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1.
Int J Syst Evol Microbiol ; 70(4): 2420-2425, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32100691

RESUMO

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.


Assuntos
Água Subterrânea/microbiologia , Micoses/microbiologia , Filogenia , Saccharomycetales/classificação , DNA Fúngico/genética , Fermentação , Georgia , Humanos , Hidrocarbonetos , Lactente , Técnicas de Tipagem Micológica , Saccharomycetales/isolamento & purificação , Análise de Sequência de DNA , Espanha , Poluentes Químicos da Água
2.
ISME J ; 12(3): 756-775, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29222443

RESUMO

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.


Assuntos
Archaea/metabolismo , Aminoácidos/metabolismo , Archaea/classificação , Archaea/genética , Archaea/isolamento & purificação , Biodiversidade , Evolução Biológica , Carbono/metabolismo , Água Doce/microbiologia , Genoma Arqueal , Genômica , Fontes Termais/microbiologia , Ferro/metabolismo , Nitrogênio/metabolismo , Ciclo do Nitrogênio , Filogenia , RNA Ribossômico 16S/genética
3.
Appl Environ Microbiol ; 83(8)2017 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-28188207

RESUMO

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.


Assuntos
Arsênico/metabolismo , Bactérias/metabolismo , Betula/microbiologia , Endófitos/metabolismo , Consórcios Microbianos/fisiologia , Rizosfera , Poluentes do Solo/metabolismo , Arsênico/farmacologia , Bactérias/química , Bactérias/classificação , Bactérias/efeitos dos fármacos , Betula/química , Betula/fisiologia , Biodegradação Ambiental , Flavobacterium/efeitos dos fármacos , Flavobacterium/isolamento & purificação , Flavobacterium/metabolismo , Concentração de Íons de Hidrogênio , Ácidos Indolacéticos/metabolismo , Resíduos Industriais , Desenvolvimento Vegetal , Folhas de Planta/química , Raízes de Plantas/química , Raízes de Plantas/microbiologia , Pseudomonas/efeitos dos fármacos , Pseudomonas/isolamento & purificação , Pseudomonas/metabolismo , Poluentes do Solo/análise
4.
Microb Biotechnol ; 7(2): 184-91, 2014 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-24418210

RESUMO

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.


Assuntos
Esterases/metabolismo , Hidrocarbonetos Aromáticos/metabolismo , Poliésteres/metabolismo , Bactérias/enzimologia , Bactérias/genética , Análise por Conglomerados , Estabilidade Enzimática , Esterases/química , Esterases/genética , Esterases/isolamento & purificação , Concentração de Íons de Hidrogênio , Filogenia , Homologia de Sequência , Especificidade por Substrato , Temperatura
5.
ISME J ; 7(1): 122-36, 2013 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-22832345

RESUMO

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.


Assuntos
Bactérias/classificação , Bactérias/isolamento & purificação , Naftalenos/toxicidade , Microbiologia do Solo , Bactérias/genética , Bactérias/metabolismo , Biodegradação Ambiental , Biodiversidade , Metagenômica , Dados de Sequência Molecular , Naftalenos/metabolismo , Filogenia , Solo/química , Poluentes do Solo/metabolismo
6.
Ann Clin Microbiol Antimicrob ; 8: 11, 2009 Apr 14.
Artigo em Inglês | MEDLINE | ID: mdl-19366439

RESUMO

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.


Assuntos
Abscesso Encefálico/microbiologia , Pneumopatias/microbiologia , Nocardiose/microbiologia , Nocardia/classificação , Nocardia/genética , Idoso de 80 Anos ou mais , DNA Bacteriano/análise , Evolução Fatal , Feminino , Humanos , Nocardia/isolamento & purificação , Fenótipo , Filogenia , Polimorfismo de Fragmento de Restrição , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
8.
Waste Manag ; 29(1): 70-7, 2009 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-18632259

RESUMO

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.


Assuntos
Reatores Biológicos , Eliminação de Resíduos/métodos , Poluentes Químicos da Água/metabolismo , Carbono/química , Nitrogênio/química , Compostos Orgânicos , Eliminação de Resíduos Líquidos/métodos , Poluentes Químicos da Água/química
9.
Diagn Microbiol Infect Dis ; 60(3): 307-11, 2008 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-18061387
10.
J Air Waste Manag Assoc ; 56(2): 137-43, 2006 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-16568796

RESUMO

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%.


Assuntos
Esterco/microbiologia , Eliminação de Resíduos Líquidos/métodos , Animais , Bactérias/classificação , Bactérias/isolamento & purificação , Bactérias/metabolismo , Biodegradação Ambiental , Reatores Biológicos , Bovinos , Contagem de Colônia Microbiana , Indústria de Laticínios , Temperatura Alta , Metais Pesados/análise
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