Competition-Mediated Antibiotic Induction in the Marine Bacterium Streptomyces tenjimariensis

Conjugative type IV secretion systems enable bacterial antagonism that operates independently of plasmid transfer

Bacterial cooperation and antagonism mediated by secretion systems are among the ways in which bacteria interact with one another. Here we report the discovery of an antagonistic property of a type IV secretion system (T4SS) sourced from a conjugative plasmid, RP4, using engineering approaches. We scrutinized the genetic determinants and suggested that this antagonistic activity is independent of molecular cargos, while we also elucidated the resistance genes. We further showed that a range of Gram-negative bacteria and a mixed bacterial population can be eliminated by this T4SS-dependent antagonism. Finally, we showed that such an antagonistic property is not limited to T4SS sourced from RP4, rather it can also be observed in a T4SS originated from another conjugative plasmid, namely R388. Our results are the first demonstration of conjugative T4SS-dependent antagonism between Gram-negative bacteria on the genetic level and provide the foundation for future mechanistic studies.

Interactions of Different Streptomyces Species and Myxococcus xanthus Affect Myxococcus Development and Induce the Production of DK-Xanthenes

The co-culturing of microorganisms is a well-known strategy to study microbial interactions in the laboratory. This approach facilitates the identification of new signals and molecules produced by one species that affects other species' behavior. In this work, we have studied the effects of the interaction of nine Streptomyces species (S. albidoflavus, S. ambofaciens, S. argillaceus, S. griseus, S. lividans, S. olivaceus, S. parvulus, S. peucetius, and S. rochei) with the predator bacteria Myxococcus xanthus, five of which (S. albidoflavus, S. griseus, S. lividans, S. olivaceus, and S. argillaceus) induce mound formation of M. xanthus on complex media (Casitone Yeast extract (CYE) and Casitone tris (CTT); media on which M. xanthus does not form these aggregates under normal culture conditions. An in-depth study on S. griseus-M. xanthus interactions (the Streptomyces strain producing the strongest effect) has allowed the identification of two siderophores produced by S. griseus, demethylenenocardamine and nocardamine, responsible for this grouping effect over M. xanthus. Experiments using pure commercial nocardamine and different concentrations of FeSO4 show that iron depletion is responsible for the behavior of M. xanthus. Additionally, it was found that molecules, smaller than 3 kDa, produced by S. peucetius can induce the production of DK-xanthenes by M. xanthus.

Ribosome-binding antibiotics increase bacterial longevity and growth efficiency

Antibiotics, by definition, reduce bacterial growth rates in optimal culture conditions; however, the real-world environments bacteria inhabit see rapid growth punctuated by periods of low nutrient availability. How antibiotics mediate population decline during these periods is poorly understood. Bacteria cannot optimize for all environmental conditions because a growth-longevity tradeoff predicts faster growth results in faster population decline, and since bacteriostatic antibiotics slow growth, they should also mediate longevity. We quantify how antibiotics, their targets, and resistance mechanisms influence longevity using populations of Escherichia coli and, as the tradeoff predicts, populations are maintained for longer if they encounter ribosome-binding antibiotics doxycycline and erythromycin, a finding that is not observed using antibiotics with alternative cellular targets. This tradeoff also predicts resistance mechanisms that increase growth rates during antibiotic treatment could be detrimental during nutrient stresses, and indeed, we find resistance by ribosomal protection removes benefits to longevity provided by doxycycline. We therefore liken ribosomal protection to a "Trojan horse" because it provides protection from an antibiotic but, during nutrient stresses, it promotes the demise of the bacteria. Seeking mechanisms to support these observations, we show doxycycline promotes efficient metabolism and reduces the concentration of reactive oxygen species. Seeking generality, we sought another mechanism that affects longevity and we found the number of doxycycline targets, namely, the ribosomal RNA operons, mediates growth and longevity even without antibiotics. We conclude that slow growth, as observed during antibiotic treatment, can help bacteria overcome later periods of nutrient stress.

Physiological and metabolic traits of Taxol biosynthesis of endophytic fungi inhabiting plants: Plant-microbial crosstalk, and epigenetic regulators

Attenuating the Taxol productivity of fungi with the subculturing and storage under axenic conditions is the challenge that halts the feasibility of fungi to be an industrial platform for Taxol production. This successive weakening of Taxol productivity by fungi could be attributed to the epigenetic down-regulation and molecular silencing of most of the gene clusters encoding Taxol biosynthetic enzymes. Thus, exploring the epigenetic regulating mechanisms controlling the molecular machinery of Taxol biosynthesis could be an alternative prospective technology to conquer the lower accessibility of Taxol by the potent fungi. The current review focuses on discussing the different molecular approaches, epigenetic regulators, transcriptional factors, metabolic manipulators, microbial communications and microbial cross-talking approaches on restoring and enhancing the Taxol biosynthetic potency of fungi to be industrial platform for Taxol production.

Effects of Trichoderma atroviride SG3403 and Bacillus subtilis 22 on the Biocontrol of Wheat Head Blight

Wheat head blight caused by Fusarium graminearum is one of the major wheat diseases in the world; therefore, it is very significant to develop an effective and environmentally friendly microbial fungicide against it. Trichoderma atroviride and Bacillus subtilis are widely applied biocontrol microorganisms with separate advantages; however, little work has been conducted for synergistically elevating the effects of biocontrol and plant promotion through the co-cultivation of the two microorganisms. Our study demonstrated that T. atroviride SG3403 is compatible with B. subtilis 22. The co-culture metabolites contained a group of antagonistic compounds which were able to inhibit F. graminearum growth and increase the activities of pathogen G protein and mitogen-activated protein kinase (MAPK) as compared with axenic culture metabolites. Additionally, the co-culture metabolites enabled us to more significantly decrease the production of gibberellin (GA), deoxynivalenol (DON), and zearalenone (ZEN) from F. graminearum, which disorganized the subcellular structure, particularly the cytoplasm of F. graminearum hyphae, relative to the axenically cultured metabolites. Furthermore, the seed-coating agent made by the co-culture had significant effects against F. graminearum infection by triggering the expression of host plant defensive genes, including PR1, PR3, PR4, PR5, ACS, and SOD. It is suggested that jasmonic acid and ethylene (JA/ET) signaling might dominate wheat's induced systemic resistance (ISR) against wheat head blight. A dry, powdered bio-seed coating agent containing the co-culture mixtures was confirmed to be a bioavailable formulation that can be applied to control wheat head blight. Taken together, the co-culture's metabolites or the metabolites and living cells might provide a basis for the further development of a new kind of microbial bio-fungicide in the future.

Production of secondary metabolites in stirred tank bioreactor co-cultures of Streptomyces noursei and Aspergillus terreus

The focus of the study was to characterize the bioprocess kinetics and secondary metabolites production in the novel microbial co-cultivation system involving Streptomyces noursei ATCC 11455 (the producer of an antifungal substance known as nystatin) and Aspergillus terreus ATCC 20542 (the source of lovastatin, a cholesterol-lowering drug). The investigated “A. terreus vs. S. noursei” stirred tank bioreactor co-cultures allowed for the concurrent development and observable biosynthetic activity of both species. In total, the production profiles of 50 secondary metabolites were monitored over the course of the study. The co-cultures were found to be effective in terms of enhancing the biosynthesis of several metabolic products, including mevinolinic acid, an acidic form of lovastatin. This work provided a methodological example of assessing the activity of a given strain in the co-culture by using the substrates which can be metabolized exclusively by this strain. Since S. noursei was shown to be incapable of lactose utilization, the observed changes in lactose levels were attributed to A. terreus and thus confirmed its viability. The study was complemented with the comparative microscopic observations of filamentous morphologies exhibited in the co-cultures and corresponding monocultures.

Adaptive laboratory evolution triggers pathogen-dependent broad-spectrum antimicrobial potency in Streptomyces

BACKGROUND

In the present study, adaptive laboratory evolution was used to stimulate antibiotic production in a Streptomyces strain JB140 (wild-type) exhibiting very little antimicrobial activity against bacterial pathogens. The seven different competition experiments utilized three serial passages (3 cycles of adaptation-selection of 15 days each) in which Streptomyces strain (wild-type) was challenged repeatedly to one (bi-culture) or two (tri-culture) or three (quadri-culture) target pathogens. The study demonstrates a simple laboratory model to study the adaptive potential of evolved phenotypes and genotypes in Streptomyces to induce antibiotic production.

RESULTS

Competition experiments resulted in the evolution of the wild-type Streptomyces strain JB140 into the seven unique mutant phenotypes that acquired the ability to constitutively exhibit increased antimicrobial activity against three bacterial pathogens Salmonella Typhi (NCIM 2051), Staphylococcus aureus (NCIM 2079), and Proteus vulgaris (NCIM 2027). The mutant phenotypes not only effectively inhibited the growth of the tested pathogens but were also observed to exhibit improved antimicrobial responses against one clinical multidrug-resistant (MDR) uropathogenic Escherichia coli (UPEC 1021) isolate. In contrast to the adaptively evolved mutants, only a weak antimicrobial activity was detected in the wild-type parental strain. To get molecular evidence of evolution, RAPD profiles of the wild-type Streptomyces and its evolved mutants were compared which revealed significant polymorphism among them.

CONCLUSION

The competition-based adaptive laboratory evolution method can constitute a platform for evolutionary engineering to select improved phenotypes (mutants) with increased antibacterial profiles against targeted pathogens.

The evolution of strategy in bacterial warfare via the regulation of bacteriocins and antibiotics

Bacteria inhibit and kill one another with a diverse array of compounds, including bacteriocins and antibiotics. These attacks are highly regulated, but we lack a clear understanding of the evolutionary logic underlying this regulation. Here, we combine a detailed dynamic model of bacterial competition with evolutionary game theory to study the rules of bacterial warfare. We model a large range of possible combat strategies based upon the molecular biology of bacterial regulatory networks. Our model predicts that regulated strategies, which use quorum sensing or stress responses to regulate toxin production, will readily evolve as they outcompete constitutive toxin production. Amongst regulated strategies, we show that a particularly successful strategy is to upregulate toxin production in response to an incoming competitor’s toxin, which can be achieved via stress responses that detect cell damage (competition sensing). Mirroring classical game theory, our work suggests a fundamental advantage to reciprocation. However, in contrast to classical results, we argue that reciprocation in bacteria serves not to promote peaceful outcomes but to enable efficient and effective attacks.

A bioprocess perspective on the production of secondary metabolites by Streptomyces in submerged co-cultures

Filamentous microorganisms are potent sources of bioactive secondary metabolites, the molecules formed in response to complex environmental signals. The chemical diversity encoded in microbial genomes is only partially revealed by following the standard microbiological approaches. Mimicking the natural stimuli through laboratory co-cultivation is one of the most effective methods of awakening the formation of high-value metabolic products. Whereas the biosynthetic outcomes of co-cultures are reviewed extensively, the bioprocess aspects of such efforts are often overlooked. The aim of the present review is to discuss the submerged co-cultivation strategies used for triggering and enhancing secondary metabolites production in Streptomyces, a heavily investigated bacterial genus exhibiting an impressive repertoire of secondary metabolites, including a vast array of antibiotics. The previously published studies on influencing the biosynthetic capabilities of Streptomyces through co-cultivation are comparatively analyzed in the bioprocess perspective, mainly with the focus on the approaches of co-culture initiation, the experimental setup, the design of experimental controls and the ways of influencing the outcomes of co-cultivation processes. These topics are discussed in the general context of secondary metabolites production in submerged microbial co-cultures by referring to the Streptomyces-related studies as illustrative examples.

Genetic variation is associated with differences in facilitative and competitive interactions in the Rhizobium leguminosarum species complex

Competitive and facilitative interactions influence bacterial community composition, diversity and functioning. However, the role of genetic diversity for determining interactions between coexisting strains of the same, or closely related, species remains poorly understood. Here, we investigated the type (facilitative/inhibitory) and potential underlying mechanisms of pairwise interactions between 24 genetically diverse bacterial strains belonging to three genospecies (gsA,C,E) of the Rhizobium leguminosarum species complex. Interactions were determined indirectly, based on secreted compounds in cell-free supernatants, and directly, as growth inhibition in cocultures. We found supernatants mediated both facilitative and inhibitory interactions that varied greatly between strains and genospecies. Overall, gsE strains indirectly suppressed growth of gsA strains, while their own growth was facilitated by other genospecies' supernatants. Similar genospecies-level patterns were observed in direct competition, where gsA showed the highest susceptibility and gsE the highest inhibition capacity. At the genetic level, increased gsA susceptibility was associated with a non-random distribution of quorum sensing and secondary metabolite genes across genospecies. Together, our results suggest that genetic variation is associated with facilitative and competitive interactions, which could be important ecological mechanisms explaining R. leguminosarum diversity.

Discovery of novel secondary metabolites encoded in actinomycete genomes through coculture

Actinomycetes are a rich source of bioactive natural products important for novel drug leads. Recent genome mining approaches have revealed an enormous number of secondary metabolite biosynthetic gene clusters (smBGCs) in actinomycetes. However, under standard laboratory culture conditions, many smBGCs are silent or cryptic. To activate these dormant smBGCs, several approaches, including culture-based or genetic engineering-based strategies, have been developed. Above all, coculture is a promising approach to induce novel secondary metabolite production from actinomycetes by mimicking an ecological habitat where cryptic smBGCs may be activated. In this review, we introduce coculture studies that aim to expand the chemical diversity of actinomycetes, by categorizing the cases by the type of coculture partner. Furthermore, we discuss the current challenges that need to be overcome to support the elicitation of novel bioactive compounds from actinomycetes.

An Analysis of Biosynthesis Gene Clusters and Bioactivity of Marine Bacterial Symbionts

Symbiotic marine bacteria have a pivotal role in drug discovery due to the synthesis of diverse biologically potential compounds. The marine bacterial phyla proteobacteria, actinobacteria and firmicutes are commonly associated with marine macro organisms and frequently reported as dominant bioactive compound producers. They can produce biologically active compounds that possess antimicrobial, antiviral, antitumor, antibiofilm and antifouling properties. Synthesis of these bioactive compounds is controlled by a set of genes of their genomes that is known as biosynthesis gene clusters (BGCs). The development in the field of biotechnology and bioinformatics has uncovered the potential BGCs of the bacterial genome and its functions. Now-a-days researchers have focused their attention on the identification of potential BGCs for the discovery of novel bioactive compounds using advanced technology. This review highlights the marine bacterial symbionts and their BGCs which are responsible for the synthesis of bioactive compounds.

Phytoplankton trigger the production of cryptic metabolites in the marine actinobacterium Salinispora tropica

Filamentous members of the phylum Actinobacteria are a remarkable source of natural products with pharmaceutical potential. The discovery of novel molecules from these organisms is, however, hindered because most of the biosynthetic gene clusters (BGCs) encoding these secondary metabolites are cryptic or silent and are referred to as orphan BGCs. While co-culture has proven to be a promising approach to unlock the biosynthetic potential of many microorganisms by activating the expression of these orphan BGCs, it still remains an underexplored technique. The marine actinobacterium Salinispora tropica, for instance, produces valuable compounds such as the anti-cancer molecule salinosporamide but half of its putative BGCs are still orphan. Although previous studies have used marine heterotrophs to induce orphan BGCs in Salinispora, its co-culture with marine phototrophs has yet to be investigated. Following the observation of an antimicrobial activity against a range of phytoplankton by S. tropica, we here report that the photosynthate released by photosynthetic primary producers influences its biosynthetic capacities with production of cryptic molecules and the activation of orphan BGCs. Our work, using an approach combining metabolomics and proteomics, pioneers the use of phototrophs as a promising strategy to accelerate the discovery of novel natural products from marine actinobacteria.

Streptomyces griseus: A new biocatalyst with N-oxygenase activity

Aromatic nitro compounds are key building blocks for many industrial syntheses and are also components of explosives, drugs and pesticides. Due to the environmentally unfriendly experimental conditions involved in their chemical syntheses, industrial processes would benefit from the use of biocatalysts. Among potentially useful enzymes, N-oxygenases, whose role is to oxygenate primary amines, are becoming relevant. These enzymes are involved in different secondary metabolic pathways in Streptomyces and in few other bacteria, forming part of the enzyme pools implicated in antibiotic synthesis. In this work, a group of Streptomyces strains, whose biomass was obtained from simple and novel culture media, were identified as new sources of N-oxygenase activity. Furthermore, the use of unspecific metabolic stimulation strategies allowed substantial improvements in the activity of whole cells as biocatalysts. It is remarkable the 6 to 50-fold increase in nitro compound yields compared to the biotransformation under standard conditions when Streptomyces griseus was the biocatalyst. In addition, biocatalyst substrate acceptance was studied in order to determine the biocatalytic potential of this enzyme.

Antibiotic drug discovery: Challenges and perspectives in the light of emerging antibiotic resistance

Amid a rising threat of antimicrobial resistance in a global scenario, our huge investments and high-throughput technologies injected for rejuvenating the key therapeutic scaffolds to suppress these rising superbugs has been diminishing severely. This has grasped world-wide attention, with increased consideration being given to the discovery of new chemical entities. Research has now proven that the relatively tiny and simpler microbes possess enhanced capability of generating novel and diverse chemical constituents with huge therapeutic leads. The usage of these beneficial organisms could help in producing new chemical scaffolds that govern the power to suppress the spread of obnoxious superbugs. Here in this review, we have explicitly focused on several appealing strategies employed for the generation of new chemical scaffolds. Also, efforts on providing novel insights on some of the unresolved questions in the production of metabolites, metabolic profiling and also the serendipity of getting "hit molecules" have been rigorously discussed. However, we are highly aware that biosynthetic pathway of different classes of secondary metabolites and their biosynthetic route is a vast topic, thus we have avoided discussion on this topic.

Effects of addition of elicitors on rimocidin biosynthesis in Streptomyces rimosus M527

The polyene macrolide rimocidin, produced by Streptomyces rimosus M527, is highly effective against a broad range of fungal plant pathogens, but at low yields. Elicitation is an effective method of stimulating the yield of bioactive secondary metabolites. In this study, the biomass and filtrate of a culture broth of Escherichia coli JM109, Bacillus subtilis WB600, Saccharomyces cerevisiae, and Fusarium oxysporum f. sp. cucumerinum were employed as elicitors to promote rimocidin production in S. rimosus M527. Adding culture broth and biomass of S. cerevisiae (A3) and F. oxysporum f. sp. cucumerinum (B4) resulted in an increase of rimocidin production by 51.2% and 68.3% respectively compared with the production under normal conditions in 5-l fermentor. In addition, quantitative RT-PCR analysis revealed that the transcriptions of ten genes (rimA to rimK) located in the gene cluster involved in rimocidin biosynthesis in A3 or B4 elicitation experimental group were all higher than those of a control group. Using a β-glucuronidase (GUS) reporter system, GUS enzyme activity assay, and Western blot analysis, we discovered that elicitation of A3 or B4 increased protein synthesis in S. rimosus M527. These results demonstrate that the addition of elicitors is a useful approach to improve rimocidin production.Key Points • An effective strategy for enhancing rimocidin production in S. rimosus M527 is demonstrated. • Overproduction of rimocidin is a result of higher expressed structural genes followed by an increase in protein synthesis.

Inhibitory interaction networks among coevolved Streptomyces populations from prairie soils

Soil microbes live within highly complex communities, where community composition, function, and evolution are the product of diverse interactions among community members. Analysis of the complex networks of interactions within communities has the potential to shed light on community stability, functioning, and evolution. However, we have little understanding of the variation in interaction networks among coevolved soil populations. We evaluated networks of antibiotic inhibitory interactions among sympatric Streptomyces communities from prairie soil. Inhibition networks differed significantly in key network characteristics from expectations under null models, largely reflecting variation among Streptomyces in the number of sympatric populations that they inhibited. Moreover, networks of inhibitory interactions within Streptomyces communities differed significantly from each other, suggesting unique network structures among soil communities from different locations. Analyses of tri-partite interactions (triads) showed that some triads were significantly over- or under- represented, and that communities differed in ‘preferred’ triads. These results suggest that local processes generate distinct structures among sympatric Streptomyces inhibition networks in soil. Understanding the properties of microbial interaction networks that generate competitive and functional capacities of soil communities will shed light on the ecological and coevolutionary history of sympatric populations, and provide a foundation for more effective management of inhibitory capacities of soil microbial communities.

Activation of silent biosynthetic pathways and discovery of novel secondary metabolites in actinomycetes by co-culture with mycolic acid-containing bacteria

Bacterial secondary metabolites (SM) are rich sources of drug leads, and in particular, numerous metabolites have been isolated from actinomycetes. It was revealed by recent genome sequence projects that actinomycetes harbor much more secondary metabolite-biosynthetic gene clusters (SM-BGCs) than previously expected. Nevertheless, large parts of SM-BGCs in actinomycetes are dormant and cryptic under the standard culture conditions. Therefore, a widely applicable methodology for cryptic SM-BGC activation is required to obtain novel SM. Recently, it was discovered that co-culturing with mycolic-acid-containing bacteria (MACB) widely activated cryptic SM-BGCs in actinomycetes. This "combined-culture" methodology (co-culture methodology using MACB as the partner of actinomycetes) is easily applicable for a broad range of actinomycetes, and indeed, 33 novel SM have been successfully obtained from 12 actinomycetes so far. In this review, the development, application, and mechanistic analysis of the combined-culture method were summarized.

The role of inter-species interactions in Salinispora specialized metabolism

Bacterial genome sequences consistently contain many more biosynthetic gene clusters encoding specialized metabolites than predicted by the compounds discovered from the respective strains. One hypothesis invoked to explain the cryptic nature of these gene clusters is that standard laboratory conditions do not provide the environmental cues needed to trigger gene expression. A potential source of such cues is other members of the bacterial community, which are logical targets for competitive interactions. In this study, we examined the effects of such interactions on specialized metabolism in the marine actinomycete Salinispora tropica. The results show that antibiotic activities and the concentration of some small molecules increase in the presence of co-occurring bacterial strains relative to monocultures. Some increases in antibiotic activity could be linked to nutrient depletion by the competitor as opposed to the production of a chemical cue. Other increases were correlated with the production of specific compounds by S. tropica. In particular, one interaction with a Vibrio sp. consistently induced antibiotic activity and was associated with parent ions that were unique to this interaction, although the associated compound could not be identified. This study provides insight into the metabolomic complexities of bacterial interactions and baseline information for future genome mining efforts.

Allelopathy-mediated competition in microbial mats from Antarctic lakes

Microbial mats are vertically stratified communities that host a complex consortium of microorganisms, dominated by cyanobacteria, which compete for available nutrients and environmental niches, within these extreme habitats. The Antarctic Dry Valleys near McMurdo Sound include a series of lakes within the drainage basin that are bisected by glacial traverses. These lakes are traditionally independent, but recent increases in glacial melting have allowed two lakes (Chad and Hoare) to become connected by a meltwater stream. Microbial mats were collected from these lakes, and cultured under identical conditions at the McMurdo Station laboratory. Replicate pairings of the microbial mats exhibited consistent patterns of growth inhibition indicative of competitive dominance. Natural products were extracted from the microbial mats, and a disk diffusion assay was utilized to show that allelochemical compounds mediate competitive interactions. Both microscopy and 16S rRNA sequencing show that these mats contain significant populations of cyanobacteria known to produce allelochemicals. Two compounds were isolated from these microbial mats that might be important in the chemical ecology of these psychrophiles. In other disk:mat pairings, including extract versus mat of origin, the allelochemicals exhibited no effect. Taken together, these results indicate that Antarctic lake microbial mats can compete via allelopathy.

Actinomycete Metabolome Induction/Suppression with N-Acetylglucosamine

The metabolite profiles of three sponge-derived actinomycetes, namely, Micromonospora sp. RV43, Rhodococcus sp. RV157, and Actinokineospora sp. EG49 were investigated after elicitation with N-acetyl-d-glucosamine. ¹H NMR fingerprint methodology was utilized to study the differences in the metabolic profiles of the bacterial extracts before and after elicitation. Our study found that the addition of N-acetyl-d-glucosamine modified the secondary metabolite profiles of the three investigated actinomycete isolates. N-Acetyl-d-glucosamine induced the production of 3-formylindole (11) and guaymasol (12) in Micromonospora sp. RV43, the siderophore bacillibactin 16, and surfactin antibiotic 17 in Rhodococcus sp. RV157 and increased the production of minor metabolites actinosporins E-H (21-24) in Actinokineospora sp. EG49. These results highlight the use of NMR fingerprinting to detect changes in metabolism following addition of N-acetyl-d-glucosamine. N-Acetyl-d-glucosamine was shown to have multiple effects including suppression of metabolites, induction of new metabolites, and increased production of minor compounds.

Antifungal activity change of Streptomyces rimosus MY02 mediated by confront culture with other microorganism

Streptomyces rimosus can produce antibacterial and antifungal antibiotics, which have important applications in medicine and agriculture. Seventy-nine microbial strains were employed to assay interaction between S. rimosus MY02 and different fungi, actinomyces, and bacteria when confront cultured on solid media. The results showed that the presence of a microorganism might affect the activity of another one. When S. rimosus MY02 confront cultured with other microorganisms, the inductive effect might be positive or negative. In this study, fungi showed to be effective elicitors, with a highest inductivity rate of 90.1%, and all of fungi showed positive induction behavior. Followed by bacteria with 59.6% of the tested bacterial strains showing positive inductivity, and the highest inductivity was 54.9%. Only six actinomyces (counting for 40% of the tested actinomyces strains) showed positive inductivity, and the highest induction rate of the strain NK413 was 34.1%. We also found that growth of most of bacteria or actinomyces which showed negative inductivity were similar or better than that of the strain MY02. However, the growth status of the strains was not positive related to inducing ability directly.

Antibiotic dialogues: induction of silent biosynthetic gene clusters by exogenous small molecules

Natural products have traditionally served as a dominant source of therapeutic agents. They are produced by dedicated biosynthetic gene clusters that assemble complex, bioactive molecules from simple precursors. Recent genome sequencing efforts coupled with advances in bioinformatics indicate that the majority of biosynthetic gene clusters are not expressed under normal laboratory conditions. Termed 'silent' or 'cryptic', these gene clusters represent a treasure trove for discovery of novel small molecules, their regulatory circuits and their biosynthetic pathways. In this review, we assess the capacity of exogenous small molecules in activating silent secondary metabolite gene clusters. Several approaches that have been developed are presented, including coculture techniques, ribosome engineering, chromatin remodeling and high-throughput elicitor screens. The rationale, applications and mechanisms attendant to each are discussed. Some general conclusions can be drawn from our analysis: exogenous small molecules comprise a productive avenue for the discovery of cryptic metabolites. Specifically, growth-inhibitory molecules, in some cases clinically used antibiotics, serve as effective inducers of silent biosynthetic gene clusters, suggesting that old antibiotics may be used to find new ones. The involvement of natural antibiotics in modulating secondary metabolism at subinhibitory concentrations suggests that they represent part of the microbial vocabulary through which inter- and intraspecies interactions are mediated.

Antimicrobial Activity of Marine Bacterial Symbionts Retrieved from Shallow Water Hydrothermal Vents

Marine sponges and other sessile macro-organisms were collected at a shallow water hydrothermal site in Eyjafjörður, Iceland. Bacteria were isolated from the organisms using selective media for actinomycetes, and the isolates were screened for antimicrobial activity. A total of 111 isolates revealed antimicrobial activity displaying different antimicrobial patterns which indicates production of various compounds. Known test strains were grown in the presence of ethyl acetate extracts from one selected isolate, and a clear growth inhibition of Staphylococcus aureus was observed down to 0.1 % extract concentration in the medium. Identification of isolates shows different species of Actinobacteria with Streptomyces sp. playing the largest role, but also members of Bacilli, Alphaproteobacteria and Gammaproteobacteria. Sponges have an excellent record regarding production of bioactive compounds, often involving microbial symbionts. At the hydrothermal vents, however, the majority of active isolates originated from other invertebrates such as sea anemones or algae. The results indicate that antimicrobial assays involving isolates in full growth can detect activity not visible by other methods. The macro-organisms inhabiting the Eyjafjörður hydrothermal vent area host diverse microbial species in the phylum Actinobacteria with antimicrobial activity, and the compounds responsible for the activity will be subject to further research.

Production of Fusaric Acid by Fusarium spp. in Pure Culture and in Solid Medium Co-Cultures

The ability of fungi isolated from nails of patients suffering from onychomycosis to induce de novo production of bioactive compounds in co-culture was examined. Comparison between the metabolite profiles produced by Sarocladium strictum, by Fusarium oxysporum, and by these two species in co-culture revealed de novo induction of fusaric acid based on HRMS. Structure confirmation of this toxin, using sensitive microflow NMR, required only three 9-cm Petri dishes of fungal culture. A targeted metabolomics study based on UHPLC-HRMS confirmed that the production of fusaric acid was strain-dependent. Furthermore, the detected toxin levels suggested that onychomycosis-associated fungal strains of the F. oxysporum and F. fujikuroi species complexes are much more frequently producing fusaric acid, and in higher amount, than strains of the F. solani species complex. Fusarium strains producing no significant amounts of this compound in pure culture, were shown to de novo produce that compound when grown in co-culture. The role of fusaric acid in fungal virulence and defense is discussed.

Metagenomic Analysis of Upwelling-Affected Brazilian Coastal Seawater Reveals Sequence Domains of Type I PKS and Modular NRPS

Marine environments harbor a wide range of microorganisms from the three domains of life. These microorganisms have great potential to enable discovery of new enzymes and bioactive compounds for industrial use. However, only ~1% of microorganisms from the environment can currently be identified through cultured isolates, limiting the discovery of new compounds. To overcome this limitation, a metagenomics approach has been widely adopted for biodiversity studies on samples from marine environments. In this study, we screened metagenomes in order to estimate the potential for new natural compound synthesis mediated by diversity in the Polyketide Synthase (PKS) and Nonribosomal Peptide Synthetase (NRPS) genes. The samples were collected from the Praia dos Anjos (Angel’s Beach) surface water—Arraial do Cabo (Rio de Janeiro state, Brazil), an environment affected by upwelling. In order to evaluate the potential for screening natural products in Arraial do Cabo samples, we used KS (keto-synthase) and C (condensation) domains (from PKS and NRPS, respectively) to build Hidden Markov Models (HMM) models. From both samples, a total of 84 KS and 46 C novel domain sequences were obtained, showing the potential of this environment for the discovery of new genes of biotechnological interest. These domains were classified by phylogenetic analysis and this was the first study conducted to screen PKS and NRPS genes in an upwelling affected sample

Investigation of Interspecies Interactions within Marine Micromonosporaceae Using an Improved Co-Culture Approach

With respect to bacterial natural products, a significant outcome of the genomic era was that the biosynthetic potential in many microorganisms surpassed the number of compounds isolated under standard laboratory growth conditions, particularly among certain members in the phylum Actinobacteria. Our group, as well as others, investigated interspecies interactions, via co-culture, as a technique to coax bacteria to produce novel natural products. While co-culture provides new opportunities, challenges exist and questions surrounding these methods remain unanswered. In marine bacteria, for example, how prevalent are interspecies interactions and how commonly do interactions result in novel natural products? In an attempt to begin to answer basic questions surrounding co-culture of marine microorganisms, we have tested both antibiotic activity-based and LC/MS-based methods to evaluate Micromonosporaceae secondary metabolite production in co-culture. Overall, our investigation of 65 Micromonosporaceae led to the identification of 12 Micromonosporaceae across three genera that produced unique metabolites in co-culture. Our results suggest that interspecies interactions were prevalent between marine Micromonosporaceae and marine mycolic acid-containing bacteria. Furthermore, our approach highlights a sensitive and rapid method for investigating interspecies interactions in search of novel antibiotics, secondary metabolites, and genes.

Elicitation of secondary metabolism in actinomycetes

Genomic sequence data have revealed the presence of a large fraction of putatively silent biosynthetic gene clusters in the genomes of actinomycetes that encode for secondary metabolites, which are not detected under standard fermentation conditions. This review focuses on the effects of biological (co-cultivation), chemical, as well as molecular elicitation on secondary metabolism in actinomycetes. Our review covers the literature until June 2014 and exemplifies the diversity of natural products that have been recovered by such approaches from the phylum Actinobacteria.

Impact of interspecific interactions on antimicrobial activity among soil bacteria

Certain bacterial species produce antimicrobial compounds only in the presence of a competing species. However, little is known on the frequency of interaction-mediated induction of antibiotic compound production in natural communities of soil bacteria. Here we developed a high-throughput method to screen for the production of antimicrobial activity by monocultures and pair-wise combinations of 146 phylogenetically different bacteria isolated from similar soil habitats. Growth responses of two human pathogenic model organisms, Escherichia coli WA321 and Staphylococcus aureus 533R4, were used to monitor antimicrobial activity. From all isolates, 33% showed antimicrobial activity only in monoculture and 42% showed activity only when tested in interactions. More bacterial isolates were active against S. aureus than against E. coli. The frequency of interaction-mediated induction of antimicrobial activity was 6% (154 interactions out of 2798) indicating that only a limited set of species combinations showed such activity. The screening revealed also interaction-mediated suppression of antimicrobial activity for 22% of all combinations tested. Whereas all patterns of antimicrobial activity (non-induced production, induced production and suppression) were seen for various bacterial classes, interaction-mediated induction of antimicrobial activity was more frequent for combinations of Flavobacteria and alpha- Proteobacteria. The results of our study give a first indication on the frequency of interference competitive interactions in natural soil bacterial communities which may forms a basis for selection of bacterial groups that are promising for the discovery of novel, cryptic antibiotics.

Co-cultivation--a powerful emerging tool for enhancing the chemical diversity of microorganisms

Marine-derived bacteria and fungi are promising sources of novel bioactive compounds that are important for drug discovery programs. However, as encountered in terrestrial microorganisms there is a high rate of redundancy that results in the frequent re-discovery of known compounds. Apparently only a part of the biosynthetic genes that are harbored by fungi and bacteria are transcribed under routine laboratory conditions which involve cultivation of axenic microbial strains. Many biosynthetic genes remain silent and are not expressed in vitro thereby seriously limiting the chemical diversity of microbial compounds that can be obtained through fermentation. In contrast to this, co-cultivation (also called mixed fermentation) of two or more different microorganisms tries to mimic the ecological situation where microorganisms always co-exist within complex microbial communities. The competition or antagonism experienced during co-cultivation is shown to lead to a significantly enhanced production of constitutively present compounds and/or to an accumulation of cryptic compounds that are not detected in axenic cultures of the producing strain. This review highlights the power of co-cultivation for increasing the chemical diversity of bacteria and fungi drawing on published studies from the marine and from the terrestrial habitat alike.

Resource use of soilborne Streptomyces varies with location, phylogeny, and nitrogen amendment

In this study, we explore variation in resource use among Streptomyces in prairie soils. Resource use patterns were highly variable among Streptomyces isolates and were significantly related to location, phylogeny, and nitrogen (N) amendment history. Streptomyces populations from soils less than 1 m apart differed significantly in their ability to use resources, indicating that drivers of resource use phenotypes in soil are highly localized. Variation in resource use within Streptomyces genetic groups was significantly associated with the location from which Streptomyces were isolated, suggesting that resource use is adapted to local environments. Streptomyces from soils under long-term N amendment used fewer resources and grew less efficiently than those from non-amended soils, demonstrating that N amendment selects for Streptomyces with more limited catabolic capacities. Finally, resource use among Streptomyces populations was correlated with soil carbon content and Streptomyces population densities. We hypothesize that variation in resource use among Streptomyces reflects adaptation to local resource availability and competitive species interactions in soil and that N amendments alter selection for resource use phenotypes.

Dithiolopyrrolone natural products: isolation, synthesis and biosynthesis

Dithiolopyrrolones are a class of antibiotics that possess the unique pyrrolinonodithiole (4H-[1,2] dithiolo [4,3-b] pyrrol-5-one) skeleton linked to two variable acyl groups. To date, there are approximately 30 naturally occurring dithiolopyrrolone compounds, including holomycin, thiolutin, and aureothricin, and more recently thiomarinols, a unique class of hybrid marine bacterial natural products containing a dithiolopyrrolone framework linked by an amide bridge with an 8-hydroxyoctanoyl chain linked to a monic acid. Generally, dithiolopyrrolone antibiotics have broad-spectrum antibacterial activity against various microorganisms, including Gram-positive and Gram-negative bacteria, and even parasites. Holomycin appeared to be active against rifamycin-resistant bacteria and also inhibit the growth of the clinical pathogen methicillin-resistant Staphylococcus aureus N315. Its mode of action is believed to inhibit RNA synthesis although the exact mechanism has yet to be established in vitro. A recent work demonstrated that the fish pathogen Yersinia ruckeri employs an RNA methyltransferase for self-resistance during the holomycin production. Moreover, some dithiolopyrrolone derivatives have demonstrated promising antitumor activities. The biosynthetic gene clusters of holomycin have recently been identified in S. clavuligerus and characterized biochemically and genetically. The biosynthetic gene cluster of thiomarinol was also identified from the marine bacterium Pseudoalteromonas sp. SANK 73390, which was uniquely encoded by two independent pathways for pseudomonic acid and pyrrothine in a novel plasmid. The aim of this review is to give an overview about the isolations, characterizations, synthesis, biosynthesis, bioactivities and mode of action of this unique family of dithiolopyrrolone natural products, focusing on the period from 1940s until now.

Future potential for anti-infectives from bacteria - how to exploit biodiversity and genomic potential

The early stages of antibiotic development include the identification of novel hit compounds. Since actinomycetes and myxobacteria are still the most important natural sources of active metabolites, we provide an overview on these producers and discuss three of the most promising approaches toward finding novel anti-infectives from microorganisms. These are defined as the use of biodiversity to find novel producers, the variation of culture conditions and induction of silent genes, and the exploitation of the genomic potential of producers via "genome mining". Challenges that exist beyond compound discovery are outlined in the last section.

Streptomyces coelicolor encodes a urate-responsive transcriptional regulator with homology to PecS from plant pathogens

Many transcriptional regulators control gene activity by responding to specific ligands. Members of the multiple-antibiotic resistance regulator (MarR) family of transcriptional regulators feature prominently in this regard, and they frequently function as repressors in the absence of their cognate ligands. Plant pathogens such as Dickeya dadantii encode a MarR homolog named PecS that controls expression of a gene encoding the efflux pump PecM in addition to other virulence genes. We report here that the soil bacterium Streptomyces coelicolor also encodes a PecS homolog (SCO2647) that regulates a pecM gene (SCO2646). S. coelicolor PecS, which exists as a homodimer, binds the intergenic region between pecS and pecM genes with high affinity. Several potential PecS binding sites were found in this intergenic region. The binding of PecS to its target DNA can be efficiently attenuated by the ligand urate, which also quenches the intrinsic fluorescence of PecS, indicating a direct interaction between urate and PecS. In vivo measurement of gene expression showed that activity of pecS and pecM genes is significantly elevated after exposure of S. coelicolor cultures to urate. These results indicate that S. coelicolor PecS responds to the ligand urate by attenuated DNA binding in vitro and upregulation of gene activity in vivo. Since production of urate is associated with generation of reactive oxygen species by xanthine dehydrogenase, we propose that PecS functions under conditions of oxidative stress.

Antagonistic interactions mediated by marine bacteria: the role of small molecules

Marine bacteria are known to produce a wide variety of structurally diverse and biologically active secondary metabolites. Considerably less is known about the ecological functions of these compounds, in part due to methodological challenges associated with this field of research. Here, we review the antagonistic activities mediated by marine bacteria with a focus on activities linked to structurally defined secondary metabolites. Bacterial antagonism has been documented against other marine bacteria as well as eukaryotes, and includes antibiosis, the inhibition of quorum sensing, larval settlement deterrence, and defense against predation. These compounds likely play important ecological roles that ultimately affect ecosystem structure and function, however, much remains to be learned before these roles can be fully appreciated. Recent technological advances coupled with a better understanding of the diverse processes mediated by secondary metabolites provide new opportunities to expand our understanding of the chemical ecology of bacterial antagonism in the marine environment.

Maternal and environmental effects on symbiont-mediated antimicrobial defense

Bacteria produce a remarkable diversity of bioactive molecules with antimicrobial properties. Despite the importance of such compounds for human medicine, little is known about the factors influencing antibiotic production in natural environments. Recently, several insects have been found to benefit from symbiont-produced antimicrobial compounds for defense against pathogenic microbes. In the European beewolf, Philanthus triangulum (Hymenoptera, Crabronidae), bacteria of the genus Streptomyces provide protection against pathogens by producing antimicrobials on the larval cocoon during hibernation, thereby significantly enhancing the survival probability of the beewolf larva. To investigate the effects of abiotic and biotic factors on antibiotic production, we exposed beewolf cocoons to different environmental conditions and quantified the amount of Streptomyces-produced antibiotics by using gas chromatography/mass spectrometry (GC/MS). The results revealed no significant influence of temperature, humidity, or pathogen load on the antibiotic amount, indicating that antibiotic production is not affected by current environmental conditions but rather may be optimized to serve as a reliable long-term protection during the unpredictable phase of beewolf hibernation. However, the amount of antibiotics was positively correlated with the symbiont population size on the cocoon, which in turn is affected by the number of Streptomyces cells provided by the mother into the brood cell. Additionally, we found a positive correlation between the amount of hydrocarbons and the number and length of bacterial cells in the antennal gland secretion, suggesting that maternal investment affects symbiont growth and, thus, antibiotic production on the larval cocoon.

Two Polyketides from a Co-culture of Two Marine-derived Fungal Strains

Co-cultivation of the fungal strains Penicillium sp. Ma(M3)V and Trichoderma sp. Gc(M2)1 in malt 2% medium led to the production of two novel, unusual polyketides, ( Z)-2-ethylhex-2-enedioic acid and ( E)-4-oxo-2-propylideneoct-7-enoic acid. Analysis of spectroscopic data enabled the structure determination of both compounds.

Complex marine natural products as potential epigenetic and production regulators of antibiotics from a marine Pseudomonas aeruginosa

Marine microbes are capable of producing secondary metabolites for defense and competition. Factors exerting an impact on secondary metabolite production of microbial communities included bioactive natural products and co-culturing. These external influences may have practical applications such as increased yields or the generation of new metabolites from otherwise silent genes in addition to reducing or limiting the production of undesirable metabolites. In this paper, we discuss the metabolic profiles of a marine Pseudomonas aeruginosa in the presence of a number of potential chemical epigenetic regulators, adjusting carbon sources and co-culturing with other microbes to induce a competitive response. As a result of these stressors certain groups of antibiotics or antimalarial agents were increased most notably when treating P. aeruginosa with sceptrin and co-culturing with another Pseudomonas sp. An interesting cross-talking event between these two Pseudomonas species when cultured together and exposed to sceptrin was observed.

Cross-Species Induction and Enhancement of Antimicrobial Properties in Response to Gamma Irradiation in Exiguobacterium sp. HKG 126

A gram positive, extreme haloalkaliphilic, radioresistant bacterium was isolated from mangrove region of Kerala (India) which was characterized as Exiguobacterium sp. HKG-126 using morphological, physiological, biochemical and molecular characterization. Present investigation was undertaken to examine Exiguobacterium sp. as a potential source of broad-spectrum antimicrobial activity and enhancement in this activity was observed due to cross-species/cross-genera induction and also in response to high dose of gamma (γ) irradiation. Individual studies on the antimicrobial activity of all the co-cultivated bacterial strains before and after mixed culture fermentation, showed excellent enhancement in antimicrobial activity of Exiguobacterium sp. against a variety of clinical pathogens. To the best of our knowledge, this is the first report showing existence of an extremely high radioresistant strain of (up to 15 kGy) Exiguobacterium sp.

Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction

Adaptation is normally viewed as the enemy of the antibiotic discovery and development process because adaptation among pathogens to antibiotic exposure leads to resistance. We present a method here that, in contrast, exploits the power of adaptation among antibiotic producers to accelerate the discovery of antibiotics. A competition-based adaptive laboratory evolution scheme is presented whereby an antibiotic-producing microorganism is competed against a target pathogen and serially passed over time until the producer evolves the ability to synthesize a chemical entity that inhibits growth of the pathogen. When multiple Streptomyces clavuligerus replicates were adaptively evolved against methicillin-resistant Staphylococcus aureus N315 in this manner, a strain emerged that acquired the ability to constitutively produce holomycin. In contrast, no holomycin could be detected from the unevolved wild-type strain. Moreover, genome re-sequencing revealed that the evolved strain had lost pSCL4, a large 1.8 Mbp plasmid, and acquired several single nucleotide polymorphisms in genes that have been shown to affect secondary metabolite biosynthesis. These results demonstrate that competition-based adaptive laboratory evolution can constitute a platform to create mutants that overproduce known antibiotics and possibly to discover new compounds as well.

Use of experimental design for the optimization of the production of new secondary metabolites by two Penicillium species

A fractional factorial design approach has been used to enhance secondary metabolite production by two Penicillium strains. The method was initially used to improve the production of bioactive extracts as a whole and subsequently to optimize the production of particular bioactive metabolites. Enhancements of over 500% in secondary metabolite production were observed for both P. oxalicum and P. citrinum. Two new alkaloids, citrinalins A (5) and B (6), were isolated and identified from P. citrinum cultures optimized for production of minor metabolites.

The sponge-associated bacterium Bacillus licheniformis SAB1: a source of antimicrobial compounds

Several bacterial cultures were isolated from sponge Halichondria sp., collected from the Gujarat coast of the Indo Pacific region. These bacterial cultures were fermented in the laboratory (100 mL) and the culture filtrate was assayed for antibiotic activity against 16 strains of clinical pathogens. Bacillus sp. (SAB1), the most potent of them and antagonistic to several clinically pathogenic Gram-positive, Gram-negative bacteria and the fungus Aspergillus fumigatus was chosen for further investigation. Analysis of the nucleotide sequence of the 16S rDNA gene of Bacillus sp. SAB1 showed a strong similarity (100%) with the 16S rDNA gene of Bacillus licheniformis HNL09. The bioactive compounds produced by Bacillus licheniformis SAB1 (GenBank accession number: DQ071568) were identified as indole (1), 3-phenylpropionic acid (2) and a dimer 4,4′-oxybis[3-phenylpropionic acid] (3) on the basis of their Fourier Transform Infrared (FTIR), Nuclear Magnetic Resonance (NMR) and Electrospray Ionization Mass Spectrometer (ESI-MS) data. There is a single reference on the natural occurrence of compound 3 from the leaves of a terrestrial herb Aptenia cordifolia in the literature, so to the best of our knowledge, this is a first report of its natural occurrence from a marine source. The recovery of bacterial strains with antimicrobial activity suggests that marine-invertebrates remain a rich source for the isolation of culturable isolates capable of producing novel bioactive secondary metabolites.