The regulatory mechanism underlying light-inducible production of carotenoids in nonphototrophic bacteria

Light inducible gene expression system for Streptomyces

The LitR/CarH family comprises adenosyl B12-based photosensory transcriptional regulators that control light-inducible carotenoid production in nonphototrophic bacteria. In this study, we established a blue-green light-inducible hyperexpression system using LitR and its partner ECF-type sigma factor LitS in streptomycin-producing Streptomyces griseus NBRC 13350. The constructed multiple-copy number plasmid, pLit19, carried five genetic elements: pIJ101rep, the thiostrepton resistance gene, litR, litS, and σLitS-recognized light-inducible crtE promoter. Streptomyces griseus transformants harboring pLit19 exhibited a light-dependent hyper-production of intracellular reporter enzymes including catechol-2,3-dioxygenase and β-glucuronidase, extracellular secreted enzymes including laccase and transglutaminase, and secondary metabolites including melanin, flaviolin, and indigoidine. Cephamycin-producing Streptomyces sp. NBRC 13304, carrying an entire actinorhodin gene cluster, exhibited light-dependent actinorhodin production after the introduction of the pLit19 shuttle-type plasmid with the pathway-specific activator actII-ORF4. Insertion of sti fragment derived from Streptomyces phaeochromogenes pJV1 plasmid into pLit19 increased its light sensitivity, allowing gene expression under weak light irradiation. The two constructed Escherichia coli-Streptomyces shuttle-type pLit19 plasmids were found to have abilities similar to those of pLit19. We successfully established an optogenetically controlled hyperproduction system for S. griseus NBRC 13350 and Streptomyces sp. NBRC 13304.

Bioactive compounds from food-grade Bacillus

Bacillus species have attracted significant attention in recent years due to their potential for producing various bioactive compounds with diverse functional properties. This review highlights bioactive substances from food-grade Bacillus strains and their applications in functional foods and nutraceuticals. The metabolic capacities of Bacillus species have allowed them to generate a wide range of bioactive substances, including vitamins, enzymes, anti-microbial peptides, and other non-ribosomal peptides. These substances have a variety of positive effects, including potential cholesterol-lowering and immune-modulatory qualities in addition to anti-oxidant and anti-bacterial actions. The uses and mechanisms of action of these bioactive chemicals can be used to improve the functional qualities and nutritional profile of food products. Examples include the use of anti-microbial peptides to increase safety and shelf life, as well as the use of Bacillus-derived enzymes in food processing to improve digestibility and sensory qualities. The exploitation of bioactive compounds from food-grade Bacillus strains presents a promising frontier in the development of functional foods and nutraceuticals with enhanced health benefits. Due to their wide range of activity and applications, they are considered as important resources for the development of novel medications, agricultural biocontrol agents, and industrial enzymes. Ongoing research into the biosynthetic pathways, functional properties, and applications of these compounds is essential to fully realize their potential in the food industry. This review underscores the significance of various bioactive compounds generated from Bacillus in tackling global issues like environmental sustainability, sustainable agriculture, and antibiotic resistance. Future developments in microbiology and biotechnology will enable us to fully utilize the potential of these amazing microbes, resulting in novel approaches to industry, agriculture, and health. © 2024 Society of Chemical Industry.

High-intensity green light potentially activates the actinorhodin biosynthetic pathway in Streptomyces coelicolor A3(2)

The development of practices that enhance the potential of actinomycetes as major antibiotic producers is a challenge in discovering new secondary metabolites. Light, an essential external stimulus for most microorganisms, could be exploited to manipulate their physiological processes. However, the effects of monochromatic green light on the production of secondary metabolites in actinomycetes have not yet been reported. In this paper, we report a novel and simple method that uses high-intensity monochromatic green light to potentially induce the production of cryptic secondary metabolites in the model actinomycete Streptomyces coelicolor A3(2). Using actinorhodin (ACT), a blue-pigmented antibiotic, and undecylprodigiosin (RED), a red-pigmented antibiotic, as indicators, we found that irradiation with high-intensity monochromatic green light-emitting diodes promoted sporulation, significantly decreased RED production, and increased ACT production. Semi-quantitative reverse transcription-polymerase chain reaction and western blot analyses revealed, for the first time, that stimulation with green light accelerated the expression of ActII-ORF4, a pathway-specific regulator of ACT biosynthesis in S. coelicolor A3(2). This approach of stimulating secondary metabolite biosynthesis pathways in actinomycetes by irradiation with high-intensity monochromatic green light is expected to facilitate the discovery of cryptic antibiotics that are not typically produced under conventional dark culture conditions. However, the effective intensity and duration of irradiation with green light that are required to activate these metabolite pathways may vary markedly among actinomycetes.

The effect of isolated probiotics from Indonesian <em>passiflora edulis</em> sims. on interferon gamma (ifn-γ) levels in peripheral blood mononuclear cell of adult tuberculosis patients <em>in vitro</em>

Background: Mycobacterium tuberculosis (M.tb) is unique because the bacteria live intracellularly and hide in macrophages so that they can escape from phagocytosis. This is one of the factors that complicate the treatment of M.tb infections. Interferon-gamma (IFN-γ) is a compound that plays an important role in macrophage activation to control intracellular pathogens. Objective: The purpose of this research is to analyze the concentration of IFN-γ in peripheral blood mononuclear cells of adult Tuberculosis patients (TB) after in vitro administration of multistrain probiotics from indigeneous Indonesian red passion fruit (Passiflora edulis Sims.). Method: The probiotics isolated from red passion fruit were introduced into Peripheral Blood Mononuclear Cell (PBMC) adult TB patients who were undergoing Anti-tuberculosis Drug Therapy (ATD) category one at the Trosobo Primary Health Center (Sidoarjo, East Java, Indonesia), and the patients who were undergoing ATD category one treatment were willing to be involved in this study. Result: The probiotics isolated from fermentation-broth of Indonesian red passion fruit were able to increase IFN-γ levels in PBMC of adult TB patients. Conclusion: The red passion fruit probiotics isolated can increase IFN-γ of adult TB patients increased from 0.82% to 23.17% after in vitro administration.

Research Progress on Cordycepin Synthesis and Methods for Enhancement of Cordycepin Production in Cordyceps militaris

C. militaris is an insect-born fungus that belongs to Ascomycota and Cordyceps. It has a variety of biological activities that can be applied in medicine, health-care products, cosmeceuticals and other fields. Cordycepin (COR) is one of the major bioactive components identified from C. militaris. Thus, C. militaris and COR have attracted extensive attention. In this study, chemical synthetic methods and the biosynthesis pathway of COR were reviewed. As commercially COR was mainly isolated from C. militaris fermentation, the optimizations for liquid and solid fermentation and genetic modifications of C. militaris to increase COR content were also summarized. Moreover, the research progress of genetic modifications of C. militaris and methods for separation and purification COR were introduced. Finally, the existing problems and future research direction of C. militaris were discussed. This study provides a reference for the production of COR in the future.

Bacillus spore-forming probiotics: benefits with concerns?

Representatives of the genus Bacillus are multifunctional microorganisms with a broad range of applications in both traditional fermentation and modern biotechnological processes. Bacillus spp. has several beneficial properties. They serve as starter cultures for various traditional fermented foods and are important biotechnological producers of enzymes, antibiotics, and bioactive peptides. They are also used as probiotics for humans, in veterinary medicine, and as feed additives for animals of agricultural importance. The beneficial effects of bacilli are well-reported and broadly acknowledged. However, with a better understanding of their positive role, many questions have been raised regarding their safety and the relevance of spore formation in the practical application of this group of microorganisms. What is the role of Bacillus spp. in the human microbial consortium? When and why did they start colonizing the gastrointestinal tract (GIT) of humans and other animals? Can spore-forming probiotics be considered as truly beneficial organisms, or should they still be approached with caution and regarded as "benefits with concerns"? In this review, we not only hope to answer the above questions but to expand the scope of the conversation surrounding bacilli probiotics.

A Molecular Survey of Bacterial Species in the Guts of Black Soldier Fly Larvae (Hermetia illucens) Reared on Two Urban Organic Waste Streams in Kenya

Globally, the expansion of livestock and fisheries production is severely constrained due to the increasing costs and ecological footprint of feed constituents. The utilization of black soldier fly (BSF) as an alternative protein ingredient to fishmeal and soybean in animal feed has been widely documented. The black soldier fly larvae (BSFL) used are known to voraciously feed and grow in contaminated organic wastes. Thus, several concerns about their safety for inclusion into animal feed remain largely unaddressed. This study evaluated both culture-dependent sequence-based and 16S rDNA amplification analysis to isolate and identify bacterial species associated with BSFL fed on chicken manure (CM) and kitchen waste (KW). The bacteria species from the CM and KW were also isolated and investigated. Results from the culture-dependent isolation strategies revealed that Providencia sp. was the most dominant bacterial species detected from the guts of BSFL reared on CM and KW. Morganella sp. and Brevibacterium sp. were detected in CM, while Staphylococcus sp. and Bordetella sp. were specific to KW. However, metagenomic studies showed that Providencia and Bordetella were the dominant genera observed in BSFL gut and processed waste substrates. Pseudomonas and Comamonas were recorded in the raw waste substrates. The diversity of bacterial genera recorded from the fresh rearing substrates was significantly higher compared to the diversity observed in the gut of the BSFL and BSF frass (leftovers of the rearing substrates). These findings demonstrate that the presence and abundance of microbiota in BSFL and their associated waste vary considerably. However, the presence of clinically pathogenic strains of bacteria in the gut of BSFL fed both substrates highlight the biosafety risk of potential vertical transmission that might occur, if appropriate pre-and-postharvest measures are not enforced.

Killing effect of deinoxanthins on cyanobloom-forming Microcystis aeruginosa: Eco-friendly production and specific activity of deinoxanthins

Cyanobacterial blooms caused mainly by Microcystis aeruginosa could be controlled using chemical and biological agents such as H₂O₂, antagonistic bacteria, and enzymes. Little is known about the possible toxic effects of bacterial membrane pigments on M. aeruginosa cells. Deinococcus metallilatus MA1002 cultured under light increased the production of several carotenoid-like compounds by upregulating two deinoxanthin biosynthesis genes: crtO and cruC. The deinoxanthin compounds were identified using thin-layer chromatography, high-performance liquid chromatography, and liquid chromatography-mass spectrometry. D. metallilatus was cultured with agricultural by-products under light to produce the deinoxanthin compounds. Soybean meal, from six tested agricultural by-products, was selected as the single factor for making an economical medium to produce deinoxanthin compounds. The growth of axenic M. aeruginosa PCC7806, as well as other xenic cyanobacteria such as Cyanobium gracile, Trichormus variabilis, and Dolichospermum circinale, were inhibited by the deinoxanthin compounds. Scanning electron microscopic images showed the complete collapse of M. aeruginosa cells under deinoxanthin treatment, probably due to its interference with cyanobacterial membrane synthesis during cellular elongation. Deinoxanthins appeared to be nontoxic to other non-cyanobacteria such as Acinetobacter, Pseudomonas, Methylobacterium, and Bacillus species, suggesting that it can be a novel candidate for preventing cyanobacterial blooms through its specific activity against cyanobacteria.

Unraveling the Underlying Heavy Metal Detoxification Mechanisms of Bacillus Species

The rise of anthropogenic activities has resulted in the increasing release of various contaminants into the environment, jeopardizing fragile ecosystems in the process. Heavy metals are one of the major pollutants that contribute to the escalating problem of environmental pollution, being primarily introduced in sensitive ecological habitats through industrial effluents, wastewater, as well as sewage of various industries. Where heavy metals like zinc, copper, manganese, and nickel serve key roles in regulating different biological processes in living systems, many heavy metals can be toxic even at low concentrations, such as mercury, arsenic, cadmium, chromium, and lead, and can accumulate in intricate food chains resulting in health concerns. Over the years, many physical and chemical methods of heavy metal removal have essentially been investigated, but their disadvantages like the generation of chemical waste, complex downstream processing, and the uneconomical cost of both methods, have rendered them inefficient,. Since then, microbial bioremediation, particularly the use of bacteria, has gained attention due to the feasibility and efficiency of using them in removing heavy metals from contaminated environments. Bacteria have several methods of processing heavy metals through general resistance mechanisms, biosorption, adsorption, and efflux mechanisms. Bacillus spp. are model Gram-positive bacteria that have been studied extensively for their biosorption abilities and molecular mechanisms that enable their survival as well as their ability to remove and detoxify heavy metals. This review aims to highlight the molecular methods of Bacillus spp. in removing various heavy metals ions from contaminated environments.

Isolation and characterization of a heavy metal- and antibiotic-tolerant novel bacterial strain from a contaminated culture plate of Chlamydomonas reinhardtii, a green micro-alga

Background:Chlamydomonas reinhardtii, a green micro-alga, is normally cultured in laboratories in Tris-Acetate Phosphate (TAP), a medium which contains acetate as the sole carbon source. Acetate in TAP can lead to occasional bacterial and fungal contamination. We isolated a yellow-pigmented bacterium from a Chlamydomonas TAP plate. It was named Clip185 based on the Chlamydomonas strain plate it was isolated from. In this article we present our work on the isolation, taxonomic identification and physiological and biochemical characterizations of Clip185. Methods: We measured sensitivities of Clip185 to five antibiotics and performed standard microbiological tests to characterize it. We partially sequenced the 16S rRNA gene of Clip185. We identified the yellow pigment of Clip185 by spectrophotometric analyses. We tested tolerance of Clip185 to six heavy metals by monitoring its growth on Lysogeny Broth (LB) media plates containing 0.5 mM -10 mM concentrations of six different heavy metals. Results: Clip185 is an aerobic, gram-positive rod, oxidase-negative, mesophilic, alpha-hemolytic bacterium. It can ferment glucose, sucrose and mannitol. It is starch hydrolysis-positive. It is very sensitive to vancomycin but resistant to penicillin and other bacterial cell membrane- and protein synthesis-disrupting antibiotics. Clip185 produces a C50 carotenoid, decaprenoxanthin, which is a powerful anti-oxidant with a commercial demand. Decaprenoxanthin production is induced in Clip185 under light. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of Clip185 revealed a 99% sequence identity to that of Microbacterium binotii strain PK1-12M and Microbacterium sp. strain MDP6. Clip185 is able to tolerate toxic concentrations of six heavy metals. Conclusions: Our results show that Clip185 belongs to the genus Microbacterium. In the future, whole genome sequencing of Clip185 will clarify if Clip185 is a new Microbacterium species or a novel strain of Microbacterium binotii, and will reveal its genes involved in antibiotic-resistance, heavy-metal tolerance and regulation of decaprenoxanthin biosynthesis.

Isolation and characterization of a heavy metal- and antibiotic-tolerant novel bacterial strain from a contaminated culture plate of Chlamydomonas reinhardtii, a green micro-alga

Background:Chlamydomonas reinhardtii, a green micro-alga, is normally cultured in laboratories in Tris-Acetate Phosphate (TAP), a medium which contains acetate as the sole carbon source. Acetate in TAP can lead to occasional bacterial and fungal contamination. We isolated a yellow-pigmented bacterium from a Chlamydomonas TAP plate. It was named Clip185 based on the Chlamydomonas strain plate it was isolated from. In this article we present our work on the isolation, taxonomic identification and physiological and biochemical characterizations of Clip185. Methods: We measured sensitivities of Clip185 to five antibiotics and performed standard microbiological tests to characterize it. We partially sequenced the 16S rRNA gene of Clip185. We identified the yellow pigment of Clip185 by spectrophotometric analyses. We tested tolerance of Clip185 to six heavy metals by monitoring its growth on Lysogeny Broth (LB) media plates containing 0.5 mM -10 mM concentrations of six different heavy metals. Results: Clip185 is an aerobic, gram-positive rod, oxidase-negative, mesophilic, alpha-hemolytic bacterium. It can ferment glucose, sucrose and mannitol. It is starch hydrolysis-positive. It is very sensitive to vancomycin but resistant to penicillin and other bacterial cell membrane- and protein synthesis-disrupting antibiotics. Clip185 produces a C50 carotenoid, decaprenoxanthin, which is a powerful anti-oxidant with a commercial demand. Decaprenoxanthin production is induced in Clip185 under light. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of Clip185 revealed a 99% sequence identity to that of Microbacterium binotii strain PK1-12M and Microbacterium sp. strain MDP6. Clip185 is able to tolerate toxic concentrations of six heavy metals. Conclusions: Our results show that Clip185 belongs to the genus Microbacterium. In the future, whole genome sequencing of Clip185 will clarify if Clip185 is a new Microbacterium species or a novel strain of Microbacterium binotii, and will reveal its genes involved in antibiotic-resistance, heavy-metal tolerance and regulation of decaprenoxanthin biosynthesis.

Ultraviolet Radiation From a Plant Perspective: The Plant-Microorganism Context

Ultraviolet (UV) radiation directly affects plants and microorganisms, but also alters the species-specific interactions between them. The distinct bands of UV radiation, UV-A, UV-B, and UV-C have different effects on plants and their associated microorganisms. While UV-A and UV-B mainly affect morphogenesis and phototropism, UV-B and UV-C strongly trigger secondary metabolite production. Short wave (<350 nm) UV radiation negatively affects plant pathogens in direct and indirect ways. Direct effects can be ascribed to DNA damage, protein polymerization, enzyme inactivation and increased cell membrane permeability. UV-C is the most energetic radiation and is thus more effective at lower doses to kill microorganisms, but by consequence also often causes plant damage. Indirect effects can be ascribed to UV-B specific pathways such as the UVR8-dependent upregulated defense responses in plants, UV-B and UV-C upregulated ROS accumulation, and secondary metabolite production such as phenolic compounds. In this review, we summarize the physiological and molecular effects of UV radiation on plants, microorganisms and their interactions. Considerations for the use of UV radiation to control microorganisms, pathogenic as well as non-pathogenic, are listed. Effects can be indirect by increasing specialized metabolites with plant pre-treatment, or by directly affecting microorganisms.

Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions

Stable isotope labeling of microbial taxa of interest and their sorting provide an efficient and direct way to answer the question "who does what?" in complex microbial communities when coupled with fluorescence in situ hybridization or downstream 'omics' analyses. We have developed a platform for automated Raman-based sorting in which optical tweezers and microfluidics are used to sort individual cells of interest from microbial communities on the basis of their Raman spectra. This sorting of cells and their downstream DNA analysis, such as by mini-metagenomics or single-cell genomics, or cultivation permits a direct link to be made between the metabolic roles and the genomes of microbial cells within complex microbial communities, as well as targeted isolation of novel microbes with a specific physiology of interest. We describe a protocol from sample preparation through Raman-activated live cell sorting. Subsequent cultivation of sorted cells is described, whereas downstream DNA analysis involves well-established approaches with abundant methods available in the literature. Compared with manual sorting, this technique provides a substantially higher throughput (up to 500 cells per h). Furthermore, the platform has very high sorting accuracy (98.3 ± 1.7%) and is fully automated, thus avoiding user biases that might accompany manual sorting. We anticipate that this protocol will empower in particular environmental and host-associated microbiome research with a versatile tool to elucidate the metabolic contributions of microbial taxa within their complex communities. After a 1-d preparation of cells, sorting takes on the order of 4 h, depending on the number of cells required.

Rufibacter hautae sp. nov., a red-pigmented bacterium from freshwater lake sediment, and proposal of Rufibacter quisquiliarum as a latter heterotypic synonym of Rufibacter ruber

A taxonomic identification using a polyphasic approach was performed on strain NBS58-1^T, which was isolated from the interfacial sediment of Taihu Lake in China. Strain NBS58-1^T was Gram-stain-negative, aerobic, non-spore-forming and catalase-positive. Phylogenetic analyses based on 16S rRNA gene and three housekeeping genes (rpoB, gyrB and dnaK) sequences supported the position that strain NBS58-1^T should be classified within the genus Rufibacter. The 16S rRNA gene sequence of strain NBS58-1^T possessed the highest similarity to Rufibacter sediminis H-1^T (96.60 %), followed by Rufibacter glacialis MDT1-10-3^T (96.17 %). And the ANI value between strain NBS58-1^T and R. glacialis MDT1-10-3^T was 79.3 %. The respiratory quinone was menaquinone 7 (MK-7). The major cellular fatty acids comprised iso-C_15 : 0 and summed feature 3. Phosphatidylethanolamine, two unidentified phospholipids and four unidentified lipids were the main polar lipids. The genomic DNA G+C content was 51.3 mol%. Based on phenotypic features and phylogenetic position, a novel species with the name Rufibacter hautae sp. nov. is proposed. The type strain is NBS58-1^T=(KACC 21309^T=MCCC 1K04037^T). We also proposed Rufibacter quisquiliarum as a latter heterotypic synonym of Rufibacter ruber.

Light Response of Pseudomonas putida KT2440 Mediated by Class II LitR, a Photosensor Homolog

Pseudomonas putida KT2440 retains three homologs (PplR1 to PplR3) of the LitR/CarH family, an adenosyl B₁₂-dependent light-sensitive MerR family transcriptional regulator. Transcriptome analysis revealed the existence of a number of photoinducible genes, including pplR1, phrB (encoding DNA photolyase), ufaM (furan-containing fatty acid synthase), folE (GTP cyclohydrolase I), cryB (cryptochrome-like protein), and multiple genes without annotated/known function. Transcriptional analysis by quantitative reverse transcription-PCR with knockout mutants of pplR1 to pplR3 showed that a triple knockout completely abolished the light-inducible transcription in P. putida, which indicates the occurrence of ternary regulation of PplR proteins. A DNase I footprint assay showed that PplR1 protein specifically binds to the promoter regions of light-inducible genes, suggesting a consensus PplR1-binding direct repeat, 5'-T(G/A)TACAN₁₂TGTA(C/T)A-3'. The disruption of B₁₂ biosynthesis cluster did not affect the light-inducible transcription; however, disruption of ppSB1-LOV (where LOV indicates "light, oxygen, or voltage") and ppSB2-LOV, encoding blue light photoreceptors adjacently located to pplR3 and pplR2, respectively, led to the complete loss of light-inducible transcription. Overall, the results suggest that the three PplRs and two PpSB-LOVs cooperatively regulate the light-inducible gene expression. The wide distribution of the pplR/ppSB-LOV cognate pair homologs in Pseudomonas spp. and related bacteria suggests that the response and adaptation to light are similarly regulated in the group of nonphototrophic bacteria.IMPORTANCE The LitR/CarH family is a new group of photosensor homologous to MerR-type transcriptional regulators. Proteins of this family are distributed to various nonphototrophic bacteria and grouped into at least five classes (I to V). Pseudomonas putida retaining three class II LitR proteins exhibited a genome-wide response to light. All three paralogs were functional and mediated photodependent activation of promoters directing the transcription of light-induced genes or operons. Two LOV (light, oxygen, or voltage) domain proteins, adjacently encoded by two litR genes, were also essential for the photodependent transcriptional control. Despite the difference in light-sensing mechanisms, the DNA binding consensus of class II LitR [T(G/A)TA(C/T)A] was the same as that of class I. This is the first study showing the actual involvement of class II LitR in light-induced transcription.

A Zeaxanthin-Producing Bacterium Isolated from the Algal Phycosphere Protects Coral Endosymbionts from Environmental Stress

Occupying less than 1% of the seas, coral reefs are estimated to harbor ∼25% of all marine species. However, the destruction of coral reefs has intensified in the face of global climate changes, such as rising seawater temperatures, which induce the overproduction of reactive oxygen species harmful to corals. Although reef-building corals form complex consortia with bacteria and photosynthetic endosymbiotic algae of the family Symbiodiniaceae, the functional roles of coral-associated bacteria remain largely elusive. By manipulating the Symbiodiniaceae bacterial community, we demonstrated that a bacterium that produces an antioxidant carotenoid could mitigate thermal and light stresses in cultured Symbiodiniaceae isolated from a reef-building coral. Therefore, this study illuminates the unexplored roles of coral-associated bacteria under stressful conditions.

Reef-building corals form a complex consortium with photosynthetic algae in the family Symbiodiniaceae and bacteria, collectively termed the coral holobiont. These bacteria are hypothesized to be involved in the stress resistance of the coral holobiont, but their functional roles remain largely elusive. Here, we show that cultured Symbiodiniaceae algae isolated from the reef-building coral Galaxea fascicularis are associated with novel bacteria affiliated with the family Flavobacteriaceae. Antibiotic treatment eliminated the bacteria from cultured Symbiodiniaceae, resulting in a decreased maximum quantum yield of PSII (variable fluorescence divided by maximum fluorescence [F_v/F_m]) and an increased production of reactive oxygen species (ROS) under thermal and light stresses. We then isolated this bacterial strain, named GF1. GF1 inoculation in the antibiotic-treated Symbiodiniaceae cultures restored the F_v/F_m and reduced the ROS production. Furthermore, we found that GF1 produces the carotenoid zeaxanthin, which possesses potent antioxidant activity. Zeaxanthin supplementation to cultured Symbiodiniaceae ameliorated the F_v/F_m and ROS production, suggesting that GF1 mitigates thermal and light stresses in cultured Symbiodiniaceae via zeaxanthin production. These findings could advance our understanding of the roles of bacteria in Symbiodiniaceae and the coral holobiont, thereby contributing to the development of novel approaches toward coral protection through the use of symbiotic bacteria and their metabolites.

Light-inducible carotenoid production controlled by a MarR-type regulator in Corynebacterium glutamicum

Carotenoid production in some non-phototropic bacteria occurs in a light-dependent manner to protect cells from photo-oxidants. Knowledge regarding the transcriptional regulator involved in the light-dependent production of carotenoids of non-phototrophic bacteria has been mainly confined to coenzyme B₁₂-based photo-sensitive regulator CarH/LitR family proteins belonging to a MerR family transcriptional regulator. In this study, we found that bacteria belonging to Micrococcales and Corynebacteriales exhibit light-dependent carotenoid-like pigment production including an amino acid-producer Corynebacterium glutamicum AJ1511. CrtR is a putative MarR family transcriptional regulator located in the divergent region of a carotenoid biosynthesis gene cluster in the genome of those bacteria. A null mutant for crtR of C. glutamicum AJ1511 exhibited constitutive production of carotenoids independent of light. A complemented strain of the crtR mutant produced carotenoids in a light-dependent manner. Transcriptional analysis revealed that the expression of carotenoid biosynthesis genes is regulated in a light-dependent manner in the wild type, while the transcription was upregulated in the crtR mutant irrespective of light. In vitro experiments demonstrated that a recombinant CrtR protein binds to the specific sequences within the intergenic region of crtR and crtE, which corresponds to −58 to −7 for crtE, and +26 to −28 for crtR with respect to the transcriptional start site, and serves as a repressor for crtE transcription directed by RNA polymerase containing SigA. Taken together, the results indicate that CrtR light-dependently controls the expression of the carotenoid gene cluster in C. glutamicum and probably closely related Actinobacteria.

Identification of Bacillus species: Implication on the quality of probiotic formulations

Spores of several Bacillus species have long history of consumption and safe use as probiotics and a variety of formulations containing these organisms are available in the global market. Considering the difficulties in the identification of Bacillus species and the poor microbiological quality of many probiotic formulations, we used three up-to-date methodological approaches for analyzing the content of ten formulations marketed in Italy and labeled to contain Bacillus spores. We compared the performance of biochemical tests based on the BCL Vitek2 card and MALDI-TOF mass spectrometry, using 16S rDNA sequencing as the reference technique. The BCL card performed well in identifying all Bacillus probiotic strains as well as the Bruker’s MALDI Biotyper. Nevertheless, the MALDI score values were sometimes lower than those indicated by the manufacturer for correct species identification. Contaminant bacteria (Lysinibacillus fusiformis, Acinetobacter baumannii, Bacillus cereus, Brevibacillus choshinensis, Bacillus licheniformis, Bacillus badius) were detected in some formulations. Characterization of the B. cereus contaminant showed the potential pathogenicity of this strain. Microbial enumeration performed by the plate count method revealed that the number of viable cells contained in many of the analyzed products differed from the labeled amount. Overall, our data show that only two of the ten analyzed formulations qualitatively and quantitatively respect what is on the label. Since probiotic properties are most often strain specific, molecular typing of isolates of the two most common Bacillus species, B. clausii and B. coagulans, was also performed. In conclusion, the majority of the analyzed products do not comply with quality requirements, most likely leading to reduced/absent efficacy of the preparation and representing a potential infective risk for consumers.

Role and Function of Class III LitR, a Photosensor Homolog from Burkholderia multivorans

The LitR/CarH protein family is an adenosyl B₁₂ (AdoB₁₂)-dependent photoreceptor family with DNA-binding activity, and its homologs are widely distributed in the genomes of diverse bacterial genera. In this investigation, we studied the role and functions of a LitR homolog from a Gram-negative soil bacterium, Burkholderia multivorans, which does not possess an AdoB₁₂-binding domain. Transcriptome analysis indicated the existence of 19 light-induced genes, including folE2, cfaB, litS, photolyase gene phrB2, and cryB, located in the region flanking litR Disruption of litR caused constitutive expression of all the light-inducible genes, while mutation in the light-induced sigma factor gene, litS, abolished the transcription of the phrB2 operon and the cfa operon, indicating that LitR and LitS play a central role in light-inducible transcription. A gel shift assay showed that recombinant protein LitR specifically binds to the promoter regions of litR and the folE2 operon, and its binding was weakened by UV-A illumination. LitR absorbs light at maximally near 340 nm and exhibited a photocyclic response and light-dependent dissociation of multimer into tetramer. The litR mutant produced a 20-fold-higher intracellular level of folate than that of the wild-type strain. Thus, the evidence suggests that LitR light-dependently regulates the transcription of litR itself and the folE2 operon, resulting in the production of folate, and then the expressed RNA polymerase complex containing σ^LitS directs the transcription of the phrB2 operon and the cfa operon. These light-dependent characteristics suggest that class III LitR, in complex with a UV-A-absorbing molecule, follows a novel light-sensing mechanism.IMPORTANCE Members of the LitR/CarH family are adenosyl B₁₂-based photosensory transcriptional regulator involved in light-inducible carotenoid production in nonphototrophic bacteria. Our study provides the first evidence of the involvement of a class III LitR, which lacks an adenosyl B₁₂-binding domain in the light response of Burkholderia multivorans belonging to betaproteobacteria. Our biochemical analysis suggests that class III LitR protein exhibits features as a photosensor including absorption of light at the UV-A region (λ_max = ca. 340 nm), photocyclic response, and light-dependent dissociation. This suggests that class III LitR associates with a UV-A-absorbing molecule, and it has a photosensing mechanism distinguishable from that of the B₁₂-based type.

A global perspective on carotenoids: Metabolism, biotechnology, and benefits for nutrition and health

Carotenoids are lipophilic isoprenoid compounds synthesized by all photosynthetic organisms and some non-photosynthetic prokaryotes and fungi. With some notable exceptions, animals (including humans) do not produce carotenoids de novo but take them in their diets. In photosynthetic systems carotenoids are essential for photoprotection against excess light and contribute to light harvesting, but perhaps they are best known for their properties as natural pigments in the yellow to red range. Carotenoids can be associated to fatty acids, sugars, proteins, or other compounds that can change their physical and chemical properties and influence their biological roles. Furthermore, oxidative cleavage of carotenoids produces smaller molecules such as apocarotenoids, some of which are important pigments and volatile (aroma) compounds. Enzymatic breakage of carotenoids can also produce biologically active molecules in both plants (hormones, retrograde signals) and animals (retinoids). Both carotenoids and their enzymatic cleavage products are associated with other processes positively impacting human health. Carotenoids are widely used in the industry as food ingredients, feed additives, and supplements. This review, contributed by scientists of complementary disciplines related to carotenoid research, covers recent advances and provides a perspective on future directions on the subjects of carotenoid metabolism, biotechnology, and nutritional and health benefits.

Bacillus As Potential Probiotics: Status, Concerns, and Future Perspectives

Spore-forming bacilli are being explored for the production and preservation of food for many centuries. The inherent ability of production of large number of secretory proteins, enzymes, antimicrobial compounds, vitamins, and carotenoids specifies the importance of bacilli in food chain. Additionally, Bacillus spp. are gaining interest in human health related functional food research coupled with their enhanced tolerance and survivability under hostile environment of gastrointestinal tract. Besides, bacilli are more stable during processing and storage of food and pharmaceutical preparations, making them more suitable candidate for health promoting formulations. Further, Bacillus strains also possess biotherapeutic potential which is connected with their ability to interact with the internal milieu of the host by producing variety of antimicrobial peptides and small extracellular effector molecules. Nonetheless, with proposed scientific evidences, commercial probiotic supplements, and functional foods comprising of Bacillus spp. had not gained much credential in general population, since the debate over probiotic vs pathogen tag of Bacillus in the research and production terrains is confusing consumers. Hence, it’s important to clearly understand the phenotypic and genotypic characteristics of selective beneficial Bacillus spp. and their substantiation with those having GRAS status, to reach a consensus over the same. This review highlights the probiotic candidature of spore forming Bacillus spp. and presents an overview of the proposed health benefits, including application in food and pharmaceutical industry. Moreover, the growing need to evaluate the safety of individual Bacillus strains as well as species on a case by case basis and necessity of more profound analysis for the selection and identification of Bacillus probiotic candidates are also taken into consideration.

Isoprenoid Pyrophosphate-Dependent Transcriptional Regulation of Carotenogenesis in Corynebacterium glutamicum

Corynebacterium glutamicum is a natural producer of the C50 carotenoid decaprenoxanthin. The crtEcg0722crtBIYEb operon comprises most of its genes for terpenoid biosynthesis. The MarR-type regulator encoded upstream and in divergent orientation of the carotenoid biosynthesis operon has not yet been characterized. This regulator, named CrtR in this study, is encoded in many actinobacterial genomes co-occurring with terpenoid biosynthesis genes. CrtR was shown to repress the crt operon of C. glutamicum since DNA microarray experiments revealed that transcript levels of crt operon genes were increased 10 to 70-fold in its absence. Transcriptional fusions of a promoter-less gfp gene with the crt operon and crtR promoters confirmed that CrtR represses its own gene and the crt operon. Gel mobility shift assays with purified His-tagged CrtR showed that CrtR binds to a region overlapping with the −10 and −35 promoter sequences of the crt operon. Isoprenoid pyrophosphates interfered with binding of CrtR to its target DNA, a so far unknown mechanism for regulation of carotenogenesis. The molecular details of protein-ligand interactions remain to be studied. Decaprenoxanthin synthesis by C. glutamicum wild type was enhanced 10 to 30-fold upon deletion of crtR and was decreased 5 to 6-fold as result of crtR overexpression. Moreover, deletion of crtR was shown as metabolic engineering strategy to improve production of native and non-native carotenoids including lycopene, β-carotene, C.p. 450 and sarcinaxanthin.