Functional genomic analysis of an efficient indole degrading bacteria strain Alcaligenes faecalis IITR89 and its biodegradation characteristics

Indole is a nitrogenous heterocyclic aromatic pollutant often detected in various environments. An efficient indole degrading bacterium strain IITR89 was isolated from River Cauvery, India, and identified as Alcaligenes faecalis subsp. phenolicus. The bacterium was found to degrade ~ 95% of 2.5 mM (293.75 mg/L) of indole within 18 h utilizing it as a sole carbon and energy source. Based on metabolite identification, the metabolic route of indole degradation is indole → (indoxyl) → isatin → (anthranilate) → salicylic acid → (catechol) → (Acetyl-CoA) → and further entering into TCA cycle. Genome sequencing of IITR89 revealed the presence of gene cluster dmpKLMNOP, encoding multicomponent phenol hydroxylase; andAbcd gene cluster, encoding anthranilate 1,2-dioxygenase ferredoxin subunit (andAb), anthranilate 1,2-dioxygenase large subunit (andAc), and anthranilate 1,2-dioxygenase small subunit (andAd); nahG, salicylate hydroxylase; catA, catechol 1,2-dioxygenase; catB, cis, cis-muconate cycloisomerase; and catC, muconolactone D-isomerase which play an active role in indole degradation. The findings strongly support the degradation potential of strain IITR89 and its possible application for indole biodegradation.

Identification of an indole biodegradation gene cluster from Providencia rettgeri and its contribution in selectively biosynthesizing Tyrian purple

Tyrian purple, mainly composed of 6, 6'-dibromoindigo, is a precious dye extracted from sea snails. In this study, we found Tyrian purple can be selectively produced by a bacterial strain GS-2 when fed with 6-bromotryptophan in the presence of tryptophan. This GS-2 strain was then identified as Providencia rettgeri based on bacterial genome sequencing analysis. An indole degradation gene cluster for indole metabolism was identified from this GS-2 strain. The heterologous expression of the indole degradation gene cluster in Escherichia coli BL21 (DE3) and in vitro enzymatic reaction demonstrated that the indole biodegradation gene cluster may contribute to selectively biosynthesizing Tyrian purple. To further explore the underlying mechanism of the selectivity, we explored the intermediates in this indole biodegradation pathway using liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry (LC-ESI-QTOF-MS/MS), which indicated that the indole biodegradation pathway in Providencia rettgeri is the catechol pathway. Interestingly, the monooxygenase GS-C co-expressed with its corresponding reductase GS-D in the cluster has better activity for the biosynthesis of Tyrian purple compared with the previously reported monooxygenase from Methylophaga aminisulfidivorans (MaFMO) or Streptomyces cattleya cytochrome P450 enzyme (CYP102G4). This is the first study to show the existence of an indole biodegradation pathway in Providencia rettgeri, and the indole biodegradation gene cluster can contribute to the selective production of Tyrian purple.

Toward Elucidating the Human Gut Microbiota-Brain Axis: Molecules, Biochemistry, and Implications for Health and Diseases

In recent years, a substantial amount of data have supported an active role of gut microbiota in mediating mammalian brain function and health. Mining gut microbiota and their metabolites for neuroprotection is enticing but requires that the fundamental biochemical details underlying such microbiota-brain crosstalk be deciphered. While a neuronal gut-brain axis (through the vagus nerve) is not disputable, accumulating studies also point to a humoral route (via blood/lymphatic circulation) by which innumerable microbial molecular cues translocate from local gut epithelia to circulation with potentials to further cross the blood-brain barrier and reach the brain. In this Perspective, we review a realm of gut microbial molecules to evaluate their fate, function, and neuroactivities in vivo as mediated by microbiota. We turn to seminal studies of neurophysiology and neurologic disease models for the elucidation of biochemical pathways that link microbiota to gut-brain signaling. In addition, we discuss opportunities and challenges for advancing the microbiota-brain axis field while calling for high-throughput discovery of microbial molecules and studies for resolving the interspecies, interorgan, and interclass interaction among these neuroactive microbial molecules.

Phosphate solubilization and indole acetic acid production by rhizosphere yeast Torulaspora globosa: improvement of culture conditions for better performance in vitro

The rhizosphere yeast Torulaspora globosa is known to produce indole acetic acid (IAA) and to solubilize minerals. Due to the prospective use of this yeast as a biostimulant for agricultural applications, this work aimed to optimize the cultural conditions for both IAA production and phosphate solubilization. For phosphate solubilization, the temperature (20, 25 and 30 °C), initial medium pH (3.0, 5.0, and 7.0), and shaker speed (without mixing, 100 rpm, 150 rpm, and 200 rpm) were considered using the one-factor-at-a-time (OFAT) design. Temperature of 25 °C, initial medium pH 7.0, and static cultures were the conditions of greatest phosphate solubilization, with 40% of the total phosphorus content solubilized from calcium phosphate (419.86 mg L-1) after 48 h. By using the response surface methodology, the maximum IAA production (217.73 µg mL-1) was obtained with the highest initial pH 7.0, the lowest nitrogen, and glucose concentrations (5 g L-1 and 10 g L-1, respectively) and the lowest agitator speed (100 rpm). Further tests indicated that nitrogen affected significantly IAA production and the absence of nitrogen in the medium promoted higher IAA production (457 µg mL-1). The results obtained here may contribute to the scaling up for industrial and agricultural applications of a yeast-based product with T. globosa.

Preparation of a Novel Solid Phase Microextraction Fiber for Headspace GC-MS Analysis of Hazardous Odorants in Landfill Leachate

The practice of odorant analysis can often be very challenging because odorants are usually composed of a host of volatile organic compounds (VOCs) at low concentrations. Preconcentration with solid phase microextraction (SPME) is a conventional technique for the enrichment of these volatile compounds before analysis by headspace gas chromatography-mass spectrometry (GC-MS). However, commercially available SPME products usually bear the defects of weak mechanical strength and high cost. In this work, novel SPME fibers were prepared by a one-pot synthesis procedure from divinylbenzene (DVB), porous carbon powder (Carbon) and polydimethylsiloxane (PDMS). Factors that influence the extraction efficiency, such as extraction temperature, extraction time, salting effects, pH, stirring rate, desorption temperature and time, were optimized. VOCs in landfills pose a great threat to human health and the environment. The new SPME fibers were successfully applied in the analysis of VOCs from the leachate of a cyanobacteria landfill. Quantification methods of major odor contributors were established, and a good linearity (r > 0.998) was obtained, with detection limits in the range of 0.30–0.50 ng/L. Compared to commercial SPME fibers, the new material has higher extraction efficacy and higher precision. Hence, it is suitable for the determination of hazardous odorants of various sources.

Anti-Virulence Activity of 3,3′-Diindolylmethane (DIM): A Bioactive Cruciferous Phytochemical with Accelerated Wound Healing Benefits

Antimicrobial resistance is among the top global health problems with antibacterial resistance currently representing the major threat both in terms of occurrence and complexity. One reason current treatments of bacterial diseases are ineffective is the occurrence of protective and resistant biofilm structures. Phytochemicals are currently being reviewed for newer anti-virulence agents. In the present study, we aimed to investigate the anti-virulence activity of 3,3′-diindolylmethane (DIM), a bioactive cruciferous phytochemical. Using a series of in vitro assays on major Gram-negative pathogens, including transcriptomic analysis, and in vivo porcine wound studies as well as in silico experiments, we show that DIM has anti-biofilm activity. Following DIM treatment, our findings show that biofilm formation of two of the most prioritized bacterial pathogens Acinetobacter baumannii and Pseudomonas aeruginosa was inhibited respectively by 65% and 70%. Combining the antibiotic tobramycin with DIM enabled a high inhibition (94%) of P. aeruginosa biofilm. A DIM-based formulation, evaluated for its wound-healing efficacy on P. aeruginosa-infected wounds, showed a reduction in its bacterial bioburden, and wound size. RNA-seq was used to evaluate the molecular mechanism underlying the bacterial response to DIM. The gene expression profile encompassed shifts in virulence and biofilm-associated genes. A network regulation analysis showed the downregulation of 14 virulence-associated super-regulators. Quantitative real-time PCR verified and supported the transcriptomic results. Molecular docking and interaction profiling indicate that DIM can be accommodated in the autoinducer- or DNA-binding pockets of the virulence regulators making multiple non-covalent interactions with the key residues that are involved in ligand binding. DIM treatment prevented biofilm formation and destroyed existing biofilm without affecting microbial death rates. This study provides evidence for bacterial virulence attenuation by DIM.

Investigation of indole biodegradation by Cupriavidus sp. strain IDO with emphases on downstream biotransformation and indigo production

Indole, as a typical N-heterocyclic aromatic pollutant, poses risks to living things; however, indole-biotransformation mechanisms remain under-discussed, especially those related to its downstream biotransformation. Here, we systematically investigated the characteristics of indole degradation by strain Cupriavidus sp. IDO. We found that Cupriavidus sp. IDO could utilize 25 to 150 mg/L indole within 40 h and identified three intermediates (2-oxindole, indigo, and isatin). Additionally, integrated genomics and proteomics analysis of the indole biotransformation mechanism in strain IDO revealed 317 proteins showing significant changes (262 upregulated and 55 downregulated) in the presence of indole. Among these, three clusters containing indole oxidoreductase, CoA-thioester ligase, and gentisate 1,2-oxidoreductase were identified as potentially responsible for upstream and downstream indole metabolism. Moreover, HPLC-MS and -omics analysis offered insight into the indole-degradation pathway in strain IDO. Furthermore, the indole oxidoreductase IndAB, which initiates indole degradation, was heterologously expressed in Escherichia coli BL21(DE3). Optimization by the response surface methodology resulted in a maximal production of 135.0 mg/L indigo by the recombination strains in tryptophan medium. This work enriches our understanding of the indole-biodegradation process and provides new insights into multiple indole-degradation pathways in natural environments.

Novel anti-adipogenic effect of CF3-allylated indole in 3T3-L1 cells

Indole derivatives from various plants are known to have health benefits because of their anti-cancer, anti-oxidant, anti-inflammatory, and anti-tubercular effects. However, their effects on adipogenesis have not been fully elucidated yet. Herein, we show that a newly synthesized indole derivative, CF₃-allylated indole, [(E)-1-(pyrimidin- 2-yl)-2-(4,4,4- trifluorobut-2-enyl)-1H-indole], effectively inhibits adipogenesis. We found that CF₃-allylated indole inhibited lipid accumulation and suppressed the expression of CCAAT/enhancer-binding protein α (C/EBPα) and peroxisome proliferator activated receptor γ (PPARγ) in 3T3-L1 cells. The inhibitory effect of CF₃-allylated indole primarily occurred at the early phase of adipocyte differentiation by increasing intracellular cyclic adenosine monophosphate (cAMP) levels and enhancing protein kinase A (PKA) and adenosine monophosphate-activated protein kinase (AMPK) signaling. Conversely, depletion of PKA or treatment with a protein kinase A inhibitor (H89) reversed such inhibitory effects of CF₃-allylated indole on adipogenesis and PPARγ expression. These results suggest that CF₃-allylated indole inhibits early stages of adipogenesis by increasing phosphorylation of PKA/AMPK, leading to decreased expression of adipogenic genes in 3T3-L1 cells. These results indicate that CF₃-allylated indole has potential for controlling initial adipocyte differentiation in metabolic disorders such as obesity.

Label-Free Quantitative Proteomic Analysis of the Global Response to Indole-3-Acetic Acid in Newly Isolated Pseudomonas sp. Strain LY1

Indole-3-acetic acid (IAA), known as a common plant hormone, is one of the most distributed indole derivatives in the environment, but the degradation mechanism and cellular response network to IAA degradation are still not very clear. The objective of this study was to elucidate the molecular mechanisms of IAA degradation at the protein level by a newly isolated strain Pseudomonas sp. LY1. Label-free quantitative proteomic analysis of strain LY1 cultivated with IAA or citrate/NH₄Cl was applied. A total of 2,604 proteins were identified, and 227 proteins have differential abundances in the presence of IAA, including 97 highly abundant proteins and 130 less abundant proteins. Based on the proteomic analysis an IAA degrading (iad) gene cluster in strain LY1 containing IAA transformation genes (organized as iadHABICDEFG), genes of the β-ketoadipate pathway for catechol and protocatechuate degradation (catBCA and pcaABCDEF) were identified. The iadA, iadB, and iadE-disrupted mutants lost the ability to grow on IAA, which confirmed the role of the iad cluster in IAA degradation. Degradation intermediates were analyzed by HPLC, LC-MS, and GC-MS analysis. Proteomic analysis and identified products suggested that multiple degradation pathways existed in strain LY1. IAA was initially transformed to dioxindole-3-acetic acid, which was further transformed to isatin. Isatin was then transformed to isatinic acid or catechol. An in-depth data analysis suggested oxidative stress in strain LY1 during IAA degradation, and the abundance of a series of proteins was upregulated to respond to the stress, including reaction oxygen species (ROS) scavenging, protein repair, fatty acid synthesis, RNA protection, signal transduction, chemotaxis, and several membrane transporters. The findings firstly explained the adaptation mechanism of bacteria to IAA degradation.

Influence of cultivation conditions on IAA - producing activity of endophytic bacterial strains isolated from morning-glory (IPOMOEA PES-CAPRAE (L.) R.Br.)

This work presents the experimental study results of the influence of the culture medium on the ability to IAA synthesis of three endophytic strains TH10R, TH11T, and TH13T from roots of Ipomoea pes-caprae. Three investigated strains give the highest IAA concentration after 96 h of cultivation. A significant increase in IAA biosynthesis was obtained by cultivating the TH10R strain in a medium containing lactose or starch as a carbon source and NH4Cl or KNO3 as a nitrogen source. The TH11T strain produces the maximum amount of IAA, using glucose or xylose and KNO3 or NH4NO3 as carbon and nitrogen sources, respectively. Sucrose is a suitable carbon source for the TH13T strain; on a sucrose-containing medium, the TH13T strain produces the highest IAA amount. The most active strain is TH10R, identified as Bacillus mycoides and named Bacillus mycoides TH10R.

Physiological Response of Corynebacterium glutamicum to Indole

The aromatic heterocyclic compound indole is widely spread in nature. Due to its floral odor indole finds application in dairy, flavor, and fragrance products. Indole is an inter- and intracellular signaling molecule influencing cell division, sporulation, or virulence in some bacteria that synthesize it from tryptophan by tryptophanase. Corynebacterium glutamicum that is used for the industrial production of amino acids including tryptophan lacks tryptophanase. To test if indole is metabolized by C. glutamicum or has a regulatory role, the physiological response to indole by this bacterium was studied. As shown by RNAseq analysis, indole, which inhibited growth at low concentrations, increased expression of genes involved in the metabolism of iron, copper, and aromatic compounds. In part, this may be due to iron reduction as indole was shown to reduce Fe³⁺ to Fe²⁺ in the culture medium. Mutants with improved tolerance to indole were selected by adaptive laboratory evolution. Among the mutations identified by genome sequencing, mutations in three transcriptional regulator genes were demonstrated to be causal for increased indole tolerance. These code for the regulator of iron homeostasis DtxR, the regulator of oxidative stress response RosR, and the hitherto uncharacterized Cg3388. Gel mobility shift analysis revealed that Cg3388 binds to the intergenic region between its own gene and the iolT2-rhcM2D2 operon encoding inositol uptake system IolT2, maleylacetate reductase, and catechol 1,2-dioxygenase. Increased RNA levels of rhcM2 in a cg3388 deletion strain indicated that Cg3388 acts as repressor. Indole, hydroquinone, and 1,2,4-trihydroxybenzene may function as inducers of the iolT2-rhcM2D2 operon in vivo as they interfered with DNA binding of Cg3388 at physiological concentrations in vitro. Cg3388 was named IhtR.

Screening and optimization of indole-3-acetic acid production by Rhizobium sp. strain using response surface methodology

BACKGROUND

The production of indole-3-acetic acid (IAA) is an essential tool for rhizobacteria to stimulate and facilitate plant growth. For this, eighty rhizobial bacteria isolated from root nodules of Acacia cyanophylla grown in different regions of Morocco were firstly screened for their ability to produce IAA. Then, IAA production by a combination of isolates and the inoculation effect on the germination of Acacia cyanophylla seeds was studied using the best performing isolates in terms of IAA production. The best IAA producer bacterial isolate (I69) was selected to optimize IAA production using response surface methodology based on the central composite design.

RESULTS

Results showed that the majority of tested isolates were able to produce IAA with a relatively higher concentration of 135 μg/ml for the isolate I69, followed by isolates I22 and I75 with respective concentrations of 116 μg/ml and 105 μg/ml IAA. The IAA production and the seed germination rate were relatively increased by the synergistic effect of I69 and I22. Later, response surface methodology was used to determine optimal operating conditions leading to IAA production optimization. Thus, an incubation temperature of 36 °C, a pH of 6.5, an incubation time of 1 day, and respective tryptophan and NaCl concentrations of 1 g/l and 0.1 g/l were optimal parameters leading to 166 μg/ml IAA which was the maximal produced concentration.

CONCLUSION

The present study highlighted that IAA-producing rhizobacteria could be harnessed to improve plant growth. Furthermore, their production can be easily controlled using response surface methodology, which represents a very useful tool for optimization.

Indigoid dyes by group E monooxygenases: mechanism and biocatalysis

Since ancient times, people have been attracted by dyes and they were a symbol of power. Some of the oldest dyes are indigo and its derivative Tyrian purple, which were extracted from plants and snails, respectively. These 'indigoid dyes' were and still are used for coloration of textiles and as a food additive. Traditional Chinese medicine also knows indigoid dyes as pharmacologically active compounds and several studies support their effects. Further, they are interesting for future technologies like organic electronics. In these cases, especially the indigo derivatives are of interest but unfortunately hardly accessible by chemical synthesis. In recent decades, more and more enzymes have been discovered that are able to produce these indigoid dyes and therefore have gained attention from the scientific community. In this study, group E monooxygenases (styrene monooxygenase and indole monooxygenase) were used for the selective oxygenation of indole (derivatives). It was possible for the first time to show that the product of the enzymatic reaction is an epoxide. Further, we synthesized and extracted indigoid dyes and could show that there is only minor by-product formation (e.g. indirubin or isoindigo). Thus, group E monooxygenase can be an alternative biocatalyst for the biosynthesis of indigoid dyes.

Indole Degradation in a Model System and in Poultry Manure by Acinetobacter spp

Indole degradation in a model system and in poultry manure was studied using an enrichment culture of two Acinetobacter species; Acinetobacter toweneri NTA1-2A and Acinetobacter guillouiae TAT1-6A. Degradation of indole was quantified using reverse phase high performance liquid chromatography (HPLC). The two strains were capable of degrading initial concentrations of indole ranging from 58.58–300 mg/L. The degradation efficiency was 66.36% (NTA1-2A), 94.87% (TAT1-6A), and 96.00% (mix) in 6 days when the initial concentration <300 mg/L. The strains were tested for enzymatic activity using 120 mg/L indole. The enzyme extracts of NTA1-2A and TAT1-6A from culture medium degraded indole completely, and no appreciable change of indole concentration was witnessed in the control group. The NTA1-2A, TAT1-6A, and the mix of strains were also used for in vivo poultry manure fermentation and removed 78.67%, 83.28%, and 83.70% of indole, respectively in 8 d. The strains showed a statistically significant difference (p < 0.05) in indole removal efficiency compared with the control, but no significant difference between the two strains and the mix in indole removal capacity. We concluded that A. toweneri NTA1-2A and A. guillouiae TAT1-6A are promising strains to remove indole and its derivatives to control the notorious odor in poultry and other livestock industries.

Characterization and functional gene analysis of a newly isolated indole-degrading bacterium Burkholderia sp. IDO3

Indole is a common N-heterocyclic pollutant as well as a signaling molecule widespread in various environmental matrices. Several bacterial strains have been reported to be able to degrade indole, while the degradation capacity and functional enzymes are poorly documented. Herein, the degradation characteristics of a newly-isolated indole-degrading strain Burkholderia sp. IDO3 were carefully investigated. Strain IDO3 exhibited superior degradation ability which could completely remove 100 mg/L indole within 14 h in mineral salt medium. It maintained comparable degradation performance under conditions of pH 4.0-9.0, temperature 25-35 °C and rotary speed 0-250 r/min, and most of the tested heavy metals and organic pollutants did not significantly affect the degradation process. Two important intermediates, i.e. isatin and anthranilate, were identified in indole degradation process. The genomic clone library technique with indigo-based screening method was successfully applied to screen the functional genes. Heterologous expression assay proved that recombinant E. coli strain carrying indole oxygenase and reductase genes iifCD could transform indole to indigo. Bioinformatic analyses indicated that the newly obtained enzyme IifC_IDO3 formed a phylogenetically separate branch from other related aromatic oxygenases. This study provides new insights into our understanding of indole degradation by Burkholderia strains and offers efficient bacterial resource for indole bioremediation.

Isolation and characterization of two Acinetobacter species able to degrade 3-methylindole

3-Methylindole (3MI) or Skatole is a volatile lipophilic organic compound produced by anoxic metabolism of L-tryptophan and associated with animal farming and industrial processing wastes. Pure cultures of bacteria capable of utilizing 3MI were isolated from chicken manure using enrichment culture techniques. The bacteria were identified as Acinetobacter toweneri NTA1-2A and Acinetobacter guillouiae TAT1-6A, based on 16S rDNA gene amplicon sequence data. The optimal temperature and pH for degradation of 3MI were established using single factor experiments. Strain tolerance was assessed over a range of initial concentrations of 3MI, and the effects of initial concentration on subsequent microbial 3MI degradation were also measured. During the degradation experiment, concentrations of 3MI were quantified by reverse-phase high-performance liquid chromatography (HPLC). The strains were capable of degrade initial concentrations of 3MI ranging from 65–200 mg/L. The degradation efficiency was >85% in 6 days for both strains when the initial concentration is less than 200 mg/L. The strains were tested for enzymatic activity using 65 mg/L 3MI. The enzyme extracts of NTA1-2A and TAT1-6A from the 3MI medium degraded 71.46% and 60.71% of 3MI respectively, but no appreciable change in 3MI concentration in the control group was witnessed. Our experiment revealed betaine and choline were identified as 3MI degradation metabolites by both strains while nitroso-pyrrolidine and beta-alaninebetaine formed by NTA1-2A and TAT1-6A strains respectively. The NTA1-2A and TAT1-6A strains removed 84.32% and 81.39% 3MI respectively from chicken manure during fermentation in 8 days and showed a statistically significant difference (P < 0.05) compared with the control group. The optimum temperature and pH were 31°C and 6 respectively, for 3MI degradation by A. toweneri NTA1-2A and A. guillouiae TAT1-6A. We concluded that A. toweneri NTA1-2A and A. guillouiae TAT1-6A are potential strains of interest to degrade 3MI and control odorant in poultry and other livestock industries.

Biodegradation and Biotransformation of Indole: Advances and Perspectives

Indole is long regarded as a typical N-heterocyclic aromatic pollutant in industrial and agricultural wastewater, and recently it has been identified as a versatile signaling molecule with wide environmental distributions. An exponentially growing number of researches have been reported on indole due to its significant roles in bacterial physiology, pathogenesis, animal behavior and human diseases. From the viewpoint of both environmental bioremediation and biological studies, the researches on metabolism and fates of indole are important to realize environmental treatment and illuminate its biological function. Indole can be produced from tryptophan by tryptophanase in many bacterial species. Meanwhile, various bacterial strains have obtained the ability to transform and degrade indole. The characteristics and pathways for indole degradation have been investigated for a century, and the functional genes for indole aerobic degradation have also been uncovered recently. Interestingly, many oxygenases have proven to be able to oxidize indole to indigo, and this historic and motivating case for biological applications has attracted intensive attention for decades. Herein, the bacteria, enzymes and pathways for indole production, biodegradation and biotransformation are systematically summarized, and the future researches on indole-microbe interactions are also prospected.

Unveiling the biotransformation mechanism of indole in a Cupriavidus sp. strain

Indole, an important signaling molecule as well as a typical N-heterocyclic aromatic pollutant, is widespread in nature. However, the biotransformation mechanisms of indole are still poorly studied. Here, we sought to unlock the genetic determinants of indole biotransformation in strain Cupriavidus sp. SHE based on genomics, proteomics and functional studies. A total of 177 proteins were notably altered (118 up- and 59 downregulated) in cells grown in indole mineral salt medium when compared with that in sodium citrate medium. RT-qPCR and gene knockout assays demonstrated that an indole oxygenase gene cluster was responsible for the indole upstream metabolism. A functional indole oxygenase, termed IndA, was identified in the cluster, and its catalytic efficiency was higher than those of previously reported indole oxidation enzymes. Furthermore, the indole downstream metabolism was found to proceed via the atypical CoA-thioester pathway rather than conventional gentisate and salicylate pathways. This unusual pathway was catalyzed by a conserved 2-aminobenzoyl-CoA gene cluster, among which the 2-aminobenzoyl-CoA ligase initiated anthranilate transformation. This study unveils the genetic determinants of indole biotransformation and will provide new insights into our understanding of indole biodegradation in natural environments and its functional studies.

Indole Biodegradation in Acinetobacter sp. Strain O153: Genetic and Biochemical Characterization

Indole is a molecule of considerable biochemical significance, acting as both an interspecies signal molecule and a building block of biological elements. Bacterial indole degradation has been demonstrated for a number of cases; however, very little is known about genes and proteins involved in this process. This study reports the cloning and initial functional characterization of genes (iif and ant cluster) responsible for indole biodegradation in Acinetobacter sp. strain O153. The catabolic cascade was reconstituted in vitro with recombinant proteins, and each protein was assigned an enzymatic function. Degradation starts with oxidation, mediated by the IifC and IifD flavin-dependent two-component oxygenase system. Formation of indigo is prevented by IifB, and the final product, anthranilic acid, is formed by IifA, an enzyme which is both structurally and functionally comparable to cofactor-independent oxygenases. Moreover, the iif cluster was identified in the genomes of a wide range of bacteria, suggesting the potential of widespread Iif-mediated indole degradation. This work provides novel insights into the genetic background of microbial indole biodegradation.IMPORTANCE The key finding of this research is identification of the genes responsible for microbial biodegradation of indole, a toxic N-heterocyclic compound. A large amount of indole is present in urban wastewater and sewage sludge, creating a demand for an efficient and eco-friendly means to eliminate this pollutant. A common strategy of oxidizing indole to indigo has the major drawback of producing insoluble material. Genes and proteins of Acinetobacter sp. strain O153 (DSM 103907) reported here pave the way for effective and indigo-free indole removal. In addition, this work suggests possible novel means of indole-mediated bacterial interactions and provides the basis for future research on indole metabolism.

Microbiota and Lipotoxicity

Obesity and metabolic syndrome is a multisystemic disorder, that is characterized by excess caloric intake and spillover lipotoxicity caused by ectopic lipid accumulation in non-adipose tissues. Low grade chronic inflammation and insulin resistance are the hallmarks of the disorder, which further aggravate the condition. Gut microbiota constitutes an indispensible part of human superorganism's energy harvesting apparatus. The dynamic composition of microbiota changes with age, life style and host metabolic background. The wealth of genetic repertoire provided by these microorganism enables to extend host's substrate processing and harvesting capability. Some of these compounds including short chain fatty acids and indole act as signalling molecules on mammalian cells and modulate their behaviour. Nonetheless, this symbiotic style of interaction is restrained by immune system. The role of chronic low grade inflammation in metabolic syndrome is well established. Treg cells are the key players that sense and reshape the composition of microbiota. In this regard, any disturbance in Treg functionality may aggravate the inflammation and shift the symbiotic balance towards dysbiosis, which is characterized by autoimmunity and insulin resistance. Thus, immune system is responsible for the modulation of host and microbiota metabolisms and Treg cells act as a bridge in between.

Continuous production of indole-3-acetic acid by immobilized cells of Arthrobacter agilis

Indole acetic acid (IAA) is a plant growth-promoting hormone used in agriculture; therefore, its continuous production is of paramount importance. IAA-producing eight bacteria were isolated from the rhizosphere of Verbascum vulcanicum. Among them, Arthrobacter agilis A17 gave maximum IAA production (75 mg/L) and this strain was used to immobilization studies. The A. agilis A17 cells were immobilized in calcium alginate for the production of IAA. Optimization of process parameters for IAA production was carried out to enhance IAA production using immobilized cells. The maximal production of IAA was 520 mg/L under the following optimal conditions: 1% mannitol, 30 °C, pH 8.0, and 24 h incubation. It was determined that the immobilized cells could be reused (13 times) for the production of IAA.

Biochemical and Genetic Bases of Indole-3-Acetic Acid (Auxin Phytohormone) Degradation by the Plant-Growth-Promoting Rhizobacterium Paraburkholderia phytofirmans PsJN

Several bacteria use the plant hormone indole-3-acetic acid (IAA) as a sole carbon and energy source. A cluster of genes (named iac) encoding IAA degradation has been reported in Pseudomonas putida 1290, but the functions of these genes are not completely understood. The plant-growth-promoting rhizobacterium Paraburkholderia phytofirmans PsJN harbors iac gene homologues in its genome, but with a different gene organization and context than those of P. putida 1290. The iac gene functions enable P. phytofirmans to use IAA as a sole carbon and energy source. Employing a heterologous expression system approach, P. phytofirmans iac genes with previously undescribed functions were associated with specific biochemical steps. In addition, two uncharacterized genes, previously unreported in P. putida and found to be related to major facilitator and tautomerase superfamilies, are involved in removal of an IAA metabolite called dioxindole-3-acetate. Similar to the case in strain 1290, IAA degradation proceeds through catechol as intermediate, which is subsequently degraded by ortho-ring cleavage. A putative two-component regulatory system and a LysR-type regulator, which apparently respond to IAA and dioxindole-3-acetate, respectively, are involved in iac gene regulation in P. phytofirmans These results provide new insights about unknown gene functions and complex regulatory mechanisms in IAA bacterial catabolism.

IMPORTANCE

This study describes indole-3-acetic acid (auxin phytohormone) degradation in the well-known betaproteobacterium P. phytofirmans PsJN and comprises a complete description of genes, some of them with previously unreported functions, and the general basis of their gene regulation. This work contributes to the understanding of how beneficial bacteria interact with plants, helping them to grow and/or to resist environmental stresses, through a complex set of molecular signals, in this case through degradation of a highly relevant plant hormone.

Metagenomic approach to characterize soil microbial diversity of Phumdi at Loktak Lake

Loktak, one of the largest freshwater lakes of India, is known for floating islands (Phumdi), being made up of a heterogeneous biomass of vegetation and soil. This ecological site represents an exclusive environmental habitat wherein the rhizospheric microbial community of Phumdi plays a key role in biogeochemical cycling of nutrients. A culture-independent whole genome shotgun sequencing based metagenomic approach was employed to unravel the composition of the microbial community and its corresponding functional potential at this environmental habitat. Proteobacteria (51%) was found to be the most dominant bacterial phylum followed by Acidobacteria (10%), Actinobacteria (9%) and Bacteroidetes (7%). Furthermore, Loktak metagenome data were compared with available metagenomes from four other aquatic habitats, varying from pristine to highly polluted eutrophic habitats. The comparative metagenomics approach aided by statistical analysis revealed that Candidatus Solibacter, Bradyrhizobium, Candidatus Koribacter, Pedosphaera, Methylobacterium, Anaeromyxobacter, Sorangium, Opitutus and Acidobacterium genera are selectively dominant at this habitat. Correspondingly, 12 different functional categories were found to be exclusively prevalent at Phumdi compared to other freshwater habitats. These differential features have been attributed to the unique habitat at Phumdi and correlated to the phenomenon of bioremediation at Loktak Lake.

Transcriptome of the Australian Mollusc Dicathais orbita Provides Insights into the Biosynthesis of Indoles and Choline Esters

Dicathais orbita is a mollusc of the Muricidae family and is well known for the production of the expensive dye Tyrian purple and its brominated precursors that have anticancer properties, in addition to choline esters with muscle-relaxing properties. However, the biosynthetic pathways that produce these secondary metabolites in D. orbita are not known. Illumina HiSeq 2000 transcriptome sequencing of hypobranchial glands, prostate glands, albumen glands, capsule glands, and mantle and foot tissues of D. orbita generated over 201 million high quality reads that were de novo assembled into 219,437 contigs. Annotation with reference to the Nr, Swiss-Prot and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases identified candidate-coding regions in 76,152 of these contigs, with transcripts for many enzymes in various metabolic pathways associated with secondary metabolite biosynthesis represented. This study revealed that D. orbita expresses a number of genes associated with indole, sulfur and histidine metabolism pathways that are relevant to Tyrian purple precursor biosynthesis, and many of which were not found in the fully annotated genomes of three other molluscs in the KEGG database. However, there were no matches to known bromoperoxidase enzymes within the D. orbita transcripts. These transcriptome data provide a significant molecular resource for gastropod research in general and Tyrian purple producing Muricidae in particular.

Biotransformation of Indole to 3-Methylindole byLysinibacillus xylanilyticusStrain MA

An indole-biotransforming strain MA was identified asLysinibacillus xylanilyticuson the basis of the 16S rRNA gene sequencing. It transforms indole completely from the broth culture in the presence of an additional carbon source (i.e., sodium succinate). Gas-chromatography-mass spectrometry identified indole-3-acetamide, indole-3-acetic acid, and 3-methylindole as transformation products. Tryptophan-2-monooxygenase activity was detected in the crude extracts of indole-induced cells of strain MA, which confirms the formation of indole-3-acetamide from tryptophan in the degradation pathway of indole. On the basis of identified metabolites and enzyme assay, we have proposed a new transformation pathway for indole degradation. Indole was first transformed to indole-3-acetamide via tryptophan. Indole-3-acetamide was then transformed to indole-3-acetic acid that was decarboxylated to 3-methylindole. This is the first report of a 3-methylindole synthesis via the degradation pathway of indole.