel bioactive compounds that can act against bacterial quorum sensing systems. These agents can attenuate the virulence of the pathogens without challenging their growth, thereby preventing the emergence of resistant strains.
Such potent anti-quorum -sensing compounds may lead to the development of alternative therapies to address the glaring problem of antibiotic resistance.
This would be of immense medical and commercial benefit.
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