Effects of in situ Fe oxide precipitation on As stabilization and soil ecological resilience under salt stress

Iron (Fe) oxide precipitation is a promising method for stabilizing arsenic (As) in contaminated soils; however, the addition of salts during the process can negatively affect soil functions. This study investigated the effects of in situ Fe oxide precipitation on As stabilization and the impact of salt stress on soil functions and microbial communities. Fe oxide precipitation reduced the concentration of bioaccessible As by 84% in the stabilized soil, resulting in the formation of ferrihydrite and lepidocrocite, as confirmed by XANES. Nevertheless, an increase in salt stress reduced barley development, microbial enzyme activities, and microbial diversity compared to those in the original soil. Despite this, the stabilized soil exhibited natural resilience and potential for enhanced microbial adaptations, with increased retention of salt-tolerant bacteria. Washing the stabilized soil with water restored EC1:5 to the level of the original soil, resulting in increased barley growth rates and enzyme activities after 5-d and 20-week incubation periods, suggesting soil function recovery. 16 S rRNA sequencing revealed the retention of salt-tolerant bacteria in the stabilized soil, while salt-removed soil exhibited an increase in Proteobacteria, which could facilitate ecological functions. Overall, Fe oxide precipitation effectively stabilized soil As and exhibited potential for restoring the natural resilience and ecological functions of soils through microbial adaptations and salt removal.

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.

Aerobic biotransformation of 6:2 fluorotelomer sulfonate by Dietzia aurantiaca J3 under sulfur-limiting conditions

The polyfluorinated alkyl substance 6:2 fluorotelomer sulfonate (6:2 FTS) has been detected in diverse environments impacted by aqueous film-forming foams used for firefighting. In this study, a bacterial strain (J3) using 6:2 FTS as a sulfur source was isolated from landfill leachate previously exposed to polyfluoroalkyl substances in New South Wales, Australia. Strain J3 shares 99.9% similarity with the 16S rRNA gene of Dietzia aurantiaca CCUG 35676^T. Genome sequencing yielded a draft genome sequence of 37 contigs with a G + C content of 69.7%. A gene cluster related to organic sulfur utilisation and assimilation was identified, that included an alkanesulfonate monooxygenase component B (ssuD), an alkanesulfonate permease protein (ssuC), an ABC transporter (ssuB), and an alkanesulfonate-binding protein (ssuA). Proteomic analyses comparing strain J3 cultures using sulfate and 6:2 FTS as sulfur source indicated that the ssu gene cluster was involved in 6:2 FTS biodegradation. Upregulated proteins included the SsuD monooxygenase, the SsuB transporter, the ABC transporter permease (SsuC), an alkanesulfonate-binding protein (SsuA), and a nitrilotriacetate monooxygenase component B. 6:2 Fluorotelomer carboxylic acid (6:2 FTCA) and 6:2 fluorotelomer unsaturated acid (6:2 FTUA) were detected as early degradation products in cultures (after 72 h) while 5:3 fluorotelomer acid (5:3 FTCA), perfluorohexanoic acid (PFHxA) and perfluoropentanoic acid (PFPeA) were detected as later degradation products (after 168 h). This work provides biochemical and metabolic insights into 6:2 FTS biodegradation by the Actinobacterium D. aurantiaca J3, informing the fate of PFAS in the environment.

Bhargavaea massiliensis sp. nov. and Dietzia massiliensis sp. nov., Novel Bacteria Species Isolated from Human Urine Samples in Nigeria

Two novel bacteria species designated Marseille-Q1000^T and Marseille-Q0999^T were isolated from urine samples of patients in Sokoto, Northwest-Nigeria. They were Gram-positive bacteria and belong to two different genera, Bhargavaea and Dietzia. The genome size and G + C content of Marseille-Q1000^T and Marseille-Q0999^T were 3.07 and 3.51 Mbp with 53.8 and 71.0 mol% G + C content, respectively. The strains exhibited unique phenotypic and genomic features that are substantially different from previously known bacterial species with standing in nomenclature. On the basis of the phenotypic, phylogenetic and genomic characteristics, strains Marseille-Q0999^T (= CSURQ0999 = DSM 112394) and Marseille-Q1000^T (= CSURQ1000 = DSM 112384) were proposed as the type strains of Bhargavaea massiliensis sp. nov., and Dietzia massiliensis sp. nov., respectively.

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.

Microbiota of the Gut-Lymph Node Axis: Depletion of Mucosa-Associated Segmented Filamentous Bacteria and Enrichment of Methanobrevibacter by Colistin Sulfate and Linco-Spectin in Pigs

Microorganisms are translocated from the gut to lymphatic tissues via immune cells, thereby challenging and training the mammalian immune system. Antibiotics alter the gut microbiome and consecutively might also affect the corresponding translocation processes, resulting in an imbalanced state between the intestinal microbiota and the host. Hence, understanding the variant effects of antibiotics on the microbiome of gut-associated tissues is of vital importance for maintaining metabolic homeostasis and animal health. In the present study, we analyzed the microbiome of (i) pig feces, ileum, and ileocecal lymph nodes under the influence of antibiotics (Linco-Spectin and Colistin sulfate) using 16S rRNA gene sequencing for high-resolution community profiling and (ii) ileocecal lymph nodes in more detail with two additional methodological approaches, i.e., cultivation of ileocecal lymph node samples and (iii) metatranscriptome sequencing of a single lymph node sample. Supplementation of medicated feed showed a local effect on feces and ileal mucosa-associated microbiomes. Pigs that received antibiotics harbored significantly reduced amounts of segmented filamentous bacteria (SFB) along the ileal mucosa (p = 0.048; 199.17-fold change) and increased amounts of Methanobrevibacter, a methanogenic Euryarchaeote in fecal samples (p = 0.005; 20.17-fold change) compared to the control group. Analysis of the porcine ileocecal lymph node microbiome exposed large differences between the viable and the dead fraction of microorganisms and the microbiome was altered to a lesser extent by antibiotics compared with feces and ileum. The core microbiome of lymph nodes was constituted mainly of Proteobacteria. RNA-sequencing of a single lymph node sample unveiled transcripts responsible for amino acid and carbohydrate metabolism as well as protein turnover, DNA replication and signal transduction. The study presented here is the first comparative study of microbial communities in feces, ileum, and its associated ileocecal lymph nodes. In each analyzed site, we identified specific phylotypes susceptible to antibiotic treatment that can have profound impacts on the host physiological and immunological state, or even on global biogeochemical cycles. Our results indicate that pathogenic bacteria, e.g., enteropathogenic Escherichia coli, could escape antibiotic treatment by translocating to lymph nodes. In general ileocecal lymph nodes harbor a more diverse and active community of microorganisms than previously assumed.

Identification of Dietzia Species in a Patient with Endophthalmitis following Penetrating Injury with Retained Intraocular Metallic Foreign Body

To the best of our knowledge, we report the first case of Dietzia species in a patient with endophthalmitis. A 47-year-old man presented to the ophthalmology department with decreased vision, redness, and minimal pain in his right eye after a foreign body struck his eye following working using a hammer and chisel. Broad-spectrum polymerase chain reaction (PCR) and deoxyribonucleic acid (DNA) sequencing targeting 16S ribosomal ribonucleic acid-(rRNA-) encoding gene on an undiluted vitreous sample revealed 100% identity with GenBank sequences of Dietzia species including D. natronolimnaea, D. dagingensis, and D. cercidiphylli. The culture of the vitreous samples demonstrated the growth of Gram-positive cocci and polymorphic rods. The isolate from the culture was identified as D. natronolimnaea using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS). The combination of surgical and medical treatment (pars plana vitrectomy and systemic and topical antibiotics) eradicated the infection successfully.

Aerobic Actinomycetes of Clinical Significance

The group of Gram-positive bacillary organisms broadly known as "aerobic actinomycetes" consists of heterogeneous and taxonomically divergent genera. They are found in a wide variety of natural and man-made environments but are rarely considered a part of the normal human flora, with infections normally originating from exogenous sources. An extensive number of genera have been described, but only a minority of these has been associated with human or veterinary health. The association with human disease is usually of an opportunistic nature, either through accidental means of inoculation or through involvement with immunocompromising conditions in the host. They cause a wide spectrum of diseases in humans, which may differ greatly between the genera and even between species, but which also may have a great amount of overlap. The occurrence of such infections is probably greater than appreciated, since many may go unrecognized. Etiologic prevalence of specific genera and species varies geographically within the United States and worldwide. Traditional phenotypic identification methods for separation of the many genera and species of aerobic actinomycetes have found great difficulties. Recent use of chemotaxonomic analyses and emerging technologies such as molecular analysis of nucleic acids, and more recently proteomics for identification to the genus/species level, has provided a far more robust technique to understand the organisms' relatedness, distribution, epidemiology, and pathogenicity in humans.

What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015

Technological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by the International Journal of Systematic and Evolutionary Microbiology Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by the Journal of Clinical Microbiology on a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015.

Identification of Dietzia spp. from Cardiac Tissue by 16S rRNA PCR in a Patient with Culture-Negative Device-Associated Endocarditis: A Case Report and Review of the Literature

The genus Dietzia was recently distinguished from other actinomycetes such as Rhodococcus. While these organisms are known to be distributed widely in the environment, over the past decade several novel species have been described and isolated from human clinical specimens. Here we describe the identification of Dietzia natronolimnaea/D. cercidiphylli by PCR amplification and sequencing of the 16S rRNA encoding gene from cardiac tissue in a patient with culture-negative device-associated endocarditis.

Fatty acids in bacterium Dietzia sp. grown on simple and complex hydrocarbons determined as FAME by GC-MS

The influence of growth substrates on the fatty acids produced by Dietzia sp. A14101 has been studied to investigate how qualitative and semi-quantitative information on fatty acids correlates with the ability of this strain to access and utilize a wide range of water-immiscible HC-substrates by modifying the FA content and thus also the properties of the cellular membrane. After incubation on different substrates and media, the profiles of fatty acids (FA) were analyzed by gas chromatography and mass spectrometry (GC-MS). The equivalent chain length (ECL) index calibration system was employed to identify FA. The effect of each substrate on the cell surface charge and on the hydrophobicity of the cellular membrane was also investigated. The results indicate that the variation of the content of saturated fatty acids (SAT-FA) versus mono-unsaturated fatty acids (MUFA) was found to be the most pronounced while branched FA exhibited much less variation in spite of different substrate regimes. The regulation of the ratio of SAT-FA and MUFA seems to be coupled with the regulation of the charge and hydrophobicity of the outer cellular surface. The exposure to a water immiscible substrate led to the development of the negative cellular surface charge, production of carotenoid-type pigments and increased hydrophobicity of the cellular surface. The specific aspects of the adaptation mechanism could have implications for bioremediation and/or (M)EOR applications.