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Microb Ecol ; 77(2): 288-303, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30019110


Two annual Baltic Sea phytoplankton blooms occur in spring and summer. The bloom intensity is determined by nutrient concentrations in the water, while the period depends on weather conditions. During the course of the bloom, dead cells sink to the sediment where their degradation consumes oxygen to create hypoxic zones (< 2 mg/L dissolved oxygen). These zones prevent the establishment of benthic communities and may result in fish mortality. The aim of the study was to determine how the spring and autumn sediment chemistry and microbial community composition changed due to degradation of diatom or cyanobacterial biomass, respectively. Results from incubation of sediment cores showed some typical anaerobic microbial processes after biomass addition such as a decrease in NO2- + NO3- in the sediment surface (0-1 cm) and iron in the underlying layer (1-2 cm). In addition, an increase in NO2- + NO3- was observed in the overlying benthic water in all amended and control incubations. The combination of NO2- + NO3- diffusion plus nitrification could not account for this increase. Based on 16S rRNA gene sequences, the addition of cyanobacterial biomass during autumn caused a large increase in ferrous iron-oxidizing archaea while diatom biomass amendment during spring caused minor changes in the microbial community. Considering that OTUs sharing lineages with acidophilic microorganisms had a high relative abundance during autumn, it was suggested that specific niches developed in sediment microenvironments. These findings highlight the importance of nitrogen cycling and early microbial community changes in the sediment due to sinking phytoplankton before potential hypoxia occurs.

Bactérias/isolamento & purificação , Cianobactérias/crescimento & desenvolvimento , Diatomáceas/crescimento & desenvolvimento , Sedimentos Geológicos/microbiologia , Fitoplâncton/crescimento & desenvolvimento , Bactérias/classificação , Bactérias/genética , Biomassa , Cianobactérias/classificação , Cianobactérias/genética , Cianobactérias/isolamento & purificação , Diatomáceas/classificação , Diatomáceas/genética , Diatomáceas/isolamento & purificação , Eutrofização , Sedimentos Geológicos/química , Nitratos/análise , Nitratos/metabolismo , Nitritos/análise , Nitritos/metabolismo , Filogenia , Fitoplâncton/classificação , Fitoplâncton/genética , Fitoplâncton/isolamento & purificação , Estações do Ano , Água do Mar/química , Água do Mar/microbiologia
Extremophiles ; 20(6): 903-913, 2016 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-27783177


Acidithiobacillus ferrivorans is an acidophilic bacterium that represents a substantial proportion of the microbial community in a low temperature mining waste stream. Due to its ability to grow at temperatures below 15 °C, it has previously been classified as 'psychrotolerant'. Low temperature-adapted microorganisms have strategies to grow at cold temperatures such as the production of cold acclimation proteins, DEAD/DEAH box helicases, and compatible solutes plus increasing their cellular membrane fluidity. However, little is known about At. ferrivorans adaptation strategies employed during culture at its temperature extremes. In this study, we report the transcriptomic response of At. ferrivorans SS3 to culture at 8 °C compared to 20 °C. Analysis revealed 373 differentially expressed genes of which, the majority were of unknown function. Only few changes in transcript counts of genes previously described to be cold adaptation genes were detected. Instead, cells cultured at cold (8 °C) altered the expression of a wide range of genes ascribed to functions in transcription, translation, and energy production. It is, therefore, suggested that a temperature of 8 °C imposed little cold stress on At. ferrivorans, underlining its adaptation to growth in the cold as well as suggesting it should be classified as a 'eurypsychrophile'.

Acidithiobacillus/genética , Resposta ao Choque Frio , Regulação Bacteriana da Expressão Gênica , RNA Mensageiro/genética , Acidithiobacillus/metabolismo , Adaptação Fisiológica , Concentração de Íons de Hidrogênio , RNA Mensageiro/metabolismo
J Microbiol Methods ; 129: 23-27, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27469351


BACKGROUND: Recent studies show that suboptimal blood levels of ß-lactam antibiotics are present in intensive care unit (ICU) patients. A common reference method for assessing drug concentrations is liquid chromatography coupled with mass-spectrometry (LC-MS) which is highly accurate but rarely available outside reference centres. Thus, our aim was to develop a microbiological method for monitoring ß-lactam antibiotic serum levels which could be used at any hospital with a microbiological laboratory. METHODS: The method was developed as a 96-well broth microdilution format to assess the concentrations of cefotaxime (CTX), meropenem (MER), and piperacillin (PIP). Patient serum containing antibiotics were diluted in suspensions of bacteria with known minimal inhibitory concentrations (MICs). Serum antibiotic concentrations were calculated by dividing the MIC with the dilution factor at which the serum inhibited growth of the bacterial suspension. Serum (n=88) from ICU patients at four hospitals in south-east Sweden were analysed and compared to LC-MS analysis. RESULTS: The overall accuracy and precision for spiked samples and patient samples was within the pre-set target of ±20.0% for all drugs. There was a significant correlation between the microbiological assay and LC-MS for the patient samples (CTX: r=0.86, n=31; MER: r=0.96, n=11; PIP: r=0.88, n=39) and the agreement around the clinical cut-off for CTX (4.0mg/l), MER (2.0mg/l) and PIP (16.0mg/l) was 90%, 100% and 87%, respectively. CONCLUSION: The microbiological method has a performance for determination of serum levels of meropenem, piperacillin and cefotaxime suitable for clinical use. It is an inexpensive method applicable in any microbiology laboratory.

Antibacterianos/sangue , Bactérias/efeitos dos fármacos , Técnicas Bacteriológicas , Estado Terminal , beta-Lactamas/sangue , Antibacterianos/farmacologia , Bactérias/crescimento & desenvolvimento , Cromatografia Líquida , Humanos , Espectrometria de Massas , Meropeném , Testes de Sensibilidade Microbiana , Suécia , Tienamicinas/sangue , Tienamicinas/farmacologia , beta-Lactamas/farmacologia
FEMS Microbiol Lett ; 363(7)2016 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-26956550


Acidithiobacillus ferrivorans is an acidophile implicated in low-temperature biomining for the recovery of metals from sulfide minerals. Acidithiobacillus ferrivorans obtains its energy from the oxidation of inorganic sulfur compounds, and genes encoding several alternative pathways have been identified. Next-generation sequencing of At. ferrivorans RNA transcripts identified the genes coding for metabolic and electron transport proteins for energy conservation from tetrathionate as electron donor. RNA transcripts suggested that tetrathionate was hydrolyzed by the tetH1 gene product to form thiosulfate, elemental sulfur and sulfate. Despite two of the genes being truncated, RNA transcripts for the SoxXYZAB complex had higher levels than for thiosulfate quinone oxidoreductase (doxDAgenes). However, a lack of heme-binding sites in soxX suggested that DoxDA was responsible for thiosulfate metabolism. Higher RNA transcript counts also suggested that elemental sulfur was metabolized by heterodisulfide reductase (hdrgenes) rather than sulfur oxygenase reductase (sor). The sulfite produced as a product of heterodisulfide reductase was suggested to be oxidized by a pathway involving the sat gene product or abiotically react with elemental sulfur to form thiosulfate. Finally, several electron transport complexes were involved in energy conservation. This study has elucidated the previously unknown At. ferrivorans tetrathionate metabolic pathway that is important in biomining.

Acidithiobacillus/genética , Acidithiobacillus/metabolismo , RNA Bacteriano/genética , Compostos de Enxofre/metabolismo , Enxofre/metabolismo , Sequência de Bases , Transporte de Elétrons/genética , Transporte de Elétrons/fisiologia , Expressão Gênica , Genoma Bacteriano , Redes e Vias Metabólicas , Oxirredução , Análise de Sequência de RNA/métodos
PLoS One ; 11(2): e0149454, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-26886224


Determining which reference genes have the highest stability, and are therefore appropriate for normalising data, is a crucial step in the design of real-time quantitative PCR (qPCR) gene expression studies. This is particularly warranted in non-model and ecologically important species for which appropriate reference genes are lacking, such as the mallard--a key reservoir of many diseases with relevance for human and livestock health. Previous studies assessing gene expression changes as a consequence of infection in mallards have nearly universally used ß-actin and/or GAPDH as reference genes without confirming their suitability as normalisers. The use of reference genes at random, without regard for stability of expression across treatment groups, can result in erroneous interpretation of data. Here, eleven putative reference genes for use in gene expression studies of the mallard were evaluated, across six different tissues, using a low pathogenic avian influenza A virus infection model. Tissue type influenced the selection of reference genes, whereby different genes were stable in blood, spleen, lung, gastrointestinal tract and colon. ß-actin and GAPDH generally displayed low stability and are therefore inappropriate reference genes in many cases. The use of different algorithms (GeNorm and NormFinder) affected stability rankings, but for both algorithms it was possible to find a combination of two stable reference genes with which to normalise qPCR data in mallards. These results highlight the importance of validating the choice of normalising reference genes before conducting gene expression studies in ducks. The fact that nearly all previous studies of the influence of pathogen infection on mallard gene expression have used a single, non-validated reference gene is problematic. The toolkit of putative reference genes provided here offers a solid foundation for future studies of gene expression in mallards and other waterfowl.

Patos/genética , Regulação da Expressão Gênica , Reação em Cadeia da Polimerase em Tempo Real/métodos , Reação em Cadeia da Polimerase em Tempo Real/normas , Animais , Estudos de Associação Genética , Padrões de Referência , Software