Genus Dietzia Research Articles

Halotolerant Benzoic Acid-Degrading Bacteria of the Genus <i>Dietzia</i>

Six benzoic acid-degrading bacteria of the genus Dietzia were isolated from the saline ecotopes of the Verkhnekamskoe and Yakshinskoe salt deposits (Perm region, Komi Republic, Russia). Benzoic acid (BA) may accumulate in ecosystems through technogenic processes, as well as during the microbiological decomposition of complex organic compounds containing an aromatic ring. The strains studied here were found to be closely related to D. psychralcaliphila, D. kunjamensis subsp. kunjamensis, D. cercidiphylli, and D. maris. It was shown that they are halotolerant and able to thrive on BA as their sole carbon and energy source in the absence of salt or in the presence of 50–70 g/L NaCl. They also contain benA genes encoding the α-subunit of benzoate 1,2-dioxygenase, the key enzyme of BA degradation. The highest level of similarity (79.32–91.38%) was observed between the nucleotide sequences of the benA genes of the strains considered and the homologous sequences of Actinomycetes representatives from genera such as Dietzia, Mycolicibacterium, Geodermatophilus, Pseudonocardia, Corynebacterium, and Raineyella. The described active BA degraders belonging to the genus Dietzia have the potential to aid in the development of bioremediation techniques for environmental objects contaminated with mono(poly)aromatic pollutants and subject to salting.

Comparative genomic analysis of the Dietzia genus: an insight into genomic diversity, and adaptation

Dietzia strains are widely distributed in the environment, presenting an opportunistic role, and some species have undetermined taxonomic characteristics. Here, we propose the existence of errors in the classification of species in this genus using comparative genomics. We performed ANI, dDDH, pangenome and genomic plasticity analyses better to elucidate the phylogenomic relationships between Dietzia strains. For this, we used 55 genomes of Dietzia downloaded from public databases that were combined with a newly sequenced. Sequence analysis of a phylogenetic tree based on genome similarity comparisons and dDDH, ANI analyses supported grouping different Dietzia species into four distinct groups. The pangenome analysis corroborated the classification of these groups, supporting the idea that some species of Dietzia could be reassigned in a possible classification into three distinct species, each containing less variability than that found within the global pangenome of all strains. Additionally, analysis of genomic plasticity based on groups containing Dietzia strains found differences in the presence and absence of symbiotic Islands and pathogenic islands related to their isolation site. We propose that the comparison of pangenome subsets together with phylogenomic approaches can be used as an alternative for the classification and differentiation of new species of the genus Dietzia.

Ontogeny, species identity, and environment dominate microbiome dynamics in wild populations of kissing bugs (Triatominae)

BackgroundKissing bugs (Triatominae) are blood-feeding insects best known as the vectors of Trypanosoma cruzi, the causative agent of Chagas’ disease. Considering the high epidemiological relevance of these vectors, their biology and bacterial symbiosis remains surprisingly understudied. While previous investigations revealed generally low individual complexity but high among-individual variability of the triatomine microbiomes, any consistent microbiome determinants have not yet been identified across multiple Triatominae species.MethodsTo obtain a more comprehensive view of triatomine microbiomes, we investigated the host-microbiome relationship of five Triatoma species sampled from white-throated woodrat (Neotoma albigula) nests in multiple locations across the USA. We applied optimised 16S rRNA gene metabarcoding with a novel 18S rRNA gene blocking primer to a set of 170 T. cruzi-negative individuals across all six instars.ResultsTriatomine gut microbiome composition is strongly influenced by three principal factors: ontogeny, species identity, and the environment. The microbiomes are characterised by significant loss in bacterial diversity throughout ontogenetic development. First instars possess the highest bacterial diversity while adult microbiomes are routinely dominated by a single taxon. Primarily, the bacterial genus Dietzia dominates late-stage nymphs and adults of T. rubida, T. protracta, and T. lecticularia but is not present in the phylogenetically more distant T. gerstaeckeri and T. sanguisuga. Species-specific microbiome composition, particularly pronounced in early instars, is further modulated by locality-specific effects. In addition, pathogenic bacteria of the genus Bartonella, acquired from the vertebrate hosts, are an abundant component of Triatoma microbiomes.ConclusionOur study is the first to demonstrate deterministic patterns in microbiome composition among all life stages and multiple Triatoma species. We hypothesise that triatomine microbiome assemblages are produced by species- and life stage-dependent uptake of environmental bacteria and multiple indirect transmission strategies that promote bacterial transfer between individuals. Altogether, our study highlights the complexity of Triatominae symbiosis with bacteria and warrant further investigation to understand microbiome function in these important vectors.26uaj7E81qJUzay5q4KdpFVideo abstract.

Pan-genomic analysis reveals that the evolution of Dietzia species depends on their living habitats.

The bacterial genus Dietzia is widely distributed in various environments. The genomes of 26 diverse strains of Dietzia, including almost all the type strains, were analysed in this study. This analysis revealed a lipid metabolism gene richness, which could explain the ability of Dietzia to live in oil related environments. The pan-genome consists of 83,976 genes assigned into 10,327 gene families, 792 of which are shared by all the genomes of Dietzia. Mathematical extrapolation of the data suggests that the Dietzia pan-genome is open. Both gene duplication and gene loss contributed to the open pan-genome, while horizontal gene transfer was limited. Dietzia strains primarily gained their diverse metabolic capacity through more ancient gene duplications. Phylogenetic analysis of Dietzia isolated from aquatic and terrestrial environments showed two distinct clades from the same ancestor. The genome sizes of Dietzia strains from aquatic environments were significantly larger than those from terrestrial environments, which was mainly due to the occurrence of more gene loss events during the evolutionary progress of the strains from terrestrial environments. The evolutionary history of Dietzia was tightly coupled to environmental conditions, and iron concentrations should be one of the key factors shaping the genomes of the Dietzia lineages.

A succession of marine bacterial communities in batch reactor experiments during the degradation of five different petroleum types

Marine microbial communities might be subjected to accidental petroleum spills; however, some bacteria can degrade it, making these specific bacteria valuable for bioremediation from petroleum contamination. Thus, characterizing the microbial communities exposed to varying types of petroleum is essential. We evaluated five enriched microbial communities from the northwest Gulf of Mexico (four from the water column and one from sediments). Enrichments were performed using five types of petroleum (extra light, light, medium, heavy and extra heavy), to reveal the microbial succession using a 16S rDNA amplicon approach. Four communities were capable of degrading from extra light to heavy petroleum. However, only the community from sediment was able to degrade the extra heavy petroleum. Successional changes in the microbial communities' structures were specific for each type of petroleum where genus Dietzia, Gordonia, Microvirga, Rhizobium, Paracoccus, Thalassobaculum, Sphingomonas, Moheibacter, Acinetobacter, Pseudohongiella, Porticoccus, Pseudoalteromonas, Pseudomonas, Shewanella, and Planctomyces presented differential abundance between the treatments.

Lipids of Dietzia sp. A14101. Part I: A study of the production dynamics of surface-active compounds

Dietzia sp. A14101 belonging to the genus Dietzia (Gram-positive bacteria, Actinomycetes, high G+C content of DNA) was isolated from an oil reservoir model column inoculated with oil-field bacteria (Bødtker et al., 2009). Low interfacial tension (IFT) values were obtained by studying intact strain cells grown on water-immiscible hydrocarbons (HC) (Kowalewski et al. (2004), Kowalewski et al. (2005). Further investigations showed that the adaptation mechanism of Dietzia sp. A14101 to toxic water-immiscible HC involved changes both on the level of fatty acids content and in the physical properties of the cellular surface (development of the negative cellular surface charge and an increased in hydrophobicity) (Hvidsten et al., 2015b). However, these changes could not explain the low IFT values observed in earlier studies of this strain. Generally, low IFT imply a production of surface active compounds of low MW that are lipids by structure (Rosenberg and Ron, 1999).In this paper, it is shown that Dietzia sp. A14101 produces a range of glycolipids on all substrates. The amount of trehalose-containing lipids increases when the strain is grown on hydrocarbons. The production peak seems to coincide with the exponential growth phase, and such increased glycolipid synthesis continues throughout the stationary phase. The results indicate that only low amounts of the hydrocarbon substrate is incorporated directly into the glycolipids produced. Most of the hydrocarbon substrate seems to be employed for the biosynthesis of the neutral lipids and higher amounts of biomass were generated on HC substrates compared to incubations on non-HC substrates.The lipid content of the cell was determined as the total lipid extract (TLE), and was further fractionated (SPE). The hydrophobic and hydrophilic moieties of the isolated surface active compounds were determined (GC–MS, TLC, DART, LC–MS). The changes in the lipid content during the culture development were monitored by 1D and 2D TLC, emulsification and oil-spreading tests.

High efficiency degradation of alkanes and crude oil by a salt-tolerant bacterium Dietzia species CN-3

A bacterial strain, CN-3, was isolated from petroleum-contaminated sediment in Bohai Bay, China. Morphological, physiological and phylogenetic analyses indicated that the strain belonged to the genus Dietzia. It was capable of utilizing a wide range of alkanes (C14–C31), aromatic compounds and crude oil as the sole carbon and energy sources. The bacterium showed high degradation rate (>80%) of the saturated hydrocarbons of crude oil in the pH range of 6–9. The degradation rate was hardly affected at a NaCl concentration up to 85 g L−1, indicating that the strain can tolerate high salinities. The real-time quantitative Polymerase Chain Reaction (PCR) results showed that the CYP153 genes could be significantly induced by C14, C15, C16, C26 and pristane, whereas the transcription level of alkB gene was increased moderately with C14, C15, C16, C26 and pristane induction condition. A high degradation extent, wide substrate range and facile conditions enhanced the potential for this bacterial strain to be used in the bioremediation of crude oil pollution.

Commentary: Oil degradation and biosurfactant production by the deep sea bacterium Dietzia maris As-13-3.

Commentary: Oil degradation and biosurfactant production by the deep sea bacterium Dietzia maris As-13-3.

Editorial: Microbiotechnology Based Surfactants and Their Applications.

This editorial is an annotation on the exciting research topic “Microbiotechnology based surfactants and their applications” that covers a compilation of original research articles, reviews and mini-reviews submitted by researchers enthusiastically working in the field of biosurfactants.

Dietziamides, novel tetramic acid dimers from Dietzia timorensis MZ-3 with antioxidative activity

Dietziamides A and B, two novel tetramic acid dimers, were isolated from the rare actinomycetes Dietzia timorensis MZ-3 in the course of our HPLC-diode array screening of our collection of terrestrial actinomycetes. The spectroscopic analysis revealed the chemical structures of the first secondary metabolites characterized in the genus Dietzia. Dietziamides A and B showed moderate DPPH (1,1-diphenyl-2-picrylhydrazyl) radical scavenging activities.

Isolation and characterization of a novel strain of genus Dietzia capable of multiple-extreme resistance

An ultraviolet (UV) radiation resistant gram-positive bacterium, Dietzia sp. MG4 strain, was isolated from the Sirch Hot Spring (Kerman, Iran), then it was identified on the basis of morphological and biochemical characteristics, and 16S rRNA gene sequencing. The effects of temperature, pH, desiccation, different percentage of NaCl, hydrogen peroxide (H2O2), mitomycin C (MMC) and high levels of radiation on viability or growth rate of MG4 strain were investigated. Also heavy metal tolerance of MG4 strain was assayed. 16S rDNA sequence of the isolate exhibited 99.69% similarity with Dietzia sp. and this result was confirmed by phylogenetic analysis. Viability of this strain was obtained D91 according to D index after exposure to 25 J/cm2 UV radiation dose, and D30 after desiccation stress (for 28 days) using flow cytometery. The D10 value for a microorganism is defined as the stress dose necessary to provide 10% survivors. Therefore, this strain showed high resistance to UV-C radiation and moderate resistance to desiccation. Optimal growth of MG4 strain was observed at pH 9, temperature of 30°C and 5% (w/v) NaCl. Isolated Dietzia was resisted up to 3 mM of nickel and 0.2 mM of mercury ions. Also this strain could tolerate 1–4% (v/v) H2O2 and 8 µg/mL of MMC as oxidant agents. To the best of our knowledge, this is the first study on multiple extreme resistant Dietzia sp. MG4 strain.

Biodegradation of two Azo dyes using Dietzia sp. PD1: process optimization using Response Surface Methodology and Artificial Neural Network

A two level three factor (23) central composite design (CCD) was applied for optimization of the selected biodegradation process variables, i.e. initial solution pH (4–8), initial dye concentration (150–400 mg L−1), and time consumed for degradation (14–48 h) for studying the biodegradation of Congo red (CR) and Indigo carmine (IC) using the isolated novel bacterial strain, Dietzia sp. PD1. This is the first report of dye degradation for the genus Dietzia obtained so far. The optimum dye degradation efficiency of Dietzia sp. PD1, obtained from RSM modeling for CR, was found to be 99.97% (at 177.63 mg L−1 of initial dye concentration at pH 5.56 for 42.64 h) and for IC it was found to be 99.95% (at pH 5.85, concentration of dye 135.62 mg L−1 and time 43.29 h) at temperature 303 K and stirring speed 150 rpm. A strong correlation existed between the input process variables and the output parameter for degradation of dye using Artificial Neural Network (ANN). The model developed using Response Surface Methodology (RSM) and ANN showed a close interaction (% deviation ~ 0.6%) with the experimental values for both the dye degradation. The ability of the isolated Dietzia sp. PD1 for degrading two dyes of different chemical structure and properties endorses the possibility of applying it for the treatment of real industrial effluent bearing a mixture of different dyes.

Oil degradation and biosurfactant production by the deep sea bacterium Dietzia maris As-13-3.

Recent investigations of extreme environments have revealed numerous bioactive natural products. However, biosurfactant-producing strains from deep sea extreme environment are largely unknown. Here, we show that Dietzia maris As-13-3 isolated from deep sea hydrothermal field could produce di-rhamnolipid as biosurfactant. The critical micelle concentration (CMC) of the purified di-rhamnolipid was determined to be 120 mgL−1, and it lowered the surface tension of water from 74 ± 0.2 to 38 ± 0.2 mN m−1. Further, the alkane metabolic pathway-related genes and di-rhamnolipid biosynthesis-related genes were also analyzed by the sequencing genome of D. maris As-13-3 and quantitative real-time PCR (Q-PCR), respectively. Q-PCR analysis showed that all these genes were induced by n-Tetradecane, n-Hexadecane, and pristane. To the best of our knowledge, this is first report about the complete pathway of the di-rhamnolipid synthesis process in the genus Dietzia. Thus, our study provided the insights into Dietzia in respects of oil degradation and biosurfactant production, and will help to evaluate the potential of Dietzia in marine oil removal.

Biosorption of Congo red and Indigo carmine by nonviable biomass of a new Dietzia strain isolated from the effluent of a textile industry

A new bacterial strain, PD1, was isolated from the effluent of a textile industry. Phylogenetic analysis based on 16S rRNA gene sequence showed that the strain belonged to the genus Dietzia. The efficacy of the dried bacterial biomass as biosorbent for removal of acid dyes, namely Congo red (CR) and Indigo carmine (IC), from aqueous solutions was studied by performing batch equilibrium tests under different operating parameters such as initial dye concentration, pH, and temperature. The amount of dye adsorbed onto Dietzia sp. PD1 decreased with increasing pH while it increased with increasing temperature. The equilibrium biosorption data showed excellent fit to Langmuir isotherm as compared to Freundlich isotherm. The maximum biosorption capacity, calculated using the Langmuir model, were 170.34 and 188.71 mg g-1 for CR and IC, respectively. Analysis of kinetic data showed that the biosorption processes followed pseudo-second-order kinetics. The numerical value of the thermodynamic parameters (ΔG0, ΔH0, and ΔS0) indicated that biosorption of CR and IC was feasible, spontaneous, and endothermic under the examined conditions. The study shows that the isolated Dietzia strain can be used as an inexpensive and efficient biosorbent for removal of acid dyes from aqueous solution.

Simple and rapid characterization of mycolic acids from Dietzia strains by using MALDI spiral-TOFMS with ultra high mass-resolving power

Mycolic acids have been used as important chemotaxonomic markers. In this study, a newly developed matrix-assisted laser desorption/ionization time-of-flight mass spectrometer with a spiral ion trajectory (MALDI spiral-TOFMS) was applied to the characterization of mycolic acids of three type strains of validated species belonging to the genus Dietzia (D. papillomatosis 105045(T), D. kunjamensis NBRC 105042(T) and D. timorensis NBRC 104184(T)), by analysis of total fatty acid methyl ester fractions. In addition, owing to the high mass-resolving power of MALDI spiral-TOFMS, adjacent peaks (0.036 Da mass differences) were successfully separated, and weak peaks corresponding to oxygenated mycolic acids were detected. For all samples, the distributions of carbon-chain lengths were mainly in the range of C30-C42 and the average number of carbon-chain lengths was about 37, which agreed reasonably well with reported results for the genus Dietzia. The number of double bonds and/or cyclopropane rings was 0-2. Relative peak intensities of each mycolic acid methyl ester were used to compare the mycolic acids of the three strains. The mycolic acids of D. papillomatosis and D. kunjamensis were characterized by a high content of mycolic acids with 0-1 double bond or cyclopropane ring and an almost equal content of mycolic acids with odd- and even-numbered carbon-chain lengths. In contrast, mycolic acids of D. timorensis were characterized by a high content of mycolic acids with 1-2 double bonds and/or cyclopropane rings with an even-numbered carbon-chain length. By using MALDI spiral-TOFMS, mycolic acids from three type strains of the genus Dietzia were characterized easily and rapidly.

Potential applications and emerging trends of species of the genus Dietzia: a review

Interest in attractive biological sources with multicriteria applications has been increasing during recent years. This study scrutinized the applications of Dietzia bacteria for future prospects. Apart from such present and well-established applications—as in therapeutic biotreatments for adult paratuberculosis animals, production of carotenoid pigments, and animal feed additives—their uses in biosurfactants and biodemulsifiers production, the pollutants bioremediation, biodegradation of petroleum hydrocarbons and crude oil and also production of extracellular polymeric substances (EPSs) have been exploited. The use of these bacteria as a biotechnological tool may lead to improve the optimization and quality assurance of food ingredients and products, the capability of degradation and remediation of environmental pollutants, and the efficiency of bioconversion systems for energy recovery and bioprocessing of value-added products.

Characterization of Canthaxanthin Isomers Isolated from a New Soil Dietzia sp. and Their Antioxidant Activities

Canthaxanthin (cx) is a potent antioxidant that is chemically synthesized at the industrial scale and has imperative applications in the cosmetic and feed industries. An orange pigmented mesophilic bacterium, designated as K44, was isolated from soil samples of Kargil, India. Biochemical tests, 16S rRNA gene sequencing, and FAME analysis of the bacterium indicated it to belong in the genus Dietzia and is distinct from human isolates. The strain showed 98% 16S rRNA gene sequence homology with Dietzia maris DSM 43102. High-performance liquid chromatography profile of the pigments isolated from K44 showed two major peaks absorbing at 465.3 and 475 nm. The liquid chromatography-mass spectrometry (LC-MS) analysis of both these peaks revealed their m/z to be 564. The molecular weights, LC-MS/MS fragmentation patterns, and lambdamax of these fractions corresponded to all-trans- (475 nm) and 9-cis-(465.3 nm) cx isomers. The antioxidant activities of cis- and trans-cx isomers isolated from this bacterium were found to differ, where the cis-isomer showed higher free radical, superoxide radical, and reactive oxygen species scavenging activities than the alltrans- isomer, suggesting that 9-cis-cx is more effective as an antioxidant than the all-trans-cx.

Characterization of bacteria of the genus Dietzia: an updated review

The aim of this study was to characterize several aspects of species of the genus Dietzia, such as current taxonomic placement, morphological and growth characteristics, biochemical reactions, cellular lipid and fatty acid composition, the amino acids and sugars of whole-cell hydrolysates and the respiratory quinone system, and genomic guanine and cytosine (G + C) content. The species chosen for study were D. aerolata, D. alimentaria, D. aurantiaca, D. cerdiciphylli, D. cinnamea, D. kunjamensis, D. lutea, D. maris, D. natronolimnaea, D. papillomatosis, D. psychralcaliphila, D. schimae, and D. timorensis. The colony morphology study revealed that the colonies were small, smooth, circular and convex. Nitrate reduction, H2S production, hydrolysis of urea, starch, and Tween 80, and the Voges–Proskauer and methyl red tests were performed for biochemical differentiation of the various Dietzia strains. Optimum growth temperature and pH for the different strains were 25–30 °C and 7–8, respectively. Among the strains studied, D. timorensis ID05-A0528T had the lowest tolerance level to NaCl (7 %). This strain was also able to utilize a wide range of compounds as the sole carbon source. Short-chain mycolic acids were present in these bacteria. The cell wall contained meso-diaminopimelic acid, arabinose, and galactose; the glycan moiety of the cell wall contained acetyl residues. The major menaquinone was MK-8 (H2). The G + C contents of the DNA ranged from 64.7 (D. alimentaria 72T) to 73 mol % (D. maris DSM 43672T). The most important phospholipids in these strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol, and phosphatidylethanolamine.

Alkane-degrading properties of Dietzia sp. H0B, a key player in the Prestige oil spill biodegradation (NW Spain)

Investigation of the alkane-degrading properties of Dietzia sp. H0B, one of the isolated Corynebacterineae strains that became dominant after the Prestige oil spill. Using molecular and chemical analyses, the alkane-degrading properties of strain Dietzia sp. H0B were analysed. This Grampositive isolate was able to grow on n-alkanes ranging from C₁₂ to C₃₈ and branched alkanes (pristane and phytane). 8-Hexadecene was detected as an intermediate of hexadecane degradation by Dietzia H0B, suggesting a novel alkane-degrading pathway in this strain. Three putative alkane hydroxylase genes (one alkB homologue and two CYP153 gene homologues of cytochrome P450 family) were PCR-amplified from Dietzia H0B and differed from previously known hydroxylase genes, which might be related to the novel degrading activity observed on Dietzia H0B. The alkane degradation activity and the alkB and CYP153 gene expression were observed constitutively regardless of the presence of the substrate, suggesting additional, novel pathways for alkane degradation. The results from this study suggest novel alkane-degrading pathways in Dietzia H0B and a genetic background coding for two different putative oil-degrading enzymes, which is mostly unexplored and worth to be subject of further functional analysis. This study increases the scarce information available about the genetic background of alkane degradation in genus Dietzia and suggests new pathways and novel expression mechanisms of alkane degradation.

Degradation of petroleum hydrocarbons (C6–C40) and crude oil by a novel Dietzia strain

A novel bacterial strain, DQ12-45-1b, was isolated from the production water of a deep subterranean oil-reservoir. Morphological, physiological and phylogenetic analyses indicated that the strain belonged to the genus Dietzia with both alkB (coding for alkane monooxygenase) and CYP153 (coding for P450 alkane hydroxylase of the cytochrome CYP153 family) genes and their induction detected. It was capable of utilizing a wide range of n-alkanes (C6–C40), aromatic compounds and crude oil as the sole carbon sources for growth. In addition, it preferentially degraded short-chain hydrocarbons (⩽C25) in the early cultivation phase and accumulated hydrocarbons with chain-lengths from C23 to C27 during later cultivation stage with crude oil as the sole carbon source. This is the first study to report the different behaviors of a bacterial species toward crude oil degradation as well as a species of Dietzia degrading a wide range of hydrocarbons.