The Ecological Coherence of Temperature and Salinity Tolerance Interaction and Pigmentation in a Non-marine Vibrio Isolated from Salar de Atacama

Improving Bioprocess Conditions for the Production of Prodigiosin Using a Marine Serratia rubidaea Strain

The enormous potential attributed to prodigiosin regarding its applicability as a natural pigment and pharmaceutical agent justifies the development of sound bioprocesses for its production. Using a Serratia rubidaea strain isolated from a shallow-water hydrothermal vent, optimization of the growth medium composition was carried out. After medium development, the bacterium temperature, light and oxygen needs were studied, as was growth inhibition by product concentration. The implemented changes led to a 13-fold increase in prodigiosin production in a shake flask, reaching 19.7 mg/L. The conditions allowing the highest bacterial cell growth and prodigiosin production were also tested with another marine strain: S. marcescens isolated from a tide rock pool was able to produce 15.8 mg/L of prodigiosin. The bioprocess with S. rubidaea was scaled up from 0.1 L shake flasks to 2 L bioreactors using the maintenance of the oxygen mass transfer coefficient (kLa) as the scale-up criterion. The implemented parameters in the bioreactor led to an 8-fold increase in product per biomass yield and to a final concentration of 293.1 mg/L of prodigiosin in 24 h.

Insights into the diversity and survival strategies of soil bacterial isolates from the Atacama Desert

The Atacama Desert, the driest, with the highest radiation, and one of the most ancient deserts in the world, is a hostile environment for life. We have a collection of 74 unique bacterial isolates after cultivation and confirmation by 16S rRNA gene sequencing. Pigmentation, biofilm formation, antimicrobial production against Escherichia coli MG1655 and Staphylococcus aureus HG003, and antibiotic resistance were assessed on these isolates. We found that approximately a third of the colonies produced pigments, 80% of isolates formed biofilms, many isolates produce growth inhibiting activities against E. coli and/or S. aureus, and many were resistant to antibiotics. The functional characterization of these isolates gives us insight into the adaptive bacterial strategies in harsh environments and enables us to learn about their possible use in agriculture, healthcare, or biotechnology.

Assessing the effect of multiple variables on the production of bioflocculant by Serratia marcescens: Flocculating activity, kinetics, toxicity, and flocculation mechanism

Bioflocculants gain attention as alternatives to chemical flocculants because they are more environmentally friendly and highly biodegradable. This study aims to improve the bioflocculant production by Serratia marcescens using one-variable-at-a-time (OVAT) analysis and analyze its flocculating activity performance, toxicity, and the flocculation mechanism. The effect of multiple variables including initial inoculum size, pH, mixing speed, temperature, growth medium, and incubation period was assessed through OVAT. Flocculating activity was then determined via jar test analysis, and toxicity test was performed using Daphnia magna and Daphnia pulex. The flocculation mechanism was determined via particle size distribution and zeta potential analysis. The optimum conditions for the improved bioflocculant production were as follows: 10% v/v initial inoculum size, pH 7, mixing speed of 150 rpm, room temperature, nutrient broth medium, and 72 h of incubation period. Scanning electron microscopy showed flake-like intact structure with coarse surface. The produced bioflocculant showed flocculating activity of 48% in 5227 ± 580 NTU initial kaolin turbidity with 1 mg/L concentration and 5% v/v dosage of bioflocculant, following the second-order kinetics. Toxicity test to D. magna and D. pulex showed the 48 h LC₅₀ values of 8.06 and 6.42 g/L, respectively; these values are greatly higher than the fabricated chemical flocculants. The flocculation process using bioflocculant produced by S. marcescens was suggested to occur via bridging mechanism because it greatly affected the particle size distribution. Results indicated that bioflocculant produced by S. marcescens is much environmentally friendly and has great potential for turbidity removal in water/wastewater.

Enhanced Prodigiosin Production in Serratia marcescens JNB5-1 by Introduction of a Polynucleotide Fragment into the pigN 3' Untranslated Region and Disulfide Bonds into O-Methyl Transferase (PigF)

In Serratia marcescens JNB5-1, prodigiosin was highly produced at 30°C, but it was noticeably repressed at ≥37°C. Our initial results demonstrated that both the production and the stability of the O-methyl transferase (PigF) and oxidoreductase (PigN) involved in the prodigiosin pathway in S. marcescens JNB5-1 sharply decreased at ≥37°C. Therefore, in this study, we improved mRNA stability and protein production using de novo polynucleotide fragments (PNFs) and the introduction of disulfide bonds, respectively, and observed their effects on prodigiosin production. Our results demonstrate that adding PNFs at the 3' untranslated regions of pigF and pigN significantly improved the mRNA half-lives of these genes, leading to an increase in the transcript and expression levels. Subsequently, the introduction of disulfide bonds in pigF improved the thermal stability, pH stability, and copper ion resistance of PigF. Finally, shake flask fermentation showed that the prodigiosin titer with the engineered S. marcescens was increased by 61.38% from 5.36 to 8.65 g/liter compared to the JNB5-1 strain at 30°C and, significantly, the prodigiosin yield increased 2.05-fold from 0.38 to 0.78 g/liter at 37°C. In this study, we revealed that the introduction of PNFs and disulfide bonds greatly improved the expression and stability of pigF and pigN, hence efficiently enhancing prodigiosin production with S. marcescens at 30 and 37°C. IMPORTANCE This study highlights a promising strategy to improve mRNA/enzyme stability and to increase production using de novo PNF libraries and the introduction of disulfide bonds into the protein. PNFs could increase the half-life of target gene mRNA and effectively prevent its degradation. Moreover, PNFs could increase the relative intensity of target genes without affecting the expression of other genes; as a result, it could alleviate the cellular burden compared to other regulatory elements such as promoters. In addition, we obtained a PigF variant with improved activity and stability by the introduction of disulfide bonds into PigF. Collectively, we demonstrate here a novel approach for improving mRNA/enzyme stability using PNFs, which results in enhanced prodigiosin production in S. marcescens at 30°C.

Evaluation of antioxidant potential of pigments extracted from Bacillus spp. and Halomonas spp. isolated from mangrove rhizosphere

The present study aimed to isolate different pigment-producing bacteria from the mangrove rhizosphere habitat and to extract their pigments for evaluating their antioxidant and sun-protective properties. Three pigment-producing bacterial cultures were isolated from soil samples and were identified by morphological analysis and 16S rDNA sequencing. The pigments were isolated by the solvent extraction method and named as MZ (Pink), Orange, and Yellow. They were characterized by Fourier Transform Infrared (FTIR) and UV-Vis spectroscopy. The sun protection factor (SPF) values of these pigments were then determined using the Mansur equation. The total polyphenol content was estimated by the Folin-Ciocâlteu method, and the antioxidant activity of the pigments was determined using DPPH (2,2-diphenyl-1-picrylhydrazyl), FRAP (ferric reducing antioxidant power), and ABTS (2,2-azinobis-3-ethyl-enzothiazoline-6-sulfonic acid) assays. The in vitro antioxidant potential of the pigments in the presence of oxidative stress (H2O2) was confirmed in the mouse macrophage cell line RAW264.7 by using the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) assay. The pigment-producing bacterial isolates were identified as Bacillus infantis (MZ), Halomonas spp. (Orange), and Bacillus spp. (Yellow). The pigments were found to be carotenoid in nature, and the SPF values were in the range of 3.99 to 5.22. All three pigments had high polyphenol content (22 to 48 μg tannic acid equivalent) and showed significant antioxidant properties in both chemical and cell line-based studies. The results of this study indicate that these pigments have the potential to be used as an antioxidant agent and can be further developed as a pharmaceutical compound.

High-level production of microbial prodigiosin: A review

Prodigiosin is a natural red pigment derived primarily from secondary metabolites of microorganisms, especially Serratia marcescens. It can also be chemically synthesized. Prodigiosin has been proven to have antitumor, antibacterial, antimalaria, anti-insect, antialgae, and immunosuppressive activities, and is gaining increasing important in the global market because of its great potential application value in clinical medicine development, environmental treatment, preparation of food additives, and so on. Due to the low efficiency of prodigiosin chemical synthesis, high-level prodigiosin of production by microorganisms are necessary for prodigiosin applications. In this paper, the production of prodigiosin by microorganism in recent decades is reviewed. The methods and strategies for increasing the yield of prodigiosin are discussed from the aspects of medium composition, additives, factors affecting production conditions, strain modification, and fermentation methods.

Toxicity of hydraulic fracturing wastewater from black shale natural-gas wells influenced by well maturity and chemical additives

Hydraulic fracturing of deep shale formations generates large volumes of wastewater that must be managed through treatment, reuse, or disposal. Produced wastewater liberates formation-derived radionuclides and contains previously uncharacterized organohalides thought to be generated within the shale well, both posing unknown toxicity to human and ecological health. Here, we assess the toxicity of 42 input media and produced fluid samples collected from four wells in the Utica formation and Marcellus Shale using two distinct endpoint screening assays. Broad spectrum acute toxicity was assessed using a bioluminescence inhibition assay employing the halotolerant bacterium Aliivibrio fischeri, while predictive mammalian cytotoxicity was evaluated using a N-acetylcysteine (NAC) thiol reactivity assay. The acute toxicity and thiol reactivity of early-stage flowback was higher than later produced fluids, with levels diminishing through time as the natural gas wells matured. Acute toxicity of early stage flowback and drilling muds were on par with the positive control, 3,5-dichlorophenol (6.8 mg L-1). Differences in both acute toxicity and thiol reactivity between paired natural gas well samples were associated with specific chemical additives. Samples from wells containing a larger diversity and concentration of organic additives resulted in higher acute toxicity, while samples from a well applying a higher composition of ammonium persulfate, a strong oxidizer, showed greater thiol reactivity, predictive of higher mammalian toxicity. Both acute toxicity and thiol reactivity are consistently detected in produced waters, in some cases present up to nine months after hydraulic fracturing. These results support that specific chemical additives, the reactions generated by the additives, or the constituents liberated from the formation by the additives contribute to the toxicity of hydraulic fracturing produced waters and reinforces the need for careful consideration of early produced fluid management.

Biotechnological Activities and Applications of Bacterial Pigments Violacein and Prodigiosin

In this review, we discuss violacein and prodigiosin, two chromogenic bacterial secondary metabolites that have diverse biological activities. Although both compounds were "discovered" more than seven decades ago, interest into their biological applications has grown in the last two decades, particularly driven by their antimicrobial and anticancer properties. These topics will be discussed in the first half of this review. The latter half delves into the current efforts of groups to produce these two compounds. This includes in both their native bacterial hosts and heterogeneously in other bacterial hosts, including discussing some of the caveats related to the yields reported in the literature, and some of the synthetic biology techniques employed in this pursuit.

The Microbiome of Neotropical Water Striders and Its Potential Role in Codiversification

Simple Summary

Insects host a highly diverse bacterial community. Although we have a good understanding of the role that this microbiome plays in insects, the composition and diversity of microbiomes associated with Neotropical freshwater insects is virtually unknown. Here, we describe, for the first time, the microbiome associated with six species of Neotropical water striders in Panama. We also performed phylogenetic analyses to explore potential codiversification or coevolution between water strider species and their associated microbiome. We found a diverse microbiome associated with the six species of water striders, with the dominant bacterial taxa belonging to the phyla Proteobacteria and Tenericutes. Although some bacterial lineages were shared across species, some lineages were also uniquely associated with different water strider species. Our results suggest that both environmental variation and host phylogenetic identity are important drivers of the microbiome associated with water striders. Understanding the evolution of the host-microbiome interaction is crucial to our understanding of Neotropical freshwater ecosystems.

Abstract

Insects host a highly diverse microbiome, which plays a crucial role in insect life. However, the composition and diversity of microbiomes associated with Neotropical freshwater insects is virtually unknown. In addition, the extent to which diversification of this microbiome is associated with host phylogenetic divergence remains to be determined. Here, we present the first comprehensive analysis of bacterial communities associated with six closely related species of Neotropical water striders in Panama. We used comparative phylogenetic analyses to assess associations between dominant bacterial linages and phylogenetic divergence among species of water striders. We found a total of 806 16S rRNA amplicon sequence variants (ASVs), with dominant bacterial taxa belonging to the phyla Proteobacteria (76.87%) and Tenericutes (19.51%). Members of the α- (e.g., Wolbachia) and γ- (e.g., Acinetobacter, Serratia) Proteobacteria, and Mollicutes (e.g., Spiroplasma) were predominantly shared across species, suggesting the presence of a core microbiome in water striders. However, some bacterial lineages (e.g., Fructobacillus, Fluviicola and Chryseobacterium) were uniquely associated with different water strider species, likely representing a distinctive feature of each species’ microbiome. These findings indicate that both host identity and environmental context are important drivers of microbiome diversity in water striders. In addition, they suggest that diversification of the microbiome is associated with diversification in water striders. Although more research is needed to establish the evolutionary consequences of host-microbiome interaction in water striders, our findings support recent work highlighting the role of bacterial community host-microbiome codiversification.

Comparative Genomics and Transcriptomics Analyses Reveal a Unique Environmental Adaptability of Vibrio fujianensis

The genus Vibrio is ubiquitous in marine environments and uses numerous evolutionary characteristics and survival strategies in order to occupy its niche. Here, a newly identified species, Vibrio fujianensis, was deeply explored to reveal a unique environmental adaptability. V. fujianensis type strain FJ201301^T shared 817 core genes with the Vibrio species in the population genomic analysis, but possessed unique genes of its own. In addition, V. fujianensis FJ201301^T was predicated to carry 106 virulence-related factors, several of which were mostly found in other pathogenic Vibrio species. Moreover, a comparative transcriptome analysis between the low-salt (1% NaCl) and high-salt (8% NaCl) condition was conducted to identify the genes involved in salt tolerance. A total of 913 unigenes were found to be differentially expressed. In a high-salt condition, 577 genes were significantly upregulated, whereas 336 unigenes were significantly downregulated. Notably, differentially expressed genes have a significant association with ribosome structural component and ribosome metabolism, which may play a role in salt tolerance. Transcriptional changes in ribosome genes indicate that V. fujianensis may have gained a predominant advantage in order to adapt to the changing environment. In conclusion, to survive in adversity, V. fujianensis has enhanced its environmental adaptability and developed various strategies to fill its niche.

The production and bioactivity of prodigiosin: quo vadis?

Prodigiosin (PG), a red tripyrrole pigment, belongs to a member of the prodiginine family and is normally secreted by various sources including Serratia marcescens and other Gram-negative bacteria. The studies of PG have received innovative devotion as a result of reported antimicrobial, larvicidal and anti-nematoid immunomodulation and antitumor properties, owing to its antibiotic and cytotoxic activities. This review provides a comprehensive summary of research undertaken toward the isolation and structural elucidation of the prodiginine family of natural products. Additionally, the current evidence-based understanding of the biological activities and medicinal potential of PG is employed to determine the efficacy, with some reports of information related to pharmacokinetics, pharmacodynamics and toxicology.

Differential Production of Pigments by Halophilic Bacteria Under the Effect of Salt and Evaluation of Their Antioxidant Activity

Microorganisms that survive in the high salt environment have been shown to be a potential source for metabolites with pharmaceutical importance. In the present study, we have investigated the effect of 5 and 10% (w/v) NaCl on growth, biochemical changes, and metabolite production in seven moderately halophilic bacteria isolated from the salterns/mangrove area of South India. Metabolite production by Bacillus VITPS3 increased by 3.18-fold in the presence of 10% (w/v) NaCl concentration. Total phenolic and flavonoid content increased in Bacillus VITPS5 (11.3-fold) and Planococcus maritimus VITP21 (5.99-fold) whereas β-carotene content was less at higher NaCl concentrations. VITP21 and VITPS5, in response to NaCl, produced metabolites with higher (6.72- and 4.91-fold) DPPH and ABTS radical scavenging activity. UV/visible spectrophotometry of the extracts confirmed the presence of flavonoids, phenolics, and related compounds. ¹H-NMR spectra indicated substantial changes in the metabolite production in response to salt concentration. Principal component analysis (PCA) revealed that VITP21 extracts exhibited the highest antioxidant activity compared with other extracts. The present study presents the first report on the comparative analysis of pigment production by moderate halophilic bacteria, in response to the effect of salt and their relation to radical scavenging property.

Biosynthesis and Bioactivity of Prodiginine Analogs in Marine Bacteria, Pseudoalteromonas: A Mini Review

The Prodiginine family consists of primarily red-pigmented tripyrrole secondary metabolites that were first characterized in the Gram-negative bacterial species Serratia marcescens and demonstrates a wide array of biological activities and applications. Derivatives of prodiginine have since been characterized in the marine γ-proteobacterium, Pseudoalteromonas. Although biosynthetic gene clusters involved in prodiginine synthesis display homology among genera, there is an evident structural difference in the resulting metabolites. This review will summarize prodiginine biosynthesis, bioactivity, and gene regulation in Pseudoalteromonas in comparison to the previously characterized species of Serratia, discuss the ecological contributions of Pseudoalteromonas in the marine microbiome and their eukaryotic hosts, and consider the importance of modern functional genomics and classic DNA manipulation to understand the overall prodiginine biosynthesis pathway.

Characterization and Salt Response in Recurrent Halotolerant Exiguobacterium sp. SH31 Isolated From Sediments of Salar de Huasco, Chilean Altiplano

Poly-extremophiles microorganisms have the capacity to inhabit hostile environments and can survive several adverse conditions that include as variations in temperature, pH, and salinity, high levels UV light and atmospheric pressure, and even the presence of toxic compounds and the formation of reactive oxygen species (ROS). A halotolerant Exiguobacterium strain was isolated from Salar de Huasco (Chilean Altiplano), a well-known shallow lake area with variable salinity levels, little human intervention, and extreme environmental conditions, which makes it ideal for the study of resistant mechanisms and the evolution of adaptations. This bacterial genus has not been extensively studied, although its cosmopolitan location indicates that it has high levels of plasticity and adaptive capacity. However, to date, there are no studies regarding the tolerance and resistance to salinity and osmotic pressure. We set out to characterize the Exiguobacterium sp. SH31 strain and describe its phenotypical and genotypical response to osmotic stress. In this context, as a first step to characterize the response to the SH31 strain to salinity and to establish the bases for a molecular study, we proposed to compare its response under three salt conditions (0, 25, and 50 g/l NaCl). Using different physiology, genomic, and transcriptomic approaches, we determined that the bacterium is able to grow properly in a NaCl concentration of up to 50 g/l; however, the best growth rate was observed at 25 g/l. Although the presence of flagella is not affected by salinity, motility was diminished at 25 g/l NaCl and abolished at 50 g/l. Biofilm formation was induced proportionally with increases in salinity, which was expected. These phenotypic results correlated with the expression of related genes: fliG and fliS Motility); opuBA and putP (transport); glnA, proC, gltA, and gbsA (compatible solutes); ywqC, bdlA, luxS y pgaC (biofilm and stress response); and therefore, we conclude that this strain effectively modifies gene expression and physiology in a differential manner when faced with different concentrations of NaCl and these modifications aid survival.

Microbial diversity of saline environments: searching for cytotoxic activities

In order to select halophilic microorganisms as a source of compounds with cytotoxic activities, a total of 135 bacterial strains were isolated from water and sediment samples collected from the Zipaquirá salt mine in the Colombian Andes. We determined the cytotoxic effects of 100 crude extracts from 54 selected organisms on the adherent murine mammary cell carcinoma 4T1 and human mammary adenocarcinoma MCF-7 cell lines. These extracts were obtained from strains of Isoptericola, Ornithinimicrobium, Janibacter, Nesterenkonia, Alkalibacterium, Bacillus, Halomonas, Chromohalobacter, Shewanella, Salipiger, Martellela, Oceanibaculum, Caenispirillum and Labrenzia. The extracts of 23 strains showed an IC₅₀ of less than 100 μg mL⁻¹. They were subsequently analyzed by LC/MS allowing dereplication of 20 compounds. The cytotoxic effect was related to a complex mixture of diketopiperazines present in many of the extracts analyzed. The greatest cytotoxic activity against both of the evaluated cell lines was obtained from the chloroform extract of Labrenzia aggregata USBA 371 which had an IC₅₀ < 6 μg mL⁻¹. Other extracts with high levels of cytotoxic activity were obtained from Bacillus sp. (IC₅₀ < 50 μg mL⁻¹) which contained several compounds such as macrolactin L and A, 7-O-succinoylmacrolactin F and iturin. Shewanella chilikensis USBA 344 also showed high levels of cytotoxic activity against both cell lines in the crude extract: an IC₅₀ < 15 μg mL⁻¹ against the 4T1 cell line and an IC₅₀ < 68 μg mL⁻¹ against the MCF-7 cell line. Nesterenkonia sandarakina CG 35, which has an IC₅₀ of 118 µg mL⁻¹ against 4T1, is a producer of diketopiperazines and 1-acetyl-β-carboline. Also, Ornithinimicrobium kibberense CG 24, which has IC₅₀ < 50 μg mL⁻¹, was a producer of diketopiperazines and lagunamycin. Our study demonstrates that these saline environments are habitats of halophilic and halotolerant bacteria that have previously unreported cytotoxic activity.