scholarly journals Characteristics of Heterotrophic Nitrifying and Aerobic Denitrifying Arthrobacter nicotianae D51 Strain in the Presence of Copper

Water ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 434 ◽  
Author(s):  
Xi Cai ◽  
Kaili Li ◽  
Tengxia He ◽  
Yaxin Wang ◽  
Xue Zhang ◽  
...  
Keyword(s):  
Nitrogen Source ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Aerobic Denitrification ◽  
Rrna Gene ◽  
Sole Nitrogen Source ◽  
Bacterium Strain ◽  
Arthrobacter Nicotianae ◽  
Nitrite Nitrate ◽  
The Impact

A heterotrophic nitrification and aerobic denitrification bacterium, strain D51, was identified as Arthrobacter nicotianae based on morphological, phospholipid fatty acids (PLFAs), and 16S rRNA gene sequence analyses. Further tests demonstrated that strain D51 had the capability to use nitrite, nitrate, or ammonium as the sole nitrogen source in the presence of Cu2+. The maximum removal efficiencies of nitrite, nitrate and ammonium were 68.97%, 78.32%, and 98.70%, respectively. Additionally, the maximum growth rate and denitrification capacity of this strain occurred in the presence of 0.05 mg·L−1 of Cu2+.However, the growth and aerobic denitrification capacity were intensively inhibited by Cu2+ at ≥0.1 mg·L−1. Moreover, gas chromatography indicated that a portion of the nitrogen was transformed into N2O when the nitrite, nitrate, and ammonium were separately used as the sole nitrogen source. This is the first study of the nitrification and denitrification ability of Arthrobacter nicotianae under aerobic conditions, and the first experiment to investigate the impact of Cu2+ concentration on the growth and denitrification ability of this bacteria. The results presented herein extend the known varieties of heterotrophic nitrifying–aerobic denitrifying bacteria and provide useful information regarding the specific bacteria for nitrogen bioremediation of industrial wastewater containing Cu2+.

scholarly journals Methanobacterium aggregans sp. nov., a hydrogenotrophic methanogenic archaeon isolated from an anaerobic digester

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1975-1980 ◽  
Author(s):  
Tobias Kern ◽  
Mary Linge ◽  
Michael Rother
Keyword(s):  
16S Rrna ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Curved Rods

A novel, strictly anaerobic, hydrogenotrophic methanogen, strain E09F.3T, was isolated from a commercial biogas plant in Germany. Cells of E09F.3T were Gram-stain-negative, non-motile, slightly curved rods, long chains of which formed large aggregates consisting of intertwined bundles of chains. Cells utilized H2+CO2 and, to a lesser extent, formate as substrates for growth and methanogenesis. The optimal growth temperature was around 40 °C; maximum growth rate was obtained at pH around 7.0 with approximately 6.8 mM NaCl. The DNA G+C content of strain E09F.3T was 39.1 mol%. Phylogenetic analyses based on 16S rRNA and mcrA gene sequences placed strain E09F.3T within the genus Methanobacterium. On the basis of 16S rRNA gene sequence similarity, strain E09F.3T was closely related to Methanobacterium congolense CT but morphological, physiological and genomic characteristics indicated that strain E09F.3T represents a novel species. The name Methanobacterium aggregans sp. nov. is proposed for this novel species, with strain E09F.3T ( = DSM 29428T = JCM 30569T) as the type strain.

Modeling the Impact of Vapor Thymol Concentration, Temperature, and Modified Atmosphere Condition on Growth Behavior of Salmonella on Raw Shrimp†

2015 ◽  
Vol 78 (2) ◽  
pp. 293-301 ◽  
Author(s):  
SIYUAN ZHOU ◽  
SHIOWSHUH SHEEN ◽  
YU-HSIN PANG ◽  
LINSHU LIU ◽  
KIT L. YAM
Keyword(s):  
Growth Rate ◽  
Maximum Growth ◽  
Lag Time ◽  
Maximum Growth Rate ◽  
Growth Behavior ◽  
Impact Factors ◽  
Modified Atmosphere ◽  
Predictive Values ◽  
Raw Shrimp ◽  
The Impact

Salmonella is a microorganism of concern on a global basis for raw shrimp. This research modeled the impact of vapor thymol concentration (0, 0.8, and 1.6 mg/liter), storage temperature (8, 12, and 16°C), and modified atmosphere condition (0.04 as in the natural atmosphere and 59.5% CO2) against the growth behavior of a Salmonella cocktail (six strains) on raw shrimp. Lag time (hour) and maximum growth rate (log CFU per gram per hour), chosen as two growth indicators, were obtained through DMFit software and then developed into polynomial as well as nonlinear modified secondary models (dimensional and/or dimensionless), consisting of two or even three impact factors in the equations. The models were validated, and results showed that the predictive values from both models demonstrated good matches to the observed experimental values, yet the prediction based on lag time was more accurate than maximum growth rate. The information will provide the food industry with insight into the potential safety risk of Salmonella growth on raw shrimp under stressed conditions.

Denitrification characteristics of a newly isolated indigenous aerobic denitrifying bacterium under oligotrophic conditions

2015 ◽  
Vol 72 (7) ◽  
pp. 1082-1088 ◽  
Author(s):  
Jun-feng Su ◽  
Kai Zhang ◽  
Ting-lin Huang ◽  
Fang Ma ◽  
Lin Guo ◽  
...  
Keyword(s):  
Nitrate Removal ◽  
Reduction Rate ◽  
Inoculum Size ◽  
Aerobic Denitrification ◽  
Rrna Gene ◽  
Box Behnken Design ◽  
Initial Ph ◽  
Bacterium Strain ◽  
Nitrate Degradation ◽  
Full Factorial

A novel indigenous bacterium, strain JM10, isolated from the oligotrophic Hei He reservoir was characterized and showed aerobic denitrification ability. JM10 was identified as Bacillus sp. by phylogenetic analysis of its 16S rRNA gene sequence. Strain JM10 displayed very high levels of activity in aerobic conditions, consuming over 94.3% NO3−-N (approximately 3.06 mg L−1) with a maximum reduction rate of 0.108 mg NO3−-N L−1 h−1. Full-factorial Box–Behnken design and response surface methodology were employed to investigate the optimal nitrate degradation conditions. The optimum conditions for nitrate degradation, at a rate of 0.140 mg L−1 h−1, were found to be an inoculum size of 16.3% v/v, initial pH of 7.6, C/N ratio of 7.4, and temperature of 27.4 °C, and the C/N ratio and temperature had the largest effect on the nitrate degradation rate. Strain JM10 was added into the water samples from Hei He reservoir and the total nitrogen and nitrate removal rates of the strain reached 66.5% and 100%, respectively. Therefore, our results demonstrate that the strain JM10 favored the bioremediation of the oligotrophic reservoir.

scholarly journals Thiomicrospira arctica sp. nov. and Thiomicrospira psychrophila sp. nov., psychrophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacteria isolated from marine Arctic sediments

2005 ◽  
Vol 55 (2) ◽  
pp. 781-786 ◽  
Author(s):  
Katrin Knittel ◽  
Jan Kuever ◽  
Anke Meyerdierks ◽  
Ruth Meinke ◽  
Rudolf Amann ◽  
...  
Keyword(s):  
Novel Species ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Sulfur Oxidizing ◽  
Sulfur Oxidizing Bacteria

Two psychrophilic, chemolithoautotrophic, sulfur-oxidizing bacteria were isolated from marine Arctic sediments sampled off the coast of Svalbard with thiosulfate as the electron donor and CO2 as carbon source. Comparative analysis of 16S rRNA gene sequences suggested that the novel strains, designated SVAL-DT and SVAL-ET, represent members of the genus Thiomicrospira. Further genotypic (DNA–DNA relatedness, DNA G+C content) and phenotypic characterization revealed that the strains represent members of two novel species. Both organisms are obligately autotrophic and strictly aerobic. Nitrate was not used as an electron acceptor. Chemolithoautotrophic growth was observed with thiosulfate, tetrathionate and sulfur. The temperature limits for growth of both strains were between −2 °C and 20·8 °C, with optima of 11·5–13·2 °C (SVAL-ET) and 14·6–15·4 °C (SVAL-DT), which is about 13–15 °C lower than the optima of all other recognized Thiomicrospira species. The maximum growth rate on thiosulfate at 14 °C was 0·14 h−1 for strain SVAL-ET and 0·2 h−1 for strain SVAL-DT. Major fatty acids of SVAL-DT are C16 : 1, C18 : 0 and C16 : 0, and those of SVAL-ET are C16 : 1, C18 : 1, C16 : 0 and C14 : 1. Cells of SVAL-DT and SVAL-ET are rods, like those of their closest relatives. To our knowledge the novel strains are the first psychrophilic, chemolithoautotrophic, sulfur-oxidizing bacteria so far described. The names Thiomicrospira arctica sp. nov. and Thiomicrospira psychrophila sp. nov. are proposed for SVAL-ET (=ATCC 700955T=DSM 13458T) and SVAL-DT (=ATCC 700954T=DSM 13453T), respectively.

scholarly journals Amplicon-sequencing of raw milk microbiota: impact of DNA extraction and library-PCR

2021 ◽  
Author(s):  
Annemarie Siebert ◽  
Katharina Hofmann ◽  
Lena Staib ◽  
Etienne V. Doll ◽  
Siegfried Scherer ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Dna Extraction ◽  
Raw Milk ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
Microbiome Analysis ◽  
Eukaryotic Dna ◽  
Selective Lysis ◽  
The Impact

Abstract The highly complex raw milk matrix challenges the sample preparation for amplicon-sequencing due to low bacterial counts and high amounts of eukaryotic DNA originating from the cow. In this study, we optimized the extraction of bacterial DNA from raw milk for microbiome analysis and evaluated the impact of cycle numbers in the library-PCR. The selective lysis of eukaryotic cells by proteinase K and digestion of released DNA before bacterial lysis resulted in a high reduction of mostly eukaryotic DNA and increased the proportion of bacterial DNA. Comparative microbiome analysis showed that a combined enzymatic and mechanical lysis procedure using the DNeasy® PowerFood® Microbial Kit with a modified protocol was best suitable to achieve high DNA quantities after library-PCR and broad coverage of detected bacterial biodiversity. Increasing cycle numbers during library-PCR systematically altered results for species and beta-diversity with a tendency to overrepresentation or underrepresentation of particular taxa. To limit PCR bias, high cycle numbers should thus be avoided. An optimized DNA extraction yielding sufficient bacterial DNA and enabling higher PCR efficiency is fundamental for successful library preparation. We suggest that a protocol using ethylenediaminetetraacetic acid (EDTA) to resolve casein micelles, selective lysis of somatic cells, extraction of bacterial DNA with a combination of mechanical and enzymatic lysis, and restriction of PCR cycles for analysis of raw milk microbiomes is optimal even for samples with low bacterial numbers. Key points • Sample preparation for high-throughput 16S rRNA gene sequencing of raw milk microbiota. • Reduction of eukaryotic DNA by enzymatic digestion. • Shift of detected microbiome caused by high cycle numbers in library-PCR.

scholarly journals Impact of Diagnosed and Undiagnosed Respiratory Pseudomonas on VAP and VAE During Long-Term Acute Care

2020 ◽  
Vol 41 (S1) ◽  
pp. s258-s259
Author(s):  
James Harrigan ◽  
Ebbing Lautenbach ◽  
Emily Reesey ◽  
Magda Wernovsky ◽  
Pam Tolomeo ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Acute Care ◽  
Statistical Significance ◽  
Rrna Gene ◽  
Care Hospital ◽  
16S Sequencing ◽  
Increased Risk ◽  
Wide Range ◽  
The Impact

Background: Clinically diagnosed ventilator-associated pneumonia (VAP) is common in the long-term acute-care hospital (LTACH) setting and may contribute to adverse ventilator-associated events (VAEs). Pseudomonas aeruginosa is a common causative organism of VAP. We evaluated the impact of respiratory P. aeruginosa colonization and bacterial community dominance, both diagnosed and undiagnosed, on subsequent P. aeruginosa VAP and VAE events during long-term acute care. Methods: We enrolled 83 patients on LTACH admission for ventilator weaning, performed longitudinal sampling of endotracheal aspirates followed by 16S rRNA gene sequencing (Illumina HiSeq), and bacterial community profiling (QIIME2). Statistical analysis was performed with R and Stan; mixed-effects models were fit to relate the abundance of respiratory Psa on admission to clinically diagnosed VAP and VAE events. Results: Of the 83 patients included, 12 were diagnosed with P. aeruginosa pneumonia during the 14 days prior to LTACH admission (known P. aeruginosa), and 22 additional patients received anti–P. aeruginosa antibiotics within 48 hours of admission (suspected P. aeruginosa); 49 patients had no known or suspected P. aeruginosa (unknown P. aeruginosa). Among the known P. aeruginosa group, all 12 patients had P. aeruginosa detectable by 16S sequencing, with elevated admission P. aeruginosa proportional abundance (median, 0.97; IQR, 0.33–1). Among the suspected P. aeruginosa group, all 22 patients had P. aeruginosa detectable by 16S sequencing, with a wide range of admission P. aeruginosa proportional abundance (median, 0.0088; IQR, 0.00012–0.31). Of the 49 patients in the unknown group, 47 also had detectable respiratory Psa, and many had high P. aeruginosa proportional abundance at admission (median, 0.014; IQR, 0.00025–0.52). Incident P. aeruginosa VAP was observed within 30 days in 4 of the known P. aeruginosa patients (33.3%), 5 of the suspected P. aeruginosa patients (22.7%), and 8 of the unknown P. aeruginosa patients (16.3%). VAE was observed within 30 days in 1 of the known P. aeruginosa patients (8.3%), 2 of the suspected P. aeruginosa patients (9.1%), and 1 of the unknown P. aeruginosa patients (2%). Admission P. aeruginosa abundance was positively associated with VAP and VAE risk in all groups, but the association only achieved statistical significance in the unknown group (type S error <0.002 for 30-day VAP and <0.011 for 30-day VAE). Conclusions: We identified a high prevalence of unrecognized respiratory P. aeruginosa colonization among patients admitted to LTACH for weaning from mechanical ventilation. The admission P. aeruginosa proportional abundance was strongly associated with increased risk of incident P. aeruginosa VAP among these patients.Funding: NoneDisclosures: None

PRODUCTION OF CYTASES ACTIVE ON BARLEY GUM BY BACTERIA OF THE GENUS BACILLUS

1953 ◽  
Vol 31 (1) ◽  
pp. 28-32 ◽  
Author(s):  
A. C. Blackwood
Keyword(s):  
Bacillus Subtilis ◽  
Enzymatic Activity ◽  
Nitrogen Source ◽  
Freeze Drying ◽  
Shake Flask ◽  
Sole Nitrogen Source ◽  
Genus Bacillus ◽  
Original Activity ◽  
Bacterial Cultures ◽  
Bacillus Genus

One hundred and fourteen bacterial cultures representing most of the species in the Bacillus genus were tested for the production of extracellular barley gum cytase. Assays were made on shake-flask cultures grown on a medium containing glucose and yeast extract. Although all the organisms had some enzymatic activity, certain strains of Bacillus subtilis gave the best yields of cytase. On a medium with asparagine as the sole nitrogen source even higher yields were obtained. The crude cytase preparations were stable and after freeze-drying most of the original activity remained.

scholarly journals Optimizing of Microalgae Scenedesmus sp. Biomass Production in Wet Market Wastewater Using Response Surface Methodology

2021 ◽  
Vol 13 (4) ◽  
pp. 2216
Author(s):  
Najeeha Mohd Apandi ◽  
Mimi Suliza Muhamad ◽  
Radin Maya Saphira Radin Mohamed ◽  
Norshuhaila Mohamed Sunar ◽  
Adel Al-Gheethi ◽  
...  
Keyword(s):  
Response Surface Methodology ◽  
Response Surface ◽  
Biomass Yield ◽  
Biomass Productivity ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Aeration Rate ◽  
Composition Analysis ◽  
Wet Market ◽  
Central Composite

The present study aimed to optimize the production of Scenedesmus sp. biomass during the phycoremediation process. The biomass productivity was optimized using face centred central composite design (FCCCD) in response surface methodology (RSM) as a function of two independent variables that included wet market wastewater concentrations (A) with a range of 10% to 75% and aeration rate (B) with a range of 0.02 to 4.0 L/min. The results revealed that the highest biomass productivity (73 mg/L/d) and maximum growth rate (1.19 day−1) was achieved with the 64.26% of (A) and 3.08 L/min of (B). The GC-MS composition analysis of the biomass yield extract revealed that the major compounds are hexadecane (25%), glaucine (16.2%), and phytol (8.33%). The presence of these compounds suggests that WMW has the potential to be used as a production medium for Scenedesmus sp. Biomass, which has several applications in the pharmaceutical and chemical industry.

scholarly journals Effects of Psychotropics on the Microbiome in Patients With Depression and Anxiety: Considerations in a Naturalistic Clinical Setting

2020 ◽  
Author(s):  
Yoshihiro Tomizawa ◽  
Shunya Kurokawa ◽  
Daiki Ishii ◽  
Katsuma Miyaho ◽  
Chiharu Ishii ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
Depressive Disorders ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Shannon Index ◽  
Rrna Gene ◽  
Depression And Anxiety ◽  
The Impact ◽  
Whole Tree

Abstract Background The antibacterial effects of psychotropics may be part of their pharmacological effects when treating depression. However, limited studies have focused on gut microbiota in relation to prescribed medication. Method We longitudinally investigated the relationship between patients’ prescribed medications and intestinal bacterial diversity in a naturalistic treatment course for patients with major depressive disorders and anxiety disorders. Patients were recruited and their stool was collected at 3 time points during their usual psychiatric treatments. Gut microbiota were analyzed using 16S rRNA gene sequencing. We examined the impact of psychotropics (i.e., antidepressants, anxiolytics, antipsychotics) on their gut microbial diversity and functions. Results We collected 246 stool samples from 40 patients. Despite no differences in microbial diversity between medication groups at the baseline, over the course of treatment, phylogenic diversity whole-tree diversity decreased in patients on antipsychotics compared with patients without (P = .027), and beta diversity followed this trend. Based on a fixed-effect model, antipsychotics predicted microbial diversity; the higher doses correlated with less diversity based on the Shannon index and phylogenic diversity whole tree (estimate = −0.00254, SE = 0.000595, P &lt; .0001; estimate = −0.02644, SE = 0.00833, P = .002, respectively). Conclusion Antipsychotics may play a role in decreasing the alpha diversity of the gut microbiome among patients with depression and anxiety, and our results indicate a relationship with medication dosage. Future studies are warranted and should consider patients’ types and doses of antipsychotics in order to further elucidate the mechanisms of gut-brain interactions in psychiatric disorders.

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