Nucleotide Second Messenger-Based Signaling in Extreme Acidophiles of the Acidithiobacillus Species Complex: Partition Between the Core and Variable Gene Complements

Cyclic and linear nucleotides are key elements of the signal transduction networks linking perception of the environment to specific cellular behavior of prokaryotes. These molecular mechanisms are particularly important in bacteria exposed to different, and frequently simultaneous, types of extreme conditions. This is the case in acidithiobacilli, a group of extremophilic bacteria thriving in highly acidic biotopes, that must also cope with significant variations in temperature, osmotic potentials and concentrations of various transition metals and metalloids. Environmental cues sensed by bacteria are transduced into differential levels of nucleotides acting as intracellular second messengers, promoting the activation or inhibition of target components and eliciting different output phenotypes. Cyclic (c) di-GMP, one of the most common bacterial second messengers, plays a key role in lifestyle changes in many bacteria, including acidithiobacilli. The presence of functional c-di-GMP-dependent signal transduction pathways in representative strains of the best-known linages of this species complex has been reported. However, a comprehensive panorama of the c-di-GMP modulated networks, the cognate input signals and output responses, are still missing for this group of extremophiles. Moreover, little fundamental understanding has been gathered for other nucleotides acting as second messengers. Taking advantage of the increasing number of sequenced genomes of the taxon, here we address the challenge of disentangling the nucleotide-driven signal transduction pathways in this group of polyextremophiles using comparative genomic tools and strategies. Results indicate that the acidithiobacilli possess all the genetic elements required to establish functional transduction pathways based in three different nucleotide-second messengers: (p)ppGpp, cyclic AMP (cAMP), and c-di-GMP. The elements related with the metabolism and transduction of (p)ppGpp and cAMP appear highly conserved, integrating signals related with nutrient starvation and polyphosphate metabolism, respectively. In contrast, c-di-GMP networks appear diverse and complex, differing both at the species and strain levels. Molecular elements of c-di-GMP metabolism and transduction were mostly found scattered along the flexible genome of the acidithiobacilli, allowing the identification of probable control modules that could be critical for substrate colonization, biofilm development and intercellular interactions. These may ultimately convey increased endurance to environmental stress and increased potential for gene sharing and adaptation to changing conditions

Application of Dispersive Liquid–Liquid Aerosol Phase Extraction to the Analysis of Total and Individual Phenolic Compounds in Fried Extra Virgin Olive Oils

Seventeen extra virgin olive oil samples from Valencian Community (Spain) were submitted to a domestic-frying process (180 °C) during different degradation times (5, 10, 30, 60, 120 min). A dispersive liquid–liquid aerosol phase extraction by using a methanol/water (50:50) extracting solution was used to isolate the polyphenol fraction. Total phenolic content (TPC) was determined, whereas the determination of seven individual target polyphenolic compounds (hydroxytyrosol, tyrosol, oleuropein, vanillic acid, p-coumaric acid, ferulic acid, and vanillin) was carried out by using ultrahigh-performance liquid chromatography coupled to a tandem mass spectrometer. Statistically significant differences in the TPC values were found for Blanqueta and Manzanilla samples from different harvesting years. The domestic-frying process impacted the TPC and the individual phenolic compounds content. Thermal treatment for 2 h gave rise to a 94% decrease in the TPC. A first-order kinetic model was suitable to accurately describe the degradation of the individual phenolic compounds.The authors wish to thank the Spanish Ministry of Science, Innovation, and Universities for the financial support (project ref. PID2021-127566NB-I00)

Acidithiobacillus ferrianus sp. nov.:an ancestral extremely acidophilic and facultatively anaerobic chemolithoautotroph

Strain MG, isolated from an acidic pond sediment on the island of Milos (Greece), is proposed as a novel species of ferrous iron- and sulfur-oxidizing Acidithiobacillus. Currently, four of the eight validated species of this genus oxidize ferrous iron, and strain MG shares many key characteristics with these four, including the capacities for catalyzing the oxidative dissolution of pyrite and for anaerobic growth via ferric iron respiration. Strain MG also grows aerobically on hydrogen and anaerobically on hydrogen coupled to ferric iron reduction. While the 16S rRNA genes of the iron-oxidizing Acidithiobacillus species (and strain MG) are located in a distinct phylogenetic clade and are closely related (98–99% 16S rRNA gene identity), genomic relatedness indexes (ANI/dDDH) revealed strong genomic divergence between strain MG and all sequenced type strains of the taxon, and placed MG as the first cultured representative of an ancestral phylotype of iron oxidizing acidithiobacilli. Strain MG is proposed as a novel species, Acidithiobacillus ferrianus sp. nov. The type strain is MGT(= DSM 107098T= JCM 33084T).Similar strains have been found as isolates or indicated by cloned 16S rRNA genes from several mineral sulfide mine sites.Indexación: Scopu

Domestication of Local Microbial Consortia for Efficient Recovery of Gold Through Top-Down Selection in Airlift Bioreactors

Extreme acidophiles play central roles in the geochemical cycling of diverse elements in low pH environments. This has been harnessed in biotechnologies such as biomining, where microorganisms facilitate the recovery of economically important metals such as gold. By generating both extreme acidity and a chemical oxidant (ferric iron) many species of prokaryotes that thrive in low pH environments not only catalyze mineral dissolution but also trigger both community and individual level adaptive changes. These changes vary in extent and direction depending on the ore mineralogy, water availability and local climate. The use of indigenous versus introduced microbial consortia in biomining practices is still a matter of debate. Yet, indigenous microbial consortia colonizing sulfidic ores that have been domesticated, i.e., selected for their ability to survive under specific polyextreme conditions, are claimed to outperform un-adapted foreign consortia. Despite this, little is known on the domestication of acidic microbial communities and the changes elicited in their members. In this study, high resolution targeted metagenomic techniques were used to analyze the changes occurring in the community structure of local microbial consortia acclimated to growing under extreme acidic conditions and adapted to endure the conditions imposed by the target mineral during biooxidation of a gold concentrate in an airlift reactor over a period of 2 years. The results indicated that operative conditions evolving through biooxidation of the mineral concentrate exerted strong selective pressures that, early on, purge biodiversity in favor of a few Acidithiobacillus spp. over other iron oxidizing acidophiles. Metagenomic analysis of the domesticated consortium present at the end of the adaptation experiment enabled reconstruction of the RVS1-MAG, a novel representative of Acidithiobacillus ferrooxidans from the Andacollo gold mineral district. Comparative genomic analysis performed with this genome draft revealed a net enrichment of gene functions related to heavy metal transport and stress management that are likely to play a significant role in adaptation and survival to adverse conditions experienced by these acidophiles during growth in presence of gold concentrates

Volatile Profile of Nuts, Key Odorants and Analytical Methods for Quantification

The presence of nuts in diets has notably increased due to their composition, and the presence of antioxidants and their unsaturated fatty acid profile has led to a considerable increase in their consumption. The volatile profile of nuts is important from different points of view. It affects consumer’s selection, influences raw material selection for the production of composite foods, dictates variety selection in breeding programs, and, from a quality perspective, its changes can indicate food degradation or alteration. A review of the published bibliography concerning the determination of volatiles in nuts has been carried out. The information retrieved has been divided into four main sections. First, a discussion on the main volatiles present in nuts is performed; next, a revision of the methods used to determine the volatiles is presented; and, finally, two sections describing how harvesting conditions, healthy state and the thermal treatment of nuts modifies their volatile profile are added. Analysis of the published bibliography denoted the complexity of volatile determination and the different variables that can modify the compounds present in the volatile fraction of nuts.The authors would like to acknowledge the Generalitat Valenciana (FEDEGENT/2018/021) for their financial support

The Type IV Secretion System of ICEAfe1: Formation of a Conjugative Pilus in Acidithiobacillus ferrooxidans

The dispersal of mobile genetic elements and their gene cargo relies on type IV secretion systems (T4SS). In this work the ICEAfe1 Tra-type T4SS nanomachine, encoded in the publicly available genome of Acidithiobacillus ferrooxidans ATCC 23270TY, was characterized in terms of its organization, conservation, expression and mating bridge formation. Twenty-one conjugative genes grouped in four genetic clusters encode the ICEAfe1 T4SS, containing all the indispensable functions for the formation and stabilization of the pili and for DNA processing. The clusters’ organization resembles that of other mobile genetic elements (such as plasmids and integrative and conjugative elements–ICEs). Sequence conservation, genetic organization and distribution of the tra system in the genomes of other sequenced Acidithiobacillus spp. suggests that the ICEAfe1 T4SS could mediate the lateral gene transfer between related bacteria. All ICEAfe1 T4SS genes are transcriptionally active and expressed from four independent operons. The transcriptional levels of selected marker genes increase in response to Mitomycin C treatment, a DNA damage elicitor that has acknowledged stimulatory effects on excision rates and gene expression of other ICEs, including ICEAfe1. Using a tailor-made pilin-antiserum against ICEAfe1 T4SS TraA pilin and epifluorescence microscopy, the presence of the conjugative pili on the cell surface of A. ferrooxidans could be demonstrated. Additionally, immunodetection assays, by immunogold, allowed the identification of pili-like extracellular structures. Together, the results obtained in this work demonstrate that the ICEAfe1 T4SS is phylogenetically conserved within the taxon, is expressed at mRNA and protein levels in vivo in the A. ferrooxidans type strain, and produces a pili-like structure of extracellular and intercellular localization in this model acidophile, supporting its functionality. Additional efforts will be required to prove conjugation of the ICEAfe1 or parts of this element through the cognate T4SS

Plan de negocios para un restaurante de comida saludable a domicilio “Healthy Food to Go”

126 Páginas incluye diagramas.Cerca de un cuarenta y cinco por ciento de la población colombiana tiene sobrepeso, un 18 por ciento lo conforman niños, según la última encuesta que data del 2005.1 Partiendo de ello, se percibe que en la actualidad la tendencia hacia una alimentación saludable cada día toma gran relevancia debido en gran medida a la aparición de múltiples enfermedades relacionadas con los malos hábitos alimentarios y al nivel de obesidad que hoy se percibe en la población. En Bucaramanga existen establecimientos que ofrecen comidas o alimentos que intentan pasar por saludables, sin embargo están muy lejos de serlo. La comida saludable no parece ser una moda pasajera existe un nuevo nicho de mercado por explotar donde se percibe una oportunidad de negocio como respuesta a una demanda en crecimiento, “HEALTHY FOOD TO GO” podría fácilmente tener una aceptación en el mercado además de ser muy rentable e innovador

Optimization and validation of a simplified methodology for simultaneous extraction of fatty acids and tocopherol homologues in peanuts

A new sample treatment methodology was developed for the simultaneous determination of oleic, linoleic, palmitic and stearic fatty acids (FA), and α-, β-, γ- and δ-tocopherol homologues in peanut samples. Usually, the determination of these compounds is carried out after oil extraction with an organic solvent at boiling temperatures of the solvent. The innovative analytical methodology developed in this work was performed in a 20 mL vial in which the FA and tocopherols were simultaneously extracted, and the derivatization of the FA was, afterwards, conducted. The reduction in analysis time from 1 h 30 min (reference methodology) to 20 min (new methodology) increased the sample throughput. Furthermore, the amount of organic solvent used decreased from 40 mL to 6 mL The new methodology was validated based on the analysis of a certified reference peanut butter sample and the results were compared to those obtained by using the reference methodology and a suitable agreement with the certified values was found. Finally, the new sample treatment approach was used to analyse toasted and fried (with and without tegument) peanuts.The authors would like to acknowledge the Packaging, Transport and Logistics Research Center (ITENE) and the Generalitat Valenciana (FEDEGENT/2018/021) for their financial support and DAMEL group© for providing some of the peanut samples

Global phylogenomic novelty of the Cas1 gene from hot spring microbial communities

The Cas1 protein is essential for the functioning of CRISPR-Cas adaptive systems. However, despite the high prevalence of CRISPR-Cas systems in thermophilic microorganisms, few studies have investigated the occurrence and diversity of Cas1 across hot spring microbial communities. Phylogenomic analysis of 2,150 Cas1 sequences recovered from 48 metagenomes representing hot springs (42–80°C, pH 6–9) from three continents, revealed similar ecological diversity of Cas1 and 16S rRNA associated with geographic location. Furthermore, phylogenetic analysis of the Cas1 sequences exposed a broad taxonomic distribution in thermophilic bacteria, with new clades of Cas1 homologs branching at the root of the tree or at the root of known clades harboring reference Cas1 types. Additionally, a new family of casposases was identified from hot springs, which further completes the evolutionary landscape of the Cas1 superfamily. This ecological study contributes new Cas1 sequences from known and novel locations worldwide, mainly focusing on under-sampled hot spring microbial mat taxa. Results herein show that circumneutral hot springs are environments harboring high diversity and novelty related to adaptive immunity systems.This work was financed in part by FONDECYT regular N° 1190998 (ANID) and Iniciativa de Investigación UnACh 2021-157-Unach. OS and JT-L were supported in part by ANID National Doctoral Scholarship (Beca de Doctorado Nacional ANID) N° 21172022 and 21171048, respectively. SG-L was supported by ANID FONDECYT Postdoctoral N° 3210547. AM-B and RQ were supported by Centro Ciencia and Vida, FB210008, Financiamiento Basal para Centros Científicos y Tecnológicos de Excelencia de ANID, and FONDECYT regular N° 1221035 (ANID). FJMM acknowledged research support by the Conselleria d’Innovació, Universitats, Ciència i Societat Digital from Generalitat Valenciana, research project PROMETEO/2021/057. BD acknowledged the Millennium Institute Center for Genome Regulation, Project ICN2021-044 supported by the ANID Millennium Scientific Initiative (Chile)

Pangenome-level analysis of nucleoid-associated proteins in the Acidithiobacillia class: insights into their functional roles in mobile genetic elements biology

Mobile genetic elements (MGEs) are relevant agents in bacterial adaptation and evolutionary diversification. Stable appropriation of these DNA elements depends on host factors, among which are the nucleoid-associated proteins (NAPs). NAPs are highly abundant proteins that bind and bend DNA, altering its topology and folding, thus affecting all known cellular DNA processes from replication to expression. Even though NAP coding genes are found in most prokaryotic genomes, their functions in host chromosome biology and xenogeneic silencing are only known for a few NAP families. Less is known about the occurrence, abundance, and roles of MGE-encoded NAPs in foreign elements establishment and mobility. In this study, we used a combination of comparative genomics and phylogenetic strategies to gain insights into the diversity, distribution, and functional roles of NAPs within the class Acidithiobacillia with a special focus on their role in MGE biology. Acidithiobacillia class members are aerobic, chemolithoautotrophic, acidophilic sulfur-oxidizers, encompassing substantial genotypic diversity attributable to MGEs. Our search for NAP protein families (PFs) in more than 90 genomes of the different species that conform the class, revealed the presence of 1,197 proteins pertaining to 12 different NAP families, with differential occurrence and conservation across species. Pangenome-level analysis revealed 6 core NAP PFs that were highly conserved across the class, some of which also existed as variant forms of scattered occurrence, in addition to NAPs of taxa-restricted distribution. Core NAPs identified are reckoned as essential based on the conservation of genomic context and phylogenetic signals. In turn, various highly diversified NAPs pertaining to the flexible gene complement of the class, were found to be encoded in known plasmids or, larger integrated MGEs or, present in genomic loci associated with MGE-hallmark genes, pointing to their role in the stabilization/maintenance of these elements in strains and species with larger genomes. Both core and flexible NAPs identified proved valuable as markers, the former accurately recapitulating the phylogeny of the class, and the later, as seed in the bioinformatic identification of novel episomal and integrated mobile elements