Rafael Ruiz de la Haba

Hypersaline soils are poly-extreme terrestrial habitats characterized by high salinity, in some cases heavy-metal contamination, temperature fluctuations, and nutrient limitation. These conditions impose strong selective pressures, and many prokaryotic inhabitants still remain uncultured. Here, we conducted an extensive culturomics study of 549 isolates from the hypersaline soils of the Odiel Saltmarshes Natural Area (Southwest Spain) and compared the results with previously generated shotgun metagenomic datasets from the same environment in order to evaluate taxonomic composition, functional potential, and ecological representativeness. Cultivation across media containing 7.5%, 15%, and 25% (w/v) total salts yielded microorganisms belonging to three major phyla: Pseudomonadota, Bacillota (Bacteria) and Halobacteriota (Archaea). At the genus level, bacterial isolates were dominated by Marinobacter, Halomonas, and Aquibacillus at 7.5% (w/v) salinity, whereas extremely halophilic archaea, including Halorubrum, Halogeometricum, and Haloarcula, were predominantly recovered from media containing 25% (w/v) salts. Among the isolates, 57 strains displayed identity values < 98.65% for 16S rRNA gene sequence comparison, suggesting their putative status as new taxa. Comparison with metagenomic datasets showed that culture-dependent approaches successfully recovered the dominant haloarchaeal groups but missed some abundant bacterial phyla, such as Gemmatimonadota. Conversely, culturomics enabled the isolation of unknown species from the rare biosphere, including representatives of the novel genus Terrihalobacillus, which are typically detected at low abundance in metagenomic datasets. Together, these results demonstrate the complementarity of culturomics and metagenomics and provide an insight into the microbial communities inhabiting the hypersaline soils of the Odiel Saltmarshes.

Background/Objectives: Flavonoids are low-molecular-weight polyphenolic compounds that are universally distributed in plants. They are a chemically varied group of secondary metabolites with a broad range of biological activity. The use of flavonoids is known to decrease the risk of many chronic diseases due to their radical scavenging, antioxidant, anti-inflammatory, anticarcinogenic, and antimutagenic properties. Limitations in the use of flavonoids include their low water solubility and poor stability, and therefore their low bioavailability. The encapsulation of flavonoids in different nanocarriers has helped to overcome this limitation. Taking this into account, in this work, the encapsulation of four flavones with several therapeutic applications—7-hydroxyflavone, 7,8-dihydroxyflavone, baicalein, and luteolin—in poly(lactic-co-glycolic) acid (PLGA)-derived polymeric nanoparticles (NPs) has been investigated. Methods: A physicochemical characterization of the NPs has been carried out using different techniques, including the evaluation of antioxidant and antimicrobial activities. Results: In all cases, the encapsulation efficiency of the four flavones in the prepared NPs was high (>90%), the zeta potential was about −31 mV, and the size was nanometric (~450 nm). The drug release from the nanoparticles was also studied, showing first-order kinetics. Statistical tools were applied to the release rate constants. The antioxidant activity and the in vitro antimicrobial activity of the free and flavone-loaded NPs were investigated, in the case of the latter using Gram-positive and Gram-negative bacteria. Results show that when the flavones are encapsulated, they retain their therapeutic properties. Conclusions: In summary, PLGA-based NPs not only prevent flavone degradation but also significantly boost solubility, ultimately optimizing bioavailability. Our results underscore these NPs as a promising platform for efficient flavone delivery.

The hypersaline soils of the Odiel Saltmarshes Natural Area in Southwest Spain harbor highly diverse microbial communities adapted to extreme conditions. However, their genomic diversity remains largely unexplored. In addition to high salinity, these soils are contaminated with heavy metals, creating a hostile environment of great interest for studying extremophilic microorganisms and their metabolic adaptations. This study aims to characterize the uncovered prokaryotic taxa as Candidatus species inhabiting the hypersaline soils of the Odiel Saltmarshes, based on their metagenomic assembled genomic sequences. The reconstructed genomes were assessed for quality based on completeness and contamination thresholds and subsequently taxonomically classified. Comparative genomic analysis of six high-quality MAGs revealed key metabolic traits related to survival under extreme salinity and heavy metal conditions. The findings provide new insights about microbial diversity of hypersaline environments and expand the catalog of known prokaryotic genomes. Detailed characterization of six novel Candidatus taxa highlights the unique adaptations of these microorganisms, enhancing our understanding of life in extreme habitats.

Antiterminators are essential components of bacterial transcriptional regulation, allowing the control of gene expression in response to fluctuating environmental conditions. Among them, RNA-binding antiterminator proteins play a major role in preventing transcription termination by binding to specific RNA sequences. These RNA-binding antiterminators have been extensively studied for their role in regulating various metabolic pathways. However, their function in modulating the physiology of pathogens requires further investigation. This review focuses on RNA-binding proteins displaying CAT (Co-AntiTerminator) or ANTAR (AmiR and NasR Transcription Antitermination Regulators) domains reported in model bacteria. In particular, their structures, mechanism of action, and target genes will be described. The involvement of the antitermination mechanisms in bacterial pathogenicity is also discussed. This knowledge is crucial for understanding the regulatory mechanisms that control bacterial virulence, and opens up exciting prospects for future research, and potentially new alternative strategies to combat infectious diseases.

Antiterminators are essential components of bacterial transcriptional regulation, allowing the control of gene expression in response to fluctuating environmental conditions. Among them, RNA-binding antiterminator proteins play a major role in preventing transcription termination by binding to specific RNA sequences. These RNA-binding antiterminators have been extensively studied for their role in regulating various metabolic pathways. However, their function in modulating the physiology of pathogens requires further investigation. This review focuses on RNA-binding proteins displaying CAT (Co-AntiTerminator) or ANTAR (AmiR and NasR Transcription Antitermination Regulators) domains reported in model bacteria. In particular, their structures, mechanism of action, and target genes will be described. The involvement of the antitermination mechanisms in bacterial pathogenicity is also discussed. This knowledge is crucial for understanding the regulatory mechanisms that control bacterial virulence, and opens up exciting prospects for future research, and potentially new alternative strategies to combat infectious diseases.

A novel moderately halophilic and alkaliphilic Gram-stain-negative, strictly aerobic, bacterial strain (N2^T) was isolated from an inland saltern in central Portugal. The taxonomic position of this isolate was determined based on polyphasic taxonomic and phylogenomic analysis. Phylogenetic analysis based on 16S rRNA gene sequences indicated that isolate N2^T belongs to the genus Fodinibius, showing the highest similarity to Fodinibius halophilus 2W32^T (98.14%). Phylogenomic analysis based on whole genomes, using the up-to-date bacterial core gene sets (92 genes), showed that strain N2^T formed a distinct monophyletic lineage within the genus Fodinibius. The cells of N2^T were motile rods that grew at temperatures between 30 and 40 °C (optimum at 35 °C), pH levels of 6.0–11.0 (optimum at pH 9.0) and salinities of 13–20 % (w/v) NaCl (optimum at 15% NaCl). Cells tested positive for oxidase and catalase activity. The predominant isoprenoid quinone was menaquinone-7 (MK-7), and the major fatty acids were iso-C_15:0, anteiso-C_15:0, C_16:1  ω6c and/or 10-methyl C_16:0. The polar lipids included two aminolipids, two glycolipids and seven phospholipids. The DNA G+C content was 42.0 mol%. Based on phylogenetic, phylogenomic, genomic, phenotypic and chemotaxonomic data, we propose that strain N2^T (=KCTC 102228^T=MCCC 1K08942^T) represents a novel species within the genus Fodinibius, with the name Fodinibius alkaliphilus sp. nov. We also propose the reclassification of Alifodinibius salipaludis as Fodinibius salipaludis sp. nov.

Phylogenetic trees are essential diagrams used in different sciences, such as evolutionary biology or taxonomy, and they depict the relationships between a given set of taxa sharing a common ancestor. So far, a multitude of tools have already been developed to infer phylogeny, and even more to visualize the resulting trees. However, editing generated graphical plots to obtain ready-to-publish figures is still a major issue. Most available tools do not take into consideration important aspects in nomenclature, such as the use of italics for taxon names or the superscript T that must be displayed after the strain/specimen designation to denote the type strain/specimen, at least not automatically. A gap also exists to easily highlight tree branches conserved across different phylogenies containing the same taxa. The lack of available tools to achieve these tasks is challenging for scientists, since manual formatting of phylogenetic trees is very time-consuming. Here, we present a tool named ‘gitana’, running in Linux/Windows/Mac operating systems with R software installed. It creates ready-to-publish trees with formatting taxon nomenclature and editing options such as rerooting, clade highlighting or collapsing, among other features. Moreover, ‘gitana’ performs node comparisons among phylogenies comprising the same taxa to identify conserved branches. ‘gitana’ is a user-friendly tool to output high-quality and ready-to-publish phylogenetic trees for users without R-coding skills. It combines dedicated functions of popular R packages for phylogeny and graphical visualization into an easy one-line-command. The users’ manual and source code are freely available at https://github.com/cristinagalisteo/gitana .

Haloarchaea, a group of extremophilic archaea, thrive in hypersaline environments characterized not only by high salinity but also by other extreme conditions, such as intense UV radiation, high osmotic pressure, heavy metal contamination, oxidative stress, and fluctuating temperatures. This study investigates the environmental adaptation strategies of species of two genera, Haloarcula and Natrinema, the second and third largest haloarchaeal genera, respectively, after Halorubrum. Comparative genomic analyses were conducted on 48 species from both genera to elucidate their genomic diversity, metabolic potential, and stress-tolerance mechanisms. The genomes revealed diverse metabolic pathways, including rhodopsin-mediated phototrophy, nitrogen assimilation, and thiamine biosynthesis, which support their survival and adaptation to extreme conditions. The analysis identified mechanisms for oxidative stress mitigation, DNA repair, “salt-in” and “salt-out” osmoregulatory strategies, adaptations to temperature shifts and heavy metal exposure, and immune defense. Experimental validation of four representative species, Haloarcula terrestris S1AR25-5A^T, Haloarcula saliterrae S1CR25-12^T, Haloarcula onubensis S3CR25-11^T, and Natrinema salsiterrestre S1CR25-10^T, isolated from the heavy-metal-rich hypersaline soils in the Odiel Saltmarshes (Huelva, Spain), demonstrated their tolerance, especially to arsenic, corroborating genomic predictions. This study advances our understanding of the resilience of haloarchaea under poly-extreme conditions and underscores their ecological significance and promise for biotechnological applications, such as the bioremediation of heavy-metal-polluted environments and the production of valuable biomolecules.

Antimicrobial resistance (AMR) poses a global threat to human, animal and environmental health. Among the multidisciplinary tasks aimed at collectively tackling the AMR crisis, surveillance, research and education stand as major priorities. Based on a crowdsourcing research strategy, the MicroMundo project, a partner of the Tiny Earth initiative in Spain and Portugal, has been developed and consolidated with success in the academic environment. The objectives are focused on promoting research and, especially, on bringing knowledge of One Health and microbiology concepts, as well as AMR awareness to the community. Following a service‐learning approach, MicroMundo integrates university and secondary/high school students in a citizen science‐based research project to collectively isolate microorganisms with the potential to produce new antibiotics from soil environments. Over the last 7 years, 32 MicroMundo hubs operating across 31 different Portuguese and Spanish universities have recruited thousands of teenagers in this quest. Here we review the outcome of this unprecedented effort from a scientific and an educational perspective.

A long-awaited taxogenomic investigation of the family Halomonadaceae by de la Haba, R. R., Arahal, D. R., Sánchez-Porro, C., Chuvochina, M., Wittouck, S., Hugenholtz, P., andVentosa, A. (2023). Front. Microbiol. 14:1293707. doi: 10.3389/fmicb.2023.1293707 In the published article, there was an error in the formation of the new combination Vreelandella utahensis, which should have been named Vreelandella halophila comb. nov. instead, using the earliest legitimate epithet of the species in application of Rule 41a (Oren et al., 2023).A correction has been made to the Taxonomic conclusions section, specifically to the Description of Vreelandella utahensis comb. nov. This section previously stated: "Description of Vreelandella utahensis comb. nov.Vreelandella utahensis (u.ta.hen'sis. N.L. fem. adj. utahensis, referring to Utah).Basonym: Halomonas utahensis Sorokin and Tindall, 2006.The description is as given in the proposal of the basonym (Sorokin and Tindall, 2006), with the following addition. The genome size of the type strain is 3.73 Mbp. The DNA G + C content is 55.8 mol%.Isolated from surface water from the North Arm of Great Salt Lake (United States).