The significance of metabolic alkalosis on acute decompensated heart failure: the ALCALOTIC study.

AIMS: To determine the prevalence and the impact on prognosis of metabolic alkalosis (MA) in patients admitted for acute heart failure (AHF). METHODS AND RESULTS: The ALCALOTIC is a multicenter, observational cohort study that prospectively included patients admitted for AHF. Patients were classified into four groups according to their acid-base status on admission: acidosis, MA, respiratory alkalosis, and normal pH (reference group for comparison). Primary endpoint was all-cause in-hospital mortality, and secondary endpoints included 30/90-day all-cause mortality, all-cause readmission, and readmission for HF. Associations between endpoints and acid-base alterations were estimated in a multivariate Cox regression model including sex, age, comorbidities, and Barthel index and expressed as hazard ratio (HR) with 95% confidence interval (95% CI). Six hundred sixty-five patients were included (84 years and 57% women), and 40% had acid-base alterations on admission: 188 (28%) acidosis and 78 (12%) alkalosis. The prevalence (95% CI) of MA was 9% (6.8-11.2%). Patients with MA were more women; had fewer comorbidities, better renal function, and higher left ventricle ejection fraction values; and received more treatment with oral acetazolamide during hospitalization and at discharge. MA was not associated with a higher risk of in-hospital mortality and 30/90-day all-cause mortality or readmissions but was associated with a significant increase in readmissions for HF at 30 and 90 days (adjusted HR [95% CI] 3.294 [1.397-7.767], p = 0.006 and 2.314 [1.075-4.978], p = 0.032). CONCLUSION: The prevalence of MA in patients admitted for AHF was 9%, and its presence was associated with more readmissions for HF but not with all-cause mortality.

The microbiome of a brownfield highly polluted with mercury and arsenic.

Abandoned brownfields represent a challenge for their recovery. To apply sustainable remediation technologies, such as bioremediation or phytoremediation, indigenous microorganisms are essential agents since they are adapted to the ecology of the soil. Better understanding of microbial communities inhabiting those soils, identification of microorganisms that drive detoxification process and recognising their needs and interactions will significantly improve the outcome of the remediation. With this in mind we have carried out a detailed metagenomic analysis to explore the taxonomic and functional diversity of the prokaryotic and eukaryotic microbial communities in soils, several mineralogically distinct types of pyrometallurgic waste, and groundwater sediments of a former mercury mining and metallurgy site which harbour very high levels of arsenic and mercury pollution. Prokaryotic and eukaryotic communities were identified, which turned out to be more diverse in the surrounding contaminated soils compared to the pyrometallurgic waste. The highest diversity loss was observed in two environments most contaminated with mercury and arsenic (stupp, a solid mercury condenser residue and arsenic-rich soot from arsenic condensers). Interestingly, microbial communities in the stupp were dominated by an overwhelming majority of archaea of the phylum Crenarchaeota, while Ascomycota and Basidiomycota fungi comprised the fungal communities of both stump and soot, results that show the impressive ability of these previously unreported microorganisms to colonize these extreme brownfield environments. Functional predictions for mercury and arsenic resistance/detoxification genes show their increase in environments with higher levels of pollution. Our work establishes the bases to design sustainable remediation methods and, equally important, to study in depth the genetic and functional mechanisms that enable the subsistence of microbial populations in these extremely selective environments.

Effective bioremediation of soil from the Burgan oil field (Kuwait) using compost: A comprehensive hydrocarbon and DNA fingerprinting study.

An innovative combination of metagenomic profiling of microbial communities and GC-MS & Pyrolysis-GC-MS fingerprinting methods were used to assess the biodegradation of contaminated soil from the Burgan oil field in Kuwait. The soil was treated with (sludge) compost in microcosms to evaluate the feasibility of this material for bioremediation purposes. The most favourable trial showed a > 80% decrease in TPH, thereby indicating strong potential for full-scale application using a cost-effective technology and thus in line with the principles of the circular economy. The microbial study showed that compost addition enhanced the organic matter and nutrient content of the soil. However, the microorganisms in the compost did not seem to play a relevant role in bioremediation, meaning that compost amendments serve as a biostimulation rather than a bioaugmentation approach. The chemical study of the distinct oil fractions revealed rapidly biodegraded compounds (alkanes, alkyl-aromatics, etc.) and others that were much more refractory (hopanes, benzohopanes, etc.). Of note, although heavy fractions are usually considered recalcitrant to biodegradation, we observed incipient degradation of the asphaltene fraction by means of double-shot thermodesorption and pyrolysis. Finally, chemical fingerprinting also revealed that the treated soil contained some of the compounds found in the compost, such as coprostanol, cholesterol, and plant sterols. This observation would support the use of these compounds as proxies to monitor the effects of compost and to adjust dosages in real-scale bioremediation treatments.

Effects of in situ Remediation With Nanoscale Zero Valence Iron on the Physicochemical Conditions and Bacterial Communities of Groundwater Contaminated With Arsenic.

Nanoscale Zero-Valent Iron (nZVI) is a cost-effective nanomaterial that is widely used to remove a broad range of metal(loid)s and organic contaminants from soil and groundwater. In some cases, this material alters the taxonomic and functional composition of the bacterial communities present in these matrices; however, there is no conclusive data that can be generalized to all scenarios. Here we studied the effect of nZVI application in situ on groundwater from the site of an abandoned fertilizer factory in Asturias, Spain, mainly polluted with arsenic (As). The geochemical characteristics of the water correspond to a microaerophilic and oligotrophic environment. Physico-chemical and microbiological (cultured and total bacterial diversity) parameters were monitored before and after nZVI application over six months. nZVI treatment led to a marked increase in Fe(II) concentration and a notable fall in the oxidation-reduction potential during the first month of treatment. A substantial decrease in the concentration of As during the first days of treatment was observed, although strong fluctuations were subsequently detected in most of the wells throughout the six-month experiment. The possible toxic effects of nZVI on groundwater bacteria could not be clearly determined from direct observation of those bacteria after staining with viability dyes. The number of cultured bacteria increased during the first two weeks of the treatment, although this was followed by a continuous decrease for the following two weeks, reaching levels moderately below the initial number at the end of sampling, and by changes in their taxonomic composition. Most bacteria were tolerant to high As(V) concentrations and showed the presence of diverse As resistance genes. A more complete study of the structure and diversity of the bacterial community in the groundwater using automated ribosomal intergenic spacer analysis (ARISA) and sequencing of the 16S rRNA amplicons by Illumina confirmed significant alterations in its composition, with a reduction in richness and diversity (the latter evidenced by Illumina data) after treatment with nZVI. The anaerobic conditions stimulated by treatment favored the development of sulfate-reducing bacteria, thereby opening up the possibility to achieve more efficient removal of As.

Wickerhamiella verensis f.a. sp. nov., a novel yeast species isolated from subsoil groundwater contaminated with hydrocarbons and from a human infection.

Yeast strains belonging to a novel anamorphic yeast species were isolated from subsoil groundwater contaminated with hydrocarbons in a metal working factory located in northern Spain, and from a human infection in the USA. Comparison of ITS sequences between the isolates revealed 0.2 % divergence between the Spanish isolates and 0.46 % divergence between those and the USA isolate. Phylogenetic analysis based on the D1/D2 domains of the LSU rRNA gene showed that these isolates belong to the Wickerhamiella clade with W. sorbophila and W. infanticola as their closest relatives. Sequence divergence between the new isolates and W. sorbophila and W. infanticola was 1.97 and 1.79 %, respectively. The isolates in the novel species are not fermentative and pseudohyphae were not produced. Sexual reproduction was not observed for individual isolates or in mixtures of isolates. Conjugation between the isolates in the novel species and close relatives W. sorbophila and W. infanticola was not observed. These data support the proposal of Wickerhamiella verensis as a novel species, with CECT 12028T as the holotype.

Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota.

Small acidophilic archaea belonging to Micrarchaeota and Parvarchaeota phyla are known to physically interact with some Thermoplasmatales members in nature. However, due to a lack of cultivation and limited genomes on hand, their biodiversity, metabolisms, and physiologies remain largely unresolved. Here, we obtained 39 genomes from acid mine drainage (AMD) and hot spring environments around the world. 16S rRNA gene based analyses revealed that Parvarchaeota were only detected in AMD and hot spring habitats, while Micrarchaeota were also detected in others including soil, peat, hypersaline mat, and freshwater, suggesting a considerable higher diversity and broader than expected habitat distribution for this phylum. Despite their small genomes (0.64-1.08 Mb), these archaea may contribute to carbon and nitrogen cycling by degrading multiple saccharides and proteins, and produce ATP via aerobic respiration and fermentation. Additionally, we identified several syntenic genes with homology to those involved in iron oxidation in six Parvarchaeota genomes, suggesting their potential role in iron cycling. However, both phyla lack biosynthetic pathways for amino acids and nucleotides, suggesting that they likely scavenge these biomolecules from the environment and/or other community members. Moreover, low-oxygen enrichments in laboratory confirmed our speculation that both phyla are microaerobic/anaerobic, based on several specific genes identified in them. Furthermore, phylogenetic analyses provide insights into the close evolutionary history of energy related functionalities between both phyla with Thermoplasmatales. These results expand our understanding of these elusive archaea by revealing their involvement in carbon, nitrogen, and iron cycling, and suggest their potential interactions with Thermoplasmatales on genomic scale.

Use of Endophytic and Rhizosphere Bacteria To Improve Phytoremediation of Arsenic-Contaminated Industrial Soils by Autochthonous Betula celtiberica.

The aim of this study was to investigate the potential of indigenous arsenic-tolerant bacteria to enhance arsenic phytoremediation by the autochthonous pseudometallophyte Betula celtiberica The first goal was to perform an initial analysis of the entire rhizosphere and endophytic bacterial communities of the above-named accumulator plant, including the cultivable bacterial species. B. celtiberica's microbiome was dominated by taxa related to Flavobacteriales, Burkholderiales, and Pseudomonadales, especially the Pseudomonas and Flavobacterium genera. A total of 54 cultivable rhizobacteria and 41 root endophytes, mainly affiliated with the phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, were isolated and characterized with respect to several potentially useful features for metal plant accumulation, such as the ability to promote plant growth, metal chelation, and/or mitigation of heavy-metal stress. Seven bacterial isolates were further selected and tested for in vitro accumulation of arsenic in plants; four of them were finally assayed in field-scale bioaugmentation experiments. The exposure to arsenic in vitro caused an increase in the total nonprotein thiol compound content in roots, suggesting a detoxification mechanism through phytochelatin complexation. In the contaminated field, the siderophore and indole-3-acetic acid producers of the endophytic bacterial consortium enhanced arsenic accumulation in the leaves and roots of Betula celtiberica, whereas the rhizosphere isolate Ensifer adhaerens strain 91R mainly promoted plant growth. Field experimentation showed that additional factors, such as soil arsenic content and pH, influenced arsenic uptake in the plant, attesting to the relevance of field conditions in the success of phytoextraction strategies.IMPORTANCE Microorganisms and plants have developed several ways of dealing with arsenic, allowing them to resist and metabolize this metalloid. These properties form the basis of phytoremediation treatments and the understanding that the interactions of plants with soil bacteria are crucial for the optimization of arsenic uptake. To address this in our work, we initially performed a microbiome analysis of the autochthonous Betula celtiberica plants growing in arsenic-contaminated soils, including endosphere and rhizosphere bacterial communities. We then proceeded to isolate and characterize the cultivable bacteria that were potentially better suited to enhance phytoextraction efficiency. Eventually, we went to the field application stage. Our results corroborated the idea that recovery of pseudometallophyte-associated bacteria adapted to a large historically contaminated site and their use in bioaugmentation technologies are affordable experimental approaches and potentially very useful for implementing effective phytoremediation strategies with plants and their indigenous bacteria.

Biochemical studies on a versatile esterase that is most catalytically active with polyaromatic esters.

Herein, we applied a community genomic approach using a naphthalene-enriched community (CN1) to isolate a versatile esterase (CN1E1) from the α/ß-hydrolase family. The protein shares low-to-medium identity (≤ 57%) with known esterase/lipase-like proteins. The enzyme is most active at 25-30°C and pH 8.5; it retains approximately 55% of its activity at 4°C and less than 8% at ≥ 55°C, which indicates that it is a cold-adapted enzyme. CN1E1 has a distinct substrate preference compared with other α/ß-hydrolases because it is catalytically most active for hydrolysing polyaromatic hydrocarbon (phenanthrene, anthracene, naphthalene, benzoyl, protocatechuate and phthalate) esters (7200-21 000 units g(-1) protein at 40°C and pH 8.0). The enzyme also accepts 44 structurally different common esters with different levels of enantio-selectivity (1.0-55 000 units g(-1) protein), including (±)-menthyl-acetate, (±)-neomenthyl acetate, (±)-pantolactone, (±)-methyl-mandelate, (±)-methyl-lactate and (±)-glycidyl 4-nitrobenzoate (in that order). The results provide the first biochemical evidence suggesting that such broad-spectrum esterases may be an ecological advantage for bacteria that mineralize recalcitrant pollutants (including oil refinery products, plasticizers and pesticides) as carbon sources under pollution pressure. They also offer a new tool for the stereo-assembly (i.e. through ester bonds) of multi-aromatic molecules with benzene rings that are useful for biology, chemistry and materials sciences for cases in which enzyme methods are not yet available.

Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation.

Microbial metabolism in aromatic-contaminated environments has important ecological implications, and obtaining a complete understanding of this process remains a relevant goal. To understand the roles of biodiversity and aromatic-mediated genetic and metabolic rearrangements, we conducted 'OMIC' investigations in an anthropogenically influenced and polyaromatic hydrocarbon (PAH)-contaminated soil with (Nbs) or without (N) bio-stimulation with calcium ammonia nitrate, NH(4)NO(3) and KH(2)PO(4) and the commercial surfactant Iveysol, plus two naphthalene-enriched communities derived from both soils (CN2 and CN1, respectively). Using a metagenomic approach, a total of 52, 53, 14 and 12 distinct species (according to operational phylogenetic units (OPU) in our work equivalent to taxonomic species) were identified in the N, Nbs, CN1 and CN2 communities, respectively. Approximately 10 out of 95 distinct species and 238 out of 3293 clusters of orthologous groups (COGs) protein families identified were clearly stimulated under the assayed conditions, whereas only two species and 1465 COGs conformed to the common set in all of the mesocosms. Results indicated distinct biodegradation capabilities for the utilisation of potential growth-supporting aromatics, which results in bio-stimulated communities being extremely fit to naphthalene utilisation and non-stimulated communities exhibiting a greater metabolic window than previously predicted. On the basis of comparing protein expression profiles and metagenome data sets, inter-alia interactions among members were hypothesised. The utilisation of curated databases is discussed and used for first time to reconstruct 'presumptive' degradation networks for complex microbial communities.

A fatal case of Nocardia otitidiscaviarum pulmonary infection and brain abscess: taxonomic characterization by molecular techniques.

We report on a rare case of pulmonary Nocardiosis and brain abscess caused by Nocardia otitidiscaviarum in an elderly woman with chronic obstructive pulmonary disease. Taxonomic identification involved phenotypic testing, restriction fragment length polymorphism (RFLP), and complete 16S rRNA gene sequencing.

A rare case of silicone mammary implant infection by Streptomyces spp. in a patient with breast reconstruction after mastectomy: taxonomic characterization using molecular techniques.

A Streptomyces sp. isolated from a patient who had had breast reconstruction after a mastectomy was identified at the species level by comparative sequence analysis of 16S ribosomal DNA (rDNA) and the hypervariable alpha-region of the 16S rDNA.

Bioreactor treatment of municipal solid waste landfill leachates: characterization of organic fractions.

Quantitative and qualitative changes in organic matter were studied at different stages of treatment in a bioreactor designed to process leachates from a municipal solid waste landfill. The particulate matter (PM) and macromolecular fractions of the dissolved organic matter with solubility properties comparable to humic (acid-insoluble) and fulvic (acid-soluble) acid fractions (AI, AS, respectively) from the incoming black liquid, the bioreactor content, and the final processed effluent were isolated, quantified, and characterized by visible and infrared (IR) spectroscopies. The macromolecular signature either aliphatic (glycopeptides, carbohydrates) or aromatic (coinciding with infrared patterns of lignin, tannins etc.) enabled us to characterize the different organic fractions during the course of microbial transformation. The results reveal significant changes in the nitrogen speciation patterns within the different organic fractions isolated from the wastewater. The final increase in the relative proportions of nitrogen in the least aromatic AS fraction during microbial transformation could be related to protein formation inside the bioreactor. After biological treatment and ultrafiltration, the amount of organic matter was reduced by approximately 70%, whereas aromaticity increased in all fractions, indicating preferential elimination of aliphatic wastewater compounds. Most of the remaining fractions at the end of the process consisted of a yellow residue rich in low molecular weight AS fractions.

A rare case of lung coinfection by Streptomyces cinereoruber and Haemophilus influenzae in a patient with severe chronic obstructive pulmonary disease: characterization at species level using molecular techniques.

Streptomyces cinereoruber isolated from a patient with severe respiratory failure that could not be identified by culture was correctly identified at the species level by comparative sequence analysis of 16S rDNA and the hypervariable alpha-region of 16S rDNA. Restriction fragment length polymorphism, morphologic, and biochemical characteristics have confirmed their identity.

Anaerobic mesophilic treatment of cattle manure in an upflow anaerobic sludge blanket reactor with prior pasteurization.

Different autonomous communities located in northern Spain have large populations of dairy cattle. In the case of Asturias, the greatest concentration of dairy farms is found in the areas near the coast, where the elimination of cattle manure by means of its use as a fertilizer may lead to environmental problems. The aim of the present research work was to study the anaerobic treatment of the liquid fraction of cattle manure at mesophilic temperature using an upflow anaerobic sludge blanket (UASB) reactor combined with a settler after a pasteurization process at 70 degrees C for 2 hr. The manure used in this study came from two different farms, with 40 and 200 cows, respectively. The manure from the smaller farm was pretreated in the laboratory by filtration through a 1-mm mesh, and the manure from the other farm was pretreated on the farm by filtration through a separator screw press (0.5-mm mesh). The pasteurization process removed the pathogenic microorganisms lacking spores, such as Enterococcus, Yersinia, Pseudomonas, and coliforms, but bacterial spores are only reduced by this treatment, not removed. The combination of a UASB reactor and a settler proved to be effective for the treatment of cattle manure. In spite of the variation in the organic loading rate and total solids in the influent during the experiment, the chemical oxygen demand (COD) of the effluent from the settler remained relatively constant, obtaining reductions in the COD of approximately 85%.