Draft genome sequence of Microbacterium oleivorans strain Wellendorf implicates heterotrophic versatility and bioremediation potential

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Anton P. Avramov

2016-12-01

Full Text Available Microbacterium oleivorans is a predominant member of hydrocarbon-contaminated environments. We here report on the genomic analysis of M. oleivorans strain Wellendorf that was isolated from an indoor door handle. The partial genome of M. oleivorans strain Wellendorf consists of 2,916,870 bp of DNA with 2831 protein-coding genes and 49 RNA genes. The organism appears to be a versatile mesophilic heterotroph potentially capable of hydrolysis a suite of carbohydrates and amino acids. Genomic analysis revealed metabolic versatility with genes involved in the metabolism and transport of glucose, fructose, rhamnose, galactose, xylose, arabinose, alanine, aspartate, asparagine, glutamate, serine, glycine, threonine and cysteine. This is the first detailed analysis of a Microbacterium oleivorans genome.

Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

Energy Technology Data Exchange (ETDEWEB)

Xie, Gary [Los Alamos National Laboratory (LANL); Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL

2011-01-01

Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer-ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi-cellulose. This bacterium is also considered as a potential probiotic. Complete genome squence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

Trimethylamine and trimethylamine N-oxide are supplementary energy sources for a marine heterotrophic bacterium: implications for marine carbon and nitrogen cycling.

Science.gov (United States)

Lidbury, Ian D E A; Murrell, J Colin; Chen, Yin

2015-03-01

Bacteria of the marine Roseobacter clade are characterised by their ability to utilise a wide range of organic and inorganic compounds to support growth. Trimethylamine (TMA) and trimethylamine N-oxide (TMAO) are methylated amines (MA) and form part of the dissolved organic nitrogen pool, the second largest source of nitrogen after N2 gas, in the oceans. We investigated if the marine heterotrophic bacterium, Ruegeria pomeroyi DSS-3, could utilise TMA and TMAO as a supplementary energy source and whether this trait had any beneficial effect on growth. In R. pomeroyi, catabolism of TMA and TMAO resulted in the production of intracellular ATP which in turn helped to enhance growth rate and growth yield as well as enhancing cell survival during prolonged energy starvation. Furthermore, the simultaneous use of two different exogenous energy sources led to a greater enhancement of chemoorganoheterotrophic growth. The use of TMA and TMAO primarily as an energy source resulted in the remineralisation of nitrogen in the form of ammonium, which could cross feed into another bacterium. This study provides greater insight into the microbial metabolism of MAs in the marine environment and how it may affect both nutrient flow within marine surface waters and the flux of these climatically important compounds into the atmosphere.

Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

Energy Technology Data Exchange (ETDEWEB)

Rhee, Mun Su [University of Florida, Gainesville; Moritz, Brelan E. [University of Florida, Gainesville; Xie, Gary [Los Alamos National Laboratory (LANL); Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Chertkov, Olga [Los Alamos National Laboratory (LANL); Brettin, Thomas S [ORNL; Han, Cliff [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Patel, Milind [University of Florida, Gainesville; Ou, Mark [University of Florida, Gainesville; Harbrucker, Roberta [University of Florida, Gainesville; Ingram, Lonnie O. [University of Florida; Shanmugam, Keelnathan T. [University of Florida

2011-01-01

Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer- ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this spo- rogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attrac- tive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi- cellulose. This bacterium is also considered as a potential probiotic. Complete genome se- quence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

Science.gov (United States)

Rhee, Mun Su; Moritz, Brélan E.; Xie, Gary; Glavina del Rio, T.; Dalin, E.; Tice, H.; Bruce, D.; Goodwin, L.; Chertkov, O.; Brettin, T.; Han, C.; Detter, C.; Pitluck, S.; Land, Miriam L.; Patel, Milind; Ou, Mark; Harbrucker, Roberta; Ingram, Lonnie O.; Shanmugam, K. T.

2011-01-01

Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 °C and pH 5.0 and ferments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 °C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemicellulose. This bacterium is also considered as a potential probiotic. Complete genome sequence of a representative strain, B. coagulans strain 36D1, is presented and discussed. PMID:22675583

Isolation of heterotrophic diazotrophic bacteria from estuarine surface waters.

Science.gov (United States)

Farnelid, Hanna; Harder, Jens; Bentzon-Tilia, Mikkel; Riemann, Lasse

2014-10-01

The wide distribution of diverse nitrogenase (nifH) genes affiliated with those of heterotrophic bacteria in marine and estuarine waters indicates ubiquity and an ecologically relevant role for heterotrophic N2 -fixers (diazotrophs) in aquatic nitrogen (N) cycling. However, the lack of cultivated representatives currently precludes an evaluation of their N2 -fixing capacity. In this study, microoxic or anoxic N-free media were inoculated with estuarine Baltic Sea surface water to select for N2 -fixers. After visible growth and isolation of single colonies on oxic plates or in anoxic agar tubes, nifH gene amplicons were obtained from 64 strains and nitrogenase activity, applying the acetylene reduction assay, was confirmed for 40 strains. Two strains, one Gammaproteobacterium affiliated with Pseudomonas and one Alphaproteobacterium affiliated with Rhodopseudomonas were shown to represent established members of the indigenous diazotrophic community in the Baltic Sea, with abundances of up to 7.9 × 10(4) and 4.7 × 10(4)  nifH copies l(-1) respectively. This study reports media for successful isolation of heterotrophic diazotrophs. The applied methodology and the obtained strains will facilitate future identification of factors controlling heterotrophic diazotrophic activity in aquatic environments, which is a prerequisite for understanding and evaluating their ecology and contribution to N cycling at local and regional scales. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Caldanaerobacter uzonensis sp. nov., an anaerobic, thermophilic, heterotrophic bacterium isolated from a hot spring.

Science.gov (United States)

Kozina, Irina V; Kublanov, Ilya V; Kolganova, Tatyana V; Chernyh, Nikolai A; Bonch-Osmolovskaya, Elizaveta A

2010-06-01

An anaerobic thermophilic bacterium, strain K67(T), was isolated from a terrestrial hot spring of Uzon Caldera, Kamchatka Peninsula. Analysis of the 16S rRNA gene sequence revealed that the novel isolate belongs to the genus Caldanaerobacter, with 95 % 16S rRNA gene sequence similarity to Caldanaerobacter subterraneus subsp. subterraneus SEBR 7858(T), suggesting that it represents a novel species of the genus Caldanaerobacter. Strain K67(T) was characterized as an obligate anaerobe, a thermophile (growth at 50-75 degrees capital ES, Cyrillic; optimum 68-70 degrees C), a neutrophile (growth at pH(25 degrees C) 4.8-8.0; optimum pH(25 degrees C) 6.8) and an obligate organotroph (growth by fermentation of various sugars, peptides and polysaccharides). Major fermentation products were acetate, H2 and CO2; ethanol, lactate and l-alanine were formed in smaller amounts. Thiosulfate stimulated growth and was reduced to hydrogen sulfide. Nitrate, sulfate, sulfite and elemental sulfur were not reduced and did not stimulate growth. Thus, according to the strain's phylogenetic position and phenotypic novelties (lower upper limit of temperature range for growth, the ability to grow on arabinose, the inability to reduce elemental sulfur and the formation of alanine as a minor fermentation product), the novel species Caldanaerobacter uzonensis sp. nov. is proposed, with the type strain K67(T) (=DSM 18923(T) =VKM capital VE, Cyrillic-2408(T)).

Draft Genome Sequence of the Efficient Bioflocculant-Producing Bacterium Paenibacillus sp. Strain A9

Science.gov (United States)

Liu, Jin-liang; Hu, Xiao-min

2013-01-01

Paenibacillus sp. strain A9 is an important bioflocculant-producing bacterium, isolated from a soil sample, and is pale pink-pigmented, aerobic, and Gram-positive. Here, we report the draft genome sequence and the initial findings from a preliminary analysis of strain A9, which is a novel species of Paenibacillus. PMID:23618713

Nitrogen Removal Characteristics of Pseudomonas putida Y-9 Capable of Heterotrophic Nitrification and Aerobic Denitrification at Low Temperature

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Yi Xu

2017-01-01

Full Text Available The cold-adapted bacterium Pseudomonas putida Y-9 was investigated and exhibited excellent capability for nitrogen removal at 15°C. The strain capable of heterotrophic nitrification and aerobic denitrification could efficiently remove ammonium, nitrate, and nitrite at an average removal rate of 2.85 mg, 1.60 mg, and 1.83 mg NL−1 h−1, respectively. Strain Y-9 performed nitrification in preference to denitrification when ammonium and nitrate or ammonium and nitrite coexisted in the solution. Meantime, the presence of nitrate had no effect on the ammonium removal rate of strain Y-9, and yet the presence of high concentration of nitrite would inhibit the cell growth and decrease the nitrification rate. The experimental results indicate that P. putida Y-9 has potential application for the treatment of wastewater containing high concentrations of ammonium along with its oxidation products at low temperature.

Antagonistic interactions between filamentous heterotrophs and the cyanobacterium Nostoc muscorum

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Wolf Sarah

2011-09-01

Full Text Available Abstract Background Little is known about interactions between filamentous heterotrophs and filamentous cyanobacteria. Here, interactions between the filamentous heterotrophic bacteria Fibrella aestuarina (strain BUZ 2 and Fibrisoma limi (BUZ 3 with an axenic strain of the autotrophic filamentous cyanobacterium Nostoc muscorum (SAG 25.82 were studied in mixed cultures under nutrient rich (carbon source present in medium and poor (carbon source absent in medium conditions. Findings F. aestuarina BUZ 2 significantly reduced the cyanobacterial population whereas F. limi BUZ 3 did not. Physical contact between heterotrophs and autotroph was observed and the cyanobacterial cells showed some level of damage and lysis. Therefore, either contact lysis or entrapment with production of extracellular compounds in close vicinity of host cells could be considered as potential modes of action. The supernatants from pure heterotrophic cultures did not have an effect on Nostoc cultures. However, supernatant from mixed cultures of BUZ 2 and Nostoc had a negative effect on cyanobacterial growth, indicating that the lytic compounds were only produced in the presence of Nostoc. The growth and survival of tested heterotrophs was enhanced by the presence of Nostoc or its metabolites, suggesting that the heterotrophs could utilize the autotrophs and its products as a nutrient source. However, the autotroph could withstand and out-compete the heterotrophs under nutrient poor conditions. Conclusions Our results suggest that the nutrients in cultivation media, which boost or reduce the number of heterotrophs, were the important factor influencing the outcome of the interplay between filamentous heterotrophs and autotrophs. For better understanding of these interactions, additional research is needed. In particular, it is necessary to elucidate the mode of action for lysis by heterotrophs, and the possible defense mechanisms of the autotrophs.

Novel heterotrophic nitrogen removal and assimilation characteristic of the newly isolated bacterium Pseudomonas stutzeri AD-1.

Science.gov (United States)

Qing, Hui; Donde, Oscar Omondi; Tian, Cuicui; Wang, Chunbo; Wu, Xingqiang; Feng, Shanshan; Liu, Yao; Xiao, Bangding

2018-04-18

AD-1, an aerobic denitrifier, was isolated from activated sludge and identified as Pseudomonas stutzeri. AD-1 completely removed NO 3 - or NO 2 - and removed 99.5% of NH 4 + during individual culturing in a broth medium with an initial nitrogen concentration of approximately 50 mg L -1 . Results showed that larger amounts of nitrogen were removed through assimilation by the bacteria. And when NH 4 + was used as the sole nitrogen source in the culture medium, neither NO 2 - nor NO 3 - was detected, thus indicating that AD-1 may not be a heterotrophic nitrifier. Only trace amount of N 2 O was detected during the denitrification process. Single factor experiments indicated that the optimal culture conditions for AD-1 were: a carbon-nitrogen ratio (C/N) of 15, a temperature of 25°C and sodium succinate or glucose as a carbon source. In conclusion, due to the ability of AD-1 to utilize nitrogen of different forms with high efficiencies for its growth while producing only trace emissions of N 2 O, the bacterium had outstanding potential to use in the bioremediation of high-nitrogen-containing wastewaters. Meanwhile, it may also be a proper candidate for biotreatment of high concentration organic wastewater. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Draft Genome Sequence of Advenella kashmirensis Strain W13003, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium

Science.gov (United States)

Jin, Decai; Zhou, Lisha; Wu, Liang; An, Wei; Zhao, Lin

2014-01-01

Advenella kashmirensis strain W13003 is a polycyclic aromatic hydrocarbon (PAH)-degrading bacterium isolated from PAH-contaminated marine sediments. Here, we report the 4.8-Mb draft genome sequence of this strain, which will provide insights into the diversity of A. kashmirensis and the mechanism of PAH degradation in the marine environment. PMID:24482505

Reduction of Mo(VI) by the bacterium Serratia sp. strain DRY5.

Science.gov (United States)

Rahman, M F A; Shukor, M Y; Suhaili, Z; Mustafa, S; Shamaan, N A; Syed, M A

2009-01-01

The need to isolate efficient heavy metal reducers for cost effective bioremediation strategy have resulted in the isolation of a potent molybdenum-reducing bacterium. The isolate was tentatively identified as Serratia sp. strain DRY5 based on the Biolog GN carbon utilization profiles and partial 16S rDNA molecular phylogeny. Strain DRY5 produced 2.3 times the amount of Mo-blue than S. marcescens strain Dr.Y6, 23 times more than E. coli K12 and 7 times more than E. cloacae strain 48. Strain DRY5 required 37 degrees C and pH 7.0 for optimum molybdenum reduction. Carbon sources such as sucrose, maltose, glucose and glycerol, supported cellular growth and molybdate reduction after 24 hr of static incubation. The most optimum carbon source that supported reduction was sucrose at 1.0% (w/v). Ammonium sulphate, ammonium chloride, glutamic acid, cysteine, and valine supported growth and molybdate reduction with ammonium sulphate as the optimum nitrogen source at 0. 2% (w/v). Molybdate reduction was optimally supported by 30 mM molybdate. The optimum concentration of phosphate for molybdate reduction was 5 mM when molybdate concentration was fixed at 30 mM and molybdate reduction was totally inhibited at 100 mM phosphate. Mo-blue produced by this strain shows a unique characteristic absorption profile with a maximum peak at 865 nm and a shoulder at 700 nm, Dialysis tubing experiment showed that 95.42% of Mo-blue was found in the dialysis tubing suggesting that the molybdate reduction seen in this bacterium was catalyzed by enzyme(s). The characteristics of isolate DRY5 suggest that it would be useful in the bioremediation ofmolybdenum-containing waste.

Draft Genome Sequence of Desulfuromonas acetexigens Strain 2873, a Novel Anode-Respiring Bacterium

KAUST Repository

Katuri, Krishna

2017-03-03

Here, we report the draft genome sequence of Desulfuromonas acetexigens strain 2873, which was originally isolated from digester sludge from a sewage treatment plant in Germany. This bacterium is capable of anode respiration with high electrochemical activity in microbial electrochemical systems. The draft genome contains 3,376 predicted protein-coding genes and putative multiheme c-type cytochromes.

Draft Genome Sequence of Desulfuromonas acetexigens Strain 2873, a Novel Anode-Respiring Bacterium

KAUST Repository

Katuri, Krishna; Albertsen, Mads; Saikaly, Pascal

2017-01-01

Here, we report the draft genome sequence of Desulfuromonas acetexigens strain 2873, which was originally isolated from digester sludge from a sewage treatment plant in Germany. This bacterium is capable of anode respiration with high electrochemical activity in microbial electrochemical systems. The draft genome contains 3,376 predicted protein-coding genes and putative multiheme c-type cytochromes.

Nitrosomonas communis strain YNSRA, an ammonia-oxidizing bacterium, isolated from the reed rhizoplane in an aquaponics plant.

Science.gov (United States)

Tokuyama, Tatsuaki; Mine, Atsusi; Kamiyama, Kaoru; Yabe, Ryuichi; Satoh, Kazuo; Matsumoto, Hirotoshi; Takahashi, Reiji; Itonaga, Koji

2004-01-01

An ammonia-oxidizing bacterium (strain YNSRA) was isolated from the rhizoplane of the reed (Phragmites communis) used in an aquaponics plant which is a wastewater treatment plant. Strain YNSRA was identified as Nitrosomonas communis by taxonomic studies. The hydroxylamine-cytochrome c reductase (HCR) of strain YNSRA was found to have a higher activity (25.60 u/mg) than that of Nitrosomonas europaea ATCC25978T (8.94 u/mg). Ribulose-1,5-bisphosphate carboxylase (RubisCO) activity was detected at very low levels in strain YNSRA, whereas strain ATCC25978T had definite activity.

Complete genome sequence of the bioleaching bacterium Leptospirillum sp. group II strain CF-1.

Science.gov (United States)

Ferrer, Alonso; Bunk, Boyke; Spröer, Cathrin; Biedendieck, Rebekka; Valdés, Natalia; Jahn, Martina; Jahn, Dieter; Orellana, Omar; Levicán, Gloria

2016-03-20

We describe the complete genome sequence of Leptospirillum sp. group II strain CF-1, an acidophilic bioleaching bacterium isolated from an acid mine drainage (AMD). This work provides data to gain insights about adaptive response of Leptospirillum spp. to the extreme conditions of bioleaching environments. Copyright © 2016 Elsevier B.V. All rights reserved.

Heterotrophic cultivation of microalgae for production of biodiesel.

Science.gov (United States)

Mohamed, Mohd Shamzi; Wei, Lai Zee; Ariff, Arbakariya B

2011-08-01

High cell density cultivation of microalgae via heterotrophic growth mechanism could effectively address the issues of low productivity and operational constraints presently affecting the solar driven biodiesel production. This paper reviews the progress made so far in the development of commercial-scale heterotrophic microalgae cultivation processes. The review also discusses on patentable concepts and innovations disclosed in the past four years with regards to new approaches to microalgal cultivation technique, improvisation on the process flow designs to economically produced biodiesel and genetic manipulation to confer desirable traits leading to much valued high lipid-bearing microalgae strains.

Aerobic and heterotrophic nitrogen removal by Enterobacter cloacae CF-S27 with efficient utilization of hydroxylamine.

Science.gov (United States)

Padhi, Soumesh Kumar; Tripathy, Swetaleena; Mohanty, Sriprakash; Maiti, Nikhil Kumar

2017-05-01

Heterotrophic bacterium, Enterobacter cloacae CF-S27 exhibited simultaneous nitrification and aerobic denitrification in presence of high concentration of hydroxylamine. With the initial nitrogen concentration of 100mgL -1 h -1 , ammonium, nitrate and nitrite removal efficiencies were 81%, 99.9% and 92.8%, while the corresponding maximum removal rates reached as high as 11.6, 15.1 and 11.2mgL -1 h -1 respectively. Quantitative amplification by real time PCR and enzyme assay demonstrated that hydroxylamine reductase gene (hao) is actively involved in hetrotrophic nitrification and aerobic denitrification process of Enterobacter cloacae CF-S27. PCR primers were designed targeting amplification of hao gene from diversified environmental soil DNA. The strain Enterobacter cloacae CF-S27 significantly maintained the undetectable amount of dissolved nitrogen throughout 60days of zero water exchange fish culture experiment in domestic wastewater. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Effect of Some Physical and Chemical Parameters on Regrowth of Aeromonas Bacterium and Heterotrophic Bacteria in Isfahan Drinking Water System

Directory of Open Access Journals (Sweden)

Sina Dobaradaran

2006-03-01

Full Text Available Aeromonas is one the gram – negative , non spor – formating rod shaping , facultatively anaerobic and opportunistic bactria that can cause systematic infections, leision and diarrhoea in human. Fairly high bactrial population in distribution system is not only of concern because of affecting consumer health but also it makes it difficult to enumerate coliform bacterium indicator. So, the relationships between aeromonas and heterotrophic bacteria growth with pH, temperature, turbidity, free residual cholornie and DO were determined in this study. ADA- V media was used in presumptive stage to count aeromonas bacteria for the first time in Iran on the basis of 1605 EPA (2001 method and used oxidase tests, trehalose fermentation and indol test in confirmative stage. R2A media was used to count HPC bacteria and other factors measured on the basis of standards. The results showed that positive cases of aeromonas bacteria and HPC increase in higher temperature and turbidity and lower pH. In contrast, positive cases of aeromonas bacteria and HPC decrease while free residual cholorine and DO increase. In addition,no positive case of aeromonas was observed in more than 0.2 mg/L concentration of free residual cholorine.

Characterization of a novel chitinase from a moderately halophilic bacterium, Virgibacillus marismortui strain M3-23

OpenAIRE

Essghaier, Badiaa; Hedi, Abdeljabbar; Bajji, Mohammed; Jijakli, Haissam; Boudabous, Abdellatif; Sadfi-Zouaoui, Najla

2012-01-01

A new chitinase produced by the moderately halophilic bacterium Virgibacillus marismortui strain M3- 23 was identified and characterized. Distinguishable characteristics of high activity and stability at different pH, temperatures and salinity of M3-23 chitinase are reported. Analysis of the catalytic domain sequence from the enzyme highlighted its relationship to glycosyl hydrolase family 18. Comparison of the deduced chitinase sequence from strain M3-23 to known chitinases from Bacillus spe...

Crassaminicella profunda gen. nov., sp. nov., an anaerobic marine bacterium isolated from deep-sea sediments.

Science.gov (United States)

Lakhal, Raja; Pradel, Nathalie; Postec, Anne; Ollivier, Bernard; Cayol, Jean-Luc; Godfroy, Anne; Fardeau, Marie-Laure; Galés, Grégoire

2015-09-01

A novel, anaerobic, chemo-organotrophic bacterium, designated strain Ra1766H(T), was isolated from sediments of the Guaymas basin (Gulf of California, Mexico) taken from a depth of 2002  m. Cells were thin, motile, Gram-stain-positive, flexible rods forming terminal endospores. Strain Ra1766H(T) grew at temperatures of 25-45 °C (optimum 30 °C), pH 6.7-8.1 (optimum 7.5) and in a salinity of 5-60 g l(-1) NaCl (optimum 30 g l(-1)). It was an obligate heterotrophic bacterium fermenting carbohydrates (glucose and mannose) and organic acids (pyruvate and succinate). Casamino acids and amino acids (glutamate, aspartate and glycine) were also fermented. The main end products from glucose fermentation were acetate, butyrate, ethanol, H2 and CO2. Sulfate, sulfite, thiosulfate, elemental sulfur, fumarate, nitrate, nitrite and Fe(III) were not used as terminal electron acceptors. The predominant cellular fatty acids were C14  : 0, C16 : 1ω7, C16 : 1ω7 DMA and C16 : 0. The main polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phospholipids. The G+C content of the genomic DNA was 33.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Ra1766H(T) was affiliated to cluster XI of the order Clostridiales, phylum Firmicutes. The closest phylogenetic relative of Ra1766H(T) was Geosporobacter subterraneus (94.2% 16S rRNA gene sequence similarity). On the basis of phylogenetic inference and phenotypic properties, strain Ra1766H(T) ( = DSM 27501(T) = JCM 19377(T)) is proposed to be the type strain of a novel species of a novel genus, named Crassaminicella profunda.

The heterocyclic ring fission and dehydroxylation of catechins and related compounds by Eubacterium sp. strain SDG-2, a human intestinal bacterium.

Science.gov (United States)

Wang, L Q; Meselhy, M R; Li, Y; Nakamura, N; Min, B S; Qin, G W; Hattori, M

2001-12-01

A human intestinal bacterium, Eubacterium (E.) sp. strain SDG-2, was tested for its ability to metabolize various (3R)- and (3S)-flavan-3-ols and their 3-O-gallates. This bacterium cleaved the C-ring of (3R)- and (3S)-flavan-3-ols to give 1,3-diphenylpropan-2-ol derivatives, but not their 3-O-gallates. Furthermore, E. sp. strain SDG-2 had the ability of p-dehydroxylation in the B-ring of (3R)-flavan-3-ols, such as (-)-catechin, (-)-epicatechin, (-)-gallocatechin and (-)-epigallocatechin, but not of (3S)-flavan-3-ols, such as (+)-catechin and (+)-epicatechin.

Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1(T)).

Science.gov (United States)

Schleheck, David; Weiss, Michael; Pitluck, Sam; Bruce, David; Land, Miriam L; Han, Shunsheng; Saunders, Elizabeth; Tapia, Roxanne; Detter, Chris; Brettin, Thomas; Han, James; Woyke, Tanja; Goodwin, Lynne; Pennacchio, Len; Nolan, Matt; Cook, Alasdair M; Kjelleberg, Staffan; Thomas, Torsten

2011-12-31

Parvibaculum lavamentivorans DS-1(T) is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Alphaproteobacteria. Strain DS-1(T) is a non-pigmented, aerobic, heterotrophic bacterium and represents the first tier member of environmentally important bacterial communities that catalyze the complete degradation of synthetic laundry surfactants. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the first completed genome sequence of the genus Parvibaculum, and the first genome sequence of a representative of the family Rhodobiaceae.

Thymidine uptake, thymidine incorporation, and thymidine kinase activity in marine bacterium isolates

International Nuclear Information System (INIS)

Jeffrey, W.H.; Paul, J.H.

1990-01-01

One assumption made in bacterial production estimates from [ 3 H]thymidine incorporation is that all heterotrophic bacteria can incorporate exogenous thymidine into DNA. Heterotrophic marine bacterium isolates from Tampa Bay, Fla., Chesapeake Bay, Md., and a coral surface microlayer were examined for thymidine uptake (transport), thymidine incorporation, the presence of thymidine kinase genes, and thymidine kinase enzyme activity. Of the 41 isolates tested, 37 were capable of thymidine incorporation into DNA. The four organisms that could not incorporate thymidine also transported the thymidine poorly and lacked thymidine kinase activity. Attempts to detect thymidine kinase genes in the marine isolates by molecular probing with gene probes made from Escherichia coli and herpes simplex virus thymidine kinase genes proved unsuccessful. To determine if the inability to incorporate thymidine was due to the lack of thymidine kinase, one organism, Vibro sp. strain DI9, was transformed with a plasmid (pGQ3) that contained an E. coli thymidine kinase gene. Although enzyme assays indicated high levels of thymidine kinase activity in transformants, these cells still failed to incorporate exogenous thymidine into DNA or to transport thymidine into cells. These results indicate that the inability of certain marine bacteria to incorporate thymidine may not be solely due to the lack of thymidine kinase activity but may also be due to the absence of thymidine transport systems

Complete genome sequences of two strains of the meat spoilage bacterium Brochothrix thermosphacta isolated from ground chicken

Science.gov (United States)

Brochothrix thermosphacta is an important meat spoilage bacterium. Here we report the genome sequences of two strains of B. thermosphacta isolated from ground chicken. The genome sequences were determined using long-read PacBio single-molecule real-time (SMRT©) technology and are the first complete ...

Draft Genome Sequence of Bacillus amyloliquefaciens EBL11, a New Strain of Plant Growth-Promoting Bacterium Isolated from Rice Rhizosphere

Science.gov (United States)

Wang, Yinghuan; Greenfield, Paul; Jin, Decai

2014-01-01

Bacillus amyloliquefaciens strain EBL11 is a bacterium that can promote plant growth by inhibiting the growth of fungi on plant surfaces and providing nutrients as a nonchemical biofertilizer. The estimated genome of this strain is 4.05 Mb in size and harbors 3,683 coding genes (CDSs). PMID:25059875

Morphological characterization of several strains of the rice-pathogenic bacterium Burkholderia glumae in North Sumatra

Science.gov (United States)

Hasibuan, M.; Safni, I.; Lisnawita; Lubis, K.

2018-02-01

Burkholderia glumae is a quarantine seed-borne bacterial pathogen causing panicle blight disease on rice. This pathogen has been detected in some locations in Java, and recently, farmers in North Sumatra have reported rice yield loss with symptoms similar with those on rice infeced by the rice-pathogenic bacterium B. glumae. This research was aimed to isolate several bacterial strains from several rice varieties in various locations in North Sumatra and characterize the morphology of the strains to detect and identify the unknown bacterial strains presumably B. glumae. Several rice seed varieties were collected from Medan and Deli Serdang Districts. The seed samples were extracted, isolated and purified, then grown in semi-selective media PPGA. The morphological characteristics of the bacterial strains were determined including Gram staining, bacterial colony’s and bacterial cell’s morphology. The results showed that of eleven strains isolated, two strains were Gram negative and nine strains were Gram positive. On the basis of colony morphology, all strains had circular form, flat elevation and cream colour while the colony margin varied, i.e. entire and undulate. Most strains had bacillus/rod shape (8 strains) and only 3 strains were coccus.

Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49

KAUST Repository

Harjes, Janno; Ryu, Tae Woo; Abdelmohsen, Usama Ramadan; Moitinho-Silva, Lucas; Horn, Hannes; Ravasi, Timothy; Hentschel, Ute

2014-01-01

The marine sponge-associated bacterium Actinokineospora sp. strain EG49 produces the antitrypanosomal angucycline-like compound actinosporin A. The draft genome of Actinokineospora sp. EG49 has a size of 7.5 megabases and a GC content of 72.8% and contains 6,629 protein-coding sequences (CDS). antiSMASH predicted 996 genes residing in 36 secondary metabolite gene clusters.

Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49

KAUST Repository

Harjes, Janno

2014-03-06

The marine sponge-associated bacterium Actinokineospora sp. strain EG49 produces the antitrypanosomal angucycline-like compound actinosporin A. The draft genome of Actinokineospora sp. EG49 has a size of 7.5 megabases and a GC content of 72.8% and contains 6,629 protein-coding sequences (CDS). antiSMASH predicted 996 genes residing in 36 secondary metabolite gene clusters.

Sulfurospirillum arcachonense sp. nov., a new microaerophilic sulfur-reducing bacterium.

Science.gov (United States)

Finster, K; Liesack, W; Tindall, B J

1997-10-01

The isolation of a new motile, gram-negative, heterotrophic, sulfur-reducing, microaerophilic, vibrioid bacterium, strain F1F6, from oxidized marine surface sediment (Arcachon Bay, French Atlantic coast) is described. Hydrogen (with acetate as the carbon source), formate (with acetate as the carbon source), pyruvate, lactate, alpha-ketoglutarate, glutarate, glutamate, and yeast extract supported growth with elemental sulfur under anaerobic conditions. Apart from H2 and formate, the oxidation of the substrates was incomplete. Microaerophilic growth was supported with hydrogen (acetate as the carbon source), formate (acetate as the carbon source), acetate, propionate, pyruvate, lactate, alpha-ketoglutarate, glutamate, yeast extract, fumarate, succinate, malate, citrate, and alanine. The isolate grew fermentatively with fumarate, succinate being the only organic product. Elemental sulfur and oxygen were the only electron acceptors used. Vitamins or amino acids were not required. The isolate was oxidase, catalase, and urease positive. Comparative 16S rDNA sequence analysis revealed a tight cluster consisting of the validly described species Sulfurospirillum deleyianum and the strains SES-3 and CCUG 13942 as the closest relatives of strain F1F6 (level of sequence similarity, 91.7 to 92.4%). Together with strain F1F6, these organisms form a novel lineage within the epsilon subclass of proteobacteria clearly separated from the described species of the genera Arcobacter, Campylobacter, Wolinella, and Helicobacter. Due to the phenotypic characteristics shared by strain F1F6 and S. deleyianum and considering their phylogenetic relationship, we propose the inclusion of strain F1F6 in the genus Sulfurospirillum, namely, as S. arcachonense sp. nov. Based on the results of this study, an emended description of the genus Sulfurospirillum is given.

Genomic analysis of Melioribacter roseus, facultatively anaerobic organotrophic bacterium representing a novel deep lineage within Bacteriodetes/Chlorobi group.

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Vitaly V Kadnikov

Full Text Available Melioribacter roseus is a moderately thermophilic facultatively anaerobic organotrophic bacterium representing a novel deep branch within Bacteriodetes/Chlorobi group. To better understand the metabolic capabilities and possible ecological functions of M. roseus and get insights into the evolutionary history of this bacterial lineage, we sequenced the genome of the type strain P3M-2(T. A total of 2838 open reading frames was predicted from its 3.30 Mb genome. The whole proteome analysis supported phylum-level classification of M. roseus since most of the predicted proteins had closest matches in Bacteriodetes, Proteobacteria, Chlorobi, Firmicutes and deeply-branching bacterium Caldithrix abyssi, rather than in one particular phylum. Consistent with the ability of the bacterium to grow on complex carbohydrates, the genome analysis revealed more than one hundred glycoside hydrolases, glycoside transferases, polysaccharide lyases and carbohydrate esterases. The reconstructed central metabolism revealed pathways enabling the fermentation of complex organic substrates, as well as their complete oxidation through aerobic and anaerobic respiration. Genes encoding the photosynthetic and nitrogen-fixation machinery of green sulfur bacteria, as well as key enzymes of autotrophic carbon fixation pathways, were not identified. The M. roseus genome supports its affiliation to a novel phylum Ignavibateriae, representing the first step on the evolutionary pathway from heterotrophic ancestors of Bacteriodetes/Chlorobi group towards anaerobic photoautotrophic Chlorobi.

Characterization of culturable heterotrophic bacteria in hydrocarbon-contaminated soil from an alpine former military site.

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Zhang, Dechao; Margesin, Rosa

2014-06-01

We characterized the culturable, heterotrophic bacterial community in soil collected from a former alpine military site contaminated with petroleum hydrocarbons. The physiologically active eubacterial community, as revealed by fluorescence-in situ-hybridization, accounted for 14.9 % of the total (DAPI-stained) bacterial community. 4.0 and 1.2 % of the DAPI-stained cells could be attributed to culturable, heterotrophic bacteria able to grow at 20 and 10 °C, respectively. The majority of culturable bacterial isolates (23/28 strains) belonged to the Proteobacteria with a predominance of Alphaproteobacteria. The remaining isolates were affiliated with the Firmicutes, Actinobacteria and Bacteroidetes. Five strains could be identified as representatives of novel species. Characterization of the 28 strains demonstrated their adaptation to the temperature and nutrient conditions prevailing in the studied soil. One-third of the strains was able to grow at subzero temperatures (-5 °C). Studies on the effect of temperature on growth and lipase production with two selected strains demonstrated their low-temperature adaptation.

Locked chromophore analogs reveal that photoactive yellow protein regulates biofilm formation in the deep sea bacterium Idiomarina loihiensis

NARCIS (Netherlands)

van der Horst, M.A.; Stalcup, T.P.; Kaledhonkar, S.; Kumauchi, M.; Hara, M.; Xie, A.; Hellingwerf, K.J.; Hoff, W.D.

2009-01-01

Idiomarina loihiensis is a heterotrophic deep sea bacterium with no known photobiology. We show that light suppresses biofilm formation in this organism. The genome of I. loihiensis encodes a single photoreceptor protein: a homologue of photoactive yellow protein (PYP), a blue light receptor with

Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T.

Directory of Open Access Journals (Sweden)

Ronald M Weiner

2008-05-01

Full Text Available The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40 is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides. We report its complete genome sequence, analysis of which identifies an unusually large number of enzymes that degrade >10 complex polysaccharides. Not only is this an extraordinary range of catabolic capability, many of the enzymes exhibit unusual architecture including novel combinations of catalytic and substrate-binding modules. We hypothesize that many of these features are adaptations that facilitate depolymerization of complex polysaccharides in the marine environment. This is the first sequenced genome of a marine bacterium that can degrade plant cell walls, an important component of the carbon cycle that is not well-characterized in the marine environment.

Draft Genome Sequence of the Phosphate-Solubilizing Bacterium Pseudomonas argentinensis Strain SA190 Isolated from the Desert Plant Indigofera argentea

KAUST Repository

Lafi, Feras Fawzi; Alam, Intikhab; Geurts, Rene; Bisseling, Ton; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged

2016-01-01

Pseudomonas argentinensis strain SA190 is a plant endophytic-inhabiting bacterium that was isolated from root nodules of the desert plant Indigofera argentea collected from the Jizan region of Saudi Arabia. Here, we report the genome sequence of SA

Genome Sequence of the Enterobacter mori Type Strain, LMG 25706, a Pathogenic Bacterium of Morus alba L. ▿

Science.gov (United States)

Zhu, Bo; Zhang, Guo-Qing; Lou, Miao-Miao; Tian, Wen-Xiao; Li, Bin; Zhou, Xue-Ping; Wang, Guo-Feng; Liu, He; Xie, Guan-Lin; Jin, Gu-Lei

2011-01-01

Enterobacter mori is a plant-pathogenic enterobacterium responsible for the bacterial wilt of Morus alba L. Here we present the draft genome sequence of the type strain, LMG 25706. To the best of our knowledge, this is the first genome sequence of a plant-pathogenic bacterium in the genus Enterobacter. PMID:21602328

Growth characteristics of a strain of iron-oxidizing bacterium and its application in bioleaching of uranium ores

International Nuclear Information System (INIS)

Zhang Rui; Liu Yajie; Gao Feng; Xu Lingling

2008-01-01

05B is a strain of iron-oxidizing bacterium which separated from a uranium ore. The effect of temperature, initial pH, inoculation amount and initial total iron concentration on the strain's growth and activities in bioleaching of uranium ores are studied. The results show that the optimum growth temperature is 40-45 degree C, the optimum inoculation pH value being 1.5-1.7, the optimum initial inoculation amount being 10%-20%, and the initial total iron concentration being not more than 5 g/L. 05B is fit for leaching of low grade uranium ores. (authors)

Genetic analysis of amino acid transport in the facultatively heterotrophic cyanobacterium Synechocystis sp. Strain 6803

International Nuclear Information System (INIS)

Labarre, J.; Thuriaux, P.; Chauvat, F.

1987-01-01

The existence of active transport systems (permeases) operating on amino acids in the photoautotrophic cyanobacterium Synechocystis sp. strain 6803 was demonstrated by following the initial rates of uptake with 14 C-labeled amino acids, measuring the intracellular pools of amino acids, and isolating mutants resistant to toxic amino acids. One class of mutants (Pfa1) corresponds to a regulatory defect in the biosynthesis of the aromatic amino acids, but two other classes (Can1 and Aza1) are defective in amino acid transport. The Can1 mutants are defective in the active transport of three basic amino acids (arginine, histidine, and lysine) and in one of two transport systems operating on glutamine. The Aza1 mutants are not affected in the transport of the basic amino acids but have lost the capacity to transport all other amino acids except glutamate. The latter amino acid is probably transported by a third permease which could be identical to the Can1-independent transport operating on glutamine. Thus, genetic evidence suggests that strain 6803 has only a small number of amino acid transport systems with fairly broad specificity and that, with the exception of glutamine, each amino acid is accumulated by only one major transport system. Compared with heterotrophic bacteria such as Escherichia coli, these permeases are rather inefficient in terms of affinity (apparent K/sub m/ ranging from 6 to 60 μM) and of V/sub max/

Survival Strategies of the Plant-Associated Bacterium Enterobacter sp. Strain EG16 under Cadmium Stress.

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Chen, Yanmei; Chao, Yuanqing; Li, Yaying; Lin, Qingqi; Bai, Jun; Tang, Lu; Wang, Shizhong; Ying, Rongrong; Qiu, Rongliang

2016-01-04

Plant-associated bacteria are of great interest because of their potential use in phytoremediation. However, their ability to survive and promote plant growth in metal-polluted soils remains unclear. In this study, a soilborne Cd-resistant bacterium was isolated and identified as Enterobacter sp. strain EG16. It tolerates high external Cd concentrations (Cd(2+) MIC, >250 mg liter(-1)) and is able to produce siderophores and the plant hormone indole-3-acetic acid (IAA), both of which contribute to plant growth promotion. Surface biosorption in this strain accounted for 31% of the total Cd accumulated. The potential presence of cadmium sulfide, shown by energy-dispersive X-ray (EDX) analysis, suggested intracellular Cd binding as a Cd response mechanism of the isolate. Cd exposure resulted in global regulation at the transcriptomic level, with the bacterium switching to an energy-conserving mode by inhibiting energy-consuming processes while increasing the production of stress-related proteins. The stress response system included increased import of sulfur and iron, which become deficient under Cd stress, and the redirection of sulfur metabolism to the maintenance of intracellular glutathione levels in response to Cd toxicity. Increased production of siderophores, responding to Cd-induced Fe deficiency, not only is involved in the Cd stress response systems of EG16 but may also play an important role in promoting plant growth as well as alleviating the Cd-induced inhibition of IAA production. The newly isolated strain EG16 may be a suitable candidate for microbially assisted phytoremediation due to its high resistance to Cd and its Cd-induced siderophore production, which is likely to contribute to plant growth promotion. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

[Isolation and characterization of Thermopirellula anaerolimosa gen. nov., sp. nov., an obligate anaerobic hydrogen-producing bacterium of the phylum Planctomycetes].

Science.gov (United States)

Liu, Dongying; Liu, Yi; Men, Xuehui; Guo, Qunqun; Guo, Rongbo; Qiu, Yanling

2012-08-04

To cultivate various yet-to-be cultured heterotrophs from anaerobic granule sludge, we used a selective culture medium with low concentrations of substrates supplemented a variety of antibiotics. An obligate anaerobic, thermophilic, hydrogen-producing bacterium, strain VM20-7(T), was isolated from an upflow anaerobic sludge blanket (UASB) reactor treating high-strength organic wastewater from isomerized sugar production processes. Cells of strain VM20-7(T) are non-motile, spherical, pear or teardrop shaped, occurring singly(o)r as aggregates (0.7 - 2.0 microm x 0.7 - 2.0 microm). Spore formation was not observed. Growth temperature ranges from 35 - 50 degrees C (optimum 45 degrees C), pH ranges from 6.0 - 8.3 (optimum 7.0 - 7.5) , NaCl tolerant concentration ranges from 0% - 0.5% (w/v, optimum 0% ). Nitrate, sulfate, thiosulfate, sulfite, elemental sulfur and Fe (III)-NTA were not used as terminal electron acceptors. Strain VM20-7(T) utilizes a wide range of carbohydrates, including glucose, maltose, ribose, xylose, sucrose, galactose, mannose, raffinose, pectin, yeast extract and xylan. Acetate and H2 are the main end products of glucose fermentation. The G + C content of the genomic DNA was 60.9 mol%. 16S rRNA gene sequence analysis revealed that it is related to the Pirellula-Rhodopirellula-Blastopirellula (PRB) clade within the order Planctomycetales (82.7 - 84.3% similarity with 16S rRNA genes of other known related species). The first obligate anaerobic bacterium within the phylum Planctomycetes was isolated with low concentration of carbohydrates and antibiotics. On the basis of the physiological and phylogenetic data, the name Thermopirellula anaerolimosa gen. nov. , sp. nov. is proposed for strain VM20-7(T) (= CGMCC 1.5169(T) = JCM 17478(T) = DSM 24165(T)).

Draft Genome of the Marine Gammaproteobacterium Halomonas titanicae

Science.gov (United States)

Sánchez-Porro, Cristina; de la Haba, Rafael R.; Cruz-Hernández, Norge; González, Juan M.; Reyes-Guirao, Cristina; Navarro-Sampedro, Laura; Carballo, Modesto

2013-01-01

Halomonas titanicae strain BH1 is a heterotrophic, aerobic marine bacterium which was isolated from rusticles of the RMS Titanic wreck. Here we report the draft genome sequence of this halophilic gammaproteobacterium. PMID:23516210

Degradation of Phenol via Phenylphosphate and Carboxylation to 4-Hydroxybenzoate by a Newly Isolated Strain of the Sulfate-Reducing Bacterium Desulfobacterium anilini▿ †

OpenAIRE

Ahn, Young-Beom; Chae, Jong-Chan; Zylstra, Gerben J.; Häggblom, Max M.

2009-01-01

A sulfate-reducing phenol-degrading bacterium, strain AK1, was isolated from a 2-bromophenol-utilizing sulfidogenic estuarine sediment enrichment culture. On the basis of phylogenetic analysis of the 16S rRNA gene and DNA homology, strain AK1 is most closely related to Desulfobacterium anilini strain Ani1 (= DSM 4660T). In addition to phenol, this organism degrades a variety of other aromatic compounds, including benzoate, 2-hydroxybenzoate, 4-hydroxybenzoate, 4-hydroxyphenylacetate, 2-aminob...

An Amoebal Grazer of Cyanobacteria Requires Cobalamin Produced by Heterotrophic Bacteria.

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Ma, Amy T; Beld, Joris; Brahamsha, Bianca

2017-05-15

Amoebae are unicellular eukaryotes that consume microbial prey through phagocytosis, playing a role in shaping microbial food webs. Many amoebal species can be cultivated axenically in rich media or monoxenically with a single bacterial prey species. Here, we characterize heterolobosean amoeba LPG3, a recent natural isolate, which is unable to grow on unicellular cyanobacteria, its primary food source, in the absence of a heterotrophic bacterium, a Pseudomonas species coisolate. To investigate the molecular basis of this requirement for heterotrophic bacteria, we performed a screen using the defined nonredundant transposon library of Vibrio cholerae , which implicated genes in corrinoid uptake and biosynthesis. Furthermore, cobalamin synthase deletion mutations in V. cholerae and the Pseudomonas species coisolate do not support the growth of amoeba LPG3 on cyanobacteria. While cyanobacteria are robust producers of a corrinoid variant called pseudocobalamin, this variant does not support the growth of amoeba LPG3. Instead, we show that it requires cobalamin that is produced by the Pseudomonas species coisolate. The diversity of eukaryotes utilizing corrinoids is poorly understood, and this amoebal corrinoid auxotroph serves as a model for examining predator-prey interactions and micronutrient transfer in bacterivores underpinning microbial food webs. IMPORTANCE Cyanobacteria are important primary producers in aquatic environments, where they are grazed upon by a variety of phagotrophic protists and, hence, have an impact on nutrient flux at the base of microbial food webs. Here, we characterize amoebal isolate LPG3, which consumes cyanobacteria as its primary food source but also requires heterotrophic bacteria as a source of corrinoid vitamins. Amoeba LPG3 specifically requires the corrinoid variant produced by heterotrophic bacteria and cannot grow on cyanobacteria alone, as they produce a different corrinoid variant. This same corrinoid specificity is also

Ralstonia syzygii, the Blood Disease Bacterium and Some Asian R. solanacearum Strains Form a Single Genomic Species Despite Divergent Lifestyles

Science.gov (United States)

Cellier, Gilles; Jacobs, Jonathan M.; Mangenot, Sophie; Barbe, Valérie; Lajus, Aurélie; Vallenet, David; Medigue, Claudine; Fegan, Mark; Allen, Caitilyn; Prior, Philippe

2011-01-01

The Ralstonia solanacearum species complex includes R. solanacearum, R. syzygii, and the Blood Disease Bacterium (BDB). All colonize plant xylem vessels and cause wilt diseases, but with significant biological differences. R. solanacearum is a soilborne bacterium that infects the roots of a broad range of plants. R. syzygii causes Sumatra disease of clove trees and is actively transmitted by cercopoid insects. BDB is also pathogenic to a single host, banana, and is transmitted by pollinating insects. Sequencing and DNA-DNA hybridization studies indicated that despite their phenotypic differences, these three plant pathogens are actually very closely related, falling into the Phylotype IV subgroup of the R. solanacearum species complex. To better understand the relationships among these bacteria, we sequenced and annotated the genomes of R. syzygii strain R24 and BDB strain R229. These genomes were compared to strain PSI07, a closely related Phylotype IV tomato isolate of R. solanacearum, and to five additional R. solanacearum genomes. Whole-genome comparisons confirmed previous phylogenetic results: the three phylotype IV strains share more and larger syntenic regions with each other than with other R. solanacearum strains. Furthermore, the genetic distances between strains, assessed by an in-silico equivalent of DNA-DNA hybridization, unambiguously showed that phylotype IV strains of BDB, R. syzygii and R. solanacearum form one genomic species. Based on these comprehensive data we propose a revision of the taxonomy of the R. solanacearum species complex. The BDB and R. syzygii genomes encoded no obvious unique metabolic capacities and contained no evidence of horizontal gene transfer from bacteria occupying similar niches. Genes specific to R. syzygii and BDB were almost all of unknown function or extrachromosomal origin. Thus, the pathogenic life-styles of these organisms are more probably due to ecological adaptation and genomic convergence during vertical

Draft Genome Sequence of the Phosphate-Solubilizing Bacterium Pseudomonas argentinensis Strain SA190 Isolated from the Desert Plant Indigofera argentea

KAUST Repository

Lafi, Feras Fawzi

2016-12-23

Pseudomonas argentinensis strain SA190 is a plant endophytic-inhabiting bacterium that was isolated from root nodules of the desert plant Indigofera argentea collected from the Jizan region of Saudi Arabia. Here, we report the genome sequence of SA190, highlighting several functional genes related to plant growth-promoting activity, environment adaption, and antifungal activity.

Degradative capacities and bioaugmentation potential of an anaerobic benzene-degrading bacterium strain DN11

Energy Technology Data Exchange (ETDEWEB)

Yuki Kasai; Yumiko Kodama; Yoh Takahata; Toshihiro Hoaki; Kazuya Watanabe [Marine Biotechnology Institute, Kamaishi (Japan)

2007-09-15

Azoarcus sp. strain DN11 is a denitrifying bacterium capable of benzene degradation under anaerobic conditions. The present study evaluated strain DN11 for its application to bioaugmentation of benzene-contaminated underground aquifers. Strain DN11 could grow on benzene, toluene, m-xylene, and benzoate as the sole carbon and energy sources under nitrate-reducing conditions, although o- and p-xylenes were transformed in the presence of toluene. Phenol was not utilized under anaerobic conditions. Kinetic analysis of anaerobic benzene degradation estimated its apparent affinity and inhibition constants to be 0.82 and 11 {mu}M, respectively. Benzene-contaminated groundwater taken from a former coal-distillation plant site in Aichi, Japan was anaerobically incubated in laboratory bottles and supplemented with either inorganic nutrients (nitrogen, phosphorus, and nitrate) alone, or the nutrients plus strain DN11, showing that benzene was significantly degraded only when DN11 was introduced. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments, and quantitative PCR revealed that DN11 decreased after benzene was degraded. Following the decrease in DN11 16S rRNA gene fragments corresponding to bacteria related to Owenweeksia hongkongensis and Pelotomaculum isophthalicum, appeared as strong bands, suggesting possible metabolic interactions in anaerobic benzene degradation. Results suggest that DN11 is potentially useful for degrading benzene that contaminates underground aquifers at relatively low concentrations. 50 refs., 6 figs., 1 tab.

Nesterenkonia sp. strain F, a halophilic bacterium producing acetone, butanol, and ethanol under aerobic conditions.

Science.gov (United States)

Amiri, Hamid; Azarbaijani, Reza; Parsa Yeganeh, Laleh; Shahzadeh Fazeli, Abolhassan; Tabatabaei, Meisam; Salekdeh, Ghasem Hosseini; Karimi, Keikhosro

2016-01-04

The moderately halophilic bacterium Nesterenkonia sp. strain F, which was isolated from Aran-Bidgol Lake (Iran), has the ability to produce acetone, butanol, and ethanol (ABE) as well as acetic and butyric acids under aerobic and anaerobic conditions. This result is the first report of ABE production with a wild microorganism from a family other than Clostridia and also the first halophilic species shown to produce butanol under aerobic cultivation. The cultivation of Nesterenkonia sp. strain F under anaerobic conditions with 50 g/l of glucose for 72 h resulted in the production of 105 mg/l of butanol, 122 mg/l of acetone, 0.2 g/l of acetic acid, and 2.5 g/l of butyric acid. Furthermore, the strain was cultivated on media with different glucose concentrations (20, 50, and 80 g/l) under aerobic and anaerobic conditions. Through fermentation with a 50 g/l initial glucose concentration under aerobic conditions, 66 mg/l of butanol, 125 mg/l of acetone, 291 mg/l of ethanol, 5.9 g/l of acetic acid, and 1.2 g/l of butyric acid were produced. The enzymes pertaining to the fermentation pathway in the strain were compared with the enzymes of Clostridium spp., and the metabolic pathway of fermentation used by Nesterenkonia sp. strain F was investigated.

Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated Leachate Ponds.

Science.gov (United States)

Hwang, C; Copeland, A; Lucas, S; Lapidus, A; Barry, K; Detter, J C; Glavina Del Rio, T; Hammon, N; Israni, S; Dalin, E; Tice, H; Pitluck, S; Chertkov, O; Brettin, T; Bruce, D; Han, C; Schmutz, J; Larimer, F; Land, M L; Hauser, L; Kyrpides, N; Mikhailova, N; Ye, Q; Zhou, J; Richardson, P; Fields, M W

2016-11-03

Alkaliphilus metalliredigens strain QYMF is an anaerobic, alkaliphilic, and metal-reducing bacterium associated with phylum Firmicutes QYMF was isolated from alkaline borax leachate ponds. The genome sequence will help elucidate the role of metal-reducing microorganisms under alkaline environments, a capability that is not commonly observed in metal respiring-microorganisms. Copyright © 2016 Hwang et al.

Draft Genome Sequence of Bacillus aryabhattai Strain PHB10, a Poly(3-Hydroxybutyrate)-Accumulating Bacterium Isolated from Domestic Sewerage.

Science.gov (United States)

Balakrishna Pillai, Aneesh; Jaya Kumar, Arjun; Thulasi, Kavitha; Reghunathan, Dinesh; Prasannakumar, Manoj; Kumarapillai, Harikrishnan

2017-10-12

Bacillus aryabhattai PHB10 is a poly(3-hydroxybutyrate) (PHB)-accumulating bacterium isolated from domestic sewerage. Here, we report the 4.19-Mb draft genome sequence, with 4,050 protein-coding genes and a G+C content of 37.5%. This sequence will be helpful in the study of the high-level PHB accumulation mechanism of the strain. Copyright © 2017 Balakrishna Pillai et al.

Draft Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum copahuensis Strain CINDEFI1 Isolated from the Geothermal Copahue System, Neuqu?n, Argentina

OpenAIRE

Willis Poratti, Graciana; Yaakop, Amira Suriaty; Chan, Chia Sing; Urbieta, M. Sof?a; Chan, Kok-Gan; Ee, Robson; Tan-Guan-Sheng, Adrian; Goh, Kian Mau; Donati, Edgardo R.

2016-01-01

Desulfotomaculum copahuensis strain CINDEFI1 is a novel spore-forming sulfate-reducing bacterium isolated from the Copahue volcano area, Argentina. Here, we present its draft genome in which we found genes related with the anaerobic respiration of sulfur compounds similar to those present in the Copahue environment.

Extracellular proteases of Halobacillus blutaparonensis strain M9, a new moderately halophilic bacterium.

Science.gov (United States)

Santos, Anderson F; Valle, Roberta S; Pacheco, Clarissa A; Alvarez, Vanessa M; Seldin, Lucy; Santos, André L S

2013-12-01

Halophilic microorganisms are source of potential hydrolytic enzymes to be used in industrial and/or biotechnological processes. In the present study, we have investigated the ability of the moderately halophilic bacterium Halobacillus blutaparonensis (strain M9), a novel species described by our group, to release proteolytic enzymes. This bacterial strain abundantly proliferated in Luria-Bertani broth supplemented with 2.5% NaCl as well as secreted proteases to the extracellular environment. The production of proteases occurred in bacterial cells grown under different concentration of salt, ranging from 0.5% to 10% NaCl, in a similar way. The proteases secreted by H. blutaparonensis presented the following properties: (i) molecular masses ranging from 30 to 80 kDa, (ii) better hydrolytic activities under neutral-alkaline pH range, (iii) expression modulated according to the culture age, (iv) susceptibility to phenylmethylsulphonyl fluoride, classifying them as serine-type proteases, (v) specific cleavage over the chymotrypsin substrate, and (vi) enzymatic stability in the presence of salt (up to 20% NaCl) and organic solvents (e.g., ether, isooctane and cyclohexane). The proteases described herein are promising for industrial practices due to its haloalkaline properties.

Genome sequence of the photoarsenotrophic bacterium Ectothiorhodospira sp. strain BSL-9, isolated from a hypersaline alkaline arsenic-rich extreme environment

Science.gov (United States)

Hernandez-Maldonado, Jaime; Stoneburner, Brendon; Boren, Alison; Miller, Laurence; Rosen, Michael R.; Oremland, Ronald S.; Saltikov, Chad W

2016-01-01

The full genome sequence of Ectothiorhodospira sp. strain BSL-9 is reported here. This purple sulfur bacterium encodes an arxA-type arsenite oxidase within the arxB2AB1CD gene island and is capable of carrying out “photoarsenotrophy” anoxygenic photosynthetic arsenite oxidation. Its genome is composed of 3.5 Mb and has approximately 63% G+C content.

Draft Genome Sequence of Aeribacillus pallidus Strain 8m3, a Thermophilic Hydrocarbon-Oxidizing Bacterium Isolated from the Dagang Oil Field (China)

OpenAIRE

Poltaraus, Andrey B.; Sokolova, Diyana S.; Grouzdev, Denis S.; Ivanov, Timophey M.; Malakho, Sophia G.; Korshunova, Alena V.; Rozanov, Aleksey S.; Tourova, Tatiyana P.; Nazina, Tamara N.

2016-01-01

The draft genome sequence of Aeribacillus pallidus strain 8m3, a thermophilic aerobic oil-oxidizing bacterium isolated from production water from the Dagang high-temperature oil field, China, is presented here. The genome is annotated to provide insights into the genomic and phenotypic diversity of the genus Aeribacillus.

Rapid Aggregation of Biofuel-Producing Algae by the Bacterium Bacillus sp. Strain RP1137

Science.gov (United States)

Powell, Ryan J.

2013-01-01

Algal biofuels represent one of the most promising means of sustainably replacing liquid fuels. However, significant challenges remain before alga-based fuels become competitive with fossil fuels. One of the largest challenges is the ability to harvest the algae in an economical and low-energy manner. In this article, we describe the isolation of a bacterial strain, Bacillus sp. strain RP1137, which can rapidly aggregate several algae that are candidates for biofuel production, including a Nannochloropsis sp. This bacterium aggregates algae in a pH-dependent and reversible manner and retains its aggregation ability after paraformaldehyde fixation, opening the possibility for reuse of the cells. The optimal ratio of bacteria to algae is described, as is the robustness of aggregation at different salinities and temperatures. Aggregation is dependent on the presence of calcium or magnesium ions. The efficiency of aggregation of Nannochloropsis oceanica IMET1 is between 70 and 95% and is comparable to that obtained by other means of harvest; however, the rate of harvest is fast, with aggregates forming in 30 s. PMID:23892750

Novel Acetone Metabolism in a Propane-Utilizing Bacterium, Gordonia sp. Strain TY-5▿

Science.gov (United States)

Kotani, Tetsuya; Yurimoto, Hiroya; Kato, Nobuo; Sakai, Yasuyoshi

2007-01-01

In the propane-utilizing bacterium Gordonia sp. strain TY-5, propane was shown to be oxidized to 2-propanol and then further oxidized to acetone. In this study, the subsequent metabolism of acetone was studied. Acetone-induced proteins were found in extracts of cells induced by acetone, and a gene cluster designated acmAB was cloned on the basis of the N-terminal amino acid sequences of acetone-induced proteins. The acmA and acmB genes encode a Baeyer-Villiger monooxygenase (BVMO) and esterase, respectively. The BVMO encoded by acmA was purified from acetone-induced cells of Gordonia sp. strain TY-5 and characterized. The BVMO exhibited NADPH-dependent oxidation activity for linear ketones (C3 to C10) and cyclic ketones (C4 to C8). Escherichia coli expressing the acmA gene oxidized acetone to methyl acetate, and E. coli expressing the acmB gene hydrolyzed methyl acetate. Northern blot analyses revealed that polycistronic transcription of the acmAB gene cluster was induced by propane, 2-propanol, and acetone. These results indicate that the acmAB gene products play an important role in the metabolism of acetone derived from propane oxidation and clarify the propane metabolism pathway of strain TY-5 (propane → 2-propanol → acetone → methyl acetate → acetic acid + methanol). This paper provides the first evidence for BVMO-dependent acetone metabolism. PMID:17071761

Draft Genome Sequence of Aeribacillus pallidus Strain 8m3, a Thermophilic Hydrocarbon-Oxidizing Bacterium Isolated from the Dagang Oil Field (China).

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Poltaraus, Andrey B; Sokolova, Diyana S; Grouzdev, Denis S; Ivanov, Timophey M; Malakho, Sophia G; Korshunova, Alena V; Rozanov, Aleksey S; Tourova, Tatiyana P; Nazina, Tamara N

2016-06-09

The draft genome sequence of Aeribacillus pallidus strain 8m3, a thermophilic aerobic oil-oxidizing bacterium isolated from production water from the Dagang high-temperature oil field, China, is presented here. The genome is annotated to provide insights into the genomic and phenotypic diversity of the genus Aeribacillus. Copyright © 2016 Poltaraus et al.

Formation of Highly Twisted Ribbons in a Carboxymethylcellulase Gene-Disrupted Strain of a Cellulose-Producing Bacterium

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Sugano, Yasushi; Shoda, Makoto; Sakakibara, Hitoshi; Oiwa, Kazuhiro; Tuzi, Satoru; Imai, Tomoya; Sugiyama, Junji; Takeuchi, Miyuki; Yamauchi, Daisuke

2013-01-01

Cellulases are enzymes that normally digest cellulose; however, some are known to play essential roles in cellulose biosynthesis. Although some endogenous cellulases of plants and cellulose-producing bacteria are reportedly involved in cellulose production, their functions in cellulose production are unknown. In this study, we demonstrated that disruption of the cellulase (carboxymethylcellulase) gene causes irregular packing of de novo-synthesized fibrils in Gluconacetobacter xylinus, a cellulose-producing bacterium. Cellulose production was remarkably reduced and small amounts of particulate material were accumulated in the culture of a cmcax-disrupted G. xylinus strain (F2-2). The particulate material was shown to contain cellulose by both solid-state 13C nuclear magnetic resonance analysis and Fourier transform infrared spectroscopy analysis. Electron microscopy revealed that the cellulose fibrils produced by the F2-2 cells were highly twisted compared with those produced by control cells. This hypertwisting of the fibrils may reduce cellulose synthesis in the F2-2 strains. PMID:23243308

Draft Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum copahuensis Strain CINDEFI1 Isolated from the Geothermal Copahue System, Neuquén, Argentina.

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Willis Poratti, Graciana; Yaakop, Amira Suriaty; Chan, Chia Sing; Urbieta, M Sofía; Chan, Kok-Gan; Ee, Robson; Tan-Guan-Sheng, Adrian; Goh, Kian Mau; Donati, Edgardo R

2016-08-18

Desulfotomaculum copahuensis strain CINDEFI1 is a novel spore-forming sulfate-reducing bacterium isolated from the Copahue volcano area, Argentina. Here, we present its draft genome in which we found genes related with the anaerobic respiration of sulfur compounds similar to those present in the Copahue environment. Copyright © 2016 Willis Poratti et al.

Characterization of the arsenite oxidizer Aliihoeflea sp. strain 2WW and its potential application in the removal of arsenic from groundwater in combination with Pf-ferritin.

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Corsini, Anna; Colombo, Milena; Muyzer, Gerard; Cavalca, Lucia

2015-09-01

A heterotrophic arsenite-oxidizing bacterium, strain 2WW, was isolated from a biofilter treating arsenic-rich groundwater. Comparative analysis of 16S rRNA gene sequences showed that it was closely related (98.7 %) to the alphaproteobacterium Aliihoeflea aesturari strain N8(T). However, it was physiologically different by its ability to grow at relatively low substrate concentrations, low temperatures and by its ability to oxidize arsenite. Here we describe the physiological features of strain 2WW and compare these to its most closely related relative, A. aestuari strain N8(T). In addition, we tested its efficiency to remove arsenic from groundwater in combination with Pf-ferritin. Strain 2WW oxidized arsenite to arsenate between pH 5.0 and 8.0, and from 4 to 30 °C. When the strain was used in combination with a Pf-ferritin-based material for arsenic removal from natural groundwater, the removal efficiency was significantly higher (73 %) than for Pf-ferritin alone (64 %). These results showed that arsenite oxidation by strain 2WW combined with Pf-ferritin-based material has a potential in arsenic removal from contaminated groundwater.

[Progress of heterotrophic studies on symbiotic corals].

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Yang, Yang-Chu-Qiao; Hong, Wen Ting; Wang, Shu Hong

2017-12-01

Heterotrophy of zooxanthellae symbiotic corals refers to the nutrition directly coming from food absorption, not the nutrition obtained from photosynthesis. Most ex situ propagation of symbiotic corals focused on the effects of irradiation, flow rate and water quality on corals, few of them involved in the demand and supply of coral heterotrophic nutrition. This paper reviewed the significance of heterotrophic nutrient supply to symbiotic corals from the sources of coral heterotrophic nutrition, the factors affecting the supply of coral heterotrophic nutrient, and the methods of how to study the coral heterotrophy. In general, the research of coral heterotrophy is just at the beginning stage, and future studies should focus on the inherent mechanism of coral feeding selection and developing more effective research methods.

Antimicrobial activity of heterotrophic bacterial communities from the marine sponge Erylus discophorus (Astrophorida, Geodiidae.

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Ana Patrícia Graça

Full Text Available Heterotrophic bacteria associated with two specimens of the marine sponge Erylus discophorus were screened for their capacity to produce bioactive compounds against a panel of human pathogens (Staphylococcus aureus wild type and methicillin-resistant S. aureus (MRSA, Bacillus subtilis, Pseudomonas aeruginosa, Acinetobacter baumanii, Candida albicans and Aspergillus fumigatus, fish pathogen (Aliivibrio fischeri and environmentally relevant bacteria (Vibrio harveyi. The sponges were collected in Berlengas Islands, Portugal. Of the 212 isolated heterotrophic bacteria belonging to Alpha- and Gammaproteobacteria, Actinobacteria and Firmicutes, 31% produced antimicrobial metabolites. Bioactivity was found against both Gram positive and Gram negative and clinically and environmentally relevant target microorganisms. Bioactivity was found mainly against B. subtilis and some bioactivity against S. aureus MRSA, V. harveyi and A. fisheri. No antifungal activity was detected. The three most bioactive genera were Pseudovibrio (47.0%, Vibrio (22.7% and Bacillus (7.6%. Other less bioactive genera were Labrenzia, Acinetobacter, Microbulbifer, Pseudomonas, Gordonia, Microbacterium, Micrococcus and Mycobacterium, Paenibacillus and Staphylococcus. The search of polyketide I synthases (PKS-I and nonribosomal peptide synthetases (NRPSs genes in 59 of the bioactive bacteria suggested the presence of PKS-I in 12 strains, NRPS in 3 strains and both genes in 3 strains. Our results show the potential of the bacterial community associated with Erylus discophorus sponges as producers of bioactive compounds.

A novel electrophototrophic bacterium Rhodopseudomonas palustris strain RP2, exhibits hydrocarbonoclastic potential in anaerobic environments

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Krishnaveni Venkidusamy

2016-07-01

Full Text Available An electrophototrophic, hydrocarbonoclastic bacterium Rhodopseudomonas palustris stain RP2 was isolated from the anodic biofilms of hydrocarbon fed microbial electrochemical remediation systems (MERS. Salient properties of the strain RP2 were direct electrode respiration, dissimilatory metal oxide reduction, spore formation, anaerobic nitrate reduction, free living diazotrophy and the ability to degrade n-alkane components of petroleum hydrocarbons in anoxic, photic environments. In acetate fed microbial electrochemical cells, a maximum current density of 305±10 mA/m2 (1000Ω was generated (power density 131.65±10 mW/m2 by strain RP2 with a coulombic efficiency of 46.7 ± 1.3%. Cyclic voltammetry studies showed that anaerobically grown cells of strain RP2 is electrochemically active and likely to transfer electrons extracellularly to solid electron acceptors through membrane bound compounds, however, aerobically grown cells lacked the electrochemical activity. The ability of strain RP2 to produce current (maximum current density 21±3 mA/m2; power density 720±7 µW/m2, 1000Ω using petroleum hydrocarbon (PH as a sole energy source was also examined using an initial concentration of 800 mg l-1 of diesel range hydrocarbons (C9- C36 with a concomitant removal of 47.4 ± 2.7% hydrocarbons in MERS. Here, we also report the first study that shows an initial evidence for the existence of a hydrocarbonoclastic behavior in the strain RP2 when grown in different electron accepting and illuminated conditions (anaerobic and MERS degradation. Such observations reveal the importance of photoorganotrophic growth in the utilization of hydrocarbons from contaminated environments. Identification of such novel petrochemical hydrocarbon degrading electricigens, not only expands the knowledge on the range of bacteria known for the hydrocarbon bioremediation but also shows a biotechnological potential that goes well beyond its applications to MERS.

Clostridium scatologenes strain SL1 isolated as an acetogenic bacterium from acidic sediments.

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Küsel, K; Dorsch, T; Acker, G; Stackebrandt, E; Drake, H L

2000-03-01

A strictly anaerobic, H2-utilizing bacterium, strain SL1, was isolated from the sediment of an acidic coal mine pond. Cells of strain SL1 were sporulating, motile, long rods with a multilayer cell wall. Growth was observed at 5-35 degrees C and pH 3.9-7.0. Acetate was the sole end product of H2 utilization and was produced in stoichiometries indicative of an acetyl-CoA-pathway-dependent metabolism. Growth and substrate utilization also occurred with CO/CO2, vanillate, syringate, ferulate, ethanol, propanol, 1-butanol, glycerine, cellobiose, glucose, fructose, mannose, xylose, formate, lactate, pyruvate and gluconate. With most substrates, acetate was the main or sole product formed. Growth in the presence of H2/CO2 or CO/CO2 was difficult to maintain in laboratory cultures. Methoxyl, carboxyl and acrylate groups of various aromatic compounds were O-demethylated, decarboxylated and reduced, respectively. Small amounts of butyrate were produced during the fermentation of sugars. The acrylate group of ferulate was reduced. Nitrate, sulfate, thiosulfate, dimethylsulfoxide and Fe(III) were not utilized as electron acceptors. Analysis of the 16S rRNA gene sequence of strain SL1 demonstrated that it is closely related to Clostridium scatologenes (99.6% sequence similarity), an organism characterized as a fermentative anaerobe but not previously shown to be capable of acetogenic growth. Comparative experiments with C. scatologenes DSM 757T demonstrated that it utilized H2/CO2 (negligible growth), CO/CO2 (negligible growth), formate, ethanol and aromatic compounds according to stoichiometries indicative of the acetyl-CoA pathway. CO dehydrogenase, formate dehydrogenase and hydrogenase activities were present in both strain SL1 and C. scatologenes DSM 757T. These results indicate that (i) sediments of acidic coal mine ponds harbour acetogens and (ii) C. scatologenes is an acetogen that tends to lose its capacity to grow acetogenically under H2/CO2 or CO/CO2 after prolonged

Proteome and membrane fatty acid analyses on Oligotropha carboxidovorans OM5 grown under chemolithoautotrophic and heterotrophic conditions.

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Debarati Paul

Full Text Available Oligotropha carboxidovorans OM5 T. (DSM 1227, ATCC 49405 is a chemolithoautotrophic bacterium able to utilize CO and H(2 to derive energy for fixation of CO(2. Thus, it is capable of growth using syngas, which is a mixture of varying amounts of CO and H(2 generated by organic waste gasification. O. carboxidovorans is capable also of heterotrophic growth in standard bacteriologic media. Here we characterize how the O. carboxidovorans proteome adapts to different lifestyles of chemolithoautotrophy and heterotrophy. Fatty acid methyl ester (FAME analysis of O. carboxidovorans grown with acetate or with syngas showed that the bacterium changes membrane fatty acid composition. Quantitative shotgun proteomic analysis of O. carboxidovorans grown in the presence of acetate and syngas showed production of proteins encoded on the megaplasmid for assimilating CO and H(2 as well as proteins encoded on the chromosome that might have contributed to fatty acid and acetate metabolism. We found that adaptation to chemolithoautotrophic growth involved adaptations in cell envelope, oxidative homeostasis, and metabolic pathways such as glyoxylate shunt and amino acid/cofactor biosynthetic enzymes.

Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1.

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Mauffrey, Florian; Cucaita, Alexandra; Constant, Philippe; Villemur, Richard

2017-01-01

Methylophaga nitratireducenticrescens strain JAM1 is a methylotrophic, marine bacterium that was isolated from a denitrification reactor treating a closed-circuit seawater aquarium. It can sustain growth under anoxic conditions by reducing nitrate ([Formula: see text]) to nitrite ([Formula: see text]). These physiological traits are attributed to gene clusters that encode two dissimilatory nitrate reductases (Nar). Strain JAM1 also contains gene clusters encoding two nitric oxide (NO) reductases and one nitrous oxide (N 2 O) reductase, suggesting that NO and N 2 O can be reduced by strain JAM1. Here we characterized further the denitrifying activities of M. nitratireducenticrescens JAM1. Series of oxic and anoxic cultures of strain JAM1 were performed with N 2 O, [Formula: see text] or sodium nitroprusside, and growth and N 2 O, [Formula: see text], [Formula: see text] and N 2 concentrations were measured. Ammonium ([Formula: see text])-free cultures were also tested to assess the dynamics of N 2 O, [Formula: see text] and [Formula: see text]. Isotopic labeling of N 2 O was performed in 15 NH 4 + -amended cultures. Cultures with the JAM1Δ narG1narG2 double mutant were performed to assess the involvement of the Nar systems on N 2 O production. Finally, RT-qPCR was used to measure the gene expression levels of the denitrification genes cytochrome bc -type nitric oxide reductase ( cnorB1 and cnorB2 ) and nitrous oxide reductase ( nosZ ), and also nnrS and norR that encode NO-sensitive regulators. Strain JAM1 can reduce NO to N 2 O and N 2 O to N 2 and can sustain growth under anoxic conditions by reducing N 2 O as the sole electron acceptor. Although strain JAM1 lacks a gene encoding a dissimilatory [Formula: see text] reductase, [Formula: see text]-amended cultures produce N 2 O, representing up to 6% of the N-input. [Formula: see text] was shown to be the key intermediate of this production process. Upregulation in the expression of c norB1 , cnorB2, nnrS and nor

Cold-Active, Heterotrophic Bacteria from the Highly Oligotrophic Waters of Lake Vanda, Antarctica

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Nicole A. Vander Schaaf

2015-07-01

Full Text Available The permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica are distinctive ecosystems that consist strictly of microbial communities. In this study, water samples were collected from Lake Vanda, a stratified Dry Valley lake whose upper waters (from just below the ice cover to nearly 60 m are highly oligotrophic, and used to establish enrichment cultures. Six strains of psychrotolerant, heterotrophic bacteria were isolated from lake water samples from a depth of 50 or 55 m. Phylogenetic analyses showed the Lake Vanda strains to be species of Nocardiaceae, Caulobacteraceae, Sphingomonadaceae, and Bradyrhizobiaceae. All Lake Vanda strains grew at temperatures near or below 0 °C, but optimal growth occurred from 18 to 24 °C. Some strains showed significant halotolerance, but no strains required NaCl for growth. The isolates described herein include cold-active species not previously reported from Dry Valley lakes, and their physiological and phylogenetic characterization broadens our understanding of these limnologically unique lakes.

Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa

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Walker M Andrew

2006-09-01

Full Text Available Abstract Background The Gram-negative, xylem-limited phytopathogenic bacterium Xylella fastidiosa is responsible for causing economically important diseases in grapevine, citrus and many other plant species. Despite its economic impact, relatively little is known about the genomic variations among strains isolated from different hosts and their influence on the population genetics of this pathogen. With the availability of genome sequence information for four strains, it is now possible to perform genome-wide analyses to identify and categorize such DNA variations and to understand their influence on strain functional divergence. Results There are 1,579 genes and 194 non-coding homologous sequences present in the genomes of all four strains, representing a 76. 2% conservation of the sequenced genome. About 60% of the X. fastidiosa unique sequences exist as tandem gene clusters of 6 or more genes. Multiple alignments identified 12,754 SNPs and 14,449 INDELs in the 1528 common genes and 20,779 SNPs and 10,075 INDELs in the 194 non-coding sequences. The average SNP frequency was 1.08 × 10-2 per base pair of DNA and the average INDEL frequency was 2.06 × 10-2 per base pair of DNA. On an average, 60.33% of the SNPs were synonymous type while 39.67% were non-synonymous type. The mutation frequency, primarily in the form of external INDELs was the main type of sequence variation. The relative similarity between the strains was discussed according to the INDEL and SNP differences. The number of genes unique to each strain were 60 (9a5c, 54 (Dixon, 83 (Ann1 and 9 (Temecula-1. A sub-set of the strain specific genes showed significant differences in terms of their codon usage and GC composition from the native genes suggesting their xenologous origin. Tandem repeat analysis of the genomic sequences of the four strains identified associations of repeat sequences with hypothetical and phage related functions. Conclusion INDELs and strain specific genes

Marinicella sediminis sp. nov., isolated from marine sediment

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A novel heterotrophic, Gram-stain-negative, aerobic, rod-shaped, pale yellow, non-motile and non-spore-forming bacterium, designated as strain F2**T, was isolated from the marine sediment collected from Weihai coastal, Shandong Province, PR China. Optimal growth occurred at 33 °C (range 10–37 °C), w...

Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1

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Florian Mauffrey

2017-11-01

Full Text Available Background Methylophaga nitratireducenticrescens strain JAM1 is a methylotrophic, marine bacterium that was isolated from a denitrification reactor treating a closed-circuit seawater aquarium. It can sustain growth under anoxic conditions by reducing nitrate ( ${\\mathrm{NO}}_{3}^{-}$ NO 3 − to nitrite ( ${\\mathrm{NO}}_{2}^{-}$ NO 2 − . These physiological traits are attributed to gene clusters that encode two dissimilatory nitrate reductases (Nar. Strain JAM1 also contains gene clusters encoding two nitric oxide (NO reductases and one nitrous oxide (N2O reductase, suggesting that NO and N2O can be reduced by strain JAM1. Here we characterized further the denitrifying activities of M. nitratireducenticrescens JAM1. Methods Series of oxic and anoxic cultures of strain JAM1 were performed with N2O, ${\\mathrm{NO}}_{3}^{-}$ NO 3 − or sodium nitroprusside, and growth and N2O, ${\\mathrm{NO}}_{3}^{-}$ NO 3 − , ${\\mathrm{NO}}_{2}^{-}$ NO 2 − and N2 concentrations were measured. Ammonium ( ${\\mathrm{NH}}_{4}^{+}$ NH 4 + -free cultures were also tested to assess the dynamics of N2O, ${\\mathrm{NO}}_{3}^{-}$ NO 3 − and ${\\mathrm{NO}}_{2}^{-}$ NO 2 − . Isotopic labeling of N2O was performed in 15NH4+-amended cultures. Cultures with the JAM1ΔnarG1narG2 double mutant were performed to assess the involvement of the Nar systems on N2O production. Finally, RT-qPCR was used to measure the gene expression levels of the denitrification genes cytochrome bc-type nitric oxide reductase (cnorB1 and cnorB2 and nitrous oxide reductase (nosZ, and also nnrS and norR that encode NO-sensitive regulators. Results Strain JAM1 can reduce NO to N2O and N2O to N2 and can sustain growth under anoxic conditions by reducing N2O as the sole electron acceptor. Although strain JAM1 lacks a gene encoding a dissimilatory ${\\mathrm{NO}}_{2}^{-}$ NO 2 − reductase, ${\\mathrm{NO}}_{3}^{-}$ NO 3 − -amended cultures produce N2O, representing up to 6% of the N

Complete genome of Martelella sp. AD-3, a moderately halophilic polycyclic aromatic hydrocarbons-degrading bacterium.

Science.gov (United States)

Cui, Changzheng; Li, Zhijie; Qian, Jiangchao; Shi, Jie; Huang, Ling; Tang, Hongzhi; Chen, Xin; Lin, Kuangfei; Xu, Ping; Liu, Yongdi

2016-05-10

Martelella sp. strain AD-3, a moderate halophilic bacterium, was isolated from a petroleum-contaminated soil with high salinity in China. Here, we report the complete genome of strain AD-3, which contains one circular chromosome and two circular plasmids. An array of genes related to metabolism of polycyclic aromatic hydrocarbons and halophilic mechanism in this bacterium was identified by the whole genome analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Marine Bacteria from Danish Coastal Waters Show Antifouling Activity against the Marine Fouling Bacterium Pseudoalteromonas sp. Strain S91 and Zoospores of the Green Alga Ulva australis Independent of Bacteriocidal Activity

DEFF Research Database (Denmark)

Bernbom, Nete; Ng, Yoke Yin; Kjelleberg, Staffan

2011-01-01

, representing the major taxonomic groups, different seasons, and isolation strategies, were tested for antiadhesive effect against the marine biofilm-forming bacterium Pseudoalteromonas sp. strain S91 and zoospores of the green alga Ulva australis. The antiadhesive effects were assessed by quantifying...... the number of strain S91 or Ulva spores attaching to a preformed biofilm of each of the 22 strains. The strongest antifouling activity was found in Pseudoalteromonas strains. Biofilms of Pseudoalteromonas piscicida, Pseudoalteromonas tunicata, and Pseudoalteromonas ulvae prevented Pseudoalteromonas S91 from...

Mixotrophic organisms become more heterotrophic with rising temperature

NARCIS (Netherlands)

Wilken, S.; Huisman, J.; Naus-Wiezer, S.; van Donk, E.

2013-01-01

The metabolic theory of ecology predicts that temperature affects heterotrophic processes more strongly than autotrophic processes. We hypothesized that this differential temperature response may shift mixotrophic organisms towards more heterotrophic nutrition with rising temperature. The hypothesis

Acidophilic algae isolated from mine-impacted environments and their roles in sustaining heterotrophic acidophiles

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David Barrie Johnson

2012-09-01

Full Text Available Two acidophilic algae, identified as strains of Chlorella protothecoides var. acidicola and Euglena mutabilis, were isolated in pure culture from abandoned copper mines in Spain and Wales and grown in pH- and temperature-controlled bioreactors. The Chlorella isolate grew optimally at pH 2.5 and 30 ˚C, with a corresponding culture doubling time of 9 hours. The isolates displayed similar tolerance (10-50 mM to four transition metals tested. Growth of the algae in liquid media was paralleled with increasing concentrations of dissolved organic carbon (DOC. Glycolic acid was identified as a significant component (12- 14% of total DOC. Protracted incubation resulted in concentrations of glycolic acid declining in both cases, and glycolic acid added to a culture of Chlorella incubated in the dark was taken up by the alga (~100% within three days. Two monosaccharides were identified in cell-free liquors of each algal isolate: fructose and glucose (Chlorella, and mannitol and glucose (Euglena. These were rapidly metabolised by acidophilic heterotrophic bacteria (Acidiphilium and Acidobacterium spp. though only fructose was utilised by the more fastidious heterotroph Acidocella aromatica. The significance of algae in promoting the growth of iron- (and sulfate- reducing heterotrophic acidophiles that are important in remediating mine-impacted waters is discussed.

Genome sequence of the pink-pigmented marine bacterium Loktanella hongkongensis type strain (UST950701-009P(T)), a representative of the Roseobacter group.

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Lau, Stanley Ck; Riedel, Thomas; Fiebig, Anne; Han, James; Huntemann, Marcel; Petersen, Jörn; Ivanova, Natalia N; Markowitz, Victor; Woyke, Tanja; Göker, Markus; Kyrpides, Nikos C; Klenk, Hans-Peter; Qian, Pei-Yuan

2015-01-01

Loktanella hongkongensis UST950701-009P(T) is a Gram-negative, non-motile and rod-shaped bacterium isolated from a marine biofilm in the subtropical seawater of Hong Kong. When growing as a monospecies biofilm on polystyrene surfaces, this bacterium is able to induce larval settlement and metamorphosis of a ubiquitous polychaete tubeworm Hydroides elegans. The inductive cues are low-molecular weight compounds bound to the exopolymeric matrix of the bacterial cells. In the present study we describe the features of L. hongkongensis strain DSM 17492(T) together with its genome sequence and annotation and novel aspects of its phenotype. The 3,198,444 bp long genome sequence encodes 3104 protein-coding genes and 57 RNA genes. The two unambiguously identified extrachromosomal replicons contain replication modules of the RepB and the Rhodobacteraceae-specific DnaA-like type, respectively.

Isolation and characterization of Halomonas sp. strain C2SS100, a hydrocarbon-degrading bacterium under hypersaline conditions.

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Mnif, S; Chamkha, M; Sayadi, S

2009-09-01

To isolate and characterize an efficient hydrocarbon-degrading bacterium under hypersaline conditions, from a Tunisian off-shore oil field. Production water collected from 'Sercina' petroleum reservoir, located near the Kerkennah island, Tunisia, was used for the screening of halotolerant or halophilic bacteria able to degrade crude oil. Bacterial strain C2SS100 was isolated after enrichment on crude oil, in the presence of 100 g l(-1) NaCl and at 37 degrees C. This strain was aerobic, Gram-negative, rod-shaped, motile, oxidase + and catalase +. Phenotypic characters and phylogenetic analysis based on the 16S rRNA gene of the isolate C2SS100 showed that it was related to members of the Halomonas genus. The degradation of several compounds present in crude oil was confirmed by GC-MS analysis. The use of refined petroleum products such as diesel fuel and lubricating oil as sole carbon source, under the same conditions of temperature and salinity, showed that significant amounts of these heterogenic compounds could be degraded. Strain C2SS100 was able to degrade hexadecane (C16). During growth on hexadecane, cells surface hydrophobicity and emulsifying activity increased indicating the production of biosurfactant by strain C2SS100. A halotolerant bacterial strain Halomonas sp. C2SS100 was isolated from production water of an oil field, after enrichment on crude oil. This strain is able to degrade hydrocarbons efficiently. The mode of hydrocarbon uptake is realized by the production of a biosurfactant which enhances the solubility of hydrocarbons and renders them more accessible for biodegradation. The biodegradation potential of the Halomonas sp. strain C2SS100 gives it an advantage for possibly application on bioremediation of water, hydrocarbon-contaminated sites under high-salinity level.

Evaluation of Arthrobacter aurescens Strain TC1 as Bioaugmentation Bacterium in Soils Contaminated with the Herbicidal Substance Terbuthylazine.

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Vera P Silva

Full Text Available In the last years the chloro-s-triazine active substance terbuthylazine has been increasingly used as an herbicide and may leave residues in the environment which can be of concern. The present study aimed at developing a bioaugmentation tool based on the soil bacterium Arthrobacter aurescens strain TC1 for the remediation of terbuthylazine contaminated soils and at examining its efficacy for both soil and aquatic compartments. First, the feasibility of growing the bioaugmentation bacterium inocula on simple sole nitrogen sources (ammonium and nitrate instead of atrazine, while still maintaining its efficiency to biodegrade terbuthylazine was shown. In sequence, the successful and quick (3 days bioremediation efficacy of ammonium-grown A. aurescens TC1 cells was proven in a natural soil freshly spiked or four-months aged with commercial terbuthylazine at a dose 10× higher than the recommended in corn cultivation, to mimic spill situations. Ecotoxicity assessment of the soil eluates towards a freshwater microalga supported the effectiveness of the bioaugmentation tool. Obtained results highlight the potential to decontaminate soil while minimizing terbuthylazine from reaching aquatic compartments via the soil-water pathway. The usefulness of this bioaugmentation tool to provide rapid environment decontamination is particularly relevant in the event of accidental high herbicide contamination. Its limitations and advantages are discussed.

Evaluation of Arthrobacter aurescens Strain TC1 as Bioaugmentation Bacterium in Soils Contaminated with the Herbicidal Substance Terbuthylazine

Science.gov (United States)

Silva, Vera P.; Moreira-Santos, Matilde; Mateus, Carla; Teixeira, Tânia; Ribeiro, Rui; Viegas, Cristina A.

2015-01-01

In the last years the chloro-s-triazine active substance terbuthylazine has been increasingly used as an herbicide and may leave residues in the environment which can be of concern. The present study aimed at developing a bioaugmentation tool based on the soil bacterium Arthrobacter aurescens strain TC1 for the remediation of terbuthylazine contaminated soils and at examining its efficacy for both soil and aquatic compartments. First, the feasibility of growing the bioaugmentation bacterium inocula on simple sole nitrogen sources (ammonium and nitrate) instead of atrazine, while still maintaining its efficiency to biodegrade terbuthylazine was shown. In sequence, the successful and quick (3 days) bioremediation efficacy of ammonium-grown A. aurescens TC1 cells was proven in a natural soil freshly spiked or four-months aged with commercial terbuthylazine at a dose 10× higher than the recommended in corn cultivation, to mimic spill situations. Ecotoxicity assessment of the soil eluates towards a freshwater microalga supported the effectiveness of the bioaugmentation tool. Obtained results highlight the potential to decontaminate soil while minimizing terbuthylazine from reaching aquatic compartments via the soil-water pathway. The usefulness of this bioaugmentation tool to provide rapid environment decontamination is particularly relevant in the event of accidental high herbicide contamination. Its limitations and advantages are discussed. PMID:26662024

Sporosalibacterium faouarense gen. nov., sp. nov., a moderately halophilic bacterium isolated from oil-contaminated soil.

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Rezgui, Raja; Ben Ali Gam, Zouhaier; Ben Hamed, Said; Fardeau, Marie-Laure; Cayol, Jean-Luc; Maaroufi, Abderrazak; Labat, Marc

2011-01-01

A novel strictly anaerobic, moderately halophilic and mesophilic bacterium, designated strain SOL3f37(T), was isolated from a hydrocarbon-polluted soil surrounding a deep petroleum environment located in south Tunisia. Cells of strain SOL3f37(T) stained Gram-positive and were motile, straight and spore-forming. Strain SOL3f37(T) had a typical Gram-positive-type cell-wall structure, unlike the thick, multilayered cell wall of its closest relative Clostridiisalibacter paucivorans. The major fatty acids were iso-C(15 : 0) (41 %), iso-C(14 : 0) 3-OH and/or iso-C(15 : 0) dimethyl acetal (21.6 %), iso-C(13 : 0) (4.4 %), anteiso-C(15 : 0) (3.9 %) and iso-C(15 : 1) (2.8 %). Strain SOL3f37(T) grew between 20 and 48 °C (optimum 40 °C) and at pH 6.2-8.1 (optimum pH 6.9). Strain SOL3f37(T) required at least 0.5 NaCl l(-1) and grew in the presence of NaCl concentrations up to 150 g l(-1) (optimum 40 g l(-1)). Yeast extract (2 g l(-1)) was required for degradation of pyruvate, fumarate, fructose, glucose and mannitol. Also, strain SOL3f37(T) grew heterotrophically on yeast extract, peptone and bio-Trypticase, but was unable to grow on Casamino acids. Sulfate, thiosulfate, sulfite, elemental sulfur, fumarate, nitrate and nitrite were not reduced. The DNA G+C content was 30.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SOL3f37(T) was a member of the family Clostridiaceae in the order Clostridiales; strain SOL3f37(T) was related to members of various genera of the family Clostridiaceae. It exhibited highest 16S rRNA gene sequence similarity (93.4 %) with Clostridiisalibacter paucivorans 37HS60(T), 91.8 % with Thermohalobacter berrensis CTT3(T) and 91.7 % with Caloranaerobacter azorensis MV1087(T). On the basis of genotypic, phenotypic and phylogenetic data, it is suggested that strain SOL3f37(T) represents a novel species in a new genus. The name Sporosalibacterium faouarense gen. nov., sp. nov. is

Isolation and characterization of Caldicellulosiruptor lactoaceticus sp. nov., an extremely thermophilic, cellulolytic, anaerobic bacterium

DEFF Research Database (Denmark)

Mladenovska, Zuzana; Mathrani, Indra M.; Ahring, Birgitte Kiær

1995-01-01

An anaerobic, extremely thermophilic, cellulolytic, non-spore-forming bacterium, strain 6A, was isolated from an alkaline hot spring in Hverageroi, Iceland. The bacterium was non-motile, rod-shaped (1.5-3.5 x 0.7 mu m) and occurred singly, in pairs or in chains and stained gram-negative. The growth...

Nitrous Oxide Reduction by an Obligate Aerobic Bacterium, Gemmatimonas aurantiaca Strain T-27.

Science.gov (United States)

Park, Doyoung; Kim, Hayeon; Yoon, Sukhwan

2017-06-15

,000 parts per million by volume [ppmv]). Although a large fraction of nosZ genes recovered from soil is affiliated with nosZ found in the genomes of the obligate aerobic phylum Gemmatimonadetes , N 2 O reduction has not yet been confirmed in any of these organisms. This study demonstrates that N 2 O is reduced by an obligate aerobic bacterium, Gemmatimonas aurantiaca strain T-27, and suggests a novel regulation mechanism for N 2 O reduction in this organism, which may also be applicable to other obligate aerobic organisms possessing nosZ genes. We expect that these findings will significantly advance the understanding of N 2 O dynamics in environments with frequent transitions between oxic and anoxic conditions. Copyright © 2017 American Society for Microbiology.

The Sterilization Effect of Cooperative Treatment of High Voltage Electrostatic Field and Variable Frequency Pulsed Electromagnetic Field on Heterotrophic Bacteria in Circulating Cooling Water

Science.gov (United States)

Gao, Xuetong; Liu, Zhian; Zhao, Judong

2018-01-01

Compared to other treatment of industrial circulating cooling water in the field of industrial water treatment, high-voltage electrostatic field and variable frequency pulsed electromagnetic field co-sterilization technology, an advanced technology, is widely used because of its special characteristics--low energy consumption, nonpoisonous and environmentally friendly. In order to get a better cooling water sterilization effect under the premise of not polluting the environment, some experiments about sterilization of heterotrophic bacteria in industrial circulating cooling water by cooperative treatment of high voltage electrostatic field and variable frequency pulsed electromagnetic field were carried out. The comparison experiment on the sterilization effect of high-voltage electrostatic field and variable frequency pulsed electromagnetic field co-sterilization on heterotrophic bacteria in industrial circulating cooling water was carried out by change electric field strength and pulse frequency. The results show that the bactericidal rate is selective to the frequency and output voltage, and the heterotrophic bacterium can only kill under the condition of sweep frequency range and output voltage. When the voltage of the high voltage power supply is 4000V, the pulse frequency is 1000Hz and the water temperature is 30°C, the sterilization rate is 48.7%, the sterilization rate is over 90%. Results of this study have important guiding significance for future application of magnetic field sterilization.

Biotransformation of pharmaceuticals under nitrification, nitratation and heterotrophic conditions

International Nuclear Information System (INIS)

Fernandez-Fontaina, E.; Gomes, I.B.; Aga, D.S.; Omil, F.; Lema, J.M.; Carballa, M.

2016-01-01

The effect of nitrification, nitratation and heterotrophic conditions on the biotransformation of several pharmaceuticals in a highly enriched nitrifying activated sludge was evaluated in this study by selective activation of ammonia oxidizing bacteria (AOB), nitrite oxidizing bacteria (NOB) and heterotrophic bacteria. Nitrifiers displayed a noticeable capacity to process ibuprofen due to hydroxylation by ammonia monooxygenase (AMO) to produce 2-hydroxy-ibuprofen. Naproxen was also biotransformed under nitrifying conditions. On the other hand, heterotrophic bacteria present in the nitrifying activated sludge (NAS) biotransformed sulfamethoxazole. In contrast, both nitrifying and heterotrophic activities were ineffective against diclofenac, diazepam, carbamazepine and trimethoprim. Similar biotransformation rates of erythromycin, roxithromycin and fluoxetine were observed under all conditions tested. Overall, results from this study give more evidence on the role of the different microbial communities present in activated sludge reactors on the biological removal of pharmaceuticals. - Highlights: • The removal of pharmaceuticals in nitrifying activated sludge (NAS) was studied. • Nitrifying activity increases biotransformation rate of ibuprofen and naproxen. • Hydroxylation of ibuprofen by ammonia monooxygenase of ammonia oxidizing bacteria • Heterotrophic activity enhances biotransformation of sulfamethoxazole in NAS. • Recalcitrance of trimethoprim, diclofenac, carbamazepine and diazepam in NAS

Biotransformation of pharmaceuticals under nitrification, nitratation and heterotrophic conditions

Energy Technology Data Exchange (ETDEWEB)

Fernandez-Fontaina, E., E-mail: eduardo.fernandez.fontaina@usc.es [Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela (Spain); Gomes, I.B. [Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela (Spain); Aga, D.S. [Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260 (United States); Omil, F.; Lema, J.M.; Carballa, M. [Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela (Spain)

2016-01-15

The effect of nitrification, nitratation and heterotrophic conditions on the biotransformation of several pharmaceuticals in a highly enriched nitrifying activated sludge was evaluated in this study by selective activation of ammonia oxidizing bacteria (AOB), nitrite oxidizing bacteria (NOB) and heterotrophic bacteria. Nitrifiers displayed a noticeable capacity to process ibuprofen due to hydroxylation by ammonia monooxygenase (AMO) to produce 2-hydroxy-ibuprofen. Naproxen was also biotransformed under nitrifying conditions. On the other hand, heterotrophic bacteria present in the nitrifying activated sludge (NAS) biotransformed sulfamethoxazole. In contrast, both nitrifying and heterotrophic activities were ineffective against diclofenac, diazepam, carbamazepine and trimethoprim. Similar biotransformation rates of erythromycin, roxithromycin and fluoxetine were observed under all conditions tested. Overall, results from this study give more evidence on the role of the different microbial communities present in activated sludge reactors on the biological removal of pharmaceuticals. - Highlights: • The removal of pharmaceuticals in nitrifying activated sludge (NAS) was studied. • Nitrifying activity increases biotransformation rate of ibuprofen and naproxen. • Hydroxylation of ibuprofen by ammonia monooxygenase of ammonia oxidizing bacteria • Heterotrophic activity enhances biotransformation of sulfamethoxazole in NAS. • Recalcitrance of trimethoprim, diclofenac, carbamazepine and diazepam in NAS.

Antagonistic bioactivity of an endophytic bacterium isolated from ...

African Journals Online (AJOL)

Antagonistic bioactivity of an endophytic bacterium isolated from Epimedium brevicornu Maxim. R He, G Wang, X Liu, C Zhang, F Lin. Abstract. Endophytic bacteria are one of the most potential biological control agents in plant disease protection. The aim of this work was to evaluate the antimicrobial activities of a strain of ...

Degradation of phenol via phenylphosphate and carboxylation to 4-hydroxybenzoate by a newly isolated strain of the sulfate-reducing bacterium Desulfobacterium anilini.

Science.gov (United States)

Ahn, Young-Beom; Chae, Jong-Chan; Zylstra, Gerben J; Häggblom, Max M

2009-07-01

A sulfate-reducing phenol-degrading bacterium, strain AK1, was isolated from a 2-bromophenol-utilizing sulfidogenic estuarine sediment enrichment culture. On the basis of phylogenetic analysis of the 16S rRNA gene and DNA homology, strain AK1 is most closely related to Desulfobacterium anilini strain Ani1 (= DSM 4660(T)). In addition to phenol, this organism degrades a variety of other aromatic compounds, including benzoate, 2-hydroxybenzoate, 4-hydroxybenzoate, 4-hydroxyphenylacetate, 2-aminobenzoate, 2-fluorophenol, and 2-fluorobenzoate, but it does not degrade aniline, 3-hydroxybenzoate, 4-cyanophenol, 2,4-dihydroxybenzoate, monohalogenated phenols, or monohalogenated benzoates. Growth with sulfate as an electron acceptor occurred with acetate and pyruvate but not with citrate, propionate, butyrate, lactate, glucose, or succinate. Strain AK1 is able to use sulfate, sulfite, and thiosulfate as electron acceptors. A putative phenylphosphate synthase gene responsible for anaerobic phenol degradation was identified in strain AK1. In phenol-grown cultures inducible expression of the ppsA gene was verified by reverse transcriptase PCR, and 4-hydroxybenzoate was detected as an intermediate. These results suggest that the pathway for anaerobic degradation of phenol in D. anilini strain AK1 proceeds via phosphorylation of phenol to phenylphosphate, followed by carboxylation to 4-hydroxybenzoate. The details concerning such reaction pathways in sulfidogenic bacteria have not been characterized previously.

Marinobacter nitratireducens sp. nov., a halophilic and lipolytic bacterium isolated from coastal surface sea water

Digital Repository Service at National Institute of Oceanography (India)

Bhumika, V.; Ravinder, K.; Korpole, S.; Srinivas, T.N.R.; AnilKumar, P.

A novel Gram-stain-negative, rod-shaped, motile bacterium, designated strain AK21^T , was isolated from coastal surface sea water at Visakhapatnam, India. The strain was positive for oxidase, catalase, lipase, L-proline arylamidase...

Quantitative analysis of an engineered CO2-fixing Escherichia coli reveals great potential of heterotrophic CO2 fixation.

Science.gov (United States)

Gong, Fuyu; Liu, Guoxia; Zhai, Xiaoyun; Zhou, Jie; Cai, Zhen; Li, Yin

2015-01-01

Production of fuels from the abundant and wasteful CO2 is a promising approach to reduce carbon emission and consumption of fossil fuels. Autotrophic microbes naturally assimilate CO2 using energy from light, hydrogen, and/or sulfur. However, their slow growth rates call for investigation of the possibility of heterotrophic CO2 fixation. Although preliminary research has suggested that CO2 fixation in heterotrophic microbes is feasible after incorporation of a CO2-fixing bypass into the central carbon metabolic pathway, it remains unclear how much and how efficient that CO2 can be fixed by a heterotrophic microbe. A simple metabolic flux index was developed to indicate the relative strength of the CO2-fixation flux. When two sequential enzymes of the cyanobacterial Calvin cycle were incorporated into an E. coli strain, the flux of the CO2-fixing bypass pathway accounts for 13 % of that of the central carbon metabolic pathway. The value was increased to 17 % when the carbonic anhydrase involved in the cyanobacterial carbon concentrating mechanism was introduced, indicating that low intracellular CO2 concentration is one limiting factor for CO2 fixation in E. coli. The engineered CO2-fixing E. coli with carbonic anhydrase was able to fix CO2 at a rate of 19.6 mg CO2 L(-1) h(-1) or the specific rate of 22.5 mg CO2 g DCW(-1) h(-1). This CO2-fixation rate is comparable with the reported rates of 14 autotrophic cyanobacteria and algae (10.5-147.0 mg CO2 L(-1) h(-1) or the specific rates of 3.5-23.7 mg CO2 g DCW(-1) h(-1)). The ability of CO2 fixation was created and improved in E. coli by incorporating partial cyanobacterial Calvin cycle and carbon concentrating mechanism, respectively. Quantitative analysis revealed that the CO2-fixation rate of this strain is comparable with that of the autotrophic cyanobacteria and algae, demonstrating great potential of heterotrophic CO2 fixation.

Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs.

Science.gov (United States)

Dedysh, S N; Liesack, W; Khmelenina, V N; Suzina, N E; Trotsenko, Y A; Semrau, J D; Bares, A M; Panikov, N S; Tiedje, J M

2000-05-01

A new genus, Methylocella, and a new species, Methylocella palustris, are proposed for three strains of methane-oxidizing bacteria isolated from acidic Sphagnum peat bogs. These bacteria are aerobic, Gram-negative, colourless, non-motile, straight and curved rods that utilize the serine pathway for carbon assimilation, multiply by normal cell division and contain intracellular poly-beta-hydroxybutyrate granules (one at each pole). These strains use methane and methanol as sole sources of carbon and energy and are moderately acidophilic organisms with growth between pH 4.5 and pH 7.0, the optimum being at pH 5.0-5.5. The temperature range for growth is 10-28 degrees C with the optimum at 15-20 degrees C. The intracytoplasmic membrane system is different from those of type I and II methanotrophs. Cells contain an extensive periplasmic space and a vesicular membrane system connected to the cytoplasmic membrane. The strains grew only on media with a low salt content (0.2-0.5 g l(-1)). All three strains were found to possess soluble methane monooxygenase and are able to fix atmospheric nitrogen via an oxygen-sensitive nitrogenase. No products were observed in a PCR with particulate methane monooxygenase-targeted primers; hybridization with a pmoA probe was also negative. The major phospholipid fatty acids are 18:1 acids. The G+C content of the DNA is 61.2 mol%. The three strains share identical 16S rRNA gene sequences and represent a novel lineage of methane-oxidizing bacteria within the alpha-subclass of the class Proteobacteria and are only moderately related to type II methanotrophs of the Methylocystis-Methylosinus group. The three strains are most closely related to the acidophilic heterotrophic bacterium Beijerinckia indica subsp. indica (96.5% 16S rDNA sequence similarity). Collectively, these strains comprise a new species and genus Methylocella palustris gen. nov., sp. nov.; strain KT (= ATCC 700799T) is the type strain.

Heterotrophic cultivation of microalgae for pigment production: A review.

Science.gov (United States)

Hu, Jianjun; Nagarajan, Dillirani; Zhang, Quanguo; Chang, Jo-Shu; Lee, Duu-Jong

Pigments (mainly carotenoids) are important nutraceuticals known for their potent anti-oxidant activities and have been used extensively as high end health supplements. Microalgae are the most promising sources of natural carotenoids and are devoid of the toxic effects associated with synthetic derivatives. Compared to photoautotrophic cultivation, heterotrophic cultivation of microalgae in well-controlled bioreactors for pigments production has attracted much attention for commercial applications due to overcoming the difficulties associated with the supply of CO 2 and light, as well as avoiding the contamination problems and land requirements in open autotrophic culture systems. In this review, the heterotrophic metabolic potential of microalgae and their uses in pigment production are comprehensively described. Strategies to enhance pigment production under heterotrophic conditions are critically discussed and the challenges faced in heterotrophic pigment production with possible alternative solutions are presented. Copyright © 2017 Elsevier Inc. All rights reserved.

Isolation and characterization of a new hydrogen-utilizing bacterium from the rumen.

Science.gov (United States)

Rieu-Lesme, F; Fonty, G; Doré, J

1995-01-01

A new H2/CO2-utilizing acetogenic bacterium was isolated from the rumen of a mature deer. This is the first report of a spore-forming Gram-negative bacterial species from the rumen. The organism was a strictly anaerobic, motile rod and was able to grow autotrophically on hydrogen and carbon dioxide. Acetate was the major product detected. Glucose, fructose and lactate were also fermented heterotrophically. The optimum pH for growth was 7.0-7.5, and the optimum temperature was 37-42 degrees C. Yeast extract was required for growth and rumen fluid was highly stimulatory. The DNA base ratio was 52.9 +/- 0.5 mol% G+C. On the basis of these characteristics and fermentation products, the isolate was considered to be different from acetogenic bacteria described previously.

Evidence of carbon fixation pathway in a bacterium from candidate phylum SBR1093 revealed with genomic analysis.

Directory of Open Access Journals (Sweden)

Zhiping Wang

Full Text Available Autotrophic CO2 fixation is the most important biotransformation process in the biosphere. Research focusing on the diversity and distribution of relevant autotrophs is significant to our comprehension of the biosphere. In this study, a draft genome of a bacterium from candidate phylum SBR1093 was reconstructed with the metagenome of an industrial activated sludge. Based on comparative genomics, this autotrophy may occur via a newly discovered carbon fixation path, the hydroxypropionate-hydroxybutyrate (HPHB cycle, which was demonstrated in a previous work to be uniquely possessed by some genera from Archaea. This bacterium possesses all of the thirteen enzymes required for the HPHB cycle; these enzymes share 30∼50% identity with those in the autotrophic species of Archaea that undergo the HPHB cycle and 30∼80% identity with the corresponding enzymes of the mixotrophic species within Bradyrhizobiaceae. Thus, this bacterium might have an autotrophic growth mode in certain conditions. A phylogenetic analysis based on the 16S rRNA gene reveals that the phylotypes within candidate phylum SBR1093 are primarily clustered into 5 clades with a shallow branching pattern. This bacterium is clustered with phylotypes from organically contaminated environments, implying a demand for organics in heterotrophic metabolism. Considering the types of regulators, such as FnR, Fur, and ArsR, this bacterium might be a facultative aerobic mixotroph with potential multi-antibiotic and heavy metal resistances. This is the first report on Bacteria that may perform potential carbon fixation via the HPHB cycle, thus may expand our knowledge of the distribution and importance of the HPHB cycle in the biosphere.

Genetic Engineering of a Radiation-Resistant Bacterium for Biodegradation of Mixed Wastes. Final Report

International Nuclear Information System (INIS)

Lidstrom, Mary E.

2003-01-01

Aqueous mixed low level wastes (MLLW) containing radionuclides, solvents, and/or heavy metals represent a serious current and future problem for DOE environmental management and cleanup. In order to provide low-cost treatment alternatives under mild conditions for such contained wastes, we have proposed to use the radiation-resistant bacterium, Deinococcus radiodurans. This project has focused on developing D. radiodurans strains for dual purpose processes: cometabolic treatment of haloorganics and other solvents and removal of heavy metals from waste streams in an above-ground reactor system. The characteristics of effective treatment strains that must be attained are: (a) high biodegradative and metal binding activity; (b) stable treatment characteristics in the absence of selection and in the presence of physiological stress; (c) survival and activity under harsh chemical conditions, including radiation. The result of this project has been a suite of strains with high biodegradative capabilities that are candidates for pilot stage treatment systems. In addition, we have determined how to create conditions to precipitate heavy metals on the surface of the bacterium, as the first step towards creating dual-use treatment strains for contained mixed wastes of importance to the DOE. Finally, we have analyzed stress response in this bacterium, to create the foundation for developing treatment processes that maximize degradation while optimizing survival under high stress conditions

Thermal adaptation of heterotrophic soil respiration in laboratory microcosms.

Science.gov (United States)

Mark A. Bradford; Brian W. Watts; Christian A. Davies

2010-01-01

Respiration of heterotrophic microorganisms decomposing soil organic carbon releases carbon dioxide from soils to the atmosphere. In the short term, soil microbial respiration is strongly dependent on temperature. In the long term, the response of heterotrophic soil respiration to temperature is uncertain. However, following established evolutionary tradeoffs, mass-...

Partitioning autotrophic and heterotrophic respiration at Howland Forest

Science.gov (United States)

Carbone, Mariah; Hollinger, Dave; Davidson, Eric; Savage, Kathleen; Hughes, Holly

2015-04-01

Terrestrial ecosystem respiration is the combined flux of CO2 to the atmosphere from above- and below-ground, plant (autotrophic) and microbial (heterotrophic) sources. Flux measurements alone (e.g., from eddy covariance towers or soil chambers) cannot distinguish the contributions from these sources, which may change seasonally and respond differently to temperature and moisture. The development of improved process-based models that can predict how plants and microbes respond to changing environmental conditions (on seasonal, interannual, or decadal timescales) requires data from field observations and experiments to distinguish among these respiration sources. We tested the viability of partitioning of soil and ecosystem respiration into autotrophic and heterotrophic components with different approaches at the Howland Forest in central Maine, USA. These include an experimental manipulation using the classic root trenching approach and targeted ∆14CO2 measurements. For the isotopic measurements, we used a two-end member mass balance approach to determine the fraction of soil respiration from autotrophic and heterotrophic sources. When summed over the course of the growing season, the trenched chamber flux (heterotrophic) accounted for 53 ± 2% of the total control chamber flux. Over the four different 14C sampling periods, the heterotrophic component ranged from 35-55% and the autotrophic component ranges 45-65% of the total flux. Next steps will include assessing the value of the flux partitioning for constraining a simple ecosystem model using a model-data fusion approach to reduce uncertainties in estimates of NPP and simulation of future soil C stocks and fluxes.

Two-stage heterotrophic and phototrophic culture strategy for algal biomass and lipid production.

Science.gov (United States)

Zheng, Yubin; Chi, Zhanyou; Lucker, Ben; Chen, Shulin

2012-01-01

A two-stage heterotrophic and phototrophic culture strategy for algal biomass and lipid production was studied, wherein high density heterotrophic cultures of Chlorellasorokiniana serve as seed for subsequent phototrophic growth. The data showed growth rate, cell density and productivity of heterotrophic C.sorokiniana were 3.0, 3.3 and 7.4 times higher than phototrophic counterpart, respectively. Hetero- and phototrophic algal seeds had similar biomass/lipid production and fatty acid profile when inoculated into phototrophic culture system. To expand the application, food waste and wastewater were tested as feedstock for heterotrophic growth, and supported cell growth successfully. These results demonstrated the advantages of using heterotrophic algae cells as seeds for open algae culture system. Additionally, high inoculation rate of heterotrophic algal seed can be utilized as an effective method for contamination control. This two-stage heterotrophic phototrophic process is promising to provide a more efficient way for large scale production of algal biomass and biofuels. Copyright © 2011 Elsevier Ltd. All rights reserved.

Echinicola shivajiensis sp. nov., a novel bacterium of the family "Cyclobacteriaceae" isolated from brackish water pond

Digital Repository Service at National Institute of Oceanography (India)

Srinivas, T.N.R.; Tryambak, B.K.; AnilKumar, P.

Strain AK12 sup(T), an orange pigmented Gramnegative, rod shaped, non-motile bacterium, was isolated fromamud sample collected froma brackishwater pond at Rampur of West Bengal, India. The strain was positive for oxidase, catalase and phosphatase...

Oceanospirillum nioense sp. nov., a marine bacterium isolated from sediment sample of Palk bay, India

Digital Repository Service at National Institute of Oceanography (India)

Krishna, K.K.; Bhumika, V.; Thomas, M.; AnilKumar, P.; Srinivas, T.N.R.

A novel Gram-negative, spiral shaped, motile bacterium, designated strain NIO-S6T, was isolated from a sediment sample collected from Offshore Rameswaram, Tamilnadu, India. Strain NIO-S6 sup(T) was found to be positive for oxidase, DNase and lysine...

A Cyanide-Induced 3-Cyanoalanine Nitrilase in the Cyanide-Assimilating Bacterium Pseudomonas pseudoalcaligenes Strain CECT 5344.

Science.gov (United States)

Acera, Felipe; Carmona, María Isabel; Castillo, Francisco; Quesada, Alberto; Blasco, Rafael

2017-05-01

Pseudomonas pseudoalcaligenes CECT 5344 is a bacterium able to assimilate cyanide as a sole nitrogen source. Under this growth condition, a 3-cyanoalanine nitrilase enzymatic activity was induced. This activity was encoded by nit4 , one of the four nitrilase genes detected in the genome of this bacterium, and its expression in Escherichia coli enabled the recombinant strain to fully assimilate 3-cyanoalanine. P. pseudoalcaligenes CECT 5344 showed a weak growth level with 3-cyanoalanine as the N source, unless KCN was also added. Moreover, a nit4 knockout mutant of P. pseudoalcaligenes CECT 5344 became severely impaired in its ability to grow with 3-cyanoalanine and cyanide as nitrogen sources. The native enzyme expressed in E. coli was purified up to electrophoretic homogeneity and biochemically characterized. Nit4 seems to be specific for 3-cyanoalanine, and the amount of ammonium derived from the enzymatic activity doubled in the presence of exogenously added asparaginase activity, which demonstrated that the Nit4 enzyme had both 3-cyanoalanine nitrilase and hydratase activities. The nit4 gene is located downstream of the cyanide resistance transcriptional unit containing cio1 genes, whose expression levels are under the positive control of cyanide. Real-time PCR experiments revealed that nit4 expression was also positively regulated by cyanide in both minimal and LB media. These results suggest that this gene cluster including cio1 and nit4 could be involved both in cyanide resistance and in its assimilation by P. pseudoalcaligenes CECT 5344. IMPORTANCE Cyanide is a highly toxic molecule present in some industrial wastes due to its application in several manufacturing processes, such as gold mining and the electroplating industry. The biodegradation of cyanide from contaminated wastes could be an attractive alternative to physicochemical treatment. P. pseudoalcaligenes CECT 5344 is a bacterial strain able to assimilate cyanide under alkaline conditions, thus

The atherogenic bacterium Porphyromonas gingivalis evades circulating phagocytes by adhering to erythrocytes

DEFF Research Database (Denmark)

Belstrøm, Daniel; Holmstrup, Palle; Damgaard, Christian

2011-01-01

A relationship between periodontitis and coronary heart disease has been investigated intensively. A pathogenic role for the oral bacterium Porphyromonas gingivalis has been suggested for both diseases. We examined whether complement activation by P. gingivalis strain ATCC 33277 allows...... the bacterium to adhere to human red blood cells (RBCs) and thereby evade attack by circulating phagocytes. On incubation with normal human serum, the P. gingivalis strain efficiently fixed complement component 3 (C3). Incubation of bacteria with washed whole blood cells suspended in autologous serum resulted...... in a dose- and time-dependent adherence to RBCs. The adherence required functionally intact complement receptor 1 (CR1; also called CD35) on the RBCs and significantly inhibited the uptake of P. gingivalis by neutrophils and B cells within 1 min of incubation (by 64% and 51%, respectively...

Genomic Analysis of a Marine Bacterium: Bioinformatics for Comparison, Evaluation, and Interpretation of DNA Sequences

Directory of Open Access Journals (Sweden)

Bhagwan N. Rekadwad

2016-01-01

Full Text Available A total of five highly related strains of an unidentified marine bacterium were analyzed through their short genome sequences (AM260709–AM260713. Genome-to-Genome Distance (GGDC showed high similarity to Pseudoalteromonas haloplanktis (X67024. The generated unique Quick Response (QR codes indicated no identity to other microbial species or gene sequences. Chaos Game Representation (CGR showed the number of bases concentrated in the area. Guanine residues were highest in number followed by cytosine. Frequency of Chaos Game Representation (FCGR indicated that CC and GG blocks have higher frequency in the sequence from the evaluated marine bacterium strains. Maximum GC content for the marine bacterium strains ranged 53-54%. The use of QR codes, CGR, FCGR, and GC dataset helped in identifying and interpreting short genome sequences from specific isolates. A phylogenetic tree was constructed with the bootstrap test (1000 replicates using MEGA6 software. Principal Component Analysis (PCA was carried out using EMBL-EBI MUSCLE program. Thus, generated genomic data are of great assistance for hierarchical classification in Bacterial Systematics which combined with phenotypic features represents a basic procedure for a polyphasic approach on unambiguous bacterial isolate taxonomic classification.

Flavobacterium nitratireducens sp. nov., an amylolytic bacterium of the family Flavobacteriaceae isolated from coastal surface seawater

Digital Repository Service at National Institute of Oceanography (India)

Nupur; Bhumika, V.; Srinivas, T.N.R.; AnilKumar, P.

A novel Gram-negative, rod-shaped, non-motile bacterium, designated strain N1 sup(T), was isolated from a marine water sample collected from the sea shore, Bay of Bengal, Visakhapatnam, India. The strain was positive for starch hydrolysis, nitrate...

Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity.

Science.gov (United States)

Tang, Kai; Zhang, Yao; Lin, Dan; Han, Yu; Chen, Chen-Tung A; Wang, Deli; Lin, Yu-Shih; Sun, Jia; Zheng, Qiang; Jiao, Nianzhi

2018-01-01

Shallow-sea hydrothermal systems experience continuous fluctuations of physicochemical conditions due to seawater influx which generates variable habitats, affecting the phylogenetic composition and metabolic potential of microbial communities. Until recently, studies of submarine hydrothermal communities have focused primarily on chemolithoautotrophic organisms, however, there have been limited studies on heterotrophic bacteria. Here, fluorescence in situ hybridization, high throughput 16S rRNA gene amplicon sequencing, and functional metagenomes were used to assess microbial communities from the shallow-sea hydrothermal system off Kueishantao Island, Taiwan. The results showed that the shallow-sea hydrothermal system harbored not only autotrophic bacteria but abundant heterotrophic bacteria. The potential for marker genes sulfur oxidation and carbon fixation were detected in the metagenome datasets, suggesting a role for sulfur and carbon cycling in the shallow-sea hydrothermal system. Furthermore, the presence of diverse genes that encode transporters, glycoside hydrolases, and peptidase indicates the genetic potential for heterotrophic utilization of organic substrates. A total of 408 cultivable heterotrophic bacteria were isolated, in which the taxonomic families typically associated with oligotrophy, copiotrophy, and phototrophy were frequently found. The cultivation-independent and -dependent analyses performed herein show that Alphaproteobacteria and Gammaproteobacteria represent the dominant heterotrophs in the investigated shallow-sea hydrothermal system. Genomic and physiological characterization of a novel strain P5 obtained in this study, belonging to the genus Rhodovulum within Alphaproteobacteria, provides an example of heterotrophic bacteria with major functional capacity presented in the metagenome datasets. Collectively, in addition to autotrophic bacteria, the shallow-sea hydrothermal system also harbors many heterotrophic bacteria with versatile

Isolation and characterization of two cryptic plasmids in the ammonia-oxidizing bacterium Nitrosomonas sp. strain ENI-11.

Science.gov (United States)

Yamagata, A; Kato, J; Hirota, R; Kuroda, A; Ikeda, T; Takiguchi, N; Ohtake, H

1999-06-01

Two plasmids were discovered in the ammonia-oxidizing bacterium Nitrosomonas sp. strain ENI-11, which was isolated from activated sludge. The plasmids, designated pAYS and pAYL, were relatively small, being approximately 1.9 kb long. They were cryptic plasmids, having no detectable plasmid-linked antibiotic resistance or heavy metal resistance markers. The complete nucleotide sequences of pAYS and pAYL were determined, and their physical maps were constructed. There existed two major open reading frames, ORF1 in pAYS and ORF2 in pAYL, each of which was more than 500 bp long. The predicted product of ORF2 was 28% identical to part of the replication protein of a Bacillus plasmid, pBAA1. However, no significant similarity to any known protein sequences was detected with the predicted product of ORF1. pAYS and pAYL had a highly homologous region, designated HHR, of 262 bp. The overall identity was 98% between the two nucleotide sequences. Interestingly, HHR-homologous sequences were also detected in the genomes of ENI-11 and the plasmidless strain Nitrosomonas europaea IFO14298. Deletion analysis of pAYS and pAYL indicated that HHR, together with either ORF1 or ORF2, was essential for plasmid maintenance in ENI-11. To our knowledge, pAYS and pAYL are the first plasmids found in the ammonia-oxidizing autotrophic bacteria.

Effect of cell immobilization on the treatment of olive mill wastewater by a total phenols, acetic acid and formic acid degrading bacterium strain

Directory of Open Access Journals (Sweden)

Errami, Mohamed

2005-06-01

Full Text Available Olive mill wastewater (OMW is a pure vegetative by-product, containing a high organic and polyphenol content and is resistant to biodegradation. Its disposal lead to major environmental pollution problems in the Mediterranean basin. An aerobic bacterium was isolated from OMW. During three consecutive diluted and supplemented OMW treatment cycles, significant abatement of its phytotoxic substances was observed. In fact, total phenols, acetic and formic acids were reduced between 33 and 64 % when cells of the isolated bacterium were grown free; and between 62 and 78 % when cells of the same isolated bacterium were grown immobilized in a polyurethane sponge. These results suggest that the bacterium culture of the new isolate would decrease the OMW phytotoxicity. Phylogenetic analysis of 16S ribosomal DNA showed that all the related sequences are members of the Enterobacteriaceae family and revealed that the isolated bacterium was characterized as a Klebsiella oxytoca strain.El alpechín (OMW es un residuo puro de la extracción del aceite de oliva, que contiene una elevada carga orgánica y de polifenoles por lo que es resistente a la degradación. Su descarga produce graves problemas de contaminación medioambiental en toda el área mediterránea. Se ha aislado una bacteria anaerobia del OMW, que , durante tres ciclos consecutivos de tratamiento del OMW diluido y suplementado, produjo una disminución significativa de las sustancias fitotóxicas del residuo. De hecho, la concentración en fenoles totales, ácido acético y ácido fórmico se redujeron entre 33 y 64 % cuando las células no estaban inmovilizadas y entre el 62 y 78 % cuando las células bacterianas se inmovilizaron en una esponja de poliuretano. Estos resultados indican que el cultivo de la nueva bacteria aislada puede disminuir la fototoxicidad del alpechín. Análisis filogenético del ribosoma 16S de DNA demostró que todas las secuencias eran miembros de la familia

Genome Sequence of Lactobacillus delbrueckii subsp. lactis CNRZ327, a Dairy Bacterium with Anti-Inflammatory Properties.

Science.gov (United States)

El Kafsi, Hela; Binesse, Johan; Loux, Valentin; Buratti, Julien; Boudebbouze, Samira; Dervyn, Rozenn; Hammani, Amal; Maguin, Emmanuelle; van de Guchte, Maarten

2014-07-17

Lactobacillus delbrueckii subsp. lactis CNRZ327 is a dairy bacterium with anti-inflammatory properties both in vitro and in vivo. Here, we report the genome sequence of this bacterium, which appears to contain no less than 215 insertion sequence (IS) elements, an exceptionally high number regarding the small genome size of the strain. Copyright © 2014 El Kafsi et al.

Does S-metolachlor affect the performance of Pseudomonas sp. strain ADP as bioaugmentation bacterium for atrazine-contaminated soils?

Directory of Open Access Journals (Sweden)

Cristina A Viegas

Full Text Available Atrazine (ATZ and S-metolachlor (S-MET are two herbicides widely used, often as mixtures. The present work examined whether the presence of S-MET affects the ATZ-biodegradation activity of the bioaugmentation bacterium Pseudomonas sp. strain ADP in a crop soil. S-MET concentrations were selected for their relevance in worst-case scenarios of soil contamination by a commercial formulation containing both herbicides. At concentrations representative of application of high doses of the formulation (up to 50 µg g(-1 of soil, corresponding to a dose approximately 50× higher than the recommended field dose (RD, the presence of pure S-MET significantly affected neither bacteria survival (~10(7 initial viable cells g(-1 of soil nor its ATZ-mineralization activity. Consistently, biodegradation experiments, in larger soil microcosms spiked with 20× or 50 × RD of the double formulation and inoculated with the bacterium, revealed ATZ to be rapidly (in up to 5 days and extensively (>96% removed from the soil. During the 5 days, concentration of S-MET decreased moderately to about 60% of the initial, both in inoculated and non-inoculated microcosms. Concomitantly, an accumulation of the two metabolites S-MET ethanesulfonic acid and S-MET oxanilic acid was found. Despite the dissipation of almost all the ATZ from the treated soils, the respective eluates were still highly toxic to an aquatic microalgae species, being as toxic as those from the untreated soil. We suggest that this high toxicity may be due to the S-MET and/or its metabolites remaining in the soil.

Growth rate characteristics of acidophilic heterotrophic organisms from mine waste rock piles

Science.gov (United States)

Yacob, T. W.; Silverstein, J.; Jenkins, J.; Andre, B. J.; Rajaram, H.

2010-12-01

Autotrophic iron oxidizing bacteria play a key role in pyrite oxidation and generation of acid mine drainage AMD. Scarcity of organic substrates in many disturbed sites insures that IOB have sufficient oxygen and other nutrients for growth. It is proposed that addition of organic carbon substrate to waste rock piles will result in enrichment of heterotrophic microorganisms limiting the role of IOB in AMD generation. Previous researchers have used the acidophilic heterotroph Acidiphilium cryptum as a model to study the effects of organic substrate addition on the pyrite oxidation/AMD cycle. In order to develop a quantitative model of effects such as competition for oxygen, it is necessary to use growth and substrate consumption rate expressions, and one approach is to choose a model strain such as A. cryptum for kinetic studies. However we have found that the growth rate characteristics of A. cryptum may not provide an accurate model of the remediation effects of organic addition to subsurface mined sites. Fluorescent in-situ hybridization (FISH) assays of extracts of mine waste rock enriched with glucose and yeast extract did not produce countable numbers of cells in the Acidiphilium genus, with a detection limit of3 x 104 cells/gram rock, despite evidence of the presence of well established heterotrophic organisms. However, an MPN enrichment produced heterotrophic population estimates of 1x107 and 1x109 cells/gram rock. Growth rate studies of A. cryptum showed that cultures took 120 hours to degrade 50% of an initial glucose concentration of 2,000 mg/L. However a mixed culture enriched from mine waste rock consumed 100% of the same amount of glucose in 24 hours. Substrate consumption data for the mixed culture were fit to a Monod growth model: {dS}/{dt} = μ_{max}S {( {X_0}/{Y} + S_0 -S )}/{(K_s +S)} Kinetic parameters were estimated utilizing a non linear regression method coupled with an ODE solver. The maximum specific growth rate of the mixed population with �

Intestinimonas butyriciproducens gen. nov., sp. nov., a novel butyrate-producing bacterium from the mouse intestine

NARCIS (Netherlands)

Kläring, K.; Hanske, L.; Bui, T.P.N.; Charrier, C.; Blaut, M.; Haller, D.; Plugge, C.M.; Clavel, T.

2013-01-01

Whilst creating a bacterial collection of strains from the mouse intestine, we isolated a Gram-negative, spore-forming, non-motile and strictly anaerobic rod-shaped bacterium from the caecal content of a TNFdeltaARE mouse. The isolate, referred to as strain SRB-521-5-IT, was originally cultured on a

Heterotrophic free-living and particle-bound bacterial cell size in the ...

Indian Academy of Sciences (India)

PRAKASH

the heterotrophic bacterial cell size in the various water bodies studied in this investigation. The possible ... seasonal changes in abundance and cell size of heterotrophic ... data, 1995) physiological stress indicated by the presence of small ...

Aliidiomarina haloalkalitolerans sp. nov., a marine bacterium isolated from coastal surface seawater

Digital Repository Service at National Institute of Oceanography (India)

Srinivas, T.N.R.; Nupur; AnilKumar, P.

A novel Gram-negative, rod shaped, motile, non-sporing strictly aerobic bacterium, designated strain AK5 sup(T), was isolated from a sea water sample collected near Visakhapatnam coast, Bay of Bengal, India. Colonies on marine agar were circular, 3...

Virus-mediated transfer of nitrogen from heterotrophic bacteria to phytoplankton

Science.gov (United States)

Shelford, Emma J.; Suttle, Curtis A.

2018-02-01

Lytic infection of bacteria by viruses releases nutrients during cell lysis and stimulates the growth of primary producers, but the path by which these nutrients flow from lysates to primary producers has not been traced. This study examines the remineralisation of nitrogen (N) from Vibrio lysates by heterotrophic bacterioplankton and its transfer to primary producers. In laboratory trials, Vibrio sp. strain PWH3a was infected with a lytic virus (PWH3a-P1) and the resulting 36.0 µmol L-1 of dissolved organic N (DON) in the lysate was added to cultures containing cyanobacteria (Synechococcus sp. strain DC2) and a natural bacterial assemblage. Based on the increase in cyanobacteria, 74 % (26.5 µmol L-1 N) of the DON in the lysate was remineralised and taken up. Lysate from Vibrio sp. strain PWH3a labeled with 15NH4+ was also added to seawater containing natural microbial communities, and in four field experiments, stable isotope analysis indicated that the uptake of 15N was 0.09 to 0.70 µmol N µg-1 of chlorophyll a. The results from these experiments demonstrate that DON from lysate can be efficiently remineralised and transferred to phytoplankton, and they provide further evidence that the viral shunt is an important link in nitrogen recycling in aquatic systems.

Isolation and characterization of a radiation resistant thermophilic bacterium from radon hot spring

International Nuclear Information System (INIS)

Liang Xinle; Yang Long; Zhang Hong; Zhang Lei

2011-01-01

A radiation resistant and thermophilic bacterium strain R4-33 was isolated from radon hot spring water samples, pretreated with 60 Co γ-rays and UV irradiation. Tests on morphological, physiological and biochemical characters, fatty acid compositions, (G + C) mol% contents, and 16S rDNA sequencing were conducted. The results showed that strain R4-33 was of rod-shape, Gram-negative, atrichous, and endospore-forming. The optimum growth temperature and pH were 60 ℃ and 7.5, respectively. The strain utilized glucose, maltose and trehalose as carbon sources, and hydrolyzed casein and starch. Its catalase positive. The strain was sensitive to penicillin, neomycin, erythromycin, vancomycin, streptomycin, gentamycin, amikacin and ampicillin. The major cellular fatty acids were C 14:1 (48.8%) and C 15:1 (15.2%). The (G + C) mol% content of DNA was 58.2%. Phylogenetic tree based on 16S rDNA sequence showed R4-33 shared highly similarity to those of species in genus Anoxybacillus, especially to that of Anoxybacillus gonensis (99.5%). Based on the above, the strain R4-33 was proposed to the evolution branch of Anoxybacillus and designated as Anoxybacillu sp. R4-33. The UV and γ-radiation tests showed that the strain R4-33 had an ability of resistance to UV of 396 J/m 2 and 60 Co γ-rays irradiation of 14.0 kGy, indicating that the strain was a radiation resistant and thermophilic bacterium. (authors)

Whole-Genome Sequence of the Purple Photosynthetic Bacterium Rhodovulum sulfidophilum Strain W4

OpenAIRE

Masuda, Shinji; Hori, Koichi; Maruyama, Fumito; Ren, Shukun; Sugimoto, Saori; Yamamoto, Nozomi; Mori, Hiroshi; Yamada, Takuji; Sato, Shusei; Tabata, Satoshi; Ohta, Hiroyuki; Kurokawa, Ken

2013-01-01

We report the draft genome sequence of the purple photosynthetic bacterium Rhodovulum sulfidophilum. The photosynthesis gene cluster comprises two segments?a unique feature among photosynthesis gene clusters of purple bacteria. The genome information will be useful for further analysis of bacterial photosynthesis.

Optimization of liquid media and biosafety assessment for algae-lysing bacterium NP23.

Science.gov (United States)

Liao, Chunli; Liu, Xiaobo; Shan, Linna

2014-09-01

To control algal bloom caused by nutrient pollution, a wild-type algae-lysing bacterium was isolated from the Baiguishan reservoir in Henan province of China and identified as Enterobacter sp. strain NP23. Algal culture medium was optimized by applying a Placket-Burman design to obtain a high cell concentration of NP23. Three minerals (i.e., 0.6% KNO3, 0.001% MnSO4·H2O, and 0.3% K2HPO4) were found to be independent factors critical for obtaining the highest cell concentration of 10(13) CFU/mL, which was 10(4) times that of the control. In the algae-lysing experiment, the strain exhibited a high lysis rate for the 4 algae test species, namely, Chlorella vulgari, Scenedesmus, Microcystis wesenbergii, and Chlorella pyrenoidosa. Acute toxicity and mutagenicity tests showed that the bacterium NP23 had no toxic and mutagenic effects on fish, even in large doses such as 10(7) or 10(9) CFU/mL. Thus, Enterobacter sp. strain NP23 has strong potential application in the microbial algae-lysing project.

BACTERIOLOGICAL PROPERTIES OF MARINE WATER IN ADRIATIC FISH FARMS: ENUMERATION OF HETEROTROPHIC BACTERIA

Directory of Open Access Journals (Sweden)

Emin Teskeredžić

2012-12-01

Full Text Available Aquaculture is currently one of the fastest growing food production sectors in the world. Increase in nutrients and organic wastes lead to general deterioration of water quality. The problem of water quality is associated with both physical and chemical factors, as well as microbiological water quality. Heterotrophic bacteria play an important role in the process of decomposition of organic matter in water environment and indicate eutrophication process. Here we present our experience and knowledge on bacterial properties of marine water in the Adriatic fish farms with European sea bass (Dicentrarchus labrax L., 1758, with an emphasis on enumeration of heterotrophic bacteria in marine water. We applied two temperatures of incubation, as well as two methods for enumeration of heterotrophic bacteria: substrate SimPlate® test and spread plate method on conventional artificial media (Marine agar and Tryptic Soy agar with added NaCl. The results of analysis of bacteriological properties of marine water in the Adriatic fish farms showed that enumeration of heterotrophic bacteria in marine water depends on the applied incubation temperature and media for enumeration. At the same time, the incubation temperature of 22C favours more intense growth of marine heterotrophic bacteria, whereas a SimPlate test gives higher values of heterotrophic bacteria. Volatile values of heterotrophic bacteria during this research indicate a possible deterioration of microbiological water quality in the Adriatic fish farms and a need for regular monitoring of marine water quality.

Thermotoga lettingae sp. nov. : a novel thermophilic, methanol-degrading bacterium isolated from a thermophilic anaerobic reactor

NARCIS (Netherlands)

Balk, M.; Weijma, J.; Stams, A.J.M.

2002-01-01

A novel, anaerobic, non-spore-forming, mobile, Gram-negative, thermophilic bacterium, strain TMO(T), was isolated from a thermophilic sulfate-reducing bioreactor operated at 65 degrees C with methanol as the sole substrate. The G C content of the DNA of strain TMO(T) was 39.2 molÐThe optimum pH,

(Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage.

KAUST Repository

Balk, Melike

2010-08-03

A mesophilic bacterium, strain An4, was isolated from an underground gas storage reservoir with methanol as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5-0.8 microm in diameter, and 2-8 microm in length, growing as single cells or in pairs. The cells grew optimally at 37 degrees C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H(2)/CO(2) to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO(2). The G+C content of the DNA was 42.6 mol%. Based on the 16S rRNA gene sequence analysis, strain An4 was most closely related to Sporomusa ovata (98% similarity). The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell-free extracts.

(Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage.

KAUST Repository

Balk, Melike; Mehboob, Farrakh; van Gelder, Antonie H; Rijpstra, W Irene C; Damsté , Jaap S Sinninghe; Stams, Alfons J M

2010-01-01

A mesophilic bacterium, strain An4, was isolated from an underground gas storage reservoir with methanol as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5-0.8 microm in diameter, and 2-8 microm in length, growing as single cells or in pairs. The cells grew optimally at 37 degrees C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H(2)/CO(2) to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO(2). The G+C content of the DNA was 42.6 mol%. Based on the 16S rRNA gene sequence analysis, strain An4 was most closely related to Sporomusa ovata (98% similarity). The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell-free extracts.

The Effectiveness of Heterotrophic Bacteria Isolated from Dumai Marine Waters of Riau, Used as Antibacterial against Pathogens in Fish Culture

Science.gov (United States)

Feliatra, F.; Nursyirwani; Tanjung, A.; Adithiya, DS; Susanna, M.; Lukystyowati, I.

2018-02-01

Heterotrophic bacteria have an important role as decomposer of organic compounds (mineralization) derived from industrial waste, decomposition of unconsumed feed, faecal, excretion of fish, and have the ability to inhibit the growth of pathogenic bacteria. We investigated the role of heterotrophic bacteria used as antibacterial against pathogens in fish culture.This research was conducted from January until March 2017. The phylogenitic of the isolated bacterial was determined by 16S rDNA sequences analysis. Antagonism test showed that the bacteria had the ability to inhibit the growth of pathogenic bacteria (Vibrio alginolyticus, Aeromonas hydrophila and Pseudomonas sp.) Three isolates (Dm5, Dm6 and Dm4) indicated high inhibition zones which were classified into strong category with the average from 10.5 to 11.8 mm toward V. alginolitycus. Other isolates were classified into medium and weak category. Based on DNA analysis of heterotrophic bacteria isolated from marine waters of industrial area and low salinity of estuarine waters twelve strains of bacteria were identified, and all had highest level of homology to Bacillus sp.,one isolates has similarity to Enterobacter cloacae, other isolates to Clostridium cetobutylicum. Most of isolated bacteria obtained from the waters of industrial area due to it received much of nutrients that very influenced the growth of bacteria.

Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog.

Science.gov (United States)

Dedysh, Svetlana N; Khmelenina, Valentina N; Suzina, Natalia E; Trotsenko, Yuri A; Semrau, Jeremy D; Liesack, Werner; Tiedje, James M

2002-01-01

A novel genus and species, Methylocapsa acidiphila gen. nov., sp. nov., are proposed for a methane-oxidizing bacterium isolated from an acidic Sphagnum peat bog. This bacterium, designated strain B2T, represents aerobic, gram-negative, colourless, non-motile, curved coccoids that form conglomerates covered by an extracellular polysaccharide matrix. The cells use methane and methanol as sole sources of carbon and energy and utilize the serine pathway for carbon assimilation. Strain B2T is a moderately acidophilic organism with growth between pH 4.2 and 7.2 and at temperatures from 10 to 30 degrees C. The cells possess a well-developed system of intracytoplasmic membranes (ICM) packed in parallel on only one side of the cell membrane. This type of ICM structure represents a novel arrangement, which was termed type III. The resting cells are Azotobacter-type cysts. Strain B2T is capable of atmospheric nitrogen fixation; it possesses particulate methane monooxygenase and does not express soluble methane monooxygenase. The major phospholipid fatty acid is 18:1omega7c and the major phospholipids are phosphatidylglycerols. The G+C content of the DNA is 63.1 mol%. This bacterium belongs to the alpha-subclass of the Proteobacteria and is most closely related to the acidophilic methanotroph Methylocella palustris KT (97.3% 16S rDNA sequence similarity). However, the DNA-DNA hybridization value between strain B2T and Methylocella palustris K(T) is only 7%. Thus, strain B2T is proposed to comprise a novel genus and species, Methylocapsa acidiphila gen. nov., sp. nov. Strain B2T (= DSM 13967T = NCIMB 13765T) is the type strain.

Clostridium geopurificans strain MJ1 sp. nov., a strictly anaerobic bacterium that grows via fermentation and reduces the cyclic nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX).

Science.gov (United States)

Kwon, Man Jae; Wei, Na; Millerick, Kayleigh; Popovic, Jovan; Finneran, Kevin

2014-06-01

A fermentative, non-spore forming, motile, rod-shaped bacterium, designated strain MJ1(T), was isolated from an RDX contaminated aquifer at a live-fire training site in Northwest NJ, United States. On the basis of 16S rRNA gene sequencing and DNA base composition, strain MJ1(T) was assigned to the Firmicutes. The DNA G+C content was 42.8 mol%. Fermentative growth was supported by glucose and citrate in a defined basal medium. The bacterium is a strict anaerobe that grows between at pH 6.0 and pH 8.0 and 18 and 37 °C. The culture did not grow with hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) as the electron acceptor or mineralize RDX under these conditions. However, MJ1(T) transformed RDX into MNX, methylenedinitramine, formaldehyde, formate, ammonium, nitrous oxide, and nitrate. The nearest phylogenetic relative with a validly published name was Desulfotomaculum guttoideum (95 % similarity). However, MJ1(T) was also related to Clostridium celerecrescens DSM 5628 (95 %), Clostridium indolis DSM 755 (94 %), and Clostridium sphenoides DSM 632 (94 %). DNA:DNA hybridization with these strains was between 6.7 and 58.7 percent. The dominant cellular fatty acids (greater than 5 % of the total, which was 99.0 % recovery) were 16:0 fatty acid methyl ester (FAME) (32.12 %), 18:1cis 11 dimethyl acetal (DMA) (16.47 %), 16:1cis 9 DMA (10.28 %), 16:1cis 9 FAME (8.10 %), and 18:1cis 9 DMA (5.36 %). On the basis of morphological, physiological, and phylogenetic data, Clostridium geopurificans is proposed as a new species in genus Clostridium, with strain MJ1(T) as the type strain.

Studies on the pathogenic bacterium of ulcer disease in Epinephelus awoara

Institute of Scientific and Technical Information of China (English)

无

2006-01-01

Studies were conducted to determine the cause of the acute mortality of cage-cultured Epinephelus awoara in the Tong'an Bay of Xiamen, China during the summer of 2002. Predominant bacteria strain TS-628 was isolated from the diseased grouper. The virulence test confirmed that TS-628 was the pathogenic bacterium. Biochemical characteristics of the isolates were determined using the automatic bacterial identification system and standard tube tests. To further confirm the identification, a 1 121 bp 16S rRNA gene sequence of the isolate was amplified by PCR, which had been deposited into Genbank (accession number: AY747308). According to the biochemical characteristics and by comparing the 16S rRNA gene homology of the isolate, the pathogenic bacterium was identified as Vibrio harveyi. Drug sensitivity tests showed that this pathogenic bacterium was sensitive to 16 antibacterials, especially to chloramphenicol and actinospectacin, but completely resistant to antibacterials likes vancomycin, penicillin, lincomycin, and so on.

Organic metabolites produced by Vibrio parahaemolyticus strain ...

African Journals Online (AJOL)

Identification and action of several antibacterial metabolites produced by a fish pathogen Vibrio parahaemolyticus strain An3 from marine ecosystem of Goa has been demonstrated. Antibacterial activity of the crude cell extract of the test bacterium has been evaluated against indicator pathogenic bacterial strains such as ...

Colwellia agarivorans sp. nov., an agar-digesting marine bacterium isolated from coastal seawater

Science.gov (United States)

A novel Gram-stain-negative, facultatively anaerobic, yellowish and agar-digesting marine bacterium, designated strain QM50**T, was isolated from coastal seawater in an aquaculture site near Qingdao, China. Phylogenetic analysis based on 16S rDNA sequences revealed that the novel isolate represented...

Photoproduction of hydrogen by a non-sulphur bacterium isolated from root zones of water fern Azolla pinnata

Energy Technology Data Exchange (ETDEWEB)

Singh, S.P.; Srivastava, S.C.; Pandey, K.D. (Banaras Hindu Univ., Varanasi (IN). Centre of Advanced Study in Botany)

1990-01-01

A photosynthetic bacterium Rhodopseudomonas sp. BHU strain 1 was isolated from the root zone of water fern Azolla pinnata. The bacterium was found to produce hydrogen with potato starch under phototrophic conditions. The immobilized bacterial cells showed sustained hydrogen production with a more than 4-fold difference over free cell suspensions. The data have been discussed in the light of possible utilization of relatively cheaper raw materials by non-sulphur bacteria to evolve hydrogen. (author).

Antifouling Activity towards Mussel by Small-Molecule Compounds from a Strain of Vibrio alginolyticus Bacterium Associated with Sea Anemone Haliplanella sp.

Science.gov (United States)

Wang, Xiang; Huang, Yanqiu; Sheng, Yanqing; Su, Pei; Qiu, Yan; Ke, Caihuan; Feng, Danqing

2017-03-28

Mussels are major fouling organisms causing serious technical and economic problems. In this study, antifouling activity towards mussel was found in three compounds isolated from a marine bacterium associated with the sea anemone Haliplanella sp. This bacterial strain, called PE2, was identified as Vibrio alginolyticus using morphology, biochemical tests, and phylogenetic analysis based on sequences of 16S rRNA and four housekeeping genes ( rpoD, gyrB, rctB, and toxR ). Three small-molecule compounds (indole, 3-formylindole, and cyclo (Pro-Leu)) were purified from the ethyl acetate extract of V. alginolyticus PE2 using column chromatography techniques. They all significantly inhibited byssal thread production of the green mussel Perna viridis , with EC 50 values of 24.45 μg/ml for indole, 50.07 μg/ml for 3-formylindole, and 49.24 μg/ml for cyclo (Pro-Leu). Previous research on the antifouling activity of metabolites from marine bacteria towards mussels is scarce. Indole, 3-formylindole and cyclo (Pro-Leu) also exhibited antifouling activity against settlement of the barnacle Balanus albicostatus (EC 50 values of 8.84, 0.43, and 11.35 μg/ml, respectively) and the marine bacterium Pseudomonas sp. (EC 50 values of 42.68, 69.68, and 39.05 μg/ml, respectively). These results suggested that the three compounds are potentially useful for environmentally friendly mussel control and/or the development of new antifouling additives that are effective against several biofoulers.

Development of a novel artificial medium based on utilization of algal photosynthetic metabolites by symbiotic heterotrophs.

Science.gov (United States)

Watanabe, K; Imase, M; Aoyagi, H; Ohmura, N; Saiki, H; Tanaka, H

2008-09-01

(i) Quantitative and qualitative analyses of photosynthetic metabolites of Chlorella sorokiniana and elucidation of the mechanism of their utilization by algal symbionts. (ii) Development of artificial medium that imitates photoautotroph-heterotroph interaction and investigation of its suitability for isolation of novel microbes from the environment. Various components, including free dissolved carbohydrates, nitrogenous compounds and vitamin, were detected and together contributed 11.1% (as carbon content) of the total photosynthetic metabolites in the medium. Utilization of these photosynthetic metabolites in algal culture broth by algal symbionts was studied. Many symbionts showed specific utilization patterns. A novel artificial extracellular released organic carbon medium, which imitated the nutritional conditions surrounding algae, was developed based on the pattern of utilization of the algal metabolites by the symbiotic heterotrophs. About 42.9% of the isolates were closely related to photoautotrophic-dependent and oligotrophic bacteria. With the novel artificial medium, it was possible to selectively isolate some bacterial strains. Synthetic bacterial growth medium is an important and basic tool for bacterial isolation from environmental samples. The current study shows that preferential separation of typical bacterial subset can be achieved by using artificial medium that mimics photosynthetic metabolites.

Heterotrophic bacterial populations in tropical sandy beaches

Digital Repository Service at National Institute of Oceanography (India)

Nair, S.; LokaBharathi, P.A.

Distribution pattern of heterotrophic bacterial flora of three sandy beaches of the west coast of India was studied. The population in these beaches was microbiologically different. Population peaks of halotolerant and limnotolerant forms were...

High genetic diversity among strains of the unindustrialized lactic acid bacterium Carnobacterium maltaromaticum in dairy products as revealed by multilocus sequence typing.

Science.gov (United States)

Rahman, Abdur; Cailliez-Grimal, Catherine; Bontemps, Cyril; Payot, Sophie; Chaillou, Stéphane; Revol-Junelles, Anne-Marie; Borges, Frédéric

2014-07-01

Dairy products are colonized with three main classes of lactic acid bacteria (LAB): opportunistic bacteria, traditional starters, and industrial starters. Most of the population structure studies were previously performed with LAB species belonging to these three classes and give interesting knowledge about the population structure of LAB at the stage where they are already industrialized. However, these studies give little information about the population structure of LAB prior their use as an industrial starter. Carnobacterium maltaromaticum is a LAB colonizing diverse environments, including dairy products. Since this bacterium was discovered relatively recently, it is not yet commercialized as an industrial starter, which makes C. maltaromaticum an interesting model for the study of unindustrialized LAB population structure in dairy products. A multilocus sequence typing scheme based on an analysis of fragments of the genes dapE, ddlA, glpQ, ilvE, pyc, pyrE, and leuS was applied to a collection of 47 strains, including 28 strains isolated from dairy products. The scheme allowed detecting 36 sequence types with a discriminatory index of 0.98. The whole population was clustered in four deeply branched lineages, in which the dairy strains were spread. Moreover, the dairy strains could exhibit a high diversity within these lineages, leading to an overall dairy population with a diversity level as high as that of the nondairy population. These results are in agreement with the hypothesis according to which the industrialization of LAB leads to a diversity reduction in dairy products. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Cellulosic ethanol production via consolidated bioprocessing by a novel thermophilic anaerobic bacterium isolated from a Himalayan hot spring.

Science.gov (United States)

Singh, Nisha; Mathur, Anshu S; Tuli, Deepak K; Gupta, Ravi P; Barrow, Colin J; Puri, Munish

2017-01-01

Cellulose-degrading thermophilic anaerobic bacterium as a suitable host for consolidated bioprocessing (CBP) has been proposed as an economically suited platform for the production of second-generation biofuels. To recognize the overall objective of CBP, fermentation using co-culture of different cellulolytic and sugar-fermenting thermophilic anaerobic bacteria has been widely studied as an approach to achieving improved ethanol production. We assessed monoculture and co-culture fermentation of novel thermophilic anaerobic bacterium for ethanol production from real substrates under controlled conditions. In this study, Clostridium sp. DBT-IOC-C19, a cellulose-degrading thermophilic anaerobic bacterium, was isolated from the cellulolytic enrichment cultures obtained from a Himalayan hot spring. Strain DBT-IOC-C19 exhibited a broad substrate spectrum and presented single-step conversion of various cellulosic and hemicellulosic substrates to ethanol, acetate, and lactate with ethanol being the major fermentation product. Additionally, the effect of varying cellulose concentrations on the fermentation performance of the strain was studied, indicating a maximum cellulose utilization ability of 10 g L -1 cellulose. Avicel degradation kinetics of the strain DBT-IOC-C19 displayed 94.6% degradation at 5 g L -1 and 82.74% degradation at 10 g L -1 avicel concentration within 96 h of fermentation. In a comparative study with Clostridium thermocellum DSM 1313, the ethanol and total product concentrations were higher by the newly isolated strain on pretreated rice straw at an equivalent substrate loading. Three different co-culture combinations were used on various substrates that presented two-fold yield improvement than the monoculture during batch fermentation. This study demonstrated the direct fermentation ability of the novel thermophilic anaerobic bacteria on various cellulosic and hemicellulosic substrates into ethanol without the aid of any exogenous enzymes

Investigation of mixotrophic, heterotrophic, and autotrophic growth of Chlorella vulgaris under agricultural waste medium.

Science.gov (United States)

Mohammad Mirzaie, M A; Kalbasi, M; Mousavi, S M; Ghobadian, B

2016-01-01

Growth of Chlorella vulgaris and its lipid production were investigated under autotrophic, heterotrophic, and mixotrophic conditions. Cheap agricultural waste molasses and corn steep liquor from industries were used as carbon and nitrogen sources, respectively. Chlorella vulgaris grew remarkably under this agricultural waste medium, which resulted in a reduction in the final cost of the biodiesel production. Maximum dry weight of 2.62 g L(-1) was obtained in mixotrophic growth with the highest lipid concentration of 0.86 g L(-1). These biomass and lipid concentrations were, respectively, 140% and 170% higher than autotrophic growth and 300% and 1200% higher than heterotrophic growth. In mixotrophic growth, independent or simultaneous occurrence of autotrophic and heterotrophic metabolisms was investigated. The growth of the microalgae was observed to take place first heterotrophically to a minimum substrate concentration with a little fraction in growth under autotrophic metabolism, and then the cells grew more autotrophically. It was found that mixotrophic growth was not a simple combination of heterotrophic and autotrophic growth.

Phosphate enhances levan production in the endophytic bacterium Gluconacetobacter diazotrophicus Pal5

Science.gov (United States)

Idogawa, Nao; Amamoto, Ryuta; Murata, Kousaku; Kawai, Shigeyuki

2014-01-01

Gluconacetobacter diazotrophicus is a gram-negative and endophytic nitrogen-fixing bacterium that has several beneficial effects in host plants; thus, utilization of this bacterium as a biofertilizer in agriculture may be possible. G. diazotrophicus synthesizes levan, a D-fructofuranosyl polymer with β-(2→6) linkages, as an exopolysaccharide and the synthesized levan improves the stress tolerance of the bacterium. In this study, we found that phosphate enhances levan production by G. diazotrophicus Pal5, a wild type strain that showed a stronger mucous phenotype on solid medium containing 28 mM phosphate than on solid medium containing 7 mM phosphate. A G. diazotrophicus Pal5 levansucrase disruptant showed only a weak mucous phenotype regardless of the phosphate concentration, indicating that the mucous phenotype observed on 28 mM phosphate medium was caused by levan. To our knowledge, this is the first report of the effect of a high concentration of phosphate on exopolysaccharide production. PMID:24717418

Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment

OpenAIRE

Pereira, Jamile Queiroz; Ambrosini, Adriana; Sant?Anna, Fernando Hayashi; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, F?bio Oliveira; Souza, Emanuel Maltempi; Brandelli, Adriano; Passaglia, Luciane M. P.

2015-01-01

Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin feathers collected in the Antarctic environment. This strain has the ability to degrade keratin at low temperatures. The A03 genome sequence provides the possibility of finding new genes with biotechnological potential to better understand its cold-adaptation mechanism and survival in cold environments.

Factors limiting heterotrophic bacterial production in the southern Pacific Ocean

Directory of Open Access Journals (Sweden)

F. Van Wambeke

2008-05-01

Full Text Available The role of potential factors limiting bacterial growth was investigated along vertical and longitudinal gradients across the South Eastern Pacific Gyre. The effects of glucose, nitrate, ammonium and phosphate additions on heterotrophic bacterial production (using leucine technique were studied in parallel in unfiltered seawater samples incubated under natural daily irradiance. The enrichments realized on the subsurface showed three types of responses. From 141° W (Marquesas plateau to approx 125° W, bacteria were not bottom-up controlled, as confirmed by the huge potential of growth in non-enriched seawater (median of enhancement factor×39 in 24 h. Within the Gyre (125° W–95° W, nitrogen alone stimulated leucine incorporation rates (median×4.2, but rapidly labile carbon (glucose became a second limiting factor (median×37 when the two elements were added. Finally from the border of the gyre to the Chilean upwelling (95° W–73° W, labile carbon was the only factor stimulating heterotrophic bacterial production. Interaction between phytoplankton and heterotrophic bacterial communities and the direct versus indirect effect of iron and macronutrients on bacterial production were also investigated in four selected sites: two sites on the vicinity of the Marquesas plateau, the centre of the gyre and the Eastern border of the gyre. Both phytoplankton and heterotrophic bacteria were limited by availability of nitrogen within the gyre, but not by iron. Iron limited phytoplankton at Marquesas plateau and at the eastern border of the gyre. However 48 h enrichment experiments were not sufficient to show any clear limitation of heterotrophic bacteria within Marquesas plateau and showed a limitation of these organisms by labile carbon in the eastern border of the Gyre.

Heterotrophic nitrification and aerobic denitrification bacterium ...

African Journals Online (AJOL)

Jane

2011-07-18

Jul 18, 2011 ... nutrient agar plates 3 times from the enrichment liquid medium. The isolates ..... growing in the logarithmic phase, the decomposition rate was higher than .... denitrification in bench-scale sequencing batch reactors. Water Res.

Enrichments of methanotrophic-heterotrophic cultures with high poly-β-hydroxybutyrate (PHB) accumulation capacities.

Science.gov (United States)

Zhang, Tingting; Wang, Xiaowei; Zhou, Jiti; Zhang, Yu

2018-03-01

Methanotrophic-heterotrophic communities were selectively enriched from sewage sludge to obtain a mixed culture with high levels of poly-β-hydroxybutyrate (PHB) accumulation capacity from methane. Methane was used as the carbon source, N 2 as sole nitrogen source, and oxygen and Cu content were varied. Copper proved essential for PHB synthesis. All cultures enriched with Cu could accumulate high content of PHB (43.2%-45.9%), while only small amounts of PHB were accumulated by cultures enriched without Cu (11.9%-17.5%). Batch assays revealed that communities grown with Cu and a higher O 2 content synthesized more PHB, which had a wider optimal CH 4 :O 2 range and produced a high PHB content (48.7%) even though in the presence of N 2 . In all methanotrophic-heterotrophic communities, both methanotrophic and heterotrophic populations showed the ability to accumulate PHB. Although methane was added as the sole carbon source, heterotrophs dominated with abundances between 77.2% and 85.6%. All methanotrophs detected belonged to type II genera, which formed stable communities with heterotrophs of different PHB production capacities. Copyright © 2017. Published by Elsevier B.V.

Modeling how soluble microbial products (SMP) support heterotrophic bacteria in autotroph-based biofilms

DEFF Research Database (Denmark)

Merkey, Brian; Rittmann, Bruce E.; Chopp, David L.

2009-01-01

. In this paper, we develop and use a mathematical model to describe a model biofilm system that includes autotrophic and heterotrophic bacteria and the key products produced by the bacteria. The model combines the methods of earlier multi-species models with a multi-component biofilm model in order to explore...... the interaction between species via exchange of soluble microbial products (SMP). We show that multiple parameter sets are able to describe the findings of experimental studies, and that heterotrophs growing on autotrophically produced SMP may pursue either r- or K-strategies to sustain themselves when SMP...... is their only substrate. We also show that heterotrophs can colonize some distance from the autotrophs and still be sustained by autotrophically produced SMP. This work defines the feasible range of parameters for utilization of SMP by heterotrophs and the nature of the interactions between autotrophs...

Genome Sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse

DEFF Research Database (Denmark)

Takamiya, Monica; Özen, Asli Ismihan; Rasmussen, Morten

2011-01-01

, catalase positive bacterium obtains energy from the metabolism of amino acids and Krebs cycle intermediates. Strain 327 was isolated from a turkey slaughter production line and is considered environmentally sensitive to food processing (cold, heat, drying) and storage conditions. The 327 whole genome...

Complete genome sequence of Klebsiella pneumoniae J1, a protein-based microbial flocculant-producing bacterium.

Science.gov (United States)

Pang, Changlong; Li, Ang; Cui, Di; Yang, Jixian; Ma, Fang; Guo, Haijuan

2016-02-20

Klebsiella pneumoniae J1 is a Gram-negative strain, which belongs to a protein-based microbial flocculant-producing bacterium. However, little genetic information is known about this species. Here we carried out a whole-genome sequence analysis of this strain and report the complete genome sequence of this organism and its genetic basis for carbohydrate metabolism, capsule biosynthesis and transport system. Copyright © 2016 Elsevier B.V. All rights reserved.

[Development of a liquid fermentation system and encystment for a nitrogen-fixing bacterium strain having biofertilizer potential].

Science.gov (United States)

Camelo-Rusinque, Mauricio; Moreno-Galván, Andrés; Romero-Perdomo, Felipe; Bonilla-Buitrago, Ruth

The indiscriminate use of chemical fertilizers has contributed to the deterioration of the biological, physical and chemical properties of the soil, resulting in the loss of its productive capacity. For this reason, the use of biofertilizers has emerged as a technological alternative. The objective of this research was to develop a suitable liquid fermentation system and encystment for the multiplication of Azotobacter chroococcum AC1 strain, a bacterium employed in a biofertilizer formulation produced at present by CARPOICA, Colombia. Sequential statistical designs were used to determine the conditions in the fermentation system. The interaction between agitation, aeration and pH was evaluated on the viable biomass (CFU/ml) of AC1. In addition, the encystment ability of the strain was evaluated using two encystment agents and the potential plant growth-promoting rhizobacteria (PGPR) activity was assessed by different techniques, such as nitrogen fixation by ARA, phosphate solubilization by the phospho-molybdenum-blue reaction and indolic compound production by colorimetric reaction using the Salkowski reagent. Results showed significant effects (p<0.05) on the viable biomass in the three conditions (pH, aeration and agitation) tested individually, in one dual interaction and one tripartite interaction, were demonstrated to have a positive effect on the response variable aeration and agitation. The addition of the two encystment agents evaluated, AE01 and AE02, demonstrated the ability of AC1 to form cysts under stress conditions. Likewise, fermentation and encystment conditions did not affect the biological activities tested. Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

Keep your Sox on: Community genomics-directed isolation and microscopic characterization of the dominant subsurface sulfur-oxidizing bacterium in a sediment aquifer

Science.gov (United States)

Mullin, S. W.; Wrighton, K. C.; Luef, B.; Wilkins, M. J.; Handley, K. M.; Williams, K. H.; Banfield, J. F.

2012-12-01

Community genomics and proteomics (proteogenomics) can be used to predict the metabolic potential of complex microbial communities and provide insight into microbial activity and nutrient cycling in situ. Inferences regarding the physiology of specific organisms then can guide isolation efforts, which, if successful, can yield strains that can be metabolically and structurally characterized to further test metagenomic predictions. Here we used proteogenomic data from an acetate-stimulated, sulfidic sediment column deployed in a groundwater well in Rifle, CO to direct laboratory amendment experiments to isolate a bacterial strain potentially involved in sulfur oxidation for physiological and microscopic characterization (Handley et al, submitted 2012). Field strains of Sulfurovum (genome r9c2) were predicted to be capable of CO2 fixation via the reverse TCA cycle and sulfur oxidation (Sox and SQR) coupled to either nitrate reduction (Nap, Nir, Nos) in anaerobic environments or oxygen reduction in microaerobic (cbb3 and bd oxidases) environments; however, key genes for sulfur oxidation (soxXAB) were not identified. Sulfidic groundwater and sediment from the Rifle site were used to inoculate cultures that contained various sulfur species, with and without nitrate and oxygen. We isolated a bacterium, Sulfurovum sp. OBA, whose 16S rRNA gene shares 99.8 % identity to the gene of the dominant genomically characterized strain (genome r9c2) in the Rifle sediment column. The 16S rRNA gene of the isolate most closely matches (95 % sequence identity) the gene of Sulfurovum sp. NBC37-1, a genome-sequenced deep-sea sulfur oxidizer. Strain OBA grew via polysulfide, colloidal sulfur, and tetrathionate oxidation coupled to nitrate reduction under autotrophic and mixotrophic conditions. Strain OBA also grew heterotrophically, oxidizing glucose, fructose, mannose, and maltose with nitrate as an electron acceptor. Over the range of oxygen concentrations tested, strain OBA was not

Dynamics of pollution-indicator and heterotrophic bacteria in sewage treatment lagoons.

OpenAIRE

Legendre, P; Baleux, B; Troussellier, M

1984-01-01

The spatio-temporal dynamics of pollution-indicator bacteria and aerobic heterotrophic bacteria were studied in the sewage treatment lagoons of an urban wastewater center after 26 months of biweekly sampling at eight stations in these lagoons. Robust statistical methods of time-series analysis were used to study successional steps (through chronological clustering) and rhythmic behavior through time (through contingency periodogram). The aerobic heterotrophic bacterial community showed two ty...

Isolation and Characterization of a Human Intestinal Bacterium Eggerthella sp. AUH-JLD49s for the Conversion of (-)-3'-Desmethylarctigenin.

Science.gov (United States)

Wang, Ye; Yu, Fei; Liu, Ming-Yue; Zhao, Yi-Kai; Wang, Dong-Ming; Hao, Qing-Hong; Wang, Xiu-Ling

2017-05-24

Arctiin is the most abundant bioactive compound contained in the Arctium lappa plant. In our previous study, we isolated one single bacterium capable of bioconverting arctigenin, an aglycone of arctiin, to 3'-desmethylarctigenin (3'-DMAG) solely. However, to date, a specific bacterium capable of producing other arctiin metabolites has not been reported. In this study, we isolated one single bacterium, which we named Eggerthella sp. AUH-JLD49s, capable of bioconverting 3'-DMAG under anaerobic conditions. The metabolite of 3'-DMAG by strain AUH-JLD49s was identified as 3'-desmethyl-4'-dehydroxyarctigenin (DMDH-AG) based on electrospray ionization mass spectrometry (ESI-MS) and 1 H and 13 C nuclear magnetic resonance spectroscopy. The bioconversion kinetics and bioconversion capacity of strain AUH-JLD49s were investigated. In addition, the metabolite DMDH-AG showed an inhibitory effect on cell growth of human colon cancer cell line HCT116 and human breast cancer cell line MDA-MB-231.

Evaluation on the microbial interactions of anaerobic ammonium oxidizers and heterotrophs in Anammox biofilm

DEFF Research Database (Denmark)

Ni, Bing-Jie; Ruscalleda, Mael; Smets, Barth F.

2012-01-01

and the affecting factors were evaluated with both experimental and modeling approaches. Fluorescent in situ hybridization (FISH) analysis illustrated that Anammox bacteria and heterotrophs accounted for 77% and 23% of the total bacteria, respectively, even without addition of an external carbon source....... Experimental results showed the heterotrophs could grow both on SMP and decay released substrate from the metabolism of the Anammox bacteria. However, heterotrophic growth in Anammox biofilm (23%) was significantly lower than that of nitrifying biofilm (30–50%). The model predictions matched well...... with the experimental observations of the bacterial distribution, as well as the nitrogenous transformations in batch and continuous experiments. The modeling results showed that low nitrogen surface loading resulted in a lower availability of SMP leading to low heterotrophic growth in Anammox biofilm, but high...

Alteration of the Canine Small-Intestinal Lactic Acid Bacterium Microbiota by Feeding of Potential Probiotics

OpenAIRE

Manninen, Titta J. K.; Rinkinen, Minna L.; Beasley, Shea S.; Saris, Per E. J.

2006-01-01

Five potentially probiotic canine fecal lactic acid bacterium (LAB) strains, Lactobacillus fermentum LAB8, Lactobacillus salivarius LAB9, Weissella confusa LAB10, Lactobacillus rhamnosus LAB11, and Lactobacillus mucosae LAB12, were fed to five permanently fistulated beagles for 7 days. The survival of the strains and their potential effects on the indigenous intestinal LAB microbiota were monitored for 17 days. Denaturing gradient gel electrophoresis (DGGE) demonstrated that the five fed LAB ...

Heterotrophic bacteria associated with the green alga

NARCIS (Netherlands)

Ismail, A.; Ktari, L.; Ahmed, M.; Bolhuis, H.; Bouhaouala-Zahar, B.; Stal, L.J.; Boudabbous, A.; El Bour, M.

2018-01-01

Heterotrophic bacteria associated with the green alga Ulva rigida, collected from the coast of Tunisia, were isolated andsubsequently identified by their 16S rRNA gene sequences and by phylogenetic analysis. The 71 isolates belong to four phyla:Proteobacteria (Alpha-and Gamma- subclasses),

Co-metabolism of DDT by the newly isolated bacterium, Pseudoxanthomonas sp. wax

Directory of Open Access Journals (Sweden)

Guangli Wang

2010-06-01

Full Text Available Microbial degradation of 1,1,1-trichloro-2,2-bis(p-chlorophenylethane (DDT is the most promising way to clean up DDT residues found in the environment. In this paper, a bacterium designated as wax, which was capable of co-metabolizing DDT with other carbon sources, was isolated from a long-term DDT-contaminated soil sample by an enrichment culture technique. The new isolate was identified as a member of the Pseudoxanthomonas sp., based on its morphological, physiological and biochemical properties, as well as by 16S rRNA gene analysis. In the presence of 100 mg l-1 glucose, the wax strain could degrade over 95% of the total DDT, at a concentration of 20 mg l-1, in 72 hours, and could degrade over 60% of the total DDT, at a concentration of 100 mg l-1, in 144 hours. The wax strain had the highest degradation efficiency among all of the documented DDT-degrading bacteria. The wax strain could efficiently degrade DDT at temperatures ranging from 20 to 37ºC, and with initial pH values ranging from 7 to 9. The bacterium could also simultaneously co-metabolize 1,1-dichloro-2,2-bis(p-chlorophenylethane (DDD, 2,2-bis(p-chlorophenyl-1,1-dichlorethylene (DDE, and other organochlorine compounds. The wax strain could also completely remove 20 mg kg-1 of DDT from both sterile and non-sterile soils in 20 days. This study demonstrates the significant potential use of Pseudoxanthomonas sp. wax for the bioremediation of DDT in the environment.

Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment.

Science.gov (United States)

Pereira, Jamile Queiroz; Ambrosini, Adriana; Sant'Anna, Fernando Hayashi; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, Fábio Oliveira; Souza, Emanuel Maltempi; Brandelli, Adriano; Passaglia, Luciane M P

2015-04-02

Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin feathers collected in the Antarctic environment. This strain has the ability to degrade keratin at low temperatures. The A03 genome sequence provides the possibility of finding new genes with biotechnological potential to better understand its cold-adaptation mechanism and survival in cold environments. Copyright © 2015 Pereira et al.

[Isolation and identification of a lactate-utilizing, butyrate-producing bacterium and its primary metabolic characteristics].

Science.gov (United States)

Liu, Wei; Zhu, Wei-yun; Yao, Wen; Mao, Sheng-yong

2007-06-01

The distal mammalian gut harbors prodigiously abundant microbes, which provide unique metabolic traits to host. A lactate-utilizing, butyrate-producing bacterium, strain LB01, was isolated from adult swine feces by utilizing modified Hungate technique with rumen liquid-independent YCFA medium supplemented with lactate as the single carbon source. It was an obligate anaerobic, Gram positive bacterium, and could utilize glucose, fructose, maltose and lactate with a large amount of gas products. 16S rRNA sequence analysis revealed that it had the high similarity with members of the genus Megasphaera. The metabolic characteristics of strain LB01 was investigated by using in vitro fermentation system. Lactate at the concentration of 65 mmol/L in YCFA medium was rapidly consumed within 9 hours and was mainly converted to propionate and butyrate after 24h. As the level of acetate declined, the concentration of butyrate rose only in the presence of glucose, suggesting that butyrate could possibly be synthesized by the acetyl CoA: butyryl CoA transferase. When co-cultured with lactic acid bacteria strain K9, strain LB01 evidently reduced the concentration of lactate produced by strain K9 and decelerated the rapid pH drop, finally producing 12.11 mmol/L butyrate and 4.06 mmol/L propionate. The metabolic characteristics that strain LB01 efficiently converts toxic lactate and excessive acetate to butyrate can prevent lactate and acetate accumulation in the large intestine and maintain the slightly acidic environment of the large intestine, consequently revealing that stain LB01 could act as a potential probiotics.

Draft Genome Sequence of Lactobacillus paracasei DmW181, a Bacterium Isolated from Wild Drosophila

OpenAIRE

Hammer, Austin J.; Walters, Amber; Carroll, Courtney; Newell, Peter D.; Chaston, John M.

2017-01-01

ABSTRACT The draft genome sequence of Lactobacillus paracasei DmW181, an anaerobic bacterium isolate from wild Drosophila flies, is reported here. Strain DmW181 possesses genes for sialic acid and mannose metabolism. The assembled genome is 3,201,429?bp, with 3,454 predicted genes.

Survey on Heterotrophic Bacterial Contamination in Bottled Mineral Water by Culture Method

Directory of Open Access Journals (Sweden)

Essmaeel Ghorbanalinezhad

2014-12-01

Full Text Available Background and Aim: This project focuses on the level of heterotrophic baceria in bottled mineral water which could be a health concern for the elderly, infants, pregnant women and immuno-compromised patients. Materials and Methods: Different brands of bottled water samples were selected randomly and evaluated for their bacteriological quality, using different specific culture media and biochemical tests. Water samples were analyzed within 24 hours of their purchase/collection. Samples were filtered with 0.45 micron and filters were plated in different media. Then media were incubated at 37˚C for 24-48 hours. Results: Morphological study and biochemical tests revealed a number of bacteria in different   brands of  bottled water. Heterotrophic bacteria(Gram positive cocci, Spore forming gram positive bacilli, non spore forming gram positive bacilli, gram negative bacilli, and gram negative coccobacilli; Pseudomonas and Stenotrophomonas counted in 70% of bottled water samples. There were no cases of fecal contamination or the presence of E.coli. Conclusions: Bottled water is not sterile and contains trace amounts of bacteria naturally present or introduced during processing. Testing drinking water for all possible pathogens is complex, time-consuming, and expensive. If only total coliform bacteria are detected in drinking water, the source is probably environmental. Since the significance of non-pathogenic heterotrophic bacteria in relation to health and diseases is not understood, there is an urgent need to establish a maximum limit for the heterotrophic count in the bottled mineral water. Growth conditions play a critical role in the recovery of heterotrophic bacteria in bottled drinking water.

Bacteria that degrade hazardous waste: The isolation of trichloroethylene-degrading methanotrophic bacteria and development of monoclonal antibodies specific to them

International Nuclear Information System (INIS)

Little, C.D.

1988-01-01

Trichloroethylene (TCE), a suspected carcinogen, is one of the most frequently reported groundwater contaminants at hazardous waste sites in the US. An aerobic, methane-oxidizing bacterium was isolated that degrades TCE in pure culture at concentrations commonly observed in contaminated groundwater. Strain 46-1, a Type I methanotrophic bacterium, degraded TCE when growing on methane or methanol, producing CO 2 and water-soluble products. Gas chromatography and 14 C radiotracer techniques were used to determine the rate, methane dependence, and mechanism of TCE biodegradation. TCE biodegradation by strain 46-1 appears to be a co-metabolic process that occurs when the organism is actively metabolizing a suitable growth substrate such as methane or methanol. Five mouse monoclonal antibodies (MABS) that specifically bind strain 46-1 were prepared by conventional hybridoma technology. These MABS are apparently biochemically distinct and were used to develop enzyme-linked and fluorescent immunoassays to detect strain 46-1 cells in environmental samples. A fluorescent immunoassay utilizing four of these MABS easily distinguished laboratory-grown 46-1 cells from other methanotrophic and heterotrophic bacteria, but failed to detect 46-1 cells in groundwater samples and cultures

Psychromonas boydii sp. nov., a gas-vacuolate, psychrophilic bacterium isolated from an Arctic sea-ice core.

Science.gov (United States)

Auman, Ann J; Breezee, Jennifer L; Gosink, John J; Schumann, Peter; Barnes, Carmen R; Kämpfer, Peter; Staley, James T

2010-01-01

A gas-vacuolate bacterium, strain 174(T), was isolated from a sea-ice core collected from Point Barrow, Alaska, USA. Comparative analysis of 16S rRNA gene sequences showed that this bacterium was most closely related to Psychromonas ingrahamii 37(T), with a similarity of >99 %. However, strain 174(T) could be clearly distinguished from closely related species by DNA-DNA hybridization; relatedness values determined by two different methods between strain 174(T) and P. ingrahamii 37(T) were 58.4 and 55.7 % and those between strain 174(T) and Psychromonas antarctica DSM 10704(T) were 46.1 and 33.1 %, which are well below the 70 % level used to define a distinct species. Phenotypic analysis, including cell size (strain 174(T) is the largest member of the genus Psychromonas, with rod-shaped cells, 8-18 microm long), further differentiated strain 174(T) from other members of the genus Psychromonas. Strain 174(T) could be distinguished from its closest relative, P. ingrahamii, by its utilization of D-mannose and D-xylose as sole carbon sources, its ability to ferment myo-inositol and its inability to use fumarate and glycerol as sole carbon sources. In addition, strain 174(T) contained gas vacuoles of two distinct morphologies and grew at temperatures ranging from below 0 to 10 degrees C and its optimal NaCl concentration for growth was 3.5 %. The DNA G+C content was 40 mol%. Whole-cell fatty acid analysis showed that 16 : 1omega7c and 16 : 0 comprised 44.9 and 26.4 % of the total fatty acid content, respectively. The name Psychromonas boydii sp. nov. is proposed for this novel species, with strain 174(T) (=DSM 17665(T) =CCM 7498(T)) as the type strain.

Influence of heterotrophic microbial growth on biological oxidation of pyrite

Energy Technology Data Exchange (ETDEWEB)

Marchand, E.A.; Silverstein, J. [University of Nevada, Reno, NV (United States). Dept. of Civil Engineering

2002-12-15

Experiments were carried out to examine the possibility that enhanced growth of heterotrophic (non-iron-oxidising) bacteria would inhibit pyrite oxidation by Acidithiobacillus ferroxidans by out-competing the more slowly growing autotrophs for oxygen, nutrients or even attachment sites on the mineral surface. Glucose was added to microcosms containing pyrite, acidic mineral solution and cultures of A-ferrooxidans and Acidiphilium acidophilus under various experimental conditions. Results suggest that encouraging the growth of heterotrophic microorganisms under acid mine drainage conditions may be a feasible strategy for decreasing both the rate and the extent of sulfide mineral oxidation. 43 refs., 8 figs., 3 tabs.

Nutrient and media recycling in heterotrophic microalgae cultures.

Science.gov (United States)

Lowrey, Joshua; Armenta, Roberto E; Brooks, Marianne S

2016-02-01

In order for microalgae-based processes to reach commercial production for biofuels and high-value products such as omega-3 fatty acids, it is necessary that economic feasibility be demonstrated at the industrial scale. Therefore, process optimization is critical to ensure that the maximum yield can be achieved from the most efficient use of resources. This is particularly true for processes involving heterotrophic microalgae, which have not been studied as extensively as phototrophic microalgae. An area that has received significant conceptual praise, but little experimental validation, is that of nutrient recycling, where the waste materials from prior cultures and post-lipid extraction are reused for secondary fermentations. While the concept is very simple and could result in significant economic and environmental benefits, there are some underlying challenges that must be overcome before adoption of nutrient recycling is viable at commercial scale. Even more, adapting nutrient recycling for optimized heterotrophic cultures presents some added challenges that must be identified and addressed that have been largely unexplored to date. These challenges center on carbon and nitrogen recycling and the implications of using waste materials in conjunction with virgin nutrients for secondary cultures. The aim of this review is to provide a foundation for further understanding of nutrient recycling for microalgae cultivation. As such, we outline the current state of technology and practical challenges associated with nutrient recycling for heterotrophic microalgae on an industrial scale and give recommendations for future work.

Cesiribacter roseus sp. nov., a pink-pigmented bacterium isolated from desert sand.

Science.gov (United States)

Liu, Ming; Qi, Huan; Luo, Xuesong; Dai, Jun; Peng, Fang; Fang, Chengxiang

2012-01-01

A pink-pigmented, Gram-negative, rod-shaped, motile, strictly aerobic bacterium, designated strain 311(T), was isolated from desert sand in Xinjiang, China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 311(T) was related closely to Cesiribacter andamanensis AMV16(T) (94.6% similarity). The DNA G+C content of strain 311(T) was 47.1 mol% and the major respiratory quinone was menaquinone 7 (MK-7). The main cellular fatty acids were C(16:1)ω5c (29.9%), iso-C(15:0) (21.9%), iso-C(17:0) 3-OH (13.3%) and summed feature 4 (iso-C(17:1) I and/or anteiso-C(17:1) B; 13.0%). Based on phenotypic and chemotaxonomic data and phylogenetic analysis, strain 311(T) is considered to represent a novel species of the genus Cesiribacter, for which the name Cesiribacter roseus sp. nov. is proposed. The type strain is 311(T) (=CCTCC AB 207142(T) =KACC 15456(T)).

Biotechnical leaching of lean ores using heterotrophic microorganisms

International Nuclear Information System (INIS)

Schwartz, W.; Naeveke, R.

1980-01-01

After reporting briefly on leaching with Thiobacillus, it is discussed whether in those cases where thiobacilli fail to work the limits of microbial leaching are reached or still other groups of microorganisms will be suitable. In this relation the great number of carbon-heterotrophic fungi and bacteria have to be considered which are partly oligotrophic and occur e.g. in weathering biotopes of rocks and minerals and which may even include heavy metals in the dissolving processes of weathering. The active agents are, as far as is known up to now, organic acids which are produced by microorganisms and given off to the medium where they may combine with metals to form water-soluble complex compounds. In order to detect and isolate suitable strains of fungi and bacteria it will be necessary to work out a screening program which proceeds from general to special selections. Experiments to identify the active agents and the conditions of their production will have to follow. It remains still an open question whether such studies will result in technical processes. Mass production processes which are possible with the carbon-autotrophic and acidophilic thiobacilli are less probable than special processes to get hold of rare and economically valuable metals whose extraction would be difficult by other means. (orig.) [de

Deferribacter thermophilus gen. nov., sp. nov., a novel thermophilic manganese- and iron-reducing bacterium isolated from a petroleum reservoir.

Science.gov (United States)

Greene, A C; Patel, B K; Sheehy, A J

1997-04-01

A thermophilic anaerobic bacterium, designated strain BMAT (T = type strain), was isolated from the production water of Beatrice oil field in the North Sea (United Kingdom). The cells were straight to bent rods (1 to 5 by 0.3 to 0.5 microns) which stained gram negative. Strain BMAT obtained energy from the reduction of manganese (IV), iron(III), and nitrate in the presence of yeast extract, peptone, Casamino Acids, tryptone, hydrogen, malate, acetate, citrate, pyruvate, lactate, succinate, and valerate. The isolate grew optimally at 60 degrees C (temperature range for growth, 50 to 65 degrees C) and in the presence of 2% (wt/vol) NaCl (NaCl range for growth, 0 to 5% [wt/vol]). The DNA base composition was 34 mol% G + C. Phylogenetic analyses of the 16S rRNA gene indicated that strain BMAT is a member of the domain Bacteria. The closest known bacterium is the moderate thermophile Flexistipes sinusarabici (similarity value, 88%). Strain BMAT possesses phenotypic and phylogenetic traits that do not allow its classification as a member of any previously described genus; therefore, we propose that this isolate should be described as a member of a novel species of a new genus, Deferribacter thermophilus gen. nov., sp. nov.

Biomass and lipid production of Chlorella protothecoides under heterotrophic cultivation on a mixed waste substrate of brewer fermentation and crude glycerol.

Science.gov (United States)

Feng, Xiaoyu; Walker, Terry H; Bridges, William C; Thornton, Charles; Gopalakrishnan, Karthik

2014-08-01

Biomass and lipid accumulation of heterotrophic microalgae Chlorella protothecoides by supplying mixed waste substrate of brewer fermentation and crude glycerol were investigated. The biomass concentrations of the old and the new C. protothecoides strains on day 6 reached 14.07 and 12.73 g/L, respectively, which were comparable to those in basal medium with supplement of glucose and yeast extract (BM-GY) (14.47 g/L for old strains and 11.43 g/L for new strains) (P>0.05). Approximately 81.5% of total organic carbon and 65.1% of total nitrogen in the mixed waste were effectively removed. The accumulated lipid productivities of the old and the new C. protothecoides strains in BM-GY were 2.07 and 1.61 g/L/day, respectively, whereas in the mixed waste, lipid productivities could reach 2.12 and 1.81 g/L/day, respectively. Our result highlights a new approach of mixing carbon-rich and nitrogen-rich wastes as economical and practical alternative substrates for biofuel production. Copyright © 2014 Elsevier Ltd. All rights reserved.

Draft Genome Sequence of Pontibacter sp. nov. BAB1700, a Halotolerant, Industrially Important Bacterium

Science.gov (United States)

Joshi, M. N.; Sharma, A. C.; Pandya, R. V.; Patel, R. P.; Saiyed, Z. M.; Saxena, A. K.

2012-01-01

Pontibacter sp. nov. BAB1700 is a halotolerant, Gram-negative, rod-shaped, pink-pigmented, menaquinone-7-producing bacterium isolated from sediments of a drilling well. The draft genome sequence of the strain, consisting of one chromosome of 4.5 Mb, revealed vital gene clusters involved in vitamin biosynthesis and resistance against various metals and antibiotics. PMID:23105068

Heterotrophic fixation of CO2 in soil

Czech Academy of Sciences Publication Activity Database

Šantrůčková, Hana; Bird, M. I.; Elhottová, Dana; Novák, Jaroslav; Picek, T.; Šimek, Miloslav; Tykva, Richard

2005-01-01

Roč. 49, č. 2 (2005), s. 218-225 ISSN 0095-3628 R&D Projects: GA ČR(CZ) GA206/02/1036; GA AV ČR(CZ) IAA6066901 Institutional research plan: CEZ:AV0Z60660521 Keywords : heterotrophic fixation * CO2 * soil Subject RIV: EH - Ecology, Behaviour Impact factor: 2.674, year: 2005

Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Alcanivorax dieselolei KS-293 Isolated from Surface Seawater in the Eastern Mediterranean Sea

KAUST Repository

Barbato, Marta

2015-12-10

We report here the draft genome sequence of Alcanivorax dieselolei KS-293, a hydrocarbonoclastic bacterium isolated from the Mediterranean Sea, by supplying diesel oil as the sole carbon source. This strain contains multiple putative genes associated with hydrocarbon degradation pathways and that are highly similar to those described in A. dieselolei type strain B5.

Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Alcanivorax dieselolei KS-293 Isolated from Surface Seawater in the Eastern Mediterranean Sea

KAUST Repository

Barbato, Marta; Mapelli, Francesca; Chouaia, Bessem; Crotti, Elena; Daffonchio, Daniele; Borin, Sara

2015-01-01

We report here the draft genome sequence of Alcanivorax dieselolei KS-293, a hydrocarbonoclastic bacterium isolated from the Mediterranean Sea, by supplying diesel oil as the sole carbon source. This strain contains multiple putative genes associated with hydrocarbon degradation pathways and that are highly similar to those described in A. dieselolei type strain B5.

Utilization of organic residues using heterotrophic microalgae and insects.

Science.gov (United States)

Pleissner, Daniel; Rumpold, Birgit A

2018-02-01

Various organic residues occur globally in the form of straw, wood, green biomass, food waste, feces, manure etc. Other utilization strategies apart from anaerobic digestion, composting and incineration are needed to make use of the whole potential of organic residues as sources of various value added compounds. This review compares the cultivation of heterotrophic microalgae and insects using organic residues as nutrient sources and illuminates their potential with regard to biomass production, productivity and yield, and utilization strategies of produced biomasses. Furthermore, cultivation processes as well as advantages and disadvantages of utilization processes are identified and discussed. It was shown that both heterotrophic algae and insects are able to reduce a sufficient amount of organic residues by converting it into biomass. The biomass composition of both organisms is similar which allows similar utilization strategies in food and feed, chemicals and materials productions. Even though insect is the more complex organism, biomass production can be carried out using simple equipment without sterilization and hydrolysis of organic residues. Contrarily, heterotrophic microalgae require a pretreatment of organic residues in form of sterilization and in most cases hydrolysis. Interestingly, the volumetric productivity of insect biomass exceeds the productivity of algal biomass. Despite legal restrictions, it is expected that microalgae and insects will find application as alternative food and feed sources in the future. Copyright © 2017 Elsevier Ltd. All rights reserved.

Draft Genome Sequence of Lactobacillus paracasei DmW181, a Bacterium Isolated from Wild Drosophila.

Science.gov (United States)

Hammer, Austin J; Walters, Amber; Carroll, Courtney; Newell, Peter D; Chaston, John M

2017-07-06

The draft genome sequence of Lactobacillus paracasei DmW181, an anaerobic bacterium isolate from wild Drosophila flies, is reported here. Strain DmW181 possesses genes for sialic acid and mannose metabolism. The assembled genome is 3,201,429 bp, with 3,454 predicted genes. Copyright © 2017 Hammer et al.

Reduction of molybdate to molybdenum blue by Klebsiella sp. strain hkeem.

Science.gov (United States)

Lim, H K; Syed, M A; Shukor, M Y

2012-06-01

A novel molybdate-reducing bacterium, tentatively identified as Klebsiella sp. strain hkeem and based on partial 16s rDNA gene sequencing and phylogenetic analysis, has been isolated. Strain hkeem produced 3 times more molybdenum blue than Serratia sp. strain Dr.Y8; the most potent Mo-reducing bacterium isolated to date. Molybdate was optimally reduced to molybdenum blue using 4.5 mM phosphate, 80 mM molybdate and using 1% (w/v) fructose as a carbon source. Molybdate reduction was optimum at 30 °C and at pH 7.3. The molybdenum blue produced from cellular reduction exhibited absorption spectrum with a maximum peak at 865 nm and a shoulder at 700 nm. Inhibitors of electron transport system such as antimycin A, rotenone, sodium azide, and potassium cyanide did not inhibit the molybdenum-reducing enzyme. Mercury, silver, and copper at 1 ppm inhibited molybdenum blue formation in whole cells of strain hkeem. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Isolation, identification, and biocontrol of antagonistic bacterium against Botrytis cinerea after tomato harvest

Directory of Open Access Journals (Sweden)

Jun-Feng Shi

Full Text Available ABSTRACT Tomato is one of the most important vegetables in the world. Decay after harvest is a major issue in the development of tomato industry. Currently, the most effective method for controlling decay after harvest is storage of tomato at low temperature combined with usage of chemical bactericide; however, long-term usage of chemical bactericide not only causes pathogen resistance but also is harmful for human health and environment. Biocontrol method for the management of disease after tomato harvest has great practical significance. In this study, antagonistic bacterium B-6-1 strain was isolated from the surface of tomato and identified as Enterobacter cowanii based on morphological characteristics and physiological and biochemical features combined with sequence analysis of 16SrDNA and ropB gene and construction of dendrogram. Effects of different concentrations of antagonistic bacterium E. cowanii suspension on antifungal activity after tomato harvest were analyzed by mycelium growth rate method. Results revealed that antifungal activity was also enhanced with increasing concentrations of antagonistic bacterium; inhibitory rates of 1 × 105 colony-forming units (cfu/mL antagonistic bacterial solution on Fusarium verticillioides, Alternaria tenuissima, and Botrytis cinerea were 46.31%, 67.48%, and 75.67%, respectively. By using in vivo inoculation method, it was further confirmed that antagonistic bacterium could effectively inhibit the occurrence of B. cinerae after tomato harvest, biocontrol effect of 1 × 109 cfu/mL zymotic fluid reached up to 95.24%, and antagonistic bacterium E. cowanii has biocontrol potential against B. cinerea after harvest of fruits and vegetables.

Isolation and characterization of a novel hydrocarbon-degrading bacterium Achromobacter sp. HZ01 from the crude oil-contaminated seawater at the Daya Bay, southern China

International Nuclear Information System (INIS)

Deng, Mao-Cheng; Li, Jing; Liang, Fu-Rui; Yi, Meisheng; Xu, Xiao-Ming; Yuan, Jian-Ping; Peng, Juan; Wu, Chou-Fei; Wang, Jiang-Hai

2014-01-01

Graphical abstract: Morphological properties of the colonies and cells of strain HZ01. (A) Colonies of strain HZ01 on the LB solid plate; (B) Gram-negative bacterium of strain HZ01 (20 × 100); (C) Scanning electron microscopy (SEM) photograph of strain HZ01 (×15,000); and (D) Transmission electronic microscopy (TEM) photograph of strain HZ01 (×5000). - Highlights: • A novel petroleum degrading bacterium HZ01 was obtained from the crude oil-contaminated seawater. • Strain HZ01 had been identified as Achromobacter sp. • Strain HZ01 could degrade the evaporated diesel oil with the degradability of 96.6%. • Strain HZ01 could effectively degrade anthracene, phenanthrene and pyrence. • Strain HZ01 may be employed to remove hydrocarbon contaminants. - Abstract: Microorganisms play an important role in the biodegradation of petroleum contaminants, which have attracted great concern due to their persistent toxicity and difficult biodegradation. In this paper, a novel hydrocarbon-degrading bacterium HZ01 was isolated from the crude oil-contaminated seawater at the Daya Bay, South China Sea, and identified as Achromobacter sp. Under the conditions of pH 7.0, NaCl 3% (w/v), temperature 28 °C and rotary speed 150 rpm, its degradability of the total n-alkanes reached up to 96.6% after 10 days of incubation for the evaporated diesel oil. Furthermore, Achromobacter sp. HZ01 could effectively utilize polycyclic aromatic hydrocarbons (PAHs) as its sole carbon source, and could remove anthracene, phenanthrene and pyrence about 29.8%, 50.6% and 38.4% respectively after 30 days of incubation. Therefore, Achromobacter sp. HZ01 may employed as an excellent degrader to develop one cost-effective and eco-friendly method for the bioremediation of marine environments polluted by crude oil

Extracellular Pectinase from a Novel Bacterium Chryseobacterium indologenes Strain SD and Its Application in Fruit Juice Clarification

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Karabi Roy

2018-01-01

Full Text Available Pectinase is one of the important enzymes of industrial sectors. Presently, most of the pectinases are of plant origin but there are only a few reports on bacterial pectinases. The aim of the present study was to isolate a novel and potential pectinase producing bacterium as well as optimization of its various parameters for maximum enzyme production. A total of forty bacterial isolates were isolated from vegetable dump waste soil using standard plate count methods. Primary screening was done by hydrolysis of pectin. Pectinase activity was determined by measuring the increase in reducing sugar formed by the enzymatic hydrolysis of pectin. Among the bacterial isolates, the isolate K6 exhibited higher pectinase activity in broth medium and was selected for further studies. The selected bacterial isolate K6 was identified as Chryseobacterium indologenes strain SD. The isolate was found to produce maximum pectinase at 37°C with pH 7.5 upon incubation for 72 hours, while cultured in production medium containing citrus pectin and yeast extract as C and N sources, respectively. During enzyme-substrate reaction phase, the enzyme exhibited its best activity at pH of 8.0 and temperature of 40°C using citrus pectin as substrate. The pectinase of the isolate showed potentiality on different types of fruit juice clarification.

Dynamic metabolic modeling of heterotrophic and mixotrophic microalgal growth on fermentative wastes.

Directory of Open Access Journals (Sweden)

Caroline Baroukh

2017-06-01

Full Text Available Microalgae are promising microorganisms for the production of numerous molecules of interest, such as pigments, proteins or triglycerides that can be turned into biofuels. Heterotrophic or mixotrophic growth on fermentative wastes represents an interesting approach to achieving higher biomass concentrations, while reducing cost and improving the environmental footprint. Fermentative wastes generally consist of a blend of diverse molecules and it is thus crucial to understand microalgal metabolism in such conditions, where switching between substrates might occur. Metabolic modeling has proven to be an efficient tool for understanding metabolism and guiding the optimization of biomass or target molecule production. Here, we focused on the metabolism of Chlorella sorokiniana growing heterotrophically and mixotrophically on acetate and butyrate. The metabolism was represented by 172 metabolic reactions. The DRUM modeling framework with a mildly relaxed quasi-steady-state assumption was used to account for the switching between substrates and the presence of light. Nine experiments were used to calibrate the model and nine experiments for the validation. The model efficiently predicted the experimental data, including the transient behavior during heterotrophic, autotrophic, mixotrophic and diauxic growth. It shows that an accurate model of metabolism can now be constructed, even in dynamic conditions, with the presence of several carbon substrates. It also opens new perspectives for the heterotrophic and mixotrophic use of microalgae, especially for biofuel production from wastes.

Negative consequences of glacial turbidity for the survival of freshwater planktonic heterotrophic flagellates.

Science.gov (United States)

Sommaruga, Ruben; Kandolf, Georg

2014-02-17

Heterotrophic (phagotrophic) flagellates are key components of planktonic food webs in freshwater and marine ecosystems because they are the main consumers of bacteria. Although they are ubiquitous in aquatic ecosystems, they were numerically undetectable in turbid glacier-fed lakes. Here we show that glacial particles had negative effects on the survival and growth of heterotrophic flagellates. The effect of glacial particles was concentration-dependent and was caused by their interference with bacterial uptake rather than by physical damage. These results are the first to reveal why establishment of heterotrophic flagellates populations is hindered in very turbid glacial lakes. Because glaciers are vanishing around the world, recently formed turbid meltwater lakes represent an excellent opportunity to understand the environmental conditions that probably shaped the establishment of lake communities at the end of the last glaciation.

Two New Cholic Acid Derivatives from the Marine Ascidian-Associated Bacterium Hasllibacter halocynthiae

Directory of Open Access Journals (Sweden)

Sung Hun Kim

2012-10-01

Full Text Available The investigation of secondary metabolites in liquid cultures of a recently discovered marine bacterium, Hasllibacter halocynthiae strain KME 002T, led to the isolation of two new cholic acid derivatives. The structures of these compounds were determined to be 3,3,12-trihydroxy-7-ketocholanic acid (1 and 3,3,12-trihydroxy-7-deoxycholanic acid (2 through HRFABMS and NMR data analyses.

Heterotrophic components of soil respiration in pastures and forests in southwestern Amazonia, Acre, Brazil

Directory of Open Access Journals (Sweden)

Eric Atlas Davidson

2008-12-01

Full Text Available In this paper we present data on soil microbial biomass and heterotrophic respiration in pastures, mature and secondary forests, in order to elucidate their contribution to total CO2 flux from soil to atmosphere. The research was conducted in Southwestern Amazonia, Acre State, Brazil. Microbial biomass was estimated using a variation of the traditional fumigation-extraction method and heterotrophic respiration was measured using respirometry flasks attached to an infrared gas analyzer. Soil microbial biomass and heterotrophic respiration did not differ statistically among pastures, mature and secondary forests. These laboratory results indicate that higher CO2 fluxes from pasture soils measured in situ are probably due to higher root respiration by pasture grasses.

Desulfuromonas thiophila sp. nov., a new obligately sulfur-reducing bacterium from anoxic freshwater sediment.

Science.gov (United States)

Finster, K; Coates, J D; Liesack, W; Pfennig, N

1997-07-01

A mesophilic, acetate-oxidizing, sulfur-reducing bacterium, strain NZ27T, was isolated from anoxic mud from a freshwater sulfur spring. The cells were ovoid, motile, and gram negative. In addition to acetate, the strain oxidized pyruvate, succinate, and fumarate. Sulfur flower could be replaced by polysulfide as an electron acceptor. Ferric nitrilotriacetic acid was reduced in the presence of pyruvate; however, this reduction did not sustain growth. These phenotypic characteristics suggested that strain NZ27T is affiliated with the genus Desulfuromonas. A phylogenetic analysis based on the results of comparative 16S ribosomal DNA sequencing confirmed that strain NZ27T belongs to the Desulfuromonas cluster in the recently proposed family "Geobacteracea" in the delta subgroup of the Proteobacteria. In addition, the results of DNA-DNA hybridization studies confirmed that strain NZ27T represents a novel species. Desulfuromonas thiophila, a name tentatively used in previous publication, is the name proposed for strain NZ27T in this paper.

Complete genome sequence of Isosphaera pallida type strain (IS1BT)

Energy Technology Data Exchange (ETDEWEB)

Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Cleland, David M [ORNL; Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Hammon, Nancy [Joint Genome Institute, Walnut Creek, California; Deshpande, Shweta [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Pagani, Ioanna [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Beck, Brian [ATCC - American Type Culture Collection; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

2011-01-01

Isosphaera pallida (ex Woronichin 1927) Giovannoni et al. 1995 is the type species of the genus Isosphaera. The species is of interest because it was the first heterotrophic bacterium known to be phototactic, and it occupies an isolated phylogenetic position within the Planctomycetaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the genus Isosphaera and the third of a member of the family Planctomycetaceae. The 5,472,964 bp long chromosome and the 56,340 bp long plasmid with a total of 3,763 protein-coding and 60 RNA genes are part of the Genomic Encyclopedia of Bacteria and Archaea project.

Elevated temperature increases carbon and nitrogen fluxes between phytoplankton and heterotrophic bacteria through physical attachment

KAUST Repository

Arandia-Gorostidi, Nestor

2016-12-06

Quantifying the contribution of marine microorganisms to carbon and nitrogen cycles and their response to predicted ocean warming is one of the main challenges of microbial oceanography. Here we present a single-cell NanoSIMS isotope analysis to quantify C and N uptake by free-living and attached phytoplankton and heterotrophic bacteria, and their response to short-term experimental warming of 4 °C. Elevated temperature increased total C fixation by over 50%, a small but significant fraction of which was transferred to heterotrophs within 12 h. Cell-to-cell attachment doubled the secondary C uptake by heterotrophic bacteria and increased secondary N incorporation by autotrophs by 68%. Warming also increased the abundance of phytoplankton with attached heterotrophs by 80%, and promoted C transfer from phytoplankton to bacteria by 17% and N transfer from bacteria to phytoplankton by 50%. Our results indicate that phytoplankton-bacteria attachment provides an ecological advantage for nutrient incorporation, suggesting a mutualistic relationship that appears to be enhanced by temperature increases.

Elevated temperature increases carbon and nitrogen fluxes between phytoplankton and heterotrophic bacteria through physical attachment

KAUST Repository

Arandia-Gorostidi, Nestor; Weber, Peter K; Alonso-Sá ez, Laura; Moran, Xose Anxelu G.; Mayali, Xavier

2016-01-01

Quantifying the contribution of marine microorganisms to carbon and nitrogen cycles and their response to predicted ocean warming is one of the main challenges of microbial oceanography. Here we present a single-cell NanoSIMS isotope analysis to quantify C and N uptake by free-living and attached phytoplankton and heterotrophic bacteria, and their response to short-term experimental warming of 4 °C. Elevated temperature increased total C fixation by over 50%, a small but significant fraction of which was transferred to heterotrophs within 12 h. Cell-to-cell attachment doubled the secondary C uptake by heterotrophic bacteria and increased secondary N incorporation by autotrophs by 68%. Warming also increased the abundance of phytoplankton with attached heterotrophs by 80%, and promoted C transfer from phytoplankton to bacteria by 17% and N transfer from bacteria to phytoplankton by 50%. Our results indicate that phytoplankton-bacteria attachment provides an ecological advantage for nutrient incorporation, suggesting a mutualistic relationship that appears to be enhanced by temperature increases.

Competition between autotrophic and heterotrophic microbial plankton for inorganic nutrients induced by variability in estuarine biophysicochemical conditions

Science.gov (United States)

Williams, A.; Quigg, A.

2016-02-01

Competition for inorganic nutrients between autotrophic and heterotrophic fractions of microbial plankton (0.2-20μm) was investigated at two stations in a sub-tropical estuary, Galveston Bay, Texas. Competition potential between these groups is enhanced because individuals are similar in size, reducing variability among their nutrient uptake efficiencies. Further, in estuaries, allochthonous supplements to autochthonous carbon may satisfy heterotrophic requirements, allowing alternative factors to limit abundance. The relative abundance of autotrophs and heterotrophs stained with SYBR Green I and enumerated on a Beckman Coulter Gallios flow cytometer were evaluated monthly during a year-long study. Shifts in the relative in situ abundance were significantly related to temperature, dissolved inorganic nitrogen (DIN), phosphorous (Pi), and total organic carbon (TOC) concentrations revealing opposing gradients of limitation by different abiotic factors. In corresponding in vitro nutrient enrichment bioassays the relative contribution of autotrophic or heterotrophic microbial plankton to significant enrichment responses varied. Only during macro- (>20μm) phytoplankton blooms do autotrophic microbial plankton respond to nutrient enrichment. Contrastingly, the heterotrophic microbial plankton responded to nutrient enrichment primarily when temperature limitation was alleviated. Therefore, the potential for autotrophic and heterotrophic microbial plankton competition for limiting nutrients is highest when autotrophic microbial plankton are also competing with larger phytoplankton during bloom events. Based on this evidence, we hypothesize that the autotrophic microbial fraction has a competitive advantage over the heterotrophs for inorganic nutrients in Galveston Bay. The observed microbial competition during estuarine phytoplankton blooms may have important consequences on biogeochemical processes including carbon and nutrient cycling.

Removal of crude petroleum hydrocarbons by heterotrophic bacteria ...

African Journals Online (AJOL)

Nitrogenous fertilizer (NPK) plant effluents from NAFCON were used in amending plots of land experimentally polluted with crude oil. Counts of heterotrophic bacteria (THBC) and fungi (TF), and of petroleum utilizing bacteria (PUB) and fungi (PUF) were monitored during an 8 weeks period. Counts obtained showed that ...

Colwellia polaris sp. nov., a psychrotolerant bacterium isolated from Arctic sea ice.

Science.gov (United States)

Zhang, De-Chao; Yu, Yong; Xin, Yu-Hua; Liu, Hong-Can; Zhou, Pei-Jin; Zhou, Yu-Guang

2008-08-01

A novel psychrotolerant, Gram-negative, aerobic bacterium, designated strain 537T, was isolated from sea-ice samples from the Arctic. Strain 537T was able to grow at 4-26 degrees C, with optimum growth occurring at 20-21 degrees C. Strain 537T had Q-8 as the major respiratory quinone and contained iso-C15:0 2-OH and/or C16:1 omega7c (22.95 %), C15:1 (17.64 %) and C17:1 omega8c (13.74 %) as the predominant cellular fatty acids. The genomic DNA G+C content was 38.9 mol%. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 537T formed a coherent cluster within the genus Colwellia. The highest level of 16S rRNA gene sequence similarity (97.5 %) exhibited by strain 537T was obtained with respect to the type strain of Colwellia aestuarii. On the basis of phenotypic, chemotaxonomic and phylogenetic properties and DNA-DNA relatedness data, strain 537T represents a novel species of the genus Colwellia, for which the name Colwellia polaris sp. nov. is proposed. The type strain is 537T (=CGMCC 1.6132T =JCM 13952T).

Methylohalobius crimeensis gen. nov., sp. nov., a moderately halophilic, methanotrophic bacterium isolated from hypersaline lakes of Crimea.

Science.gov (United States)

Heyer, Jürgen; Berger, Ursula; Hardt, Martin; Dunfield, Peter F

2005-09-01

A novel genus and species are proposed for two strains of methanotrophic bacteria isolated from hypersaline lakes in the Crimean Peninsula of Ukraine. Strains 10Ki(T) and 4Kr are moderate halophiles that grow optimally at 1-1.5 M (5.8-8.7%, w/v) NaCl and tolerate NaCl concentrations from 0.2 M up to 2.5 M (1.2-15%). This optimum and upper limit are the highest for any methanotrophic bacterium known to date. The strains are Gram-negative, aerobic, non-pigmented, motile, coccoid to spindle-shaped bacteria that grow on methane or methanol only and utilize the ribulose monophosphate pathway for carbon assimilation. They are neutrophilic (growth occurs only in the range pH 6.5-7.5) and mesophilic (optimum growth occurs at 30 degrees C). On the basis of 16S rRNA gene sequence phylogeny, strains 10Ki(T) and 4Kr represent a type I methanotroph within the 'Gammaproteobacteria'. However, the 16S rRNA gene sequence displays <91.5 % identity to any public-domain sequence. The most closely related methanotrophic bacterium is the thermophilic strain HB. The DNA G+C content is 58.7 mol%. The major phospholipid fatty acids are 18:1omega7 (52-61%), 16:0 (22-23%) and 16:1omega7 (14-20%). The dominance of 18:1 over 16:0 and 16:1 fatty acids is unique among known type I methanotrophs. The data suggest that strains 10Ki(T) and 4Kr should be considered as belonging to a novel genus and species of type I methanotrophic bacteria, for which the name Methylohalobius crimeensis gen. nov., sp. nov. is proposed. Strain 10Ki(T) (=DSM 16011(T)=ATCC BAA-967(T)) is the type strain.

Examination of the Anaerobic Growth of Campylobacter concisus Strains

Directory of Open Access Journals (Sweden)

Hoyul Lee

2014-01-01

Full Text Available Campylobacter concisus is an oral bacterium that is associated with intestinal diseases. C. concisus was previously described as a bacterium that requires H2-enriched microaerobic conditions for growth. The level of H2 in the oral cavity is extremely low, suggesting that C. concisus is unlikely to have a microaerobic growth there. In this study, the anaerobic growth of C. concisus was investigated. The growth of fifty-seven oral C. concisus strains and six enteric C. concisus strains under various atmospheric conditions including anaerobic conditions with and without H2 was examined. The atmospheric conditions were generated using commercially available gas-generation systems. C. concisus putative virulence proteins were identified using mass spectrometry analysis. Under anaerobic conditions, 92% of the oral C. concisus strains (52/57 and all six enteric strains grew without the presence of H2 and the presence of H2 greatly increased C. concisus growth. An oral C. concisus strain was found to express a number of putative virulence proteins and the expression levels of these proteins were not affected by H2. The levels of H2 appeared to affect the optimal growth of C. concisus. This study provides useful information in understanding the natural colonization site and pathogenicity of C. concisus.

Draft genome sequence of Therminicola potens strain JR

Energy Technology Data Exchange (ETDEWEB)

Byrne-Bailey, K.G.; Wrighton, K.C.; Melnyk, R.A.; Agbo, P.; Hazen, T.C.; Coates, J.D.

2010-07-01

'Thermincola potens' strain JR is one of the first Gram-positive dissimilatory metal-reducing bacteria (DMRB) for which there is a complete genome sequence. Consistent with the physiology of this organism, preliminary annotation revealed an abundance of multiheme c-type cytochromes that are putatively associated with the periplasm and cell surface in a Gram-positive bacterium. Here we report the complete genome sequence of strain JR.

Phosphorus uptake of an arbuscular mycorrhizal fungus is not effected by the biocontrol bacterium ¤Burkholderia cepacia¤

DEFF Research Database (Denmark)

Ravnskov, S.; Larsen, J.; Jakobsen, I.

2002-01-01

The biocontrol bacterium Burkholderia cepacia is known to suppress a broad range of root pathogenic fungi, while its impact on other beneficial non-target organisms such as arbuscular mycorrhizal (AM) fungi is unknown. Direct interactions between five B. cepacia strains and the AM fungus, Glomus ...

Novel insight into the role of heterotrophic dinoflagellates in the fate of crude oil in the sea

Science.gov (United States)

Almeda, Rodrigo; Connelly, Tara L.; Buskey, Edward J.

2014-12-01

Although planktonic protozoans are likely to interact with dispersed crude oil after a spill, protozoan-mediated processes affecting crude oil pollution in the sea are still not well known. Here, we present the first evidence of ingestion and defecation of physically or chemically dispersed crude oil droplets (1-86 μm in diameter) by heterotrophic dinoflagellates, major components of marine planktonic food webs. At a crude oil concentration commonly found after an oil spill (1 μL L-1), the heterotrophic dinoflagellates Noctiluca scintillans and Gyrodinium spirale grew and ingested ~0.37 μg-oil μg-Cdino-1 d-1, which could represent ~17% to 100% of dispersed oil in surface waters when heterotrophic dinoflagellates are abundant or bloom. Egestion of faecal pellets containing crude oil by heterotrophic dinoflagellates could contribute to the sinking and flux of toxic petroleum hydrocarbons in coastal waters. Our study indicates that crude oil ingestion by heterotrophic dinoflagellates is a noteworthy route by which petroleum enters marine food webs and a previously overlooked biological process influencing the fate of crude oil in the sea after spills.

Elemental sulfur and thiosulfate disproportionation by Desulfocapsa sulfoexigens sp. nov., a new anaerobic bacterium isolated from marine surface sediment.

Science.gov (United States)

Finster, K; Liesack, W; Thamdrup, B

1998-01-01

A mesophilic, anaerobic, gram-negative bacterium, strain SB164P1, was enriched and isolated from oxidized marine surface sediment with elemental sulfur as the sole energy substrate in the presence of ferrihydrite. Elemental sulfur was disproportionated to hydrogen sulfide and sulfate. Growth was observed exclusively in the presence of a hydrogen sulfide scavenger, e.g., ferrihydrite. In the absence of a scavenger, sulfide and sulfate production were observed but no growth occurred. Strain SB164P1 grew also by disproportionation of thiosulfate and sulfite. With thiosulfate, the growth efficiency was higher in ferrihydrite-supplemented media than in media without ferrihydrite. Growth coupled to sulfate reduction was not observed. However, a slight sulfide production occurred in cultures incubated with formate and sulfate. Strain SB164P1 is the first bacterium described that grows chemolithoautotrophically exclusively by the disproportionation of inorganic sulfur compounds. Comparative 16S rDNA sequencing analysis placed strain SB164P1 into the delta subclass of the class Proteobacteria. Its closest relative is Desulfocapsa thiozymogenes, and slightly more distantly related are Desulfofustis glycolicus and Desulforhopalus vacuolatus. This phylogenetic cluster of organisms, together with members of the genus Desulfobulbus, forms one of the main lines of descent within the delta subclass of the Proteobacteria. Due to the common phenotypic characteristics and the phylogenetic relatedness to Desulfocapsa thiozymogenes, we propose that strain SB164P1 be designated the type strain of Desulfocapsa sulfoexigens sp. nov.

Pyruvic Oxime Nitrification and Copper and Nickel Resistance by a Cupriavidus pauculus, an Active Heterotrophic Nitrifier-Denitrifier

OpenAIRE

Ramirez, Miguel; Obrzydowski, Jennifer; Ayers, Mary; Virparia, Sonia; Wang, Meijing; Stefan, Kurtis; Linchangco, Richard; Castignetti, Domenic

2014-01-01

Heterotrophic nitrifiers synthesize nitrogenous gasses when nitrifying ammonium ion. A Cupriavidus pauculus, previously thought an Alcaligenes sp. and noted as an active heterotrophic nitrifier-denitrifier, was examined for its ability to produce nitrogen gas (N2) and nitrous oxide (N2O) while heterotrophically nitrifying the organic substrate pyruvic oxime [CH3–C(NOH)–COOH]. Neither N2 nor N2O were produced. Nucleotide and phylogenetic analyses indicated that the organism is a member of a g...

Desulfotomaculum arcticum sp nov., a novel spore-formin, moderately thermophilic, sulfate-reducing bacterium isolated from a permanently cold fjord sediment of Svalbard

DEFF Research Database (Denmark)

Vandieken, V.; Knoblauch, C.; Jørgensen, BB

2006-01-01

Strain 15 T is a novel spore-forming, sulfate-reducing bacterium isolated from a permanently cold fjord sediment of Svalbard. Sulfate could be replaced by sulfite or thiosulfate. Hydrogen, formate, lactate, propionate, butyrate, hexanoate, methanol, ethanol, propanol, butanol, pyruvate, malate, s...... related to Desulfotomaculum thermosapovorans MLF(T) (93-5% 16S rRNA gene sequence similarity). Strain 15 T represents a novel species, for which the name Desulfotomaculurn arcticum sp. nov. is proposed. The type strain is strain 15 T (=DSM 17038(T)=jCM 12923(T))....

Thermaerobacter litoralis sp. nov., a strictly aerobic and thermophilic bacterium isolated from a coastal hydrothermal field

DEFF Research Database (Denmark)

Tanaka, Reiji; Kawaichi, Satoshi; Nishimura, Hiroshi

2006-01-01

A novel thermophilic bacterium, strain KW1T, was isolated from a coastal hydrothermal field on the Satsuma Peninsula, Kagoshima Prefecture, Japan. The variably Gram-stained cells were motile rods with flagella, did not form spores and proliferated at 52-78°C (optimum, 70°C), pH 5-8 (optimum, pH 7...

The Biology of Heterotrophic N2-fixing Bacteria in Marine and Estuarine Waters

DEFF Research Database (Denmark)

Bentzon-Tilia, Mikkel

Biological nitrogen (N)2 fixation is of paramount importance for marine N cycling and for life in the oceans in general. It represents the sole mechanism by which microorganisms can channel inert atmospheric N2 gas into biomass and hence it may fuel a significant fraction of primary production...... heterotrophic isolates, this thesis aims at addressing these unknowns. It was found that heterotrophic diazotrophs were present and active in environments previously not associated with N2 fixation e.g. suboxic basins of the Baltic Sea and estuarine surface waters. In these environments they contributed...... with significant amounts fixed N2, suggesting that a reevaluation of the significance of N fixation in suboxic waters and estuarine coastal waters is warranted. It was also documented that heterotrophic diazotrophs could be enriched in culture based on their ability to utilize N2 as the sole N source...

Marivirga lumbricoides sp. nov., a marine bacterium isolated from the South China Sea.

Science.gov (United States)

Xu, Yongle; Zhang, Rui; Li, Qipei; Liu, Keshao; Jiao, Nianzhi

2015-02-01

A novel, aerobic, heterotrophic, orange-pigmented, Gram-staining-negative, rod-shaped, gliding bacterial strain, designated JLT2000(T), was isolated from surface water of the South China Sea. The strain was oxidase- and catalase-positive. The major cellular fatty acids of strain JLT2000 T: were C12 : 0, iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 0. MK-7 was the major respiratory quinone and the major polar lipids were phosphatidylcholine and phosphatidylethanolamine. The genomic DNA G+C content of strain JLT2000(T) was 37.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JLT2000(T) formed a branch within the genus Marivirga, but was clearly separated from the two established species of this genus, Marivirga tractuosa and Marivirga sericea. The 16S rRNA gene sequence similarity of strain JLT2000(T) with the type strains of these two species was 95.8 % and 96.1 %, respectively. Strain JLT2000(T) had a shorter cell length and wider growth range in different temperatures and salinities than those of Marivirga tractuosa NBRC 15989(T) and Marivirga sericea NBRC 15983(T). In addition, strain JLT2000(T) could utilize more carbon sources and hydrolyse more polymers than Marivirga tractuosa NBRC 15989(T) and Marivirga sericea NBRC 15983(T). Based on this polyphasic analysis, strain JLT2000(T) represents a novel species of the genus Marivirga, for which the name Marivirga lumbricoides sp. nov. is proposed. The type strain is JLT2000(T) ( = JCM 18012(T) = CGMCC 1.10832(T)). © 2015 IUMS.

Gold nanoparticles synthesized by Geobacillus sp. strain ID17 a thermophilic bacterium isolated from Deception Island, Antarctica

Science.gov (United States)

2013-01-01

Background The use of microorganisms in the synthesis of nanoparticles emerges as an eco-friendly and exciting approach, for production of nanoparticles due to its low energy requirement, environmental compatibility, reduced costs of manufacture, scalability, and nanoparticle stabilization compared with the chemical synthesis. Results The production of gold nanoparticles by the thermophilic bacterium Geobacillus sp. strain ID17 is reported in this study. Cells exposed to Au3+ turned from colourless into an intense purple colour. This change of colour indicates the accumulation of intracellular gold nanoparticles. Elemental analysis of particles composition was verified using TEM and EDX analysis. The intracellular localization and particles size were verified by TEM showing two different types of particles of predominant quasi-hexagonal shape with size ranging from 5–50 nm. The mayority of them were between 10‒20 nm in size. FT-IR was utilized to characterize the chemical surface of gold nanoparticles. This assay supports the idea of a protein type of compound on the surface of biosynthesized gold nanoparticles. Reductase activity involved in the synthesis of gold nanoparticles has been previously reported to be present in others microorganisms. This reduction using NADH as substrate was tested in ID17. Crude extracts of the microorganism could catalyze the NADH-dependent Au3+ reduction. Conclusions Our results strongly suggest that the biosynthesis of gold nanoparticles by ID17 is mediated by enzymes and NADH as a cofactor for this biological transformation. PMID:23919572

Draft Genome Sequence of Ochrobactrum intermedium Strain SA148, a Plant Growth-Promoting Desert Rhizobacterium

KAUST Repository

Lafi, Feras Fawzi; Alam, Intikhab; Geurts, Rene; Bisseling, Ton; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged

2017-01-01

Ochrobactrum intermedium strain SA148 is a plant growth-promoting bacterium isolated from sandy soil in the Jizan area of Saudi Arabia. Here, we report the 4.9-Mb draft genome sequence of this strain, highlighting different pathways characteristic

DNA type analysis to differentiate strains of Xylophilus ampelinus from Europe and Hokkaido, Japan

OpenAIRE

Komatsu, Tsutomu; Shinmura, Akinori; Kondo, Norio

2016-01-01

Strains of the bacterium Xylophilus ampelinus were collected from Europe and Hokkaido, Japan. Genomic fingerprints generated from 43 strains revealed four DNA types (A-D) using the combined results of Rep-, ERIC-, and Box-PCR. Genetic variation was found among the strains examined; strains collected from Europe belonged to DNA types A or B, and strains collected from Hokkaido belonged to DNA types C or D. However, strains belonging to each DNA type showed the same pathogenicity to grapevines ...

The fate of a nitrobenzene-degrading bacterium in pharmaceutical wastewater treatment sludge.

Science.gov (United States)

Ren, Yuan; Yang, Juan; Chen, Shaoyi

2015-12-01

This paper describes the fate of a nitrobenzene-degrading bacterium, Klebsiella oxytoca NBA-1, which was isolated from a pharmaceutical wastewater treatment facility. The 90-day survivability of strain NBA-1 after exposure to sludge under anaerobic and aerobic conditions was investigated. The bacterium was inoculated into sludge amended with glucose and p-chloronitrobenzene (p-CNB) to compare the bacterial community variations between the modified sludge and nitrobenzene amendment. The results showed that glucose had no obvious effect on nitrobenzene biodegradation in the co-metabolism process, regardless of the presence/absence of oxygen. When p-CNB was added under anaerobic conditions, the biodegradation rate of nitrobenzene remained unchanged although p-CNB inhibited the production of aniline. The diversity of the microbial community increased and NBA-1 continued to be one of the dominant strains. Under aerobic conditions, the degradation rate of both nitrobenzene and p-CNB was only 20% of that under anaerobic conditions. p-CNB had a toxic effect on the microorganisms in the sludge so that most of the DGGE (denaturing gradient gel electrophoresis) bands, including that of NBA-1, began to disappear under aerobic conditions after 90days of exposure. These data show that the bacterial community was stable under anaerobic conditions and the microorganisms, including NBA-1, were more resistant to the adverse environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

Anaerostipes caccae gen. nov., sp. nov., a new saccharolytic, acetate-utilising, butyrate-producing bacterium from human faeces.

Science.gov (United States)

Schwiertz, Andreas; Hold, Georgina L; Duncan, Sylvia H; Gruhl, Barbel; Collins, Matthew D; Lawson, Paul A; Flint, Harry J; Blaut, Michael

2002-04-01

Two strains of a previously undescribed Eubacterium-like bacterium were isolated from human faeces. The strains are Gram-variable, obligately anaerobic, catalase negative, asporogenous rod-shaped cells which produced acetate, butyrate and lactate as the end products of glucose metabolism. The two isolates displayed 99.9% 16S rRNA gene sequence similarity to each other and treeing analysis demonstrated the faecal isolates are far removed from Eubacterium sensu stricto and that they represent a new subline within the Clostridium coccoides group of organisms. Based on phenotypic and phylogenetic criteria, it is proposed that the two strains from faeces be classified as a new genus and species, Anaerostipes caccae. The type strain of Anaerostipes caccae is NCIMB 13811T (= DSM 14662T).

Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1T, a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification

NARCIS (Netherlands)

Berben, T.; Sorokin, D.Y.; Ivanova, N.; Pati, A.; Kyrpides, N.; Goodwin, L.A; Woyke, T.; Muyzer, G.

2015-01-01

Thioalkalivibrio thiocyanodenitrificans strain ARhD 1 T is a motile, Gram-negative bacterium isolated from soda lakes that belongs to the Gammaproteobacteria. It derives energy for growth and carbon fixation from the oxidation of sulfur compounds, most notably thiocyanate, and so is a

Draft genome sequence of Bacillus okhensis Kh10-101T, a halo-alkali tolerant bacterium from Indian saltpan

Directory of Open Access Journals (Sweden)

Pilla Sankara Krishna

2015-12-01

Full Text Available We report the 4.86-Mb draft genome sequence of Bacillus okhensis strain Kh10-101T, a halo-alkali tolerant rod shaped bacterium isolated from a salt pan near port of Okha, India. This bacterium is a potential model to study the molecular response of bacteria to salt as well as alkaline stress, as it thrives under both high salt and high pH conditions. The draft genome consist of 4,865,284 bp with 38.2% G + C, 4952 predicted CDS, 157 tRNAs and 8 rRNAs. Sequence was deposited at DDBJ/EMBL/GenBank under the project accession JRJU00000000.

Draft Genome Sequence of MCPA-Degrading Sphingomonas sp. Strain ERG5, Isolated from a Groundwater Aquifer in Denmark

DEFF Research Database (Denmark)

Nielsen, Tue Kjærgaard; Kot, Witold; Sørensen, Sebastian R

2015-01-01

Sphingomonas sp. strain ERG5 was isolated from a bacterial community, originating from a groundwater aquifer polluted with low pesticide concentrations. This bacterium degrades 2-methyl-4-chlorophenoxyacetic acid (MCPA) in a wide spectrum of concentrations and has been shown to function in bioaug......Sphingomonas sp. strain ERG5 was isolated from a bacterial community, originating from a groundwater aquifer polluted with low pesticide concentrations. This bacterium degrades 2-methyl-4-chlorophenoxyacetic acid (MCPA) in a wide spectrum of concentrations and has been shown to function...

Temperature regulation of marine heterotrophic prokaryotes increases latitudinally as a breach between bottom-up and top-down controls

KAUST Repository

Moran, Xose Anxelu G.; Gasol, Josep M.; Pernice, Massimo C.; Mangot, Jean-Franç ois; Massana, Ramon; Lara, Elena; Vaqué , Dolors; Duarte, Carlos M.

2017-01-01

Planktonic heterotrophic prokaryotes make up the largest living biomass and process most organic matter in the ocean. Determining when and where the biomass and activity of heterotrophic prokaryotes are controlled by resource availability (bottom

Complete genome sequence of Paenibacillus sp. strain JDR-2

Science.gov (United States)

Virginia Chow; Guang Nong; Franz J. St. John; John D. Rice; Ellen Dickstein; Olga Chertkov; David Bruce; Chris Detter; Thomas Brettin; James Han; Tanja Woyke; Sam Pitluck; Matt Nolan; Amrita Pati; Joel Martin; Alex Copeland; Miriam L. Land; Lynne Goodwin; Jeffrey B. Jones; Lonnie O. Ingram; Keelnathan T. Shanmugam; James F. Preston

2012-01-01

Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium isolated from sweetgum (Liquidambar styraciflua) wood, is able to efficiently depolymerize, assimilate and metabolize 4-O-methylglucuronoxylan, the predominant structural component of hardwood hemicelluloses. A basis for this capability was first supported by...

Permanent draft genome of the malachite-green-tolerant bacterium Rhizobium sp. MGL06.

Science.gov (United States)

Liu, Yang; Wang, Runping; Zeng, Runying

2014-12-01

Rhizobium sp. MGL06, the first Rhizobium isolate from a marine environment, is a malachite-green-tolerant bacterium with a broader salinity tolerance (range: 0.5% to 9%) than other rhizobia. This study sequences and annotates the draft genome sequence of this strain. Genome sequence information provides a basis for analyzing the malachite green tolerance, broad salinity adaptation, nitrogen fixation properties, and taxonomic classification of the isolate. Copyright © 2014 Elsevier B.V. All rights reserved.

Primary and heterotrophic productivity relate to multikingdom diversity in a hypersaline mat

Energy Technology Data Exchange (ETDEWEB)

Bernstein, Hans C.; Brislawn, Colin J.; Dana, Karl; Flores-Wentz, Tobias; Cory, Alexandra B.; Fansler, Sarah J.; Fredrickson, James K.; Moran, James J.

2017-10-01

Benthic microbial ecosystems are widespread yet knowledge gaps still remain on the relationships between the diversity of species across kingdoms and productivity. Here, we ask two fundamental questions: 1) How does species diversity relate to the rates of primary and heterotrophic productivity? 2) How do diel variations in light-energy inputs influence productivity and microbiome diversity? To answer these questions, microbial mats from a magnesium sulfate hypersaline Lake were used to establish microcosms. Both the number and relatedness between bacterial and eukaryotic taxa in the microbiome were assayed via amplicon based sequencing of 16S and 18S rRNA genes over two diel cycles. These results correlated with biomass productivity obtained from substrate-specific 13C stable isotope incorporation that enabled comparisons between primary and heterotrophic productivity. Both bacterial and eukaryotic species richness and evenness were related only to the rates of 13C labeled glucose and acetate biomass incorporation. Interestingly, measures of these heterotrophic relationships changed from positive and negative correlations depending on carbon derived from glucose and acetate, respectively. Bacterial and eukaryotic diversity of this ecosystem is also controlled, in part, energy constraints imposed by changing irradiance over a diel cycle.

‘Lactobacillus raoultii’ sp. nov., a new bacterium isolated from the vaginal flora of a woman with bacterial vaginosis

Directory of Open Access Journals (Sweden)

B. Nicaise

2018-01-01

Full Text Available We report the isolation of a new bacterium species, ‘Lactobacillus raoultii’ strain Marseille P4006 (CSUR P4006, isolated from a vaginal sample of a 45-year-old woman with bacterial vaginosis. Keywords: Bacterial vaginosis, culturomics, emerging bacteria, human microbiota, Lactobacillus raoultii, vaginal microbiota

Draft genome sequence of Xylella fastidiosa pear leaf scorch strain in Taiwan

Science.gov (United States)

The draft genome sequence of Xylella fastidiosa pear leaf scorch strain (PLS229) isolated from pear cultivar Hengshan (Pyrus pyrifolia) in Taiwan is reported. The bacterium has a genome size of 2,733,013 bp with a G+C content of 53.1%. The PLS229 strain genome was annotated to have 3,259 open readin...

Isolation and characterization of Alicycliphilus denitrificans strain BC, which grows on benzene with chlorate as the electron acceptor

NARCIS (Netherlands)

Weelink, S.A.B.; Tan, N.C.G.; Broeke, H. ten; Kieboom, C. van den; Doesburg, W. van; Langenhoff, A.A.M.; Gerritse, J.; Junca, H.; Stams, A.J.M.

2008-01-01

A bacterium, strain BC, was isolated from a benzene-degrading chlorate-reducing enrichment culture. Strain BC degrades benzene in conjunction with chlorate reduction. Cells of strain BC are short rods that are 0.6 μm wide and 1 to 2 μm long, are motile, and stain gram negative. Strain BC grows on

Calorimetry and thermodynamic aspects of heterotrophic, mixotrophic, and phototrophic growth

NARCIS (Netherlands)

Stockar, von U.; Marison, I.; Janssen, M.G.J.; Patino, R.

2011-01-01

A simple stoichiometric model is proposed linking the biomass yield to the enthalpy and Gibbs energy changes in chemo-heterotrophic, mixotrophic, and photo-autotrophic microbial growth. A comparison with calorimetric experiments on the algae Chlorella vulgaris and Chlorella sorokiniana confirmed the

Bioleaching of Zn, Ni and Fe from contaminated sediments of water reservoir Ružín I with using heterotrophic bacterial strains

Directory of Open Access Journals (Sweden)

Katarína Jablonovská

2012-12-01

Full Text Available This study investigates the bioleaching of the zinc polluted sediment from water reservoir Ružín I using heterotrophic bacterialstrains ubiquitous in sediment environment. The effect of bacterial activity, pH, iron solubilization and precipitation and bioleachingmedium were evaluated. The pH value controls the bacterial activity during the leaching process. Addition of glucose to the bioleachingmedium accelerated the bioleaching rate. The results indicates, that the leachibility of zinc depend on the geochemical formsand surface interaction between metal and sediment fraction. Sequential chemical extraction confirm, that Zn was predominantly boundto the iron-manganese oxides.

Behavior of the meat-borne bacterium Lactobacillus sakei during its transit through the gastrointestinal tracts of axenic and conventional mice.

Science.gov (United States)

Chiaramonte, Fabrizio; Blugeon, Sébastien; Chaillou, Stéphane; Langella, Philippe; Zagorec, Monique

2009-07-01

A Lactobacillus sakei strain named FLEC01 was isolated from human feces and characterized genotypically. Comparison of the genetic features of this strain with those of both the meat-borne L. sakei strain 23K and another human isolate, LTH5590, showed that they belong to different but closely related clusters. The three L. sakei strains did not persist and only transited through the gastrointestinal tracts (GITs) of conventional C3H/HeN mice. In contrast, they all colonized the GITs of axenic mice and rapidly reached a population of 10(9) CFU/g of feces, which remained stable until day 51. Five days after mice were fed, a first subpopulation, characterized by small colonies, appeared and reached 50% of the total L. sakei population in mice. Fifteen to 21 days after feeding, a second subpopulation, characterized by rough colonies, appeared. It coexisted with the two other populations until day 51, and its cell shapes were also affected, suggesting a dysfunction of the cell division or cell wall. No clear difference between the behaviors of the meat-borne strain and the two human isolates in both conventional and axenic mice was observed, suggesting that L. sakei is a food-borne bacterium rather than a commensal one and that its presence in human feces originates from diet. Previous observations of Escherichia coli strains suggest that the mouse GIT environment could induce mutations to increase their survival and colonization capacities. Here, we observed similar mutations concerning a food-grade gram-positive bacterium for the first time.

Accumulation of fatty acids in Chlorella vulgaris under heterotrophic conditions in relation to activity of acetyl-CoAcarboxylase, temperature, and co-immobilization with Azospirillum brasilense [corrected].

Science.gov (United States)

Leyva, Luis A; Bashan, Yoav; Mendoza, Alberto; de-Bashan, Luz E

2014-10-01

The relation between fatty acid accumulation, activity of acetyl-CoA carboxylase (ACC), and consequently lipid accumulation was studied in the microalgae Chlorella vulgaris co-immobilized with the plant growth-promoting bacterium Azospirillum brasilense under dark heterotrophic conditions with Na acetate as a carbon source. In C. vulgaris immobilized alone, cultivation experiments for 6 days showed that ACC activity is directly related to fatty acid accumulation, especially in the last 3 days. In co-immobilization experiments, A. brasilense exerted a significant positive effect over ACC activity, increased the quantity in all nine main fatty acids, increased total lipid accumulation in C. vulgaris, and mitigated negative effects of nonoptimal temperature for growth. No correlation between ACC activity and lipid accumulation in the cells was established for three different temperatures. This study demonstrated that the interaction between A. brasilense and C. vulgaris has a significant effect on fatty acid and lipid accumulation in the microalgae.

Accumulation fatty acids of in Chlorella vulgaris under heterotrophic conditions in relation to activity of acetyl-CoA carboxylase, temperature, and co-immobilization with Azospirillum brasilense

Science.gov (United States)

Leyva, Luis A.; Bashan, Yoav; Mendoza, Alberto; de-Bashan, Luz E.

2014-10-01

The relation between fatty acid accumulation, activity of acetyl-CoA carboxylase (ACC), and consequently lipid accumulation was studied in the microalgae Chlorella vulgaris co-immobilized with the plant growth-promoting bacterium Azospirillum brasilense under dark heterotrophic conditions with Na acetate as a carbon source. In C. vulgaris immobilized alone, cultivation experiments for 6 days showed that ACC activity is directly related to fatty acid accumulation, especially in the last 3 days. In co-immobilization experiments, A. brasilense exerted a significant positive effect over ACC activity, increased the quantity in all nine main fatty acids, increased total lipid accumulation in C. vulgaris, and mitigated negative effects of nonoptimal temperature for growth. No correlation between ACC activity and lipid accumulation in the cells was established for three different temperatures. This study demonstrated that the interaction between A. brasilense and C. vulgaris has a significant effect on fatty acid and lipid accumulation in the microalgae.

Microbacter margulisiae gen. nov., sp. nov., a novel propionigenic bacterium isolated from sediments of an acid rock drainage pond

NARCIS (Netherlands)

Sanchez Andrea, I.; Luis Sanz, J.; Stams, A.J.M.

2014-01-01

A novel anaerobic propionigenic bacterium, strain ADRIT, was isolated from sediment of an acid rock drainage environment (Tinto River, Spain). Cells were small (0.4-0.6 x 1-1.7 µm), non-motile and non-spore forming rods. Cells possessed a Gram-negative cell wall structure and were vancomycin

Noncontiguous finished genome sequence and description of Paenibacillus antibioticophila sp. nov. GD11T, the type strain of Paenibacillus antibioticophila

Directory of Open Access Journals (Sweden)

G. Dubourg

2015-11-01

Full Text Available Paenibacillus antibioticophila strain GD11T sp. nov. is the type strain of a new species within the genus Paenibacillus. This strain, whose genome is described here, was isolated from human faeces of a 63-year-old woman with multidrug-resistant tuberculosis who was receiving numerous antibiotics at the time of stool collection. P. antibioticophila is a Gram-positive aerobic bacterium. We describe here the features of this bacterium, together with the complete genome sequence and annotation. The 5 562 631 bp long genome contains 5084 protein-coding and 71 RNA genes.

Albibacter methylovorans gen. nov., sp. nov., a novel aerobic, facultatively autotrophic and methylotrophic bacterium that utilizes dichloromethane.

Science.gov (United States)

Doronina, N V; Trotsenko, Y A; Tourova, T P; Kuznetsov, B B; Leisinger, T

2001-05-01

A novel genus, Albibacter, with one species, Albibacter methylovorans sp. nov., is proposed for a facultatively chemolithotrophic and methylotrophic bacterium (strain DM10T) with the ribulose bisphosphate (RuBP) pathway of C1 assimilation. The bacterium is a Gram-negative, aerobic, asporogenous, nonmotile, colourless rod that multiplies by binary fission. The organism utilizes dichloromethane, methanol, methylamine, formate and CO2/H2, as well as a variety of polycarbon compounds, as carbon and energy sources. It is neutrophilic and mesophilic. The major cellular fatty acids are straight-chain unsaturated C18:1, saturated C16:0 and cyclopropane C19:0 acids. The main ubiquinone is Q-10. The dominant phospholipids are phosphatidyl ethanolamine, phosphatidyl glycerol, phosphatidyl choline and cardiolipin. The DNA G+C content is 66.7 mol%. Strain DM10T has a very low degree of DNA-DNA hybridization (4-7%) with the type species of the genera Paracoccus, Xanthobacter, Blastobacter, Angulomicrobium, Ancylobacter and Ralstonia of RuBP pathway methylobacteria. Another approach, involving comparative 16S rDNA analysis, has shown that the novel isolate represents a separate branch within the alpha-2 subgroup of the Proteobacteria. The type species of the new genus is Albibacter methylovorans sp. nov.; the type strain is DM10T (= VKM B-2236T = DSM 13819T).

Kocuria polaris sp. nov., an orange-pigmented psychrophilic bacterium isolated from an Antarctic cyanobacterial mat sample.

Science.gov (United States)

Reddy, Gundlapally S N; Prakash, Jogadhenu S S; Prabahar, Vadivel; Matsumoto, Genki I; Stackebrandt, Erko; Shivaji, Sisinthy

2003-01-01

Strain CMS 76orT, an orange-pigmented bacterium, was isolated from a cyanobacterial mat sample from a pond located in McMurdo Dry Valley, Antarctica. On the basis of chemotaxonomic and phylogenetic properties, strain CMS 76orT was identified as a member of the genus Kocuria. It exhibited a 16S rDNA similarity of 99.8% and DNA-DNA similarity of 71% with Kocuria rosea (ATCC 186T). Phenotypic traits confirmed that strain CMS 78orT and K. rosea were well differentiated. Furthermore, strain CMS 76orT could be differentiated from the other reported species of Kocuria, namely Kocuria kristinae (ATCC 27570T), Kocuria varians (ATCC 15306T), Kocuria rhizophila (DSM 11926T) and Kocuria palustris (DSM 11025T), on the basis of a number of phenotypic features. Therefore, it is proposed that strain CMS 76orT (= MTCC 3702T = DSM 14382T) be assigned to a novel species of the genus Kocuria, as Kocuria polaris.

Elemental sulfur and thiosulfate disproportionation by Desulfocapsa sulfoexigens sp. nov., a new anaerobic bacterium isolated from marine surface sediment

DEFF Research Database (Denmark)

Finster, Kai; Liesack, Werner; Thamdrup, Bo

1998-01-01

A mesophilic, anaerobic, gram-negative bacterium, strain SB164P1, was enriched and isolated from oxidized marine surface sediment with elemental sulfur as the sole energy substrate in the presence of ferrihydrite. Elemental sulfur was disproportionated to hydrogen sulfide and sulfate. Growth was ...

Biochemical and genetical analysis reveal a new clade of biovar 3 Dickeya spp. strains isolated from potato in Europe

NARCIS (Netherlands)

Slawiak, M.; Beckhoven, van J.R.C.M.; Speksnijder, A.G.C.L.; Czajkowski, R.L.; Grabe, G.; Wolf, van der J.M.

2009-01-01

Sixty-five potato strains of the soft rot-causing plant pathogenic bacterium Dickeya spp., and two strains from hyacinth, were characterised using biochemical assays, REP-PCR genomic finger printing, 16S rDNA and dnaX sequence analysis. These methods were compared with nineteen strains representing

Draft Genome Sequence of the Soil Bacterium Burkholderia terrae Strain BS001, Which Interacts with Fungal Surface Structures

DEFF Research Database (Denmark)

Nazir, Rashid; Hansen, Martin A.; Sorensen, Soren

2012-01-01

Burkholderia terrae BS001 is a soil bacterium which was originally isolated from the mycosphere of the ectomycorrhizal fungus Laccaria proxima. It exhibits a range of fungus-interacting traits which reveal its propensity to actively interact at fungal interfaces. Here, we present the approximately...

Circadian cycles in growth and feeding rates of heterotrophic protist plankton

DEFF Research Database (Denmark)

Jakobsen, Hans Henrik; Strom, S.L.

2004-01-01

Growth and feeding rates of four species of planktonic marine heterotrophic protists showed pronounced diel cycles. In most cases, rates were higher during the day and lower at night. However, for the ciliate Strobilidium sp., growth was highest at night. In another ciliate species, Balanion...... comatum, no day-night difference in growth and feeding rates was found. Maintenance of day-night rate differences during 24-h exposures to continuous darkness demonstrated that most of these protists had circadian cycles. The heterotrophic dinoflagellate Oxyrrhis marina exhibited a clear irradiance...... to culturing in a day: night light cycle in O. marina and found that resetting the circadian cycle in this dinoflagellate temporarily arrested growth and feeding. We suggest that protists use a time-integrated light threshold rather than an instantaneous irradiance to maintain the circadian cell cycle...

Complete genome of Pandoraea pnomenusa RB-38, an oxalotrophic bacterium isolated from municipal solid waste landfill site.

Science.gov (United States)

Lim, Yan-Lue; Ee, Robson; Yong, Delicia; Tee, Kok-Keng; Yin, Wai-Fong; Chan, Kok-Gan

2015-11-20

Pandoraea pnomenusa RB-38 is a bacterium isolated from a former sanitary landfill site. Here, we present the complete genome of P. pnomenusa RB38 in which an oxalate utilization pathway was identified. The genome analysis suggested the potential of this strain as an effective biocontrol agent against oxalate-producing phytopathogens. Copyright © 2015 Elsevier B.V. All rights reserved.

Autotrophic and heterotrophic activity in Arctic first-year sea ice

DEFF Research Database (Denmark)

Søgaard, Dorte Haubjerg; Kristensen, Morten; Rysgaard, Søren

2010-01-01

in plastic bags with subsequent melting and measurements of changes in total O2 concentrations. The standard incubations showed that the annual succession followed a distinctive pattern, with a low, almost balancing heterotrophic and autotrophic activity during February and March. This period was followed...

UV-induced variability of the amylolytic thermophilic bacterium Bacillus diastaticus

International Nuclear Information System (INIS)

Murygina, V.P.

1978-01-01

UV-induced variability of a thermophilic bacterium Bacillus diastaticus 13 by amylase formation has been studied. It has been shown, that variability limits in amylase biosynthesis vary from 2.2 to 158.7% under UV irradiation. At 41.8x10 2 erg/mm 2 UV dose a ''plus-variant'' designated as the UV1 mutant has been prepared. Its subsequent selection without using mutagene permitted to select the UV 1-25 variant, exceeding the initial strain in amylase biosynthesis by 43.3%. Under UV irradiation two low-active in biosynthesis amylases of the mutant were prepared. Demands for growth factors of some mutant have been studied as well

UV-induced variability of the amylolytic thermophilic bacterium Bacillus diastaticus

Energy Technology Data Exchange (ETDEWEB)

Murygina, V P

1978-03-01

Ultroviolet-radioinduced variability in analyase biosynthesis of a thermophilic bacterium Bacillus diastaticus 13, has been studied. It has been shown that amylase biosynthesis varies from 2.2 to 158.7% under UV irradiation. At 41.8x10/sup 2/ erg/mm/sup 2/ UV dose, a ''plus-variant'' designated as the UV1 mutant has been prepared. Its subsequent selection without using mutagene permitted to select the UV 1-25 variant, exceeding the initial strain in amylase biosynthesis by 43.3%. Under UV irradiation, two mutants with reduced amylose biosynthesis activity were prepared. Demands for growth factors by some mutants have been studied as well.

Draft genome sequence of a caprolactam degrader bacterium: Pseudomonas taiwanensis strain SJ9

Directory of Open Access Journals (Sweden)

Sung-Jun Hong

Full Text Available Abstract Pseudomonas taiwanensis strain SJ9 is a caprolactam degrader, isolated from industrial wastewater in South Korea and considered to have the potential for caprolactam bioremediation. The genome of this strain is approximately 6.2 Mb (G + C content, 61.75% with 6,010 protein-coding sequences (CDS, of which 46% are assigned to recognized functional genes. This draft genome of strain SJ9 will provide insights into the genetic basis of its caprolactam-degradation ability.

Amerindian Helicobacter pylori strains go extinct, as european strains expand their host range.

Directory of Open Access Journals (Sweden)

Maria G Domínguez-Bello

Full Text Available We studied the diversity of bacteria and host in the H. pylori-human model. The human indigenous bacterium H. pylori diverged along with humans, into African, European, Asian and Amerindian groups. Of these, Amerindians have the least genetic diversity. Since niche diversity widens the sets of resources for colonizing species, we predicted that the Amerindian H. pylori strains would be the least diverse. We analyzed the multilocus sequence (7 housekeeping genes of 131 strains: 19 cultured from Africans, 36 from Spanish, 11 from Koreans, 43 from Amerindians and 22 from South American Mestizos. We found that all strains that had been cultured from Africans were African strains (hpAfrica1, all from Spanish were European (hpEurope and all from Koreans were hspEAsia but that Amerindians and Mestizos carried mixed strains: hspAmerind and hpEurope strains had been cultured from Amerindians and hpEurope and hpAfrica1 were cultured from Mestizos. The least genetically diverse H. pylori strains were hspAmerind. Strains hpEurope were the most diverse and showed remarkable multilocus sequence mosaicism (indicating recombination. The lower genetic structure in hpEurope strains is consistent with colonization of a diversity of hosts. If diversity is important for the success of H. pylori, then the low diversity of Amerindian strains might be linked to their apparent tendency to disappear. This suggests that Amerindian strains may lack the needed diversity to survive the diversity brought by non-Amerindian hosts.

The abundance and diversity of heterotrophic bacteria as a function of harvesting frequency of duckweed (Lemna minor L.) in recirculating aquaculture systems.

Science.gov (United States)

Ardiansyah, A; Fotedar, R

2016-07-01

Duckweed (Lemna minor L.) is a potential biofilter for nutrient removal and acts as a substrate for heterotrophic bacteria in recirculating aquaculture systems (RAS). Here, we determined the effects of harvesting frequency of duckweed on heterotrophic bacteria in RAS. Twelve independent RAS consisting of fish-rearing tank, biofilter tank and waste-collection tank were used to study the interactions between duckweed harvest frequencies up to 6 days and the composition, abundance and diversity of heterotrophic bacteria. After 36 days, heterotrophic bacteria in the biofilter tank were primarily Gram-negative cocci or ovoid, coccobacilli, Gram-negative bacilli and Gram-positive bacilli. Most bacterial genera were Bacillus and Pseudomonas while the least common was Acinetobacter. Duckweed harvested after every 2 days produced the highest specific growth rates (SGR) and total harvested biomass of duckweed, but harboured less abundant bacteria, whereas 6-day harvests had a higher growth index (GI) of duckweed than 2-day harvests, but caused a poor relationship between SGR and biomass harvest with the abundance and diversity of heterotrophic bacteria. Stronger correlations (R(2)  > 0·65) between duckweed SGR and biomass harvest with the heterotrophic bacteria diversity were observed at 4-day harvest frequency and the control. This study provides significant information on the interaction between the harvest frequency of duckweed and the composition, abundance and diversity of heterotrophic bacteria in recirculating aquaculture systems (RAS). Different harvest frequencies significantly influence the abundance and diversity of heterotrophic bacteria, which in turn may influence the nitrogen uptake efficiency of the system. The research is useful in improving the efficiency of removing nitrogenous metabolites in RAS directly by the duckweed and associated heterotrophic bacteria. © 2016 The Society for Applied Microbiology.

Marine Bacteria from Danish Coastal Waters Show Antifouling Activity against the Marine Fouling Bacterium Pseudoalteromonas sp. Strain S91 and Zoospores of the Green Alga Ulva australis Independent of Bacteriocidal Activity▿†

Science.gov (United States)

Bernbom, Nete; Ng, Yoke Yin; Kjelleberg, Staffan; Harder, Tilmann; Gram, Lone

2011-01-01

The aims of this study were to determine if marine bacteria from Danish coastal waters produce antifouling compounds and if antifouling bacteria could be ascribed to specific niches or seasons. We further assess if antibacterial effect is a good proxy for antifouling activity. We isolated 110 bacteria with anti-Vibrio activity from different sample types and locations during a 1-year sampling from Danish coastal waters. The strains were identified as Pseudoalteromonas, Phaeobacter, and Vibrionaceae based on phenotypic tests and partial 16S rRNA gene sequence similarity. The numbers of bioactive bacteria were significantly higher in warmer than in colder months. While some species were isolated at all sampling locations, others were niche specific. We repeatedly isolated Phaeobacter gallaeciensis at surfaces from one site and Pseudoalteromonas tunicata at two others. Twenty-two strains, representing the major taxonomic groups, different seasons, and isolation strategies, were tested for antiadhesive effect against the marine biofilm-forming bacterium Pseudoalteromonas sp. strain S91 and zoospores of the green alga Ulva australis. The antiadhesive effects were assessed by quantifying the number of strain S91 or Ulva spores attaching to a preformed biofilm of each of the 22 strains. The strongest antifouling activity was found in Pseudoalteromonas strains. Biofilms of Pseudoalteromonas piscicida, Pseudoalteromonas tunicata, and Pseudoalteromonas ulvae prevented Pseudoalteromonas S91 from attaching to steel surfaces. P. piscicida killed S91 bacteria in the suspension cultures, whereas P. tunicata and P. ulvae did not; however, they did prevent adhesion by nonbactericidal mechanism(s). Seven Pseudoalteromonas species, including P. piscicida and P. tunicata, reduced the number of settling Ulva zoospores to less than 10% of the number settling on control surfaces. The antifouling alpP gene was detected only in P. tunicata strains (with purple and yellow pigmentation), so

Noncontiguous finished genome sequence and description of Virgibacillus massiliensis sp. nov., a moderately halophilic bacterium isolated from human gut

Directory of Open Access Journals (Sweden)

S. Khelaifia

2015-11-01

Full Text Available Strain Vm-5T was isolated from the stool specimen of a 10-year-old Amazonian boy. This bacterium is a Gram-positive, strictly aerobic rod, motile by a polar flagellum. Here we describe its phenotypic characteristics and complete genome sequence. The 4 353 177 bp long genome exhibits a G + C content of 36.87% and contains 4394 protein-coding and 125 predicted RNA genes. Phylogenetically and genetically, strain Vm-c is a member of the genus Virgibacillus but is distinct enough to be classified as a new species. We propose the creation of V. massiliensis sp. nov., whose type strain is strain Vm-5T (CSUR P971 = DSM 28587.

Draft Genome Sequence of Ochrobactrum intermedium Strain SA148, a Plant Growth-Promoting Desert Rhizobacterium

KAUST Repository

Lafi, Feras Fawzi

2017-03-03

Ochrobactrum intermedium strain SA148 is a plant growth-promoting bacterium isolated from sandy soil in the Jizan area of Saudi Arabia. Here, we report the 4.9-Mb draft genome sequence of this strain, highlighting different pathways characteristic of plant growth promotion activity and environmental adaptation of SA148.

Complete genome sequence of the aerobically denitrifying thermophilic bacterium Chelatococcus daeguensis TAD1

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Yunlong Yang

Full Text Available ABSTRACT Chelatococcus daeguensis TAD1 is a themophilic bacterium isolated from a biotrickling filter used to treat NOx in Ruiming Power Plant, located in Guangzhou, China, which shows an excellent aerobic denitrification activity at high temperature. The complete genome sequence of this strain was reported in the present study. Genes related to the aerobic denitrification were identified through whole genome analysis. This work will facilitate the mechanism of aerobic denitrification and provide evidence for its potential application in the nitrogen removal.

Burkholderia jiangsuensis sp. nov., a methyl parathion degrading bacterium, isolated from methyl parathion contaminated soil.

Science.gov (United States)

Liu, Xu-Yun; Li, Chun-Xiu; Luo, Xiao-Jing; Lai, Qi-Liang; Xu, Jian-He

2014-09-01

A methyl parathion (MP) degrading bacterial strain, designated MP-1(T), was isolated from a waste land where pesticides were formerly manufactured in Jiangsu province, China. Polyphasic taxonomic studies showed that MP-1(T) is a Gram-stain-negative, non-spore-forming, rod-shaped and motile bacterium. The bacterium could grow at salinities of 0-1 % (w/v) and temperatures of 15-40 °C. Strain MP-1(T) could reduce nitrate to nitrite, utilize d-glucose and l-arabinose, but not produce indole, or hydrolyse gelatin. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that MP-1(T) belongs to the genus Burkholderia, showing highest sequence similarity to Burkholderia grimmiae DSM 25160(T) (98.5 %), and similar strains including Burkholderia zhejiangensis OP-1(T) (98.2 %), Burkholderia choica LMG 22940(T) (97.5 %), Burkholderia glathei DSM 50014(T) (97.4 %), Burkholderia terrestris LMG 22937(T) (97.2 %) and Burkholderia telluris LMG 22936(T) (97.0 %). In addition, the gyrB and recA gene segments of strain MP-1(T) exhibited less than 89.0 % and 95.1 % similarities with the most highly-related type strains indicated above. The G+C content of strain MP-1(T) was 62.6 mol%. The major isoprenoid quinone was ubiquinone Q-8. The predominant polar lipids comprised phosphatidyl ethanolamine, phosphatidyl glycerol, aminolipid and phospholipid. The principal fatty acids in strain MP-1(T) were C18 : 1ω7c/C18 : 1ω6c (23.3 %), C16 : 0 (16.8 %), cyclo-C17 : 0 (15.0 %), C16 : 1ω7c/C16 : 1ω6 (8.5 %), cyclo-C19 : 0ω8c (8.1 %), C16 : 1 iso I/C14 : 0 3-OH (5.7 %), C16 : 0 3-OH (5.6 %) and C16 : 02-OH (5.1 %). The DNA-DNA relatedness values between strain MP-1(T) and the three type strains (B. grimmiae DSM 25160(T), B. zhejiangensis OP-1(T) and B. glathei DSM 50014(T)) ranged from 24.6 % to 37.4 %. In accordance with phenotypic and genotypic characteristics, strain MP-1(T) represents a novel

Distribution and enzymatic activity of heterotrophic bacteria decomposing selected macromolecular compounds in a Baltic Sea sandy beach

Science.gov (United States)

Podgórska, B.; Mudryk, Z. J.

2003-03-01

The potential capability to decompose macromolecular compounds, and the level of extracellular enzyme activities were determined in heterotrophic bacteria isolated from a sandy beach in Sopot on the Southern Baltic Sea coast. Individual isolates were capable of hydrolysing a wide spectrum of organic macromolecular compounds. Lipids, gelatine, and DNA were hydrolyzed most efficiently. Only a very small percentage of strains were able to decompose cellulose, and no pectinolytic bacteria were found. Except for starch-hydrolysis, no significant differences in the intensity of organic compound decomposition were recorded between horizontal and vertical profiles of the studied beach. Of all the studied extracellular enzymes, alkaline phosphatase, esterase lipase, and leucine acrylaminidase were most active; in contrast, the activity α-fucosidase, α-galactosidase and β-glucouronidase was the weakest. The level of extracellular enzyme activity was similar in both sand layers.

Xenophilus arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from soil.

Science.gov (United States)

Li, Qin-Fen; Sun, Li-Na; Kwon, Soon-Wo; Chen, Qing; He, Jian; Li, Shun-Peng; Zhang, Jun

2014-06-01

A Gram-reaction-negative, aerobic, motile, rod-shaped, arsenite [As(III)]-resistant bacterium, designated strain YW8(T), was isolated from agricultural soil. 16S rRNA gene sequence analysis showed over 97% sequence similarity to strains of the environmental species Xenophilus azovorans, Xenophilus aerolatus, Simplicispira metamorpha, Variovorax soli, and Xylophilus ampelinus. However, the phylogenetic tree indicated that strain YW8(T) formed a separate clade from Xenophilus azovorans. DNA-DNA hybridization experiments showed that the DNA-DNA relatedness values between strain YW8(T) and its closest phylogenetic neighbours were below 24.2-35.5%, which clearly separated the strain from these closely related species. The major cellular fatty acids of strain YW8(T) were C(16 : 0), C(17 : 0) cyclo, C(18 : 1)ω7c, and summed feature 3(C(16 : 1)ω6c and/or C(16 : 1)ω7c). The genomic DNA G+C content was 69.3 mol%, and the major respiratory quinone was ubiquinone-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, an unknown polar lipid and phosphatidylserine. The major polyamines were 2-hydroxyputrescine and putrescine. On the basis of morphological, physiological and biochemical characteristics, phylogenetic position, DNA-DNA hybridization and chemotaxonomic data, strain YW8(T) is considered to represent a novel species of the genus Xenophilus, for which the name Xenophilus arseniciresistens sp. nov. is proposed; the type strain is YW8(T) ( = CCTCC AB2012103(T) = KACC 16853(T)). © 2014 IUMS.

Draft genome sequence of Bradyrhizobium sp. strain BR 3267, an elite strain recommended for cowpea inoculation in Brazil

Directory of Open Access Journals (Sweden)

Jean Luiz Simões-Araújo

Full Text Available Abstract The strain BR 3267 is a nitrogen-fixing symbiotic bacteria isolated from soil of semi-arid area of Brazilian Northeast using cowpea as the trap plant. This strain is used as commercial inoculant for cowpea and presents high efficient in nitrogen fixation as consequence of its adaptation potential to semi-arid conditions. We report here the draft genome sequence of Bradyrhizobium sp. strain BR 3267, an elite bacterium used as inoculant for cowpea. Whole genome sequencing of BR 3267 using Illumina MiSeq sequencing technology has 55 scaffolds with a total genome size of 7,904,309 bp and C+G 63%. Annotation was added by the RAST prokaryotic genome annotation service and has shown 7314 coding sequences and 52 RNA genes.

The moisture response of soil heterotrophic respiration: interaction with soil properties

DEFF Research Database (Denmark)

Moyano, F E; Vasilyeva, N; Bouckaert, L

2012-01-01

the heterotrophic respiration response to moisture have limited empirical support and introduce an uncertainty of at least 4% in global soil carbon stock predictions by 2100. The necessity of improving the representation of this relationship in models has been highlighted in recent studies. Here we present a data......Soil moisture is of primary importance for predicting the evolution of soil carbon stocks and fluxes, both because it strongly controls organic matter decomposition and because it is predicted to change at global scales in the following decades. However, the soil functions used to model......-driven analysis of soil moisture-respiration relations based on 90 soils. With the use of linear models we show how the relationship between soil heterotrophic respiration and different measures of soil moisture is consistently affected by soil properties. The empirical models derived include main effects...

Non-Redfield, nutrient synergy and flexible internal elemental stoichiometry in a marine bacterium.

Science.gov (United States)

Trautwein, Kathleen; Feenders, Christoph; Hulsch, Reiner; Ruppersberg, Hanna S; Strijkstra, Annemieke; Kant, Mirjam; Vagts, Jannes; Wünsch, Daniel; Michalke, Bernhard; Maczka, Michael; Schulz, Stefan; Hillebrand, Helmut; Blasius, Bernd; Rabus, Ralf

2017-05-01

The stoichiometric constraints of algal growth are well understood, whereas there is less knowledge for heterotrophic bacterioplankton. Growth of the marine bacterium Phaeobacter inhibens DSM 17395, belonging to the globally distributed Roseobacter group, was studied across a wide concentration range of NH4+ and PO43-. The unique dataset covers 415 different concentration pairs, corresponding to 207 different molar N:P ratios (from 10-2 to 105). Maximal growth (by growth rate and biomass yield) was observed within a restricted concentration range at N:P ratios (∼50-120) markedly above Redfield. Experimentally determined growth parameters deviated to a large part from model predictions based on Liebig's law of the minimum, thus implicating synergistic co-limitation due to biochemical dependence of resources. Internal elemental ratios of P. inhibens varied with external nutrient supply within physiological constraints, thus adding to the growing evidence that aquatic bacteria can be flexible in their internal elemental composition. Taken together, the findings reported here revealed that P. inhibens is well adapted to fluctuating availability of inorganic N and P, expected to occur in its natural habitat (e.g. colonized algae, coastal areas). Moreover, this study suggests that elemental variability in bacterioplankton needs to be considered in the ecological stoichiometry of the oceans. © FEMS 2017.

RARE OCCURRENCE OF HETEROTROPHIC BACTERIA WITH PATHOGENIC POTENTIAL IN POTABLE WATER

Science.gov (United States)

Since the discovery of Legionella pneumophila, an opportunistic pathogen that is indigenous to water, microbiologists have speculated that there may be other opportunistic pathogens among the numerous heterotrophic bacteria found in potable water. The USEPA developed a series of...

Draft Genome Sequence of the Antagonistic Rhizosphere Bacterium Serratia plymuthica Strain PRI-2C

NARCIS (Netherlands)

Garbeva, P.; van Elsas, J.D.; de Boer, W.

Serratia plymuthica strain PRI-2C is a rhizosphere bacterial strain with antagonistic activity against different plant pathogens. Here we present the 5.39-Mb (G+C content, 55.67%) draft genome sequence of S. plymuthica strain PRI-2C with the aim of providing insight into the genomic basis of its

Molecular identification of phosphate solubilizing bacterium ...

African Journals Online (AJOL)

A phosphate solubilizing bacterium was isolated from the rhizosphere soil of upland rice and identified by 16S rRNA gene sequencing. The gene sequence showed 99% homology with Alcaligenes faecalis. Based on the gene sequence homology, it was identified as A. faecalis. Interaction effect of this bacterium on growth ...

“Nigerium massiliense” gen. nov., sp. nov., a new bacterium isolated from the gut from a patient with acute malnutrition

Directory of Open Access Journals (Sweden)

Sory Ibrahima Traore

2016-09-01

Full Text Available We propose the main characteristics of a new bacterium named “Nigerium massiliense” strain SIT5 (CSURP1302 that was isolated from the stool of a 2-year-old Nigerian child suffering from kwashiorkor, a form of severe acute malnutrition. Keywords: Culturomics, Taxonomy, Genomics, Taxono-genomics, “Nigerium massiliense”

Extreme furfural tolerance of a soil bacterium Enterobacter cloacae GGT036.

Science.gov (United States)

Choi, Sun Young; Gong, Gyeongtaek; Park, Hong-Sil; Um, Youngsoon; Sim, Sang Jun; Woo, Han Min

2015-01-10

Detoxification process of cellular inhibitors including furfural is essential for production of bio-based chemicals from lignocellulosic biomass. Here we isolated an extreme furfural-tolerant bacterium Enterobacter cloacae GGT036 from soil sample collected in Mt. Gwanak, Republic of Korea. Among isolated bacteria, only E. cloacae GGT036 showed cell growth with 35 mM furfural under aerobic culture. Compared to the maximal half inhibitory concentration (IC50) of well-known industrial strains Escherichia coli (24.9 mM furfural) and Corynebacterium glutamicum (10 mM furfural) based on the cell density, IC50 of E. cloacae GGT036 (47.7 mM) was significantly higher after 24 h, compared to E. coli and C. glutamicum. Since bacterial cell growth was exponentially inhibited depending on linearly increased furfural concentrations in the medium, we concluded that E. cloacae GGT036 is an extreme furfural-tolerant bacterium. Recently, the complete genome sequence of E. cloacae GGT036 was announced and this could provide an insight for engineering of E. cloacae GGT036 itself or other industrially relevant bacteria. Copyright © 2014 Elsevier B.V. All rights reserved.

High quality draft genome sequence of the moderately halophilic bacterium Pontibacillus yanchengensis Y32(T) and comparison among Pontibacillus genomes.

Science.gov (United States)

Huang, Jing; Qiao, Zi Xu; Tang, Jing Wei; Wang, Gejiao

2015-01-01

Pontibacillus yanchengensis Y32(T) is an aerobic, motile, Gram-positive, endospore-forming, and moderately halophilic bacterium isolated from a salt field. In this study, we describe the features of P. yanchengensis strain Y32(T) together with a comparison with other four Pontibacillus genomes. The 4,281,464 bp high-quality-draft genome of strain Y32(T) is arranged into 153 contigs containing 3,965 protein-coding genes and 77 RNA encoding genes. The genome of strain Y32(T) possesses many genes related to its halophilic character, flagellar assembly and chemotaxis to support its survival in a salt-rich environment.

Akkermansia glycaniphila sp. nov., an anaerobic mucin-degrading bacterium isolated from reticulated python faeces.

Science.gov (United States)

Ouwerkerk, Janneke P; Aalvink, Steven; Belzer, Clara; de Vos, Willem M

2016-11-01

A Gram-stain-negative, non-motile, strictly anaerobic, oval-shaped, non-spore-forming bacterium (strain PytT) was isolated from reticulated python faeces. Strain PytT was capable of using mucin as sole carbon, energy and nitrogen source. Cells could grow singly, in pairs, and were also found to aggregate. Scanning electron microscopy revealed the presence of filamentous structures connecting individual bacterial cells. Strain PytT could grow on a limited number of single sugars, including N-acetylglucosamine, N-acetylgalactosamine, glucose, lactose and galactose, but only when a plentiful protein source was provided. Phylogenetic analysis based on 16S rRNA gene sequencing showed strain PytT to belong to the Verrucomicrobiae class I, family Akkermansiaceae, genus Akkermansia, with Akkermansia muciniphila MucT as the closest relative (94.4 % sequence similarity). DNA-DNA hybridization revealed low relatedness of 28.3 % with A. muciniphila MucT. The G+C content of DNA from strain PytT was 58.2 mol%. The average nucleotide identity (ANI) of the genome of strain PytT compared to the genome of strain MucT was 79.7 %. Chemotaxonomic data supported the affiliation of strain PytT to the genus Akkermansia. Based on phenotypic, phylogenetic and genetic characteristics, strain PytT represents a novel species of the genus Akkermansia, for which the name Akkermansia glycaniphila sp. nov. is proposed. The type strain is PytT (=DSM 100705T=CIP 110913T).

Economic Game Theory to Model the Attenuation of Virulence of an Obligate Intracellular Bacterium.

Science.gov (United States)

Tago, Damian; Meyer, Damien F

2016-01-01

Diseases induced by obligate intracellular pathogens have a large burden on global human and animal health. Understanding the factors involved in the virulence and fitness of these pathogens contributes to the development of control strategies against these diseases. Based on biological observations, a theoretical model using game theory is proposed to explain how obligate intracellular bacteria interact with their host. The equilibrium in such a game shows that the virulence and fitness of the bacterium is host-triggered and by changing the host's defense system to which the bacterium is confronted, an evolutionary process leads to an attenuated strain. Although, the attenuation procedure has already been conducted in practice in order to develop an attenuated vaccine (e.g., with Ehrlichia ruminantium), there was a lack of understanding of the theoretical basis behind this process. Our work provides a model to better comprehend the existence of different phenotypes and some underlying evolutionary mechanisms for the virulence of obligate intracellular bacteria.

Desulfotomaculum arcticum sp. nov., a novel spore-forming, moderately thermophilic, sulfate-reducing bacterium isolated from a permanently cold fjord sediment of Svalbard

DEFF Research Database (Denmark)

Vandieken, Verona; Knoblauch, Christian; Jørgensen, Bo Barker

2006-01-01

Strain 15T is a novel spore-forming, sulfate-reducing bacterium isolated from a permanently cold fjord sediment of Svalbard. Sulfate could be replaced by sulfite or thiosulfate. Hydrogen, formate, lactate, propionate, butyrate, hexanoate, methanol, ethanol, propanol, butanol, pyruvate, malate...

[Isolation, identification and characterization of a diethylstilbestrol-degrading bacterial strain Serratia sp].

Science.gov (United States)

Xu, Ran-Fang; Sun, Min-Xia; Liu, Juan; Wang, Hong; Li, Xin; Zhu, Xue-Zhu; Ling, Wan-Ting

2014-08-01

Utilizing the diethylstilbestrol (DES)-degrading bacteria to biodegrade DES is a most reliable technique for cleanup of DES pollutants from the environment. However, little information is available heretofore on the isolation of DES-degrading bacteria and their DES removal performance in the environment. A novel bacterium capable of degrading DES was isolated from the activated sludge of a wastewater treatment plant. According to its morphology, physiochemical characteristics, and 16S rDNA sequence analysis, this strain was identified as Serratia sp.. The strain was an aerobic bacterium, and it could degrade 68.3% of DES (50 mg x L(-1)) after culturing for 7 days at 30 degrees C, 150 r x min(-1) in shaking flasks. The optimal conditions for DES biodegradation by the obtained strain were 30 degrees C, 40-60 mg x L(-1) DES, pH 7.0, 5% of inoculation volume, 0 g x L(-1) of added NaCl, and 10 mL of liquid medium volume in 100 mL flask.

Large-scale bioreactor production of the herbicide-degrading Aminobacter sp. strain MSH1

DEFF Research Database (Denmark)

Schultz-Jensen, Nadja; Knudsen, Berith Elkær; Frkova, Zuzana

2014-01-01

The Aminobacter sp. strain MSH1 has potential for pesticide bioremediation because it degrades the herbicide metabolite 2,6-dichlorobenzamide (BAM). Production of the BAM-degrading bacterium using aerobic bioreactor fermentation was investigated. A mineral salt medium limited for carbon and with ......The Aminobacter sp. strain MSH1 has potential for pesticide bioremediation because it degrades the herbicide metabolite 2,6-dichlorobenzamide (BAM). Production of the BAM-degrading bacterium using aerobic bioreactor fermentation was investigated. A mineral salt medium limited for carbon...... and with an element composition similar to the strain was generated. The optimal pH and temperature for strain growth were determined using shaker flasks and verified in bioreactors. Glucose, fructose, and glycerol were suitable carbon sources for MSH1 (μ =0.1 h−1); slower growth was observed on succinate and acetic...... acid (μ =0.01 h−1). Standard conditions for growth of theMSH1 strain were defined at pH 7 and 25 °C, with glucose as the carbon source. In bioreactors (1 and 5 L), the specific growth rate of MSH1 increased from μ =0.1 h−1 on traditional mineral salt medium to μ =0.18 h−1 on the optimized mineral salt...

Halomonas titanicae sp. nov., a halophilic bacterium isolated from the RMS Titanic.

Science.gov (United States)

Sánchez-Porro, Cristina; Kaur, Bhavleen; Mann, Henrietta; Ventosa, Antonio

2010-12-01

A Gram-negative, heterotrophic, aerobic, non-endospore-forming, peritrichously flagellated and motile bacterial strain, designated BH1(T), was isolated from samples of rusticles, which are formed in part by a consortium of micro-organisms, collected from the RMS Titanic wreck site. The strain grew optimally at 30-37°C, pH 7.0-7.5 and in the presence of 2-8 % (w/v) NaCl. We carried out a polyphasic taxonomic study in order to characterize the strain in detail. Phylogenetic analyses based on 16S rRNA gene sequence comparison indicated that strain BH1(T) clustered within the branch consisting of species of Halomonas. The most closely related type strains were Halomonas neptunia (98.6 % 16S rRNA sequence similarity), Halomonas variabilis (98.4 %), Halomonas boliviensis (98.3 %) and Halomonas sulfidaeris (97.5 %). Other closely related species were Halomonas alkaliphila (96.5 % sequence similarity), Halomonas hydrothermalis (96.3 %), Halomonas gomseomensis (96.3 %), Halomonas venusta (96.3 %) and Halomonas meridiana (96.2 %). The major fatty acids of strain BH1(T) were C(18 : 1)ω7c (36.3 %), C(16 : 0) (18.4 %) and C(19 : 0) cyclo ω8c (17.9 %). The DNA G+C content was 60.0 mol% (T(m)). Ubiquinone 9 (Q-9) was the major lipoquinone. The phenotypic features, fatty acid profile and DNA G+C content further supported the placement of strain BH1(T) in the genus Halomonas. DNA-DNA hybridization values between strain BH1(T) and H. neptunia CECT 5815(T), H. variabilis DSM 3051(T), H. boliviensis DSM 15516(T) and H. sulfidaeris CECT 5817(T) were 19, 17, 30 and 29 %, respectively, supporting the differential taxonomic status of BH1(T). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain BH1(T) is considered to represent a novel species, for which the name Halomonas titanicae sp. nov. is proposed. The type strain is BH1(T) (=ATCC BAA-1257(T) =CECT 7585(T) =JCM 16411(T) =LMG 25388(T)).

Complete genome of Pseudomonas sp. strain L10.10, a psychrotolerant biofertilizer that could promote plant growth.

Science.gov (United States)

See-Too, Wah Seng; Lim, Yan-Lue; Ee, Robson; Convey, Peter; Pearce, David A; Yin, Wai-Fong; Chan, Kok Gan

2016-03-20

Pseudomonas sp. strain L10.10 (=DSM 101070) is a psychrotolerant bacterium which was isolated from Lagoon Island, Antarctica. Analysis of its complete genome sequence indicates its possible role as a plant-growth promoting bacterium, including nitrogen-fixing ability and indole acetic acid (IAA)-producing trait, with additional suggestion of plant disease prevention attributes via hydrogen cyanide production. Copyright © 2016 Elsevier B.V. All rights reserved.

Isolation of a human intestinal anaerobe, Bifidobacterium sp. strain SEN, capable of hydrolyzing sennosides to sennidins.

OpenAIRE

Akao, T; Che, Q M; Kobashi, K; Yang, L; Hattori, M; Namba, T

1994-01-01

A strictly anaerobic bacterium capable of metabolizing sennosides was isolated from human feces and identified as Bifidobacterium sp., named strain SEN. The bacterium hydrolyzed sennosides A and B to sennidins A and B via sennidin A and B 8-monoglucosides, respectively. Among nine species of Bifidobacterium having beta-glucosidase activity, only Bifidobacterium dentium and B. adolescentis metabolized sennoside B to sennidin B, suggesting that the sennoside-metabolizing bacteria produce a nove...

Culturing Heterotrophic Protists from the Baltic Sea: Mostly the "Usual Suspects" but a Few Novelties as Well.

Science.gov (United States)

Weber, Felix; Mylnikov, Alexander P; Jürgens, Klaus; Wylezich, Claudia

2017-03-01

The study of cultured strains has a long tradition in protistological research and has greatly contributed to establishing the morphology, taxonomy, and ecology of many protist species. However, cultivation-independent techniques, based on 18S rRNA gene sequences, have demonstrated that natural protistan assemblages mainly consist of hitherto uncultured protist lineages. This mismatch impedes the linkage of environmental diversity data with the biological features of cultured strains. Thus, novel taxa need to be obtained in culture to close this knowledge gap. In this study, traditional cultivation techniques were applied to samples from coastal surface waters and from deep oxygen-depleted waters of the Baltic Sea. Based on 18S rRNA gene sequencing, 126 monoclonal cultures of heterotrophic protists were identified. The majority of the isolated strains were affiliated with already cultured and described taxa, mainly chrysophytes and bodonids. This was likely due to "culturing bias" but also to the eutrophic nature of the Baltic Sea. Nonetheless, ~ 12% of the isolates in our culture collection showed highly divergent 18S rRNA gene sequences compared to those of known organisms and thus may represent novel taxa, either at the species level or at the genus level. Moreover, we also obtained evidence that some of the isolated taxa are ecologically relevant, under certain conditions, in the Baltic Sea. © 2016 The Author(s) Journal of Eukaryotic Microbiology © 2016 International Society of Protistologists.

Halomonas indalinina sp.nov., a moderately halophilic bacterium isolated from a solar saltern in Cabo de Gata, Al,eria, southern Spain

NARCIS (Netherlands)

Cabrera, A.; Aguilera, M.; Fuentes Enriquez de Salamanca, S.; Incerti, C.; Russell, N.J.; Ramos-Cormenzana, A.; Monteoliva-Sanchez, M.

2007-01-01

moderately halophilic bacterium, strain CG2.1T, isolated from a solar saltern at Cabo de Gata, a wildlife reserve located in the province of Almería, southern Spain, was subjected to a polyphasic taxonomic study. This organism was an aerobic, motile, Gram-negative rod that produced orange-pigmented

Putative N₂-fixing heterotrophic bacteria associated with dinoflagellate-Cyanobacteria consortia in the low-nitrogen Indian Ocean

DEFF Research Database (Denmark)

Farnelid, H.; Tarangkoon, Woraporn; Hansen, Gert

2010-01-01

that the symbionts fix gaseous nitrogen (N2). Individual heterotrophic dinoflagellates containing cyanobacterial symbionts were isolated from the open Indian Ocean and off Western Australia, and characterized using light microscopy, transmission electron microscopy (TEM), and nitrogenase (nifH) gene amplification......, cloning, and sequencing. Cyanobacteria, heterotrophic bacteria and eukaryotic algae were recognized as symbionts of the heterotrophic dinoflagellates. nifH gene sequences were obtained from 23 of 37 (62%) specimens of dinoflagellates (Ornithocercus spp. and Amphisolenia spp.). Interestingly, only 2...... specimens contained cyanobacterial nifH sequences, while 21 specimens contained nifH genes related to heterotrophic bacteria. Of the 137 nifH sequences obtained 68% were most similar to Alpha-, Beta-, and Gammaproteobacteria, 8% clustered with anaerobic bacteria, and 5% were related to second alternative...

Pseudomonas aestus sp. nov., a plant growth-promoting bacterium isolated from mangrove sediments.

Science.gov (United States)

Vasconcellos, Rafael L F; Santos, Suikinai Nobre; Zucchi, Tiago Domingues; Silva, Fábio Sérgio Paulino; Souza, Danilo Tosta; Melo, Itamar Soares

2017-10-01

Strain CMAA 1215 T , a Gram-reaction-negative, aerobic, catalase positive, polarly flagellated, motile, rod-shaped (0.5-0.8 × 1.3-1.9 µm) bacterium, was isolated from mangrove sediments, Cananéia Island, Brazil. Analysis of the 16S rRNA gene sequences showed that strain CMAA 1215 T forms a distinct phyletic line within the Pseudomonas putida subclade, being closely related to P. plecoglossicida ATCC 700383 T , P. monteilii NBRC 103158 T , and P. taiwanensis BCRC 17751 T of sequence similarity of 98.86, 98.73, and 98.71%, respectively. Genomic comparisons of the strain CMAA 1215 T with its closest phylogenetic type strains using average nucleotide index (ANI) and DNA:DNA relatedness approaches revealed 84.3-85.3% and 56.0-63.0%, respectively. A multilocus sequence analysis (MLSA) performed concatenating 16S rRNA, gyrB and rpoB gene sequences from the novel species was related with Pseudomonas putida subcluster and formed a new phylogenetic lineage. The phenotypic, physiological, biochemical, and genetic characteristics support the assignment of CMAA 1215 T to the genus Pseudomonas, representing a novel species. The name Pseudomonas aestus sp.nov. is proposed, with CMAA 1215 T (=NRRL B-653100 T  = CBMAI 1962 T ) as the type strain.

Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1T), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta

Energy Technology Data Exchange (ETDEWEB)

Abt, Birte; Han, Cliff; Scheuner, Carmen; Lu, Megan; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxane; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Huntemann, Marcel; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Gronow, Sabine; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Detter, John C.

2012-05-25

Spirochaeta coccoides Dröge et al. 2006 is a member of the genus Spirochaeta Ehrenberg 1835, one of the oldest named genera within the Bacteria. S. coccoides is an obligately anaerobic, Gram-negative, non-motile, spherical bacterium that was isolated from the hindgut contents of the termite Neotermes castaneus. The species is of interest because it may play an important role in the digestion of breakdown products from cellulose and hemicellulose in the termite gut. Here we provide a taxonomic re-evaluation for strain SPN1T, and based on physiological and genomic characteristics, we propose its reclassification as a novel species in the genus Sphaerochaeta, a recently published sister group of the Spirochaeta. The 2,227,296 bp long genome of strain SPN1T with its 1,866 protein-coding and 58 RNA genes is a part of the GenomicEncyclopedia of Bacteria and Archaea project.

Growth of a Strictly Anaerobic Bacterium on Furfural (2-Furaldehyde)

Science.gov (United States)

Brune, Gerhard; Schoberth, Siegfried M.; Sahm, Hermann

1983-01-01

A strictly anaerobic bacterium was isolated from a continuous fermentor culture which converted the organic constituents of sulfite evaporator condensate to methane and carbon dioxide. Furfural is one of the major components of this condensate. This furfural isolate could degrade furfural as the sole source of carbon and energy in a defined mineral-vitamin-sulfate medium. Acetic acid was the major fermentation product. This organism could also use ethanol, lactate, pyruvate, or fumarate and contained cytochrome c3 and desulfoviridin. Except for furfural degradation, the characteristics of the furfural isolate were remarkably similar to those of the sulfate reducer Desulfovibrio gigas. The furfural isolate has been tentatively identified as Desulfovibrio sp. strain F-1. Images PMID:16346423

A bacterium that can grow by using arsenic instead of phosphorus

Energy Technology Data Exchange (ETDEWEB)

Wolfe-Simon, F; Blum, J S; Kulp, T R; Gordon, G W; Hoeft, S E; Pett-Ridge, J; Stolz, J F; Webb, S M; Weber, P K; Davies, P W; Anbar, A D; Oremland, R S

2010-11-01

Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur and phosphorus. Although these six elements make up nucleic acids, proteins and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, CA, which substitutes arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical significance.

A bacterium that can grow by using arsenic instead of phosphorus.

Science.gov (United States)

Wolfe-Simon, Felisa; Switzer Blum, Jodi; Kulp, Thomas R; Gordon, Gwyneth W; Hoeft, Shelley E; Pett-Ridge, Jennifer; Stolz, John F; Webb, Samuel M; Weber, Peter K; Davies, Paul C W; Anbar, Ariel D; Oremland, Ronald S

2011-06-03

Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Although these six elements make up nucleic acids, proteins, and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here, we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, California, that is able to substitute arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.

Aggregation of the rhizospheric bacterium Azospirillum brasilense in response to oxygen

Science.gov (United States)

Abdoun, Hamid; McMillan, Mary; Pereg, Lily

2016-04-01

Azospirillum brasilense spp. have ecological, scientific and agricultural importance. As model plant growth promoting rhizobacteria they interact with a large variety of plants, including important food and cash crops. Azospirillum strains are known for their production of plant growth hormones that enhance root systems and for their ability to fix nitrogen. Azospirillum cells transform in response to environmental cues. The production of exopolysaccharides and cell aggregation during cellular transformation are important steps in the attachment of Azospirillum to roots. We investigate signals that induce cellular transformation and aggregation in the Azospirillum and report on the importance of oxygen to the process of aggregation in this rhizospheric bacterium.

Echinicola rosea sp. nov., a marine bacterium isolated from surface seawater.

Science.gov (United States)

Liang, Pan; Sun, Jia; Li, Hao; Liu, Minyuan; Xue, Zhaocheng; Zhang, Yao

2016-09-01

A novel Gram-stain-negative, rod-shaped, gliding, halotolerant, aerobic, light-pink-pigmented bacterium, strain JL3085T, was isolated from surface water of the South China Sea (16° 49' 4″ N 112° 20' 24″ E; temperature: 28.3 °C, salinity: 34.5%). The major respiratory quinone was menaquinone 7 (MK-7). The polar lipids of strain JL3085T comprised phosphatidylethanolamine, four unidentified phospholipids and three unidentified lipids. The major fatty acids were iso-C15 : 0, summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 0 3-OH, iso-C17 : 1ω9c, C17 : 1ω6c, anteiso-C15 : 0 and C16 : 1ω5c. The DNA G+C content of strain JL3085T was 43.8 mol%. 16S rRNA gene sequence analysis indicated that strain JL3085T was affiliated with the genus Echinicola, a member of the phylum Bacteroidetes, and was related most closely to Echinicola vietnamensis KMM 6221T (96.8 % similarity). DNA-DNA relatedness between strain JL3085T and E. vietnamensis KMM 6221T was 27.5 %. Based on the evidence presented here, strain JL3085T is regarded as representing a novel species of the genus Echinicola, for which the name Echinicola rosea sp. nov. is proposed. The type strain is JL3085T (=NBRC 111782T=CGMCC 1.15407T).

Heterotrophic bacterial production and metabolic balance during the VAHINE mesocosm experiment in the New Caledonia lagoon

Science.gov (United States)

Van Wambeke, France; Pfreundt, Ulrike; Barani, Aude; Berthelot, Hugo; Moutin, Thierry; Rodier, Martine; Hess, Wolfgang R.; Bonnet, Sophie

2016-06-01

Studies investigating the fate of diazotrophs through the microbial food web are lacking, although N2 fixation can fuel up to 50 % of new production in some oligotrophic oceans. In particular, the role played by heterotrophic prokaryotes in this transfer is largely unknown. In the frame of the VAHINE (VAriability of vertical and tropHIc transfer of diazotroph derived N in the south wEst Pacific) experiment, three replicate large-volume (˜ 50 m3) mesocosms were deployed for 23 days in the new Caledonia lagoon and were intentionally fertilized on day 4 with dissolved inorganic phosphorus (DIP) to stimulate N2 fixation. We specifically examined relationships between heterotrophic bacterial production (BP) and N2 fixation or primary production, determined bacterial growth efficiency and established carbon budgets. BP was statistically higher during the second phase of the experiment (P2: days 15-23), when chlorophyll biomass started to increase compared to the first phase (P1: days 5-14). Phosphatase alkaline activity increased drastically during the second phase of the experiment, showing adaptations of microbial populations after utilization of the added DIP. Notably, among autotrophs, Synechococcus abundances increased during P2, possibly related to its capacity to assimilate leucine and to produce alkaline phosphatase. Bacterial growth efficiency based on the carbon budget (27-43 %), was notably higher than generally cited for oligotrophic environments and discussed in links with the presence of abundant species of bacteria expressing proteorhodopsin. The main fates of gross primary production (particulate + dissolved) were respiration (67 %) and export through sedimentation (17 %). BP was highly correlated with particulate primary production and chlorophyll biomass during both phases of the experiment but was slightly correlated, and only during P2 phase, with N2 fixation rates. Heterotrophic bacterial production was strongly stimulated after mineral N enrichment

Inference of Interactions in Cyanobacterial-Heterotrophic Co-Cultures via Transcriptome Sequencing

Energy Technology Data Exchange (ETDEWEB)

Beliaev, Alex S.; Romine, Margaret F.; Serres, Margaret; Bernstein, Hans C.; Linggi, Bryan E.; Markillie, Lye Meng; Isern, Nancy G.; Chrisler, William B.; Kucek, Leo A.; Hill, Eric A.; Pinchuk, Grigoriy; Bryant, Donald A.; Wiley, H. S.; Fredrickson, Jim K.; Konopka, Allan

2014-04-29

We employed deep sequencing technology to identify transcriptional adaptation of the euryhaline unicellular cyanobacterium Synechococcus sp. PCC 7002 and the marine facultative aerobe Shewanella putrefaciens W3-18-1 to growth in a co-culture and infer the effect of carbon flux distributions on photoautotroph-heterotroph interactions. The overall transcriptome response of both organisms to co-cultivation was shaped by their respective physiologies and growth constraints. Carbon limitation resulted in the expansion of metabolic capacities which was manifested through the transcriptional upregulation of transport and catabolic pathways. While growth coupling occurred via lactate oxidation or secretion of photosynthetically fixed carbon, there was evidence of specific metabolic interactions between the two organisms. On one hand, the production and excretion of specific amino acids (methionine and alanine) by the cyanobacterium correlated with the putative downregulation of the corresponding biosynthetic machinery of Shewanella W3-18-1. On the other hand, the broad and consistent decrease of mRNA levels for many Fe-regulated Synechococcus 7002 genes during co-cultivation suggested increased Fe availability as well as more facile and energy-efficient mechanisms for Fe acquisition by the cyanobacterium. Furthermore, evidence pointed at potentially novel interactions between oxygenic photoautotrophs and heterotrophs related to the oxidative stress response as transcriptional patterns suggested that Synechococcus 7002 rather than Shewanella W3-18-1 provided scavenging functions for reactive oxygen species under co-culture conditions. This study provides an initial insight into the complexity of photoautotrophic-heterotrophic interactions and brings new perspectives of their role in the robustness and stability of the association.

Complete Genome Sequence of the Pigmented Streptococcus thermophilus Strain JIM8232

Science.gov (United States)

Delorme, Christine; Bartholini, Claire; Luraschi, Mélanie; Pons, Nicolas; Loux, Valentin; Almeida, Mathieu; Guédon, Eric; Gibrat, Jean-François; Renault, Pierre

2011-01-01

Streptococcus thermophilus is a dairy species commonly used in the manufacture of cheese and yogurt. Here, we report the complete sequence of S. thermophilus strain JIM8232, isolated from milk and which produces a yellow pigment, an atypical trait for this bacterium. PMID:21914889

Culture conditions of Roseobacter strain 27-4 affect its attachment and biofilm formation as quantified by real-time PCR

DEFF Research Database (Denmark)

Bruhn, Jesper Bartholin; Haagensen, Janus Anders Juul; Bagge-Ravn, D.

2006-01-01

The fish probiotic bacterium Roseobacter strain 27-4 grows only as rosettes and produces its antibacterial compound under static growth conditions. It forms three-dimensional biofilms when precultured under static conditions. We quantified attachment of Roseobacter strain 27-4 using a direct real...

Noncontiguous finished genome sequence and description of Planococcus massiliensis sp. nov., a moderately halophilic bacterium isolated from the human gut

Directory of Open Access Journals (Sweden)

E.H. Seck

2016-03-01

Full Text Available We propose the main phenotypic characteristics and the complete genome sequence and annotation of Planococcus massiliensis strain ES2T (= CSUR P1103 = DSM 28915, the type strain of P. massiliensis sp. nov., isolated from a faeces sample collected from a healthy Senegalese man. It is an aerobic, Gram-positive, moderately halophilic, motile and rod-shaped bacterium. The 3 357 017 bp long genome exhibits a G+C content of 46.0% and contains 3357 protein-coding genes and 48 RNA genes.

Factors governing the pH in a heterotrophic, turbid, tidal estuary

NARCIS (Netherlands)

Hofmann, A.F.; Meysman, F.J.R.; Soetaert, K.; Middelburg, J.J.

2009-01-01

A method to quantify the influence of kinetically modelled biogeochemical processes on the pH of an ecosystem with time variable acid-base dissociation constants is presented and applied to the heterotrophic, turbid Scheldt estuary (SW Netherlands, N Belgium). Nitrification is identified as the main

Bacterium oxidizing carbon monoxide

Energy Technology Data Exchange (ETDEWEB)

Kistner, A

1953-01-01

Present-day knowledge of the microbiological oxidation of carbon monoxide is based on doubtful observations and imperfect experimental procedures. By making use of shake cultures in contact with gas mixtures containing high concentrations of CO and by employing liquid enrichment media with a low content of organic matter and solid media of the same composition with not more than 1.2% agar, it proved possible to isolate a co-oxidizing bacterium of the genus hydrogenomonas from sewage sludge. For the first time irrefutable proof has been given of the oxidation of carbon monoxide by a pure culture of a bacterium, both in growing cultures and in resting cell suspensions. 12 references.

Relative contributions of Vibrio polysaccharide and quorum sensing to the resistance of Vibrio cholerae to predation by heterotrophic protists.

Directory of Open Access Journals (Sweden)

Shuyang Sun

Full Text Available Protozoan grazing is a major mortality factor faced by bacteria in the environment. Vibrio cholerae, the causative agent of the disease cholera, is a natural inhabitant of aquatic ecosystems, and its survival depends on its ability to respond to stresses, such as predation by heterotrophic protists. Previous results show that grazing pressure induces biofilm formation and enhances a smooth to rugose morphotypic shift, due to increased expression of Vibrio polysaccharide (VPS. In addition to negatively controlling vps genes, the global quorum sensing (QS regulator, HapR, plays a role in grazing resistance as the ΔhapR strain is efficiently consumed while the wild type (WT is not. Here, the relative and combined contributions of VPS and QS to grazing resistance were investigated by exposing VPS and HapR mutants and double mutants in VPS and HapR encoding genes at different phases of biofilm development to amoeboid and flagellate grazers. Data show that the WT biofilms were grazing resistant, the VPS mutants were less resistant than the WT strain, but more resistant than the QS mutant strain, and that QS contributes to grazing resistance mainly in mature biofilms. In addition, grazing effects on biofilms of mixed WT and QS mutant strains were investigated. The competitive fitness of each strain in mixed biofilms was determined by CFU and microscopy. Data show that protozoa selectively grazed the QS mutant in mixed biofilms, resulting in changes in the composition of the mixed community. A small proportion of QS mutant cells which comprised 4% of the mixed biofilm biovolume were embedded in grazing resistant WT microcolonies and shielded from predation, indicating the existence of associational protection in mixed biofilms.

The Heterotrophic Bacterial Response During the Meso-scale Southern Ocean Iron Experiment (SOFeX)

Science.gov (United States)

Oliver, J. L.; Barber, R. T.; Ducklow, H. W.

2002-12-01

Previous meso-scale iron enrichments have demonstrated the stimulatory effect of iron on primary productivity and the accelerated flow of carbon into the surface ocean foodweb. In stratified waters, heterotrophic activity can work against carbon export by remineralizing POC and/or DOC back to CO2, effectively slowing the biological pump. To assess the response of heterotrophic activity to iron enrichment, we measured heterotrophic bacterial production and abundance during the Southern Ocean Iron Experiment (SOFeX). Heterotrophic bacterial processes primarily affect the latter of the two carbon export mechanisms, removal of DOC to the deep ocean. Heterotrophic bacterial production (BP), measured via tritiated thymidine (3H-TdR) and leucine (3H-Leu) incorporation, increased ~40% over the 18-d observation period in iron fertilized waters south of the Polar Front (South Patch). Also, South Patch BP was 61% higher than in the surrounding unfertilized waters. Abundance, measured by flow cytometry (FCM) and acridine orange direct counts (AODC), also increased in the South Patch from 3 to 5 x 108 cells liter-1, a 70% increase. Bacterial biomass increased from ~3.6 to 6.3 μg C liter-1, a clear indication that production rates exceeded removal rates (bactivory, viral lysis) over the course of 18 days. Biomass within the fertilized patch was 11% higher than in surrounding unfertilized waters reflecting a similar trend. This pattern is in contrast to SOIREE where no accumulation of biomass was observed. High DNA-containing (HDNA) cells detected by FCM also increased over time in iron fertilized waters from 20% to 46% relative to the total population suggesting an active subpopulation of cells that were growing faster than the removal rates. In iron fertilized waters north of the Polar Front (North Patch), BP and abundance were ~90% and 80% higher, respectively, than in unfertilized waters. Our results suggest an active bacterial population that responded to iron fertilization

Roots affect the response of heterotrophic soil respiration to temperature in tussock grass microcosms.

Science.gov (United States)

Graham, Scott L; Millard, Peter; Hunt, John E; Rogers, Graeme N D; Whitehead, David

2012-07-01

While the temperature response of soil respiration (R(S)) has been well studied, the partitioning of heterotrophic respiration (R(H)) by soil microbes from autotrophic respiration (R(A)) by roots, known to have distinct temperature sensitivities, has been problematic. Further complexity stems from the presence of roots affecting R(H), the rhizosphere priming effect. In this study the short-term temperature responses of R(A) and R(H) in relation to rhizosphere priming are investigated. Temperature responses of R(A), R(H) and rhizosphere priming were assessed in microcosms of Poa cita using a natural abundance δ(13)C discrimination approach. The temperature response of R(S) was found to be regulated primarily by R(A), which accounted for 70 % of total soil respiration. Heterotrophic respiration was less sensitive to temperature in the presence of plant roots, resulting in negative priming effects with increasing temperature. The results emphasize the importance of roots in regulating the temperature response of R(S), and a framework is presented for further investigation into temperature effects on heterotrophic respiration and rhizosphere priming, which could be applied to other soil and vegetation types to improve models of soil carbon turnover.

Draft Genome Sequence of Komagataeibacter intermedius Strain AF2, a Producer of Cellulose, Isolated from Kombucha Tea.

Science.gov (United States)

Dos Santos, Renato Augusto Corrêa; Berretta, Andresa Aparecida; Barud, Hernane da Silva; Ribeiro, Sidney José Lima; González-García, Laura Natalia; Zucchi, Tiago Domingues; Goldman, Gustavo H; Riaño-Pachón, Diego M

2015-12-03

Here, we present the draft genome sequence of Komagataeibacter intermedius strain AF2, which was isolated from Kombucha tea and is capable of producing cellulose, although at lower levels compared to another bacterium from the same environment, K. rhaeticus strain AF1. Copyright © 2015 dos Santos et al.

Biodegradation pathway of L-glutamatediacetate by Rhizobium radiobacter strain BG-1

NARCIS (Netherlands)

Ginkel, van C.G.; Geerts, R.; Nguyen, P.D.; Plugge, C.M.

2008-01-01

An aerobic bacterium was isolated from activated sludge in a medium containing l-glutamate-N,N-diacetate (l-GLDA) as sole carbon and energy source. The isolate was identified as a Rhizobium radiobacter species. Besides l-GLDA, the strain utilized nitrilotriacetate (NTA) and proposed intermediates in

Complete genome sequence of Vibrio anguillarum strain NB10, a virulent isolate from the Gulf of Bothnia.

Science.gov (United States)

Holm, Kåre Olav; Nilsson, Kristina; Hjerde, Erik; Willassen, Nils-Peder; Milton, Debra L

2015-01-01

Vibrio anguillarum causes a fatal hemorrhagic septicemia in marine fish that leads to great economical losses in aquaculture world-wide. Vibrio anguillarum strain NB10 serotype O1 is a Gram-negative, motile, curved rod-shaped bacterium, isolated from a diseased fish on the Swedish coast of the Gulf of Bothnia, and is slightly halophilic. Strain NB10 is a virulent isolate that readily colonizes fish skin and intestinal tissues. Here, the features of this bacterium are described and the annotation and analysis of its complete genome sequence is presented. The genome is 4,373,835 bp in size, consists of two circular chromosomes and one plasmid, and contains 3,783 protein-coding genes and 129 RNA genes.

Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome.

Directory of Open Access Journals (Sweden)

Tim van Opijnen

2016-09-01

Full Text Available The interaction between an antibiotic and bacterium is not merely restricted to the drug and its direct target, rather antibiotic induced stress seems to resonate through the bacterium, creating selective pressures that drive the emergence of adaptive mutations not only in the direct target, but in genes involved in many different fundamental processes as well. Surprisingly, it has been shown that adaptive mutations do not necessarily have the same effect in all species, indicating that the genetic background influences how phenotypes are manifested. However, to what extent the genetic background affects the manner in which a bacterium experiences antibiotic stress, and how this stress is processed is unclear. Here we employ the genome-wide tool Tn-Seq to construct daptomycin-sensitivity profiles for two strains of the bacterial pathogen Streptococcus pneumoniae. Remarkably, over half of the genes that are important for dealing with antibiotic-induced stress in one strain are dispensable in another. By confirming over 100 genotype-phenotype relationships, probing potassium-loss, employing genetic interaction mapping as well as temporal gene-expression experiments we reveal genome-wide conditionally important/essential genes, we discover roles for genes with unknown function, and uncover parts of the antibiotic's mode-of-action. Moreover, by mapping the underlying genomic network for two query genes we encounter little conservation in network connectivity between strains as well as profound differences in regulatory relationships. Our approach uniquely enables genome-wide fitness comparisons across strains, facilitating the discovery that antibiotic responses are complex events that can vary widely between strains, which suggests that in some cases the emergence of resistance could be strain specific and at least for species with a large pan-genome less predictable.

Enterobacter siamensis sp. nov., a transglutaminase-producing bacterium isolated from seafood processing wastewater in Thailand.

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Khunthongpan, Suwannee; Bourneow, Chaiwut; H-Kittikun, Aran; Tanasupawat, Somboon; Benjakul, Soottawat; Sumpavapol, Punnanee

2013-01-01

A novel strain of Enterobacter, C2361(T), a Gram-negative, non-spore-forming, rod-shaped and facultative anaerobic bacterium with the capability to produce transglutaminase, was isolated from seafood processing wastewater collected from a treatment pond of a seafood factory in Songkhla Province, Thailand. Phylogenetic analyses and phenotypic characteristics, including chemotaxonomic characteristics, showed that the strain was a member of the genus Enterobacter. The 16S rRNA gene sequence similarities between strain C2361(T) and Enterobacter cloacae subsp. cloacae ATCC 13047(T) and Enterobacter cloacae subsp. dissolvens LMG 2683(T) were 97.5 and 97.5%, respectively. Strain C2361(T) showed a low DNA-DNA relatedness with the above-mentioned species. The major fatty acids were C16:0, C17:0cyclo and C14:0. The DNA G+C content was 53.0 mol%. On the basis of the polyphasic evidence gathered in this study, it should be classified as a novel species of the genus Enterobacter for which the name Enterobacter siamensis sp. nov. is proposed. The type strain is C2361(T) (= KCTC 23282(T) = NBRC 107138(T)).

Spatial Variability of Cyanobacteria and Heterotrophic Bacteria in Lake Taihu (China).

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Qian, Haifeng; Lu, Tao; Song, Hao; Lavoie, Michel; Xu, Jiahui; Fan, Xiaoji; Pan, Xiangliang

2017-09-01

Cyanobacterial blooms frequently occur in Lake Taihu (China), but the intertwined relationships between biotic and abiotic factors modulating the frequency and duration of the blooms remain enigmatic. To better understand the relationships between the key abiotic and biotic factors and cyanobacterial blooms, we measured the abundance and diversity of prokaryotic organisms by high-throughput sequencing, the abundance of key genes involved in microcystin production and nitrogen fixation or loss as well as several physicochemical parameters at several stations in Lake Taihu during a cyanobacterial bloom of Microcystis sp.. Measurements of the copy number of denitrification-related genes and 16S rRNA analyses show that denitrification potential and denitrifying bacteria abundance increased in concert with non-diazotrophic cyanobacteria (Microcystis sp.), suggesting limited competition between cyanobacteria and heterotrophic denitrifiers for nutrients, although potential bacteria-mediated N loss may hamper Microcystis growth. The present study provides insight into the importance of different abiotic and biotic factors in controlling cyanobacteria and heterotrophic bacteria spatial variability in Lake Taihu.

Isolation of a strain of Acidithiobacillus caldus and its role in bioleaching of chalcopyrite

Energy Technology Data Exchange (ETDEWEB)

Zhou, Q.G.; Bo, F.; Bo, Z.H.; Xi, L.; Jian, G.; Fei, L.F.; Hua, C.X. [Central South University of Technology, Changsha (China)

2007-09-15

A moderately thermophilic and acidophilic sulfur-oxidizing bacterium named S-2, was isolated from coal heap drainage. The bacterium was motile, Gramnegative, rod-shaped, measured 0.4 to 0.6 by 1 to 2 gm, and grew optimally at 42-45{sup o}C and an initial pH of 2.5. The strain S-2 grew autotrophically by using elemental sulfur, sodium thiosulfate and potassium tetrathionate as energy sources. The strain did not use organic matter and inorganic minerals including ferrous sulfate, pyrite and chalcopyrite as energy sources. The morphological, biochemical, physiological characterization and analysis based on 16S rRNA gene sequence indicated that the strain S2 is most closely related to Acidithiobacillus caldus (> 99% similarity in gene sequence). The combination of the strain S-2 with Leptospirillum ferriphilum or Acidithiobacillus ferrooxidans in chalcopyrite bioleaching improved the copper-leaching efficiency. Scanning electron microscope (SEM) analysis revealed that the chalcopyrite surface in a mixed culture of Leptospirillum ferriphilum and Acidithiobacillus caldus was heavily etched. The energy dispersive X-ray (EDX) analysis indicated that Acidithiobacillus caldus has the potential role to enhance the recovery of copper from chalcopyrite by oxidizing the sulfur formed during the bioleaching progress.

Novel insight into the role of heterotrophic dinoflagellates in the fate of crude oil in the sea

DEFF Research Database (Denmark)

Almeda, Rodrigo; Connelly, Tara L.; Buskey, Edward J.

2014-01-01

Although planktonic protozoans are likely to interact with dispersed crude oil after a spill, protozoan-mediated processes affecting crude oil pollution in the sea are still not well known. Here, we present the first evidence of ingestion and defecation of physically or chemically dispersed crude...... to 0.37 mu g-oil mg-C-dino (-1) d(-1), which could represent similar to 17% to 100% of dispersed oil in surface waters when heterotrophic dinoflagellates are abundant or bloom. Egestion of faecal pellets containing crude oil by heterotrophic dinoflagellates could contribute to the sinking and flux...... of toxic petroleum hydrocarbons in coastal waters. Our study indicates that crude oil ingestion by heterotrophic dinoflagellates is a noteworthy route by which petroleum enters marine food webs and a previously overlooked biological process influencing the fate of crude oil in the sea after spills....

Yersinia ruckeri sp. nov., the redmouth (RM) bacterium

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Ewing, W.H.; Ross, A.J.; Brenner, Don J.; Fanning, G. R.

1978-01-01

Cultures of the redmouth (RM) bacterium, one of the etiological agents of redmouth disease in rainbow trout (Salmo gairdneri) and certain other fishes, were characterized by means of their biochemical reactions, by deoxyribonucleic acid (DNA) hybridization, and by determination of guanine-plus-cytosine (G+C) ratios in DNA. The DNA relatedness studies confirmed the fact that the RM bacteria are members of the family Enterobacteriaceae and that they comprise a single species that is not closely related to any other species of Enterobacteriaceae. They are about 30% related to species of both Serratia and Yersinia. A comparison of the biochemical reactions of RM bacteria and serratiae indicated that there are many differences between these organisms and that biochemically the RM bacteria are most closely related to yersiniae. The G+C ratios of RM bacteria were approximated to be between 47.5 and 48.5% These values are similar to those of yersiniae but markedly different from those of serratiae. On the basis of their biochemical reactions and their G+C ratios, the RM bacteria are considered to be a new species of Yersinia, for which the name Yersinia ruckeri is proposed. Strain 2396-61 (= ATCC 29473) is designated the type strain of the species.

Isolation and life cycle characterization of lytic viruses infecting heterotrophic bacteria and cyanobacteria

DEFF Research Database (Denmark)

Middelboe, Mathias; Chan, Amy; Bertelsen, Sif Koldborg

2010-01-01

Basic knowledge on viruses infecting heterotrophic bacteria and cyanobacteria is key to future progress in understanding the role of viruses in aquatic systems and the influence of virus–host interactions on microbial mortality, biogeochemical cycles, and genetic exchange. Such studies require......, and discusses the applications and limitations of different isolation procedures. Most work on phage isolation has been carried out with aerobic heterotrophic bacteria and cyanobacteria, culturable both on agar plates and in enriched liquid cultures. The procedures presented here are limited to lytic viruses...... infecting such hosts. In addition to the isolation procedures, methods for life cycle characterization (one-step growth experiments) of bacteriophages and cyanophages are described. Finally, limitations and drawbacks of the proposed methods are assessed and discussed...

Inhibitory activity of an extract from a marine bacterium Halomonas sp. HSB07 against the red-tide microalga Gymnodinium sp. (Pyrrophyta)

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Liu, Juan; Li, Fuchao; Liu, Ling; Jiang, Peng; Liu, Zhaopu

2013-11-01

In recent years, red tides occurred frequently in coastal areas worldwide. Various methods based on the use of clay, copper sulfate, and bacteria have been successful in controlling red tides to some extent. As a new defensive agent, marine microorganisms are important sources of compounds with potent inhibitory bioactivities against red-tide microalgae, such as Gymnodinium sp. (Pyrrophyta). In this study, we isolated a marine bacterium, HSB07, from seawater collected from Hongsha Bay, Sanya, South China Sea. Based on its 16S rRNA gene sequence and biochemical characteristics, the isolated strain HSB07 was identified as a member of the genus Halomonas. A crude ethyl acetate extract of strain HSB07 showed moderate inhibition activity against Gymnodinium sp. in a bioactive prescreening experiment. The extract was further separated into fractions A, B, and C by silica gel column chromatography. Fractions B and C showed strong inhibition activities against Gymnodinium. This is the first report of inhibitory activity of secondary metabolites of a Halomonas bacterium against a red-tide-causing microalga.

Draft genome sequence of Bradyrhizobium sp. strain BR 3262, an effective microsymbiont recommended for cowpea inoculation in Brazil.

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Simões-Araújo, Jean Luiz; Leite, Jakson; Marie Rouws, Luc Felicianus; Passos, Samuel Ribeiro; Xavier, Gustavo Ribeiro; Rumjanek, Norma Gouvêa; Zilli, Jerri Édson

The strain BR 3262 was isolated from nodule of cowpea (Vigna unguiculata L. Walp) growing in soil of the Atlantic Forest area in Brazil and it is reported as an efficient nitrogen fixing bacterium associated to cowpea. Firstly, this strain was assigned as Bradyrhizobium elkanii, however, recently a more detailed genetic and molecular characterization has indicated it could be a Bradyrhizobium pachyrhizi species. We report here the draft genome sequence of B. pachyrhizi strain BR 3262, an elite bacterium used as inoculant for cowpea. The whole genome with 116 scaffolds, 8,965,178bp and 63.8% of C+G content for BR 3262 was obtained using Illumina MiSeq sequencing technology. Annotation was added by the RAST prokaryotic genome annotation service and shown 8369 coding sequences, 52 RNAs genes, classified in 504 subsystems. Published by Elsevier Editora Ltda.

Draft genome sequence of Bradyrhizobium sp. strain BR 3262, an effective microsymbiont recommended for cowpea inoculation in Brazil

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Jean Luiz Simões-Araújo

Full Text Available Abstract The strain BR 3262 was isolated from nodule of cowpea (Vigna unguiculata L. Walp growing in soil of the Atlantic Forest area in Brazil and it is reported as an efficient nitrogen fixing bacterium associated to cowpea. Firstly, this strain was assigned as Bradyrhizobium elkanii, however, recently a more detailed genetic and molecular characterization has indicated it could be a Bradyrhizobium pachyrhizi species. We report here the draft genome sequence of B. pachyrhizi strain BR 3262, an elite bacterium used as inoculant for cowpea. The whole genome with 116 scaffolds, 8,965,178 bp and 63.8% of C+G content for BR 3262 was obtained using Illumina MiSeq sequencing technology. Annotation was added by the RAST prokaryotic genome annotation service and shown 8369 coding sequences, 52 RNAs genes, classified in 504 subsystems.

Burkholderia insulsa sp. nov., a facultatively chemolithotrophic bacterium isolated from an arsenic-rich shallow marine hydrothermal system.

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Rusch, Antje; Islam, Shaer; Savalia, Pratixa; Amend, Jan P

2015-01-01

Enrichment cultures inoculated with hydrothermally influenced nearshore sediment from Papua New Guinea led to the isolation of an arsenic-tolerant, acidophilic, facultatively aerobic bacterial strain designated PNG-April(T). Cells of this strain were Gram-stain-negative, rod-shaped, motile and did not form spores. Strain PNG-April(T) grew at temperatures between 4 °C and 40 °C (optimum 30-37 °C), at pH 3.5 to 8.3 (optimum pH 5-6) and in the presence of up to 2.7% NaCl (optimum 0-1.0%). Both arsenate and arsenite were tolerated up to concentrations of at least 0.5 mM. Metabolism in strain PNG-April(T) was strictly respiratory. Heterotrophic growth occurred with O2 or nitrate as electron acceptors, and aerobic lithoautotrophic growth was observed with thiosulfate or nitrite as electron donors. The novel isolate was capable of N2-fixation. The respiratory quinones were Q-8 and Q-7. Phylogenetically, strain PNG-April(T) belongs to the genus Burkholderia and shares the highest 16S rRNA gene sequence similarity with the type strains of Burkholderia fungorum (99.8%), Burkholderia phytofirmans (98.8%), Burkholderia caledonica (98.4%) and Burkholderia sediminicola (98.4%). Differences from these related species in several physiological characteristics (lipid composition, carbohydrate utilization, enzyme profiles) and DNA-DNA hybridization suggested the isolate represents a novel species of the genus Burkholderia, for which we propose the name Burkholderia insulsa sp. nov. The type strain is PNG-April(T) ( = DSM 28142(T) = LMG 28183(T)). © 2015 IUMS.

Intraspecies diversity of Lactobacillus sakei response to oxidative stress and variability of strain performance in mixed strains challenges.

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Guilbaud, Morgan; Zagorec, Monique; Chaillou, Stéphane; Champomier-Vergès, Marie-Christine

2012-04-01

Lactobacillus sakei is a meat-borne lactic acid bacterium species exhibiting a wide genomic diversity. We have investigated the diversity of response to various oxidative compounds, between L. sakei strains, among a collection representing the genomic diversity. We observed various responses to the different compounds as well as a diversity of response depending on the aeration conditions used for cell growth. A principal component analysis revealed two main phenotypic groups, partially correlating with previously described genomic clusters. We designed strains mixes composed of three different strains, in order to examine the behavior of each strain, when cultured alone or in the presence of other strains. The strains composing the mixtures were chosen as diverse as possible, i.e. exhibiting diverse responses to oxidative stress and belonging to different genomic clusters. Growth and survival rates of each strain were monitored under various aeration conditions, with or without heme supplementation. The results obtained suggest that some strains may act as "helper" or "burden" strains depending on the oxidative conditions encountered during incubation. This study confirms that resistance to oxidative stress is extremely variable within the L. sakei species and that this property should be considered when investigating starter performance in the complex meat bacterial ecosystems. Copyright © 2011 Elsevier Ltd. All rights reserved.

[Isolation and identification of Mn oxidizing bacterium Aminobacter sp. H1 and its oxidation mechanism].

Science.gov (United States)

Yan, Ping; Jiang, Li-Ying; Chen, Jian-Meng; He, Zhi-Min; Xiao, Shao-Dan; Jiang, Yi-Feng

2014-04-01

A bacterium with high manganese oxidizing activity was isolated from a biological manganese removal filter and named as H1. Based on its characteristics and the analysis of 16S rDNA sequence, the strain H1 belonged to the genus Aminobacter sp. and its manganese oxidizing ability had never been reported. In this paper, the microbiologic properties of the strain H1, the manganese oxidation mechanisms and characteristics of biogenic manganese oxides were investigated. The results showed that the maximal tolerant Mn concentration of strain H1 was 50 mmol x L(-1), and Mn(II) could be completely removed by strain H1 when the concentration was lower than 10 mmol x L(-1). Strain H1 could oxidize Mn2+ by both the production of manganese oxidizing activity factor and alkaline metabolites during growth, which were synthesized in the cell and then secreted into extracellular culture medium. During the oxidation process, the intermediate of soluble Mn(III) was detected. SEM showed that the biogenic manganese oxides were amorphous and poorly-crystalline, and it closely combined with bacteria. The components of the biogenic manganese oxides produced by strain H1 were identified as MnCO3, MnOOH, Mn3O4 and MnO2 by XRD, XPS and SEM-EDX.

Biological removal of nitrate and ammonium under aerobic atmosphere by Paracoccus versutus LYM.

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Shi, Zhuang; Zhang, Yu; Zhou, Jiti; Chen, Mingxiang; Wang, Xiaojun

2013-11-01

The bacterium isolated from sea sludge Paracoccus versutus LYM was characterized with the ability of aerobic denitrification. Strain LYM performs perfect activity in aerobically converting over 95% NO3(-)-N (approximate 400mg L(-1)) to gaseous products via nitrite with maximum reduction rate 33 mg NO3(-)-N L(-1) h(-1). Besides characteristic of aerobic denitrification, strain LYM was confirmed in terms of the ability to be heterotrophic nitrification and aerobic denitrification (HNAD) with few accumulations of intermediates. After the nitrogen balance and enzyme assays, the putative nitrogen pathway of HNAD could be NH4(+) → NH2OH → NO2(-)→ NO3(-), then NO3(-) was denitrified to gaseous products via nitrite. N2 was sole denitrification product without any detection of N2O by gas chromatography. Strain LYM could also simultaneously remove ammonium and additional nitrate. Meanwhile, the accumulated nitrite had inhibitory effect on ammonium reduction rate. Copyright © 2013 Elsevier Ltd. All rights reserved.

Genome sequences of two Leuconostoc pseudomesenteroides strains isolated from Danish dairy starter cultures

DEFF Research Database (Denmark)

Pedersen, Thomas Bæk; Kot, Witold Piotr; Hansen, L.H.

2014-01-01

The lactic acid bacterium Leuconostoc pseudomesenteroides can be found in mesophilic cheese starters, where it produces aromatic compounds from, e.g., citrate. Here, we present the draft genome sequences of two L. pseudomesenteroides strains isolated from traditional Danish cheese starters....

The Lipid A from the Haloalkaliphilic Bacterium Salinivibrio sharmensis Strain BAGT

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Maria Michela Corsaro

2013-01-01

Full Text Available Lipid A is a major constituent of the lipopolysaccharides (or endotoxins, which are complex amphiphilic macromolecules anchored in the outer membrane of Gram-negative bacteria. The glycolipid lipid A is known to possess the minimal chemical structure for LPSs endotoxic activity, able to cause septic shock. Lipid A isolated from extremophiles is interesting, since very few cases of pathogenic bacteria have been found among these microorganisms. In some cases their lipid A has shown to have an antagonist activity, i.e., it is able to interact with the immune system of the host without triggering a proinflammatory response by blocking binding of substances that could elicit such a response. However, the relationship between the structure and the activity of these molecules is far from being completely clear. A deeper knowledge of the lipid A chemical structure can help the understanding of these mechanisms. In this manuscript, we present our work on the complete structural characterization of the lipid A obtained from the lipopolysaccharides (LPS of the haloalkaliphilic bacterium Salinivibrio sharmensis. Lipid A was obtained from the purified LPS by mild acid hydrolysis. The lipid A, which contains different number of fatty acids residues, and its partially deacylated derivatives were completely characterized by means of electrospray ionization Fourier transform ion cyclotron (ESI FT-ICR mass spectrometry and chemical analysis.

Phenotypical and molecular responses of Arabidopsis thaliana roots as a result of inoculation with the auxin-producing bacterium Azospirillum brasilense.

Science.gov (United States)

Spaepen, Stijn; Bossuyt, Stijn; Engelen, Kristof; Marchal, Kathleen; Vanderleyden, Jos

2014-02-01

The auxin-producing bacterium Azospirillum brasilense Sp245 can promote the growth of several plant species. The model plant Arabidopsis thaliana was chosen as host plant to gain an insight into the molecular mechanisms that govern this interaction. The determination of differential gene expression in Arabidopsis roots after inoculation with either A. brasilense wild-type or an auxin biosynthesis mutant was achieved by microarray analysis. Arabidopsis thaliana inoculation with A. brasilense wild-type increases the number of lateral roots and root hairs, and elevates the internal auxin concentration in the plant. The A. thaliana root transcriptome undergoes extensive changes on A. brasilense inoculation, and the effects are more pronounced at later time points. The wild-type bacterial strain induces changes in hormone- and defense-related genes, as well as in plant cell wall-related genes. The A. brasilense mutant, however, does not elicit these transcriptional changes to the same extent. There are qualitative and quantitative differences between A. thaliana responses to the wild-type A. brasilense strain and the auxin biosynthesis mutant strain, based on both phenotypic and transcriptomic data. This illustrates the major role played by auxin in the Azospirillum-Arabidopsis interaction, and possibly also in other bacterium-plant interactions. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Studies on mangrove swamps of Goa 1. Heterotrophic bacterial flora from mangrove swamps

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Matondkar, S.G.P; Mathani, S; Mavinkurve, S

Heterotrophic bacterial flora from the mangrove swamps of Goa consisted of physiologically active organisms exhibiting cellulolytic, pectinolytic, amylolytic, proteolytic and H2S forming activities, throughout the year. Coryneform and Bacillus were...

Analysis of the genetic variation in Mycobacterium tuberculosis strains by multiple genome alignments

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Morales Juan

2008-11-01

Full Text Available Abstract Background The recent determination of the complete nucleotide sequence of several Mycobacterium tuberculosis (MTB genomes allows the use of comparative genomics as a tool for dissecting the nature and consequence of genetic variability within this species. The multiple alignment of the genomes of clinical strains (CDC1551, F11, Haarlem and C, along with the genomes of laboratory strains (H37Rv and H37Ra, provides new insights on the mechanisms of adaptation of this bacterium to the human host. Findings The genetic variation found in six M. tuberculosis strains does not involve significant genomic rearrangements. Most of the variation results from deletion and transposition events preferentially associated with insertion sequences and genes of the PE/PPE family but not with genes implicated in virulence. Using a Perl-based software islandsanalyser, which creates a representation of the genetic variation in the genome, we identified differences in the patterns of distribution and frequency of the polymorphisms across the genome. The identification of genes displaying strain-specific polymorphisms and the extrapolation of the number of strain-specific polymorphisms to an unlimited number of genomes indicates that the different strains contain a limited number of unique polymorphisms. Conclusion The comparison of multiple genomes demonstrates that the M. tuberculosis genome is currently undergoing an active process of gene decay, analogous to the adaptation process of obligate bacterial symbionts. This observation opens new perspectives into the evolution and the understanding of the pathogenesis of this bacterium.

Gracilibacillus aidingensis sp. nov., a novel moderately halophilic bacterium isolated from Aiding salt lake.

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Guan, Tong-Wei; Tian, Lei; Li, En-Yuan; Tang, Shu-Kun; Zhang, Xiao-Ping

2017-11-01

A novel Gram-positive, aerobe, moderately halophilic bacterium was isolated from saline soil of Aiding lake in Xinjiang, north-west of China, designated strain YIM 98001 T . Cells were rod-shaped, motile and grew at 5-20% (w/v) NaCl (optimum 10%), pH 6-10 (optimum pH 7.0) and 4-45 °C (optimum 37 °C). The major cellular fatty acids were anteiso C 15:0 , anteiso C 17:0 , iso C 15:0 . The predominant respiratory quinone was MK-7. Diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid were the major polar lipids. Meso-diaminopimelic acid was the diagnostic diamino acid of the cell-wall peptidoglycan. The G+C content was 36.46 mol%. 16S rRNA gene sequence analysis showed that the strain belongs to the family Bacillaceae, with the highest sequence similarity to the type strain Gracilibacillus thailandensis TP2-8 T (96.84%), followed by Gracilibacillus saliphilus YIM 91119 T (96.78%) and Gracilibacillus ureilyticus MF38 T (96.57%), thus confirming the affiliation of strain YIM 98001 T to the genus Gracilibacillus. The polyphasic approach indicates that strain YIM 98001 T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus aidingensis is proposed. The type strain is YIM 98001 T (=KCTC 42683 T  = DSMZ 104330 T ).

Trophic interactions among the heterotrophic components of plankton in man-made peat pools

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Michał Niedźwiecki

2017-03-01

Full Text Available Man-made peat pools are permanent freshwater habitats developed due to non-commercial man-made peat extraction. Yet, they have not been widely surveyed in terms of ecosystem functioning, mainly regarding the complexity of heterotrophic components of the plankton. In this study we analysed distribution and trophic interrelations among heterotrophic plankton in man-made peat pools located in different types of peatbogs. We found that peat pools showed extreme differences in environmental conditions that occurred to be important drivers of distribution of microplankton and metazooplankton. Abundance of bacteria and protozoa showed significant differences, whereas metazooplankton was less differentiated in density among peat pools. In all peat pools stress-tolerant species of protozoa and metazoa were dominant. In each peat pool five trophic functional groups were distinguished. The abundance of lower functional trophic groups (bacteria, heterotrophic nanoflagellates (HNF and ciliates feeding on bacteria and HNF was weakly influenced by environmental drivers and was highly stable in all peat pool types. Higher functional trophic groups (naupli, omnivorous and carnivorous ciliates, cladocerans, adult copepods and copepodites were strongly influenced by environmental variables and exhibited lower stability. Our study contributes to comprehensive knowledge of the functioning of peat bogs, as our results have shown that peat pools are characterized by high stability of the lowest trophic levels, which can be crucial for energy transfer and carbon flux through food webs.

Thermincola carboxydiphila gen. nov., sp. nov., a novel anaerobic, carboxydotrophic, hydrogenogenic bacterium from a hot spring of the Lake Baikal area.

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Sokolova, Tatyana G; Kostrikina, Nadezhda A; Chernyh, Nikolai A; Kolganova, Tatjana V; Tourova, Tatjana P; Bonch-Osmolovskaya, Elizaveta A

2005-09-01

A novel anaerobic, thermophilic, alkalitolerant bacterium, strain 2204(T), was isolated from a hot spring of the Baikal Lake region. The cells of strain 2204(T) were straight rods of variable length, Gram-positive with an S-layer, motile with one to two lateral flagella, and often formed aggregates of 3-15 cells. The isolate was shown to be an obligate anaerobe oxidizing CO and producing equimolar quantities of H(2) and CO(2) according to the equation CO+H(2)O-->CO(2)+H(2). No organic substrates were used as energy sources. For lithotrophic growth on CO, 0.2 g acetate or yeast extract l(-1) was required but did not support growth in the absence of CO. Growth was observed in the temperature range 37-68 degrees C, the optimum being 55 degrees C. The pH range for growth was 6.7-9.5, the optimum pH being 8.0. The generation time under optimal conditions was 1.3 h. The DNA G+C content was 45 mol%. Penicillin, erythromycin, streptomycin, rifampicin, vancomycin and tetracycline completely inhibited both growth and CO utilization by strain 2204(T). Thus, isolate 2204(T) was found to be the first known moderately thermophilic and alkalitolerant H(2)-producing anaerobic carboxydotroph. The novel bacterium fell within the cluster of the family Peptococcaceae within the low-G+C-content Gram-positive bacteria, where it formed a separate branch. On the basis of morphological, physiological and phylogenetic features, strain 2204(T) should be assigned to a novel genus and species, for which the name Thermincola carboxydiphila gen. nov., sp. nov. is proposed. The type strain is strain 2204(T) (=DSM 17129(T)=VKM B-2283(T)=JCM 13258(T)).

Uptake, Accumulation and Toxicity of Silver Nanoparticle in Autotrophic Plants, and Heterotrophic Microbes: A Concentric Review

Science.gov (United States)

Tripathi, Durgesh K.; Tripathi, Ashutosh; Shweta; Singh, Swati; Singh, Yashwant; Vishwakarma, Kanchan; Yadav, Gaurav; Sharma, Shivesh; Singh, Vivek K.; Mishra, Rohit K.; Upadhyay, R. G.; Dubey, Nawal K.; Lee, Yonghoon; Chauhan, Devendra K.

2017-01-01

Nanotechnology is a cutting-edge field of science with the potential to revolutionize today’s technological advances including industrial applications. It is being utilized for the welfare of mankind; but at the same time, the unprecedented use and uncontrolled release of nanomaterials into the environment poses enormous threat to living organisms. Silver nanoparticles (AgNPs) are used in several industries and its continuous release may hamper many physiological and biochemical processes in the living organisms including autotrophs and heterotrophs. The present review gives a concentric know-how of the effects of AgNPs on the lower and higher autotrophic plants as well as on heterotrophic microbes so as to have better understanding of the differences in effects among these two groups. It also focuses on the mechanism of uptake, translocation, accumulation in the plants and microbes, and resulting toxicity as well as tolerance mechanisms by which these microorganisms are able to survive and reduce the effects of AgNPs. This review differentiates the impact of silver nanoparticles at various levels between autotrophs and heterotrophs and signifies the prevailing tolerance mechanisms. With this background, a comprehensive idea can be made with respect to the influence of AgNPs on lower and higher autotrophic plants together with heterotrophic microbes and new insights can be generated for the researchers to understand the toxicity and tolerance mechanisms of AgNPs in plants and microbes. PMID:28184215

Biosynthesis and characterization of polyhydroxyalkanoates produced by an extreme halophilic bacterium, Halomonas nitroreducens, isolated from hypersaline ponds.

Science.gov (United States)

Cervantes-Uc, J M; Catzin, J; Vargas, I; Herrera-Kao, W; Moguel, F; Ramirez, E; Rincón-Arriaga, S; Lizama-Uc, G

2014-10-01

Morphological, biochemical and genotypic characterization of a halophilic bacterium isolated from hypersaline ponds located at Las Coloradas (Río Lagartos, Yucatán, Mexico). Characterization of polymer produced by this strain was also performed. Twenty strains were isolated from water samples of salt ponds and selected based on both morphological features and their PHA storage capacity, which were determined by SEM and staining methods with Nile red and Nile blue, respectively; strains were also analysed by the fluorescence imaging technique. Among them, JCCOL25.8 strain showed the highest production of PHA's reason why phenotypic and genotypic characterization was performed; this strain was identified as Halomonas nitroreducens. Polymer produced by this strain was characterized by FTIR, DSC, GPC and EDX spectroscopy. Results indicated that the biosynthesized polymer was polyhydroxybutyrate (PHB) which had a melting peak at 170°C and a crystallinity percentage of about 36%. Based on phenotypic and genotypic aspects, JCCOL25.8 strain was identified as H. nitroreducens and it was capable to accumulate PHB. To our knowledge, there is only one study published on the biosynthesis of PHA's by H. nitroreducens strains, although the characterization of the obtained polymer was not reported. © 2014 The Society for Applied Microbiology.

Occurrence of heterotrophic and coliform bacteria in liquid hand soaps from bulk refillable dispensers in public facilities.

Science.gov (United States)

Chattman, Marisa; Gerba, Sheri L; Maxwell, Charles P

2011-03-01

The goal of the study discussed in this article was to determine the occurrence of heterotrophic and coliform bacteria in liquid soap from bulk refillable dispensers, obtained from restrooms in a variety of public facilities. A total of 541 samples was collected from five U.S. cities. Liquid soap from dispensers in public areas was found to contain heterotrophic and coliform bacterial numbers averaging more than 106 CFU/mL in 24.8% of the dispensers.

Screening and Molecular Identification of New Microbial Strains for Production of Enzymes of Biotechnological Interest

Directory of Open Access Journals (Sweden)

Imen Ghazala

Full Text Available ABSTRACT: This research focused on isolation, identification and characterization of new strains of fungi and bacteria, which were able to produce extracellular xylanase, mannanase, pectinase and α-amylase. Fungi isolates were identified on the basis of analyses of 18S gene sequencing and internal transcribed spacer region. The closest phylogenetic neighbors according to 18S gene sequence and ITS region data for the two isolates M1 and SE were Aspergillus fumigatus and Aspergillus sydowii, respectively. I4 was identified as Bacillus mojavensis on the basis of the 16S rRNA gene sequencing and biochemical properties. The enzyme production was evaluated by cultivating the isolated microorganisms in liquid-state bioprocess using wheat bran as carbon source. Two fungi (M1, and SE and one bacterium (I4 strains were found to be xylanase producer, and several were proven to be outstanding producers of microbial xylanase. The strains producing xylanase secreted variable amounts of starch-debranching enzymes and produced low level β-mannan-degrading enzyme systems. The bacterium strain was found to be capable of producing pectinolytic enzymes on wheat bran at high level. Some of the strains have good potential for use as sources of important industrial enzymes.

Can heterotrophic uptake of dissolved organic carbon and zooplankton mitigate carbon budget deficits in annually bleached corals?

Science.gov (United States)

Levas, Stephen; Grottoli, Andréa G.; Schoepf, Verena; Aschaffenburg, Matthew; Baumann, Justin; Bauer, James E.; Warner, Mark E.

2016-06-01

Annual coral bleaching events due to increasing sea surface temperatures are predicted to occur globally by the mid-century and as early as 2025 in the Caribbean, and severely impact coral reefs. We hypothesize that heterotrophic carbon (C) in the form of zooplankton and dissolved organic carbon (DOC) is a significant source of C to bleached corals. Thus, the ability to utilize multiple pools of fixed carbon and/or increase the amount of fixed carbon acquired from one or more pools of fixed carbon (defined here as heterotrophic plasticity) could underlie coral acclimatization and persistence under future ocean-warming scenarios. Here, three species of Caribbean coral— Porites divaricata, P. astreoides, and Orbicella faveolata—were experimentally bleached for 2.5 weeks in two successive years and allowed to recover in the field. Zooplankton feeding was assessed after single and repeat bleaching, while DOC fluxes and the contribution of DOC to the total C budget were determined after single bleaching, 11 months on the reef, and repeat bleaching. Zooplankton was a large C source for P. astreoides, but only following single bleaching. DOC was a source of C for single-bleached corals and accounted for 11-36 % of daily metabolic demand (CHARDOC), but represented a net loss of C in repeat-bleached corals. In repeat-bleached corals, DOC loss exacerbated the negative C budgets in all three species. Thus, the capacity for heterotrophic plasticity in corals is compromised under annual bleaching, and heterotrophic uptake of DOC and zooplankton does not mitigate C budget deficits in annually bleached corals. Overall, these findings suggest that some Caribbean corals may be more susceptible to repeat bleaching than to single bleaching due to a lack of heterotrophic plasticity, and coral persistence under increasing bleaching frequency may ultimately depend on other factors such as energy reserves and symbiont shuffling.

Novel Poly[(R-3-Hydroxybutyrate]-Producing Bacterium Isolated from a Bolivian Hypersaline Lake

Directory of Open Access Journals (Sweden)

María Soledad Marqués-Calvo

2013-01-01

Full Text Available Poly[(R-3-hydroxybutyrate] (PHB constitutes a biopolymer synthesized from renewable resources by various microorganisms. This work focuses on finding a new PHB-producing bacterium capable of growing in conventional media used for industrial biopolymer production, its taxonomical identification, and characterization of its biopolymer. Thus, a bacterial isolation process was carried out from environmental samples of water and mud. Among the isolates, strain S29 was selected and used in a fed-batch fermentation to generate a biopolymer. This biopolymer was recovered and identified as PHB homopolymer. Surprisingly, it featured several fractions of different molecular masses, and thermal properties unusual for PHB. Hence, the microorganism S29, genetically identified as a new strain of Bacillus megaterium, proved to be interesting not only due to its growth and PHB accumulation kinetics under the investigated cultivation conditions, but also due to the thermal properties of the produced PHB.

Molasses as C source for heterotrophic bacteria production on solid fish waste

NARCIS (Netherlands)

Schneider, O.; Sereti, V.; Eding, E.H.; Verreth, J.A.J.

2006-01-01

The drumfilter effluent from a recirculation aquaculture system (RAS) can be used as substrate for heterotrophic bacteria production. These bacteria can be reused as aquatic feed. In RAS drumfilter effluents are organic carbon deficient for bacteria production. This is due to nitrogen accumulation

Burkholderia susongensis sp. nov., a mineral-weathering bacterium isolated from weathered rock surface.

Science.gov (United States)

Gu, Jia-Yu; Zang, Sheng-Gang; Sheng, Xia-Fang; He, Lin-Yan; Huang, Zhi; Wang, Qi

2015-03-01

A novel type of mineral-weathering bacterium was isolated from the weathered surface of rock (mica schist) collected from Susong (Anhui, China). Cells of strain L226(T) were Gram-stain-negative. The strain grew optimally at 30 °C, with 1 % (w/v) NaCl and at pH 7.0 in trypticase soy broth. On the basis of 16S rRNA gene phylogeny, strain L226(T) was shown to belong to the genus Burkholderia and the closest phylogenetic relatives were Burkholderia sprentiae WSM5005(T) (98.3 %), Burkholderia acidipaludis NBRC 101816(T) (98.2 %), Burkholderia tuberum STM678(T) (97.2 %) and Burkholderia diazotrophica JPY461(T) (97.1 %). The DNA G+C content was 63.5 mol% and the respiratory quinone was Q-8. The major fatty acids were C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c. The polar lipid profile of strain L226(T) consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, unknown lipids and unidentified aminophospholipids. Based on the low level of DNA-DNA relatedness (ranging from 25.8 % to 34.4 %) to the tested type strains of species of the genus Burkholderia and unique phenotypic characteristics, it is suggested that strain L226(T) represents a novel species of the genus Burkholderia, for which the name Burkholderia susongensis sp. nov., is proposed. The type strain is L226(T) ( = CCTCC AB2014142(T) = JCM 30231(T)). © 2015 IUMS.

Draft Genome Sequence of Zobellia sp. Strain OII3, Isolated from the Coastal Zone of the Baltic Sea.

Science.gov (United States)

Harms, Henrik; Poehlein, Anja; Thürmer, Andrea; König, Gabriele M; Schäberle, Till F

2017-09-07

Zobellia sp. strain OII3 was isolated from a marine environmental sample due to its heterotrophic lifestyle, i.e., using Escherichia coli cells as prey. It shows strong agar-lytic activity. The genome was assembled into 41 contigs with a total size of 5.4 Mb, revealing the genetic basis for natural product biosynthesis. Copyright © 2017 Harms et al.

Methylobacterium oryzae sp. nov., an aerobic, pink-pigmented, facultatively methylotrophic, 1-aminocyclopropane-1-carboxylate deaminase-producing bacterium isolated from rice.

Science.gov (United States)

Madhaiyan, Munusamy; Kim, Byung-Yong; Poonguzhali, Selvaraj; Kwon, Soon-Wo; Song, Myung-Hee; Ryu, Jeoung-Hyun; Go, Seung-Joo; Koo, Bon-Sung; Sa, Tong-Min

2007-02-01

A pink-pigmented, facultatively methylotrophic bacterium, strain CBMB20T, isolated from stem tissues of rice, was analysed by a polyphasic approach. Strain CBMB20T utilized 1-aminocyclopropane 1-carboxylate (ACC) as a nitrogen source and produced ACC deaminase. It was related phylogenetically to members of the genus Methylobacterium. 16S rRNA gene sequence analysis indicated that strain CBMB20T was most closely related to Methylobacterium fujisawaense, Methylobacterium radiotolerans and Methylobacterium mesophilicum; however, DNA-DNA hybridization values were less than 70 % with the type strains of these species. The DNA G+C content of strain CBMB20T was 70.6 mol%. The study presents a detailed phenotypic characterization of strain CBMB20T that allows its differentiation from other Methylobacterium species. In addition, strain CBMB20T is the only known member of the genus Methylobacterium to be described from the phyllosphere of rice. Based on the data presented, strain CBMB20T represents a novel species in the genus Methylobacterium, for which the name Methylobacterium oryzae sp. nov. is proposed, with strain CBMB20T (=DSM 18207T=LMG 23582T=KACC 11585T) as the type strain.

Effects of intense agricultural practices on heterotrophic processes in streams

Energy Technology Data Exchange (ETDEWEB)

Piscart, Christophe [Universite Claude Bernard Lyon 1 - Laboratoire d' Ecologie des Hydrosystemes Fluviaux - UMR CNRS 5023 - Campus Doua, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex (France); Universite de Rennes 1 - UMR CNRS ECOBIO 6553 - Campus Beaulieu, 263 Av. du General Leclerc, 35042 Rennes Cedex (France)], E-mail: christophe.piscart@univ-lyon1.fr; Genoel, Romuald [Universite de Rennes 1 - UMR CNRS ECOBIO 6553 - Campus Beaulieu, 263 Av. du General Leclerc, 35042 Rennes Cedex (France); Doledec, Sylvain [Universite Claude Bernard Lyon 1 - Laboratoire d' Ecologie des Hydrosystemes Fluviaux - UMR CNRS 5023 - Campus Doua, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex (France); Chauvet, Eric [Universite Paul Sabatier de Toulouse - Laboratoire EcoLab - UMR CNRS 5245, 29 rue Jeanne Marvig, 31055 Toulouse Cedex 4 (France); Marmonier, Pierre [Universite Claude Bernard Lyon 1 - Laboratoire d' Ecologie des Hydrosystemes Fluviaux - UMR CNRS 5023 - Campus Doua, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex (France); Universite de Rennes 1 - UMR CNRS ECOBIO 6553 - Campus Beaulieu, 263 Av. du General Leclerc, 35042 Rennes Cedex (France)

2009-03-15

In developed countries, changes in agriculture practices have greatly accelerated the degradation of the landscape and the functioning of adjacent aquatic ecosystems. Such alteration can in turn impair the services provided by aquatic ecosystems, namely the decomposition of organic matter, a key process in most small streams. To study this alteration, we recorded three measures of heterotrophic activity corresponding to microbial hydrolasic activity (FDA hydrolysis) and leaf litter breakdown rates with (k{sub c}) and without invertebrates (k{sub f}) along a gradient of contrasted agricultural pressures. Hydrolasic activity and k{sub f} reflect local/microhabitat conditions (i.e. nutrient concentrations and organic matter content of the sediment) but not land use while k{sub c} reflects land-use conditions. k{sub c}, which is positively correlated with the biomass of Gammaridae, significantly decreased with increasing agricultural pressure, contrary to the taxonomic richness and biomass of Trichoptera and Plecoptera. Gammaridae may thus be considered a key species for organic matter recycling in agriculture-impacted streams. - This study highlights the consequences of intensive agricultural practices on heterotrophic processes in streams along a strong gradient of perturbation.

Depth Dependent Relationships between Temperature and Ocean Heterotrophic Prokaryotic Production

KAUST Repository

Lønborg, Christian

2016-06-07

Marine prokaryotes play a key role in cycling of organic matter and nutrients in the ocean. Using a unique dataset (>14,500 samples), we applied a space-for-time substitution analysis to assess the temperature dependence of prokaryotic heterotrophic production (PHP) in epi- (0-200 m), meso- (201-1000 m) and bathypelagic waters (1001-4000 m) of the global ocean. Here, we show that the temperature dependence of PHP is fundamentally different between these major oceanic depth layers, with an estimated ecosystem-level activation energy (E) of 36 ± 7 kJ mol for the epipelagic, 72 ± 15 kJ mol for the mesopelagic and 274 ± 65 kJ mol for the bathypelagic realm. We suggest that the increasing temperature dependence with depth is related to the parallel vertical gradient in the proportion of recalcitrant organic compounds. These Ea predict an increased PHP of about 5, 12, and 55% in the epi-, meso-, and bathypelagic ocean, respectively, in response to a water temperature increase by 1°C. Hence, there is indication that a major thus far underestimated feedback mechanism exists between future bathypelagic ocean warming and heterotrophic prokaryotic activity.

Depth Dependent Relationships between Temperature and Ocean Heterotrophic Prokaryotic Production

KAUST Repository

Lø nborg, Christian; Cuevas, L. Antonio; Reinthaler, Thomas; Herndl, Gerhard J.; Gasol, Josep M.; Moran, Xose Anxelu G.; Bates, Nicholas R.; á lvarez-Salgado, Xosé A.

2016-01-01

Marine prokaryotes play a key role in cycling of organic matter and nutrients in the ocean. Using a unique dataset (>14,500 samples), we applied a space-for-time substitution analysis to assess the temperature dependence of prokaryotic heterotrophic production (PHP) in epi- (0-200 m), meso- (201-1000 m) and bathypelagic waters (1001-4000 m) of the global ocean. Here, we show that the temperature dependence of PHP is fundamentally different between these major oceanic depth layers, with an estimated ecosystem-level activation energy (E) of 36 ± 7 kJ mol for the epipelagic, 72 ± 15 kJ mol for the mesopelagic and 274 ± 65 kJ mol for the bathypelagic realm. We suggest that the increasing temperature dependence with depth is related to the parallel vertical gradient in the proportion of recalcitrant organic compounds. These Ea predict an increased PHP of about 5, 12, and 55% in the epi-, meso-, and bathypelagic ocean, respectively, in response to a water temperature increase by 1°C. Hence, there is indication that a major thus far underestimated feedback mechanism exists between future bathypelagic ocean warming and heterotrophic prokaryotic activity.

Complete genome sequence of Kytococcus sedentarius type strain (strain 541T)

Energy Technology Data Exchange (ETDEWEB)

Sims, David; Brettin, Thomas; Detter, John C.; Han, Cliff; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Chen, Feng; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ovchinnikova, Galina; Pati, Amrita; Ivanova, Natalia; Mavrommatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; D' haeseleer, Patrick; Chain, Patrick; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Schneider, Susanne; Goker, Markus; Pukall, Rudiger; Kyrpides, Nikos C.; Klenk, Hans-Peter

2009-05-20

Kytococcus sedentarius (ZoBell and Upham 1944) Stackebrandt et al. 1995 is the type strain of the species, and is of phylogenetic interest because of its location in the Dermacoccaceae, a poorly studied family within the actinobacterial suborder Micrococcineae. K. sedentarius is known for the production of oligoketide antibiotics as well as for its role as an opportunistic pathogen causing valve endocarditis, hemorrhagic pneumonia, and pitted keratolysis. It is strictly aerobic and can only grow when several amino acids are provided in the medium. The strain described in this report is a free-living, nonmotile, Gram-positive bacterium, originally isolated from a marine environment. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Dermacoccaceae and the 2,785,024 bp long single replicon genome with its 2639 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Isolation and characterization of a new CO-utilizing strain, Thermoanaerobacter thermohydrosulfuricus subsp. carboxydovorans, isolated from a geothermal spring in Turkey.

KAUST Repository

Balk, Melike

2009-08-23

A novel anaerobic, thermophilic, Gram-positive, spore-forming, and sugar-fermenting bacterium (strain TLO) was isolated from a geothermal spring in Ayaş, Turkey. The cells were straight to curved rods, 0.4-0.6 microm in diameter and 3.5-10 microm in length. Spores were terminal and round. The temperature range for growth was 40-80 degrees C, with an optimum at 70 degrees C. The pH optimum was between 6.3 and 6.8. Strain TLO has the capability to ferment a wide variety of mono-, di-, and polysaccharides and proteinaceous substrates, producing mainly lactate, next to acetate, ethanol, alanine, H(2), and CO(2). Remarkably, the bacterium was able to grow in an atmosphere of up to 25% of CO as sole electron donor. CO oxidation was coupled to H(2) and CO(2) formation. The G + C content of the genomic DNA was 35.1 mol%. Based on 16S rRNA gene sequence analysis and the DNA-DNA hybridization data, this bacterium is most closely related to Thermoanaerobacter thermohydrosulfuricus and Thermoanaerobacter siderophilus (99% similarity for both). However, strain TLO differs from Thermoanaerobacter thermohydrosulfuricus in important aspects, such as CO-utilization and lipid composition. These differences led us to propose that strain TLO represents a subspecies of Thermoanaerobacter thermohydrosulfuricus, and we therefore name it Thermoanaerobacter thermohydrosulfuricus subsp. carboxydovorans.

Isolation and characterization of a new CO-utilizing strain, Thermoanaerobacter thermohydrosulfuricus subsp. carboxydovorans, isolated from a geothermal spring in Turkey.

KAUST Repository

Balk, Melike; Heilig, Hans G H J; van Eekert, Miriam H A; Stams, Alfons J M; Rijpstra, Irene C; Sinninghe-Damsté , Jaap S; de Vos, Willem M; Kengen, Servé W M

2009-01-01

A novel anaerobic, thermophilic, Gram-positive, spore-forming, and sugar-fermenting bacterium (strain TLO) was isolated from a geothermal spring in Ayaş, Turkey. The cells were straight to curved rods, 0.4-0.6 microm in diameter and 3.5-10 microm in length. Spores were terminal and round. The temperature range for growth was 40-80 degrees C, with an optimum at 70 degrees C. The pH optimum was between 6.3 and 6.8. Strain TLO has the capability to ferment a wide variety of mono-, di-, and polysaccharides and proteinaceous substrates, producing mainly lactate, next to acetate, ethanol, alanine, H(2), and CO(2). Remarkably, the bacterium was able to grow in an atmosphere of up to 25% of CO as sole electron donor. CO oxidation was coupled to H(2) and CO(2) formation. The G + C content of the genomic DNA was 35.1 mol%. Based on 16S rRNA gene sequence analysis and the DNA-DNA hybridization data, this bacterium is most closely related to Thermoanaerobacter thermohydrosulfuricus and Thermoanaerobacter siderophilus (99% similarity for both). However, strain TLO differs from Thermoanaerobacter thermohydrosulfuricus in important aspects, such as CO-utilization and lipid composition. These differences led us to propose that strain TLO represents a subspecies of Thermoanaerobacter thermohydrosulfuricus, and we therefore name it Thermoanaerobacter thermohydrosulfuricus subsp. carboxydovorans.

Bacterial abundance, communities and heterotrophic activities in the coastal waters off Tamil Nadu

Digital Repository Service at National Institute of Oceanography (India)

Ramaiah, N.; Raghukumar, C.; Sheelu, G.; Chandramohan, D.

Culturable aerobic heterotrophic bacterial (CAHB) numbers, total direct counts (TDC), bacterial generic composition and uptake of labelled glucose by natural microbial assemblages were studied from a few selected coastal sites off Tamil Nadu. A high...

Ultrastructure and Development of Pasteuria sp. (S-1 strain), an Obligate Endoparasite of Belonolaimus longicaudatus (Nemata: Tylenchida).

Science.gov (United States)

Giblin-Davis, R M; Williams, D S; Wergin, W P; Dickson, D W; Hewlett, T E; Bekal, S; Becker, J O

2001-12-01

Pasteuria sp., strain S-1, is a gram-positive, obligate endoparasitic bacterium that uses the phytoparasitic sting nematode, Belonolaimus longicaudatus, as its host in Florida. The host attachment of S-1 appears to be specific to the genus Belonolaimus with development occurring only in juveniles and adults of B. longicaudatus. This bacterium is characterized from other described species of Pasteuria using ultrastructure of the mature endospore. Penetration, development, and sporogenesis were elucidated with TEM, LTSEM, and SEM and are similar to other nematode-specific Pasteuria. Recent analysis of 16S rDNA sequence homology confirms its congeneric ranking with other Pasteuria species and strains from nematodes and cladocerans, and corroborates ultrastructural, morphological, morphometric, and host-range evidence suggesting separate species status.

Membrane biofouling in a wastewater nitrification reactor: microbial succession from autotrophic colonization to heterotrophic domination

KAUST Repository

Lu, Huijie

2015-10-22

Membrane biofouling is a complex process that involves bacterial adhesion, extracellular polymeric substances (EPS) excretion and utilization, and species interactions. To obtain a better understanding of the microbial ecology of biofouling process, this study conducted rigorous, time-course analyses on the structure, EPS and microbial composition of the fouling layer developed on ultrafiltration membranes in a nitrification bioreactor. During a 14-day fouling event, three phases were determined according to the flux decline and microbial succession patterns. In Phase I (0-2 days), small sludge flocs in the bulk liquid were selectively attached on membrane surfaces, leading to the formation of similar EPS and microbial community composition as the early biofilms. Dominant populations in small flocs, e.g., Nitrosomonas, Nitrobacter, and Acinetobacter spp., were also the major initial colonizers on membranes. In Phase II (2-4 d), fouling layer structure, EPS composition, and bacterial community went through significant changes. Initial colonizers were replaced by fast-growing and metabolically versatile heterotrophs (e.g., unclassified Sphingobacteria). The declining EPS polysaccharide to protein (PS:PN) ratios could be correlated well with the increase in microbial community diversity. In Phase III (5-14 d), heterotrophs comprised over 90% of the community, whereas biofilm structure and EPS composition remained relatively stable. In all phases, AOB and NOB were constantly found within the top 40% of the fouling layer, with the maximum concentrations around 15% from the top. The overall microbial succession pattern from autotrophic colonization to heterotrophic domination implied that MBR biofouling could be alleviated by forming larger bacterial flocs in bioreactor suspension (reducing autotrophic colonization), and by designing more specific cleaning procedures targeting dominant heterotrophs during typical filtration cycles.

The influence of the organophosphorus insecticides acephate and parathion upon the heterotrophic bacteria of two freshwater ecosystems

International Nuclear Information System (INIS)

Albright, L.J.; Geen, G.H.; Gasith, A.; Mozel, Y.; Perry, A.S.

1983-01-01

The effect of acephate and parathion on the heterotrophic bacteria of freshwater ecosystems was studied in a dystrophic west coast Canadian lake and in an eutrophic Israeli fish pond. The limnocorrals were treated with 1-25 ppm of acephate and 30-40 ppb of parathion respectively. Bacterial populations, glucose heterotrophic activities and bacterial and algal productivities were studied using 3 H and 14 C radioisotopes. It is concluded that the two ecosystems are not extensively affected by the pesticide concentrations used

Competitive Interactions Between Incompatible Mutants of the Social Bacterium Myxococcus xanthus DK1622

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Ya Gong

2018-06-01

Full Text Available Due to the high similarity in their requirements for space and food, close bacterial relatives may be each other's strongest competitors. Close bacterial relatives often form visible boundaries to separate their swarming colonies, a phenomenon termed colony-merger incompatibility. While bacterial species are known to have many incompatible strains, it is largely unclear which traits lead to multiple incompatibilities and the interactions between multiple incompatible siblings. To investigate the competitive interactions of closely related incompatible strains, we mutated Myxococcus xanthus DK1622, a predatory bacterium with complex social behavior. From 3392 random transposon mutations, we obtained 11 self-identification (SI deficient mutants that formed unmerged colony boundaries with the ancestral strain. The mutations were at nine loci with unknown functions and formed nine independent SI mutants. Compared with their ancestral strain, most of the SI mutants showed reduced growth, swarming and development abilities, but some remained unchanged from their monocultures. When pairwise mixed with their ancestral strain for co-cultivation, these mutants exhibited improved, reduced or unchanged competitive abilities compared with the ancestral strain. The sporulation efficiencies were affected by the DK1622 partner, ranging from almost complete inhibition to 360% stimulation. The differences in competitive growth between the SI mutants and DK1622 were highly correlated with the differences in their sporulation efficiencies. However, the competitive efficiencies of the mutants in mixture were inconsistent with their growth or sporulation abilities in monocultures. We propose that the colony-merger incompatibility in M. xanthus is associated with multiple independent genetic loci, and the incompatible strains hold competitive interaction abilities, which probably determine the complex relationships between multiple incompatible M. xanthus strains and

Genome Sequence of Carbon Dioxide-Sequestering Serratia sp. Strain ISTD04 Isolated from Marble Mining Rocks

OpenAIRE

Kumar, Manish; Gazara, Rajesh Kumar; Verma, Sandhya; Kumar, Madan; Verma, Praveen Kumar; Thakur, Indu Shekhar

2016-01-01

The Serratia sp. strain ISTD04 has been identified as a carbon dioxide (CO2)-sequestering bacterium isolated from marble mining rocks in the Umra area, Rajasthan, India. This strain grows chemolithotrophically on media that contain sodium bicarbonate (NaHCO3) as the sole carbon source. Here, we report the genome sequence of 5.07?Mb Serratia sp. ISTD04.

Isolation of a human intestinal anaerobe, Bifidobacterium sp. strain SEN, capable of hydrolyzing sennosides to sennidins.

Science.gov (United States)

Akao, T; Che, Q M; Kobashi, K; Yang, L; Hattori, M; Namba, T

1994-01-01

A strictly anaerobic bacterium capable of metabolizing sennosides was isolated from human feces and identified as Bifidobacterium sp., named strain SEN. The bacterium hydrolyzed sennosides A and B to sennidins A and B via sennidin A and B 8-monoglucosides, respectively. Among nine species of Bifidobacterium having beta-glucosidase activity, only Bifidobacterium dentium and B. adolescentis metabolized sennoside B to sennidin B, suggesting that the sennoside-metabolizing bacteria produce a novel type of beta-glucosidase capable of hydrolyzing sennosides to sennidins. PMID:8161172

Insights into Brevibacillus borstelensis AK1 through Whole Genome Sequencing: A Thermophilic Bacterium Isolated from a Hot Spring in Saudi Arabia

KAUST Repository

Khalil, Amjad B.

2018-05-24

Brevibacillus borstelensis AK1 is a thermophile which grows between the temperatures of 45°C and 70°C. The present study is an extended genome report of B. borstelensis AK1 along with the morphological characterization. The strain is isolated from a hot spring in Saudi Arabia (southeast of the city Gazan). It is observed that the strain AK1 is rod-shaped, motile, and strictly aerobic bacterium. The whole genome sequence resulted in 29 contigs with a total length of 5,155,092 bp. In total, 3,946 protein-coding genes and 139 RNA genes were identified. Comparison with the previously submitted strains of B. borstelensis strains illustrates that strain AK1 has a small genome size but high GC content. The strain possesses putative genes for degradation of a wide range of substrates including polyethylene (plastic) and long-chain hydrocarbons. These genomic features may be useful for future environmental/biotechnological applications.

Insights into Brevibacillus borstelensis AK1 through Whole Genome Sequencing: A Thermophilic Bacterium Isolated from a Hot Spring in Saudi Arabia

KAUST Repository

Khalil, Amjad B.; Neelamegam, Sivakumar; Arslan, Muhammad; Saleem, Hamna; Alqarawi, Sami

2018-01-01

Brevibacillus borstelensis AK1 is a thermophile which grows between the temperatures of 45°C and 70°C. The present study is an extended genome report of B. borstelensis AK1 along with the morphological characterization. The strain is isolated from a hot spring in Saudi Arabia (southeast of the city Gazan). It is observed that the strain AK1 is rod-shaped, motile, and strictly aerobic bacterium. The whole genome sequence resulted in 29 contigs with a total length of 5,155,092 bp. In total, 3,946 protein-coding genes and 139 RNA genes were identified. Comparison with the previously submitted strains of B. borstelensis strains illustrates that strain AK1 has a small genome size but high GC content. The strain possesses putative genes for degradation of a wide range of substrates including polyethylene (plastic) and long-chain hydrocarbons. These genomic features may be useful for future environmental/biotechnological applications.

Closed Genome Sequence of Phytopathogen Biocontrol Agent Bacillus velezensis Strain AGVL-005, Isolated from Soybean.

Science.gov (United States)

Pylro, Victor Satler; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini; Morais, Daniel Kumazawa; Varani, Alessandro de Mello; Andreote, Cristiane Cipolla Fasanella; Bernardo, Eduardo Roberto de Almeida; Zucchi, Tiago

2018-02-15

We report here the closed and near-complete genome sequence and annotation of Bacillus velezensis strain AGVL-005, a bacterium isolated from soybean seeds in Brazil and used for phytopathogen biocontrol. Copyright © 2018 Pylro et al.

Separating Autotrophic and Heterotrophic Respiration in Streams and the Importance for Carbon Cycling: a Preliminary Study

Science.gov (United States)

Bozeman, M.; Raymond, P.

2005-05-01

Autotrophic and heterotrophic organisms confer different effects on nutrient cycling, especially on carbon (C). In stream ecosystems, net ecosystem production determines the amount and form of C exported; however any transformation due to different respiratory (R) mechanisms are not separated. These mechanisms highly influence the form and lability of the C transported. To understand the current state of knowledge and estimate the importance of autotrophic versus heterotrophic R, we obtained a range of respiratory rates from the literature and modeled effects of different balances of rates on bulk dissolved inorganic and organic C chemistry. Preliminary results show that a wide range of estimates of autotrophic R exist and that these can effect bulk properties of exported C. While specific effects are highly dependent upon physical structure of the study watershed, we offer that separating R mechanisms provides further insight into ecosystem C cycling. We also propose a method to measure autotrophic and heterotrophic R at the ecosystem scale and obtain watershed-level estimates of the importance of these processes on C cycling.

Micro-electrolysis/retinervus luffae-based simultaneous autotrophic and heterotrophic denitrification for low C/N wastewater treatment.

Science.gov (United States)

Li, Jinlong; Li, Desheng; Cui, Yuwei; Xing, Wei; Deng, Shihai

2017-07-01

Nitrogen bioremediation in organic insufficient wastewater generally requires an extra carbon source. In this study, nitrate-contaminated wastewater was treated effectively through simultaneous autotrophic and heterotrophic denitrification based on micro-electrolysis carriers (MECs) and retinervus luffae fructus (RLF), respectively. The average nitrate and total nitrogen removal rates reached 96.3 and 94.0% in the MECs/RLF-based autotrophic and heterotrophic denitrification (MRAHD) system without ammonia and nitrite accumulation. The performance of MRAHD was better than that of MEC-based autotrophic denitrification for the wastewater treatment with low carbon nitrogen (COD/N) ratio. Real-time quantitative polymerase chain reaction (qPCR) revealed that the relative abundance of nirS-type denitrifiers attached to MECs (4.9%) and RLF (5.0%) was similar. Illumina sequencing suggested that the dominant genera were Thiobacillus (7.0%) and Denitratisoma (5.7%), which attached to MECs and RLF, respectively. Sulfuritalea was discovered as the dominant genus in the middle of the reactor. The synergistic interaction between autotrophic and heterotrophic denitrifiers played a vital role in the mixotrophic substrate environment.

Treatment of cattle-slaughterhouse wastewater and the reuse of sludge for biodiesel production by microalgal heterotrophic bioreactors

Directory of Open Access Journals (Sweden)

Mariana Manzoni Maroneze

2014-12-01

Full Text Available Microalgal heterotrophic bioreactors are a potential technological development that can convert organic matter, nitrogen and phosphorus of wastewaters into a biomass suitable for energy production. The aim of this work was to evaluate the performance of microalgal heterotrophic bioreactors in the secondary treatment of cattle-slaughterhouse wastewater and the reuse of microalgal sludge for biodiesel production. The experiments were performed in a bubble column bioreactor using the microalgae Phormidium sp. Heterotrophic microalgal bioreactors removed 90 % of the chemical oxygen demand, 57 % of total nitrogen and 52 % of total phosphorus. Substantial microalgal sludge is produced in the process (substrate yield coefficient of 0.43 mg sludge mg chemical oxygen demand−¹, resulting in a biomass with high potential for producing biodiesel (ester content of more than 99 %, cetane number of 55, iodine value of 73.5 g iodine 100 g−¹, unsaturation degree of ~75 % and a cold filter plugging point of 5 ºC.

Bacterial biomass and heterotrophic potential in the waters of the Chesapeake Bay plume and contiguous continental shelf

Science.gov (United States)

Kator, H. I.; Zubkoff, P. L.

1981-01-01

Seasonal baseline data on bacterial biomass and heterotrophic uptake in the Chesapeake Bay plume and contiguous Atlantic Ocean shelf waters are discussed. Viable count bacterial numbers in surface water samples collected during June 1980 ranged from a maximum of 190,000 MPN (most probable number)/ml at the Bay mouth to a minimum of 7900 MPN/ml offshore. Similarly, direct count densities ranged from 1,800,000 BU (bacterial units)/ml to 24,000 BU/ml. Heterotrophic potential (V max) was largest at the Bay mouth and lowest offshore. Biomass and V max values usually decreased with depth although subsurface maxima were occasionally observed at inshore stations. Correlation of biomass and heterotrophic potential data with selected hydrographic variables was determind with a nonparametric statistic. Results indicate viable counts are positively and significantly correlated with total chlorophyll, temperature, direct count and V max during June 1980; significant negative correlations are obtained with salinity and depth. Calculations of bacterial standing crop are discussed.

Nitrate-Dependent Degradation of Acetone by Alicycliphilus and Paracoccus Strains and Comparison of Acetone Carboxylase Enzymes ▿

Science.gov (United States)

Dullius, Carlos Henrique; Chen, Ching-Yuan; Schink, Bernhard

2011-01-01

A novel acetone-degrading, nitrate-reducing bacterium, strain KN Bun08, was isolated from an enrichment culture with butanone and nitrate as the sole sources of carbon and energy. The cells were motile short rods, 0.5 to 1 by 1 to 2 μm in size, which gave Gram-positive staining results in the exponential growth phase and Gram-negative staining results in the stationary-growth phase. Based on 16S rRNA gene sequence analysis, the isolate was assigned to the genus Alicycliphilus. Besides butanone and acetone, the strain used numerous fatty acids as substrates. An ATP-dependent acetone-carboxylating enzyme was enriched from cell extracts of this bacterium and of Alicycliphilus denitrificans K601T by two subsequent DEAE Sepharose column procedures. For comparison, acetone carboxylases were enriched from two additional nitrate-reducing bacterial species, Paracoccus denitrificans and P. pantotrophus. The products of the carboxylase reaction were acetoacetate and AMP rather than ADP. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of cell extracts and of the various enzyme preparations revealed bands corresponding to molecular masses of 85, 78, and 20 kDa, suggesting similarities to the acetone carboxylase enzymes described in detail for the aerobic bacterium Xanthobacter autotrophicus strain Py2 (85.3, 78.3, and 19.6 kDa) and the phototrophic bacterium Rhodobacter capsulatus. Protein bands were excised and compared by mass spectrometry with those of acetone carboxylases of aerobic bacteria. The results document the finding that the nitrate-reducing bacteria studied here use acetone-carboxylating enzymes similar to those of aerobic and phototrophic bacteria. PMID:21841031

Genome Sequence of Lactococcus lactis subsp. lactis NCDO 2118, a GABA-Producing Strain

DEFF Research Database (Denmark)

Oliveira, Letícia C; Saraiva, Tessália D L; Soares, Siomar C

2014-01-01

Lactococcus lactis subsp. lactis NCDO 2118 is a nondairy lactic acid bacterium, a xylose fermenter, and a gamma-aminobutyric acid (GABA) producer isolated from frozen peas. Here, we report the complete genome sequence of L. lactis NCDO 2118, a strain with probiotic potential activity....

A bacterium that degrades and assimilates poly(ethylene terephthalate).

Science.gov (United States)

Yoshida, Shosuke; Hiraga, Kazumi; Takehana, Toshihiko; Taniguchi, Ikuo; Yamaji, Hironao; Maeda, Yasuhito; Toyohara, Kiyotsuna; Miyamoto, Kenji; Kimura, Yoshiharu; Oda, Kohei

2016-03-11

Poly(ethylene terephthalate) (PET) is used extensively worldwide in plastic products, and its accumulation in the environment has become a global concern. Because the ability to enzymatically degrade PET has been thought to be limited to a few fungal species, biodegradation is not yet a viable remediation or recycling strategy. By screening natural microbial communities exposed to PET in the environment, we isolated a novel bacterium, Ideonella sakaiensis 201-F6, that is able to use PET as its major energy and carbon source. When grown on PET, this strain produces two enzymes capable of hydrolyzing PET and the reaction intermediate, mono(2-hydroxyethyl) terephthalic acid. Both enzymes are required to enzymatically convert PET efficiently into its two environmentally benign monomers, terephthalic acid and ethylene glycol. Copyright © 2016, American Association for the Advancement of Science.

The Effect of Aluminium on Antibacterial Properties and the Content of Some Fatty Acids in Microalgae, Chlorella vulgaris Beijernick, under Heterotrophic and Autotrophic Conditions

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Hossein Abbaspour

2017-01-01

Full Text Available Microalgae are a group of organisms, which have a significant potential for industrial applications. These algae contain large amounts of lipids compounds that are beneficial to health, have antibacterial properties, and their extracted oil can be used for biofuel. In this study, microalgae Chlorella vulgaris Beijernick was grown in the culture medium BG-11 containing aluminium (AlCl3 under autotrophic and heterotrophic conditions. In each case, survival and growth, dry weight, internal aluminium content of the sample, antibacterial properties, the content of fatty acids accumulated in the algae and secreted into the culture medium in the logarithmic growth phase were studied. Aluminium significantly increased (P < .05 growth and dry weight in autotrophic treatment compared to the heterotrophic one. Most antibacterial properties were observed in methanol extracts of heterotrophic treatments containing 0.05% glucose. Aluminium also decreased fatty acids accumulation in the algae and increased fatty acids excretion into the culture medium in heterotrophic treatment compared to the autotrophic treatment. Survival of the sample was maintained in heterotrophic conditions and showed growth without lag phase, which is indicative of rapid acclimation of organisms in heterotrophic conditions. It seems that the mentioned characteristics make the single-celled green algae Chlorella vulgaris more efficient in different ways.

Unicellular cyanobacteria synechocystis accommodate heterotrophic bacteria with varied enzymatic and metal resistance properties

Digital Repository Service at National Institute of Oceanography (India)

Anas, A.; Sageer, S.; Jasmin, C.; Vijayan, V.; Pavanan, P.; Athiyanathil, S.; Nair, S.

unicellular cyanobacterium Synechocystis sp. that came from a heavy metal contaminated region of Cochin estuary, southwest coast of India. Based on 16S rRNA gene sequence similarities, the heterotrophic bacteria were grouped into three phyla: namely...

Complete Genome Sequence of Bacillus vallismortis NBIF-001, a Novel Strain from Shangri-La, China, That Has High Activity against Fusarium oxysporum.

Science.gov (United States)

Liu, Xiaoyan; Min, Yong; Huang, Daye; Zhou, Ronghua; Fang, Wei; Liu, Cuijun; Rao, Ben; Zhang, Guangyang; Wang, Kaimei; Yang, Ziwen

2017-11-30

Bacillus vallismortis NBIF-001, a Gram-positive bacterium, was isolated from soil in Shangri-La, China. Here, we provide the complete genome sequence of this bacterium, which has a 3,929,787-bp-long genome, including 4,030 protein-coding genes and 195 RNA genes. This strain possesses a number of genes encoding virulence factors of pathogens. Copyright © 2017 Liu et al.

Heterotrophic nitrogen removal in Bacillus sp. K5: involvement of a novel hydroxylamine oxidase.

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Yang, Yunlong; Lin, Ershu; Huang, Shaobin

2017-12-01

An aerobic denitrifying bacterium isolated from a bio-trickling filter treating NOx, Bacillus sp. K5, is able to convert ammonium to nitrite, in which hydroxylamine oxidase (HAO) plays a critical role. In the present study, the performance for simultaneous nitrification and denitrification was investigated with batch experiments and an HAO was purified by an anion-exchange and gel-filtration chromatography from strain K5. The purified HAO's molecular mass was determined by SDS-PAGE and its activity by measuring the change in the concentration of ferricyanide, the electron acceptor. Results showed that as much as 87.8 mg L -1 ammonium-N was removed without nitrite accumulation within 24 hours in the sodium citrate medium at C/N of 15. The HAO isolated from the strain K5 was approximately 71 KDa. With hydroxylamine (NH 2 OH) as a substrate and potassium ferricyanide as an electron acceptor, the enzyme was capable of oxidizing NH 2 OH to nitrite in vitro when the pH varied from 7 to 9 and temperature ranged from 25 °C to 40 °C. This is the first time that an HAO has been purified from the Bacillus genus, and the findings revealed that it is distinctive in its molecular mass and enzyme properties.

Draft Genome Sequence of Plant Growth–Promoting Micrococcus luteus Strain K39 Isolated from Cyperus conglomeratus in Saudi Arabia

KAUST Repository

Lafi, Feras Fawzi; Ramirez Prado, Juan Sebastian; Alam, Intikhab; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged

2017-01-01

Micrococcus luteus strain K39 is an endophyte bacterium isolated from roots of the desert plant Cyperus conglomeratus collected from the Red Sea shore, Thuwal, Saudi Arabia. The draft genome sequence of strain K39 revealed a number of enzymes involved in salinity and oxidative stress tolerance or having herbicide-resistance activity.

Draft Genome Sequence of Plant Growth–Promoting Micrococcus luteus Strain K39 Isolated from Cyperus conglomeratus in Saudi Arabia

KAUST Repository

Lafi, Feras Fawzi

2017-01-27

Micrococcus luteus strain K39 is an endophyte bacterium isolated from roots of the desert plant Cyperus conglomeratus collected from the Red Sea shore, Thuwal, Saudi Arabia. The draft genome sequence of strain K39 revealed a number of enzymes involved in salinity and oxidative stress tolerance or having herbicide-resistance activity.

Nitrogen transformation under different dissolved oxygen levels by the anoxygenic phototrophic bacterium Marichromatium gracile.

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Hong, Xuan; Chen, Zhongwei; Zhao, Chungui; Yang, Suping

2017-06-01

Marichromatium gracile: YL28 (M. gracile YL28) is an anoxygenic phototrophic bacterial strain that utilizes ammonia, nitrate, or nitrite as its sole nitrogen source during growth. In this study, we investigated the removal and transformation of ammonium, nitrate, and nitrite by M. gracile YL28 grown in a combinatorial culture system of sodium acetate-ammonium, sodium acetate-nitrate and sodium acetate-nitrite in response to different initial dissolved oxygen (DO) levels. In the sodium acetate-ammonium system under aerobic conditions (initial DO = 7.20-7.25 mg/L), we detected a continuous accumulation of nitrate and nitrite. However, under semi-anaerobic conditions (initial DO = 4.08-4.26 mg/L), we observed a temporary accumulation of nitrate and nitrite. Interestingly, under anaerobic conditions (initial DO = 0.36-0.67 mg/L), there was little accumulation of nitrate and nitrite, but an increase in nitrous oxide production. In the sodium acetate-nitrite system, nitrite levels declined slightly under aerobic conditions, and nitrite was completely removed under semi-anaerobic and anaerobic conditions. In addition, M. gracile YL28 was able to grow using nitrite as the sole nitrogen source in situations when nitrogen gas produced by denitrification was eliminated. Taken together, the data indicate that M. gracile YL28 performs simultaneous heterotrophic nitrification and denitrification at low-DO levels and uses nitrite as the sole nitrogen source for growth. Our study is the first to demonstrate that anoxygenic phototrophic bacteria perform heterotrophic ammonia-oxidization and denitrification under anaerobic conditions.

MODELING OF MIXED CHEMOSTAT CULTURES OF AN AEROBIC BACTERIUM, COMAMONAS-TESTOSTERONI, AND AN ANAEROBIC BACTERIUM, VEILLONELLA-ALCALESCENS - COMPARISON WITH EXPERIMENTAL-DATA

NARCIS (Netherlands)

GERRITSE, J; SCHUT, F; GOTTSCHAL, JC

A mathematical model of mixed chemostat cultures of the obligately aerobic bacterium Comamonas testosteroni and the anaerobic bacterium Veillonella alcalescens grown under dual limitation Of L-lactate and oxygen was constructed. The model was based on Michaelis-Menten-type kinetics for the

Competitive Dominance by a Bacteriocin-Producing Vibrio harveyi Strain.

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Hoyt, P R; Sizemore, R K

1982-09-01

Vibrio (Beneckea) harveyi, a bioluminescent marine bacterium, has been shown to produce a bacteriocin-like substance the production of which is mediated by a plasmid. This substance is assumed to be proteinaceous because of its sensitivity to certain proteolytic enzymes. It is stable at low temperatures and can be concentrated by ammonium sulfate precipitation or negative-pressure dialysis. The molecular weight of the bacteriocin was determined to be 2.4 x 10 by molecular exclusion chromatography. Competition experiments indicated that bacteriocin-producing strains predominated over cured variants of the same strain in broth culture experiments. We studied several environmental parameters (pH, salinity, temperature, nutrient concentration) to determine their effects on the competitive advantage bestowed on a bacteriocin-producing strain. Under simulated free-living conditions, no competitive advantage attributable to bacteriocin production was observed. In a simulated enteric habitat, a bacteriocin-producing strain showed dramatic (>90%) inhibition of the sensitive strain within 24 h.

Membrane biofouling in a wastewater nitrification reactor: Microbial succession from autotrophic colonization to heterotrophic domination.

Science.gov (United States)

Lu, Huijie; Xue, Zheng; Saikaly, Pascal; Nunes, Suzana P; Bluver, Ted R; Liu, Wen-Tso

2016-01-01

Membrane biofouling is a complex process that involves bacterial adhesion, extracellular polymeric substances (EPS) excretion and utilization, and species interactions. To obtain a better understanding of the microbial ecology of biofouling process, this study conducted rigorous, time-course analyses on the structure, EPS and microbial composition of the fouling layer developed on ultrafiltration membranes in a nitrification bioreactor. During a 14-day fouling event, three phases were determined according to the flux decline and microbial succession patterns. In Phase I (0-2 days), small sludge flocs in the bulk liquid were selectively attached on membrane surfaces, leading to the formation of similar EPS and microbial community composition as the early biofilms. Dominant populations in small flocs, e.g., Nitrosomonas, Nitrobacter, and Acinetobacter spp., were also the major initial colonizers on membranes. In Phase II (2-4 d), fouling layer structure, EPS composition, and bacterial community went through significant changes. Initial colonizers were replaced by fast-growing and metabolically versatile heterotrophs (e.g., unclassified Sphingobacteria). The declining EPS polysaccharide to protein (PS:PN) ratios could be correlated well with the increase in microbial community diversity. In Phase III (5-14 d), heterotrophs comprised over 90% of the community, whereas biofilm structure and EPS composition remained relatively stable. In all phases, AOB and NOB were constantly found within the top 40% of the fouling layer, with the maximum concentrations around 15% from the top. The overall microbial succession pattern from autotrophic colonization to heterotrophic domination implied that MBR biofouling could be alleviated by forming larger bacterial flocs in bioreactor suspension (reducing autotrophic colonization), and by designing more specific cleaning procedures targeting dominant heterotrophs during typical filtration cycles. Copyright © 2015 Elsevier Ltd. All

Quorum sensing activity of Citrobacter amalonaticus L8A, a bacterium isolated from dental plaque.

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Goh, Share-Yuan; Khan, Saad Ahmed; Tee, Kok Keng; Abu Kasim, Noor Hayaty; Yin, Wai-Fong; Chan, Kok-Gan

2016-02-10

Cell-cell communication is also known as quorum sensing (QS) that happens in the bacterial cells with the aim to regulate their genes expression in response to increased cell density. In this study, a bacterium (L8A) isolated from dental plaque biofilm was identified as Citrobacter amalonaticus by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). Its N-acylhomoserine-lactone (AHL) production was screened by using two types of AHL biosensors namely Chromobacterium violaceum CV026 and Escherichia coli [pSB401]. Citrobacter amalonaticus strain L8A was identified and confirmed producing numerous types of AHL namely N-butyryl-L-homoserine lactone (C4-HSL), N-hexanoyl-L-homoserine lactone (C6-HSL), N-octanoyl-L-homoserine lactone (C8-HSL) and N-hexadecanoyl-L-homoserine lactone (C16-HSL). We performed the whole genome sequence analysis of this oral isolate where its genome sequence reveals the presence of QS signal synthase gene and our work will pave the ways to study the function of the related QS genes in this bacterium.

Nocardioides daejeonensis sp. nov., a denitrifying bacterium isolated from sludge in a sewage-disposal plant.

Science.gov (United States)

Woo, Sung-Geun; Srinivasan, Sathiyaraj; Yang, Jihoon; Jung, Yong-An; Kim, Myung Kyum; Lee, Myungjin

2012-05-01

Strain MJ31(T), a gram-reaction-positive, aerobic, rod-shaped, non-motile bacterium, was isolated from a sludge sample collected at the Daejeon sewage-disposal plant, in South Korea, and characterized in order to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MJ31(T) belonged to the genus Nocardioides, appearing most closely related to Nocardioides dubius KSL-104(T) (98.6 % sequence similarity), Nocardioides jensenii DSM 20641(T) (97.6 %), Nocardioides daedukensis MDN22(T) (97.2 %) and Nocardioides mesophilus MSL-22(T) (97.0 %). The chemotaxonomic properties of strain MJ31(T) were consistent with those of the genus Nocardioides: MK-8(H(4)) was the predominant menaquinone, iso-C(16 : 0), iso-C(17 : 0) and C(18 : 1)ω9c were the predominant cellular fatty acids, and the cell-wall peptidoglycan was based on LL-2,6-diaminopimelic acid. The genomic DNA G+C content of strain MJ31(T) was 71.2 mol%. Some differential phenotypic properties and low DNA-DNA relatedness values (<28 %) with the type strains of closely related species indicated that strain MJ31(T) represents a novel species, for which the name Nocardioides daejeonensis sp. nov. is proposed. The type strain is MJ31(T) ( = KCTC 19772(T) = JCM 16922(T)).

Bacillus tamaricis sp. nov., an alkaliphilic bacterium isolated from a Tamarix cone soil.

Science.gov (United States)

Zhang, Yong-Guang; Zhou, Xing-Kui; Guo, Jian-Wei; Xiao, Min; Wang, Hong-Fei; Wang, Yun; Bobodzhanova, Khursheda; Li, Wen-Jun

2018-02-01

A Gram-stain-positive, alkaliphilic bacterium, designated EGI 80668 T , was isolated from a Tamarix cone soil in Xinjiang, north-west China. Cells were facultatively anaerobic, terminal endospore-forming and motile by means of peritrichous flagella. Colonies were yellowish and the cells showed oxidase-negative and catalase-positive reactions. Strain EGI 80668 T grew at pH 8.0-10.0 and with 0-10 % (w/v) NaCl (optimally at pH 9.0 and with 1-2 % NaCl) on marine agar 2216. The predominant menaquinone was MK-7. The major fatty acids were anteiso-C17 : 0 and anteiso-C15 : 0. The cellular polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unknown phospholipids and one unknown aminophospholipid. The G+C content of the genomic DNA was 38.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EGI 80668 T was affiliated to the genus Bacillus. The highest 16S rRNA gene sequence similarity between strain EGI 80668 T and a member of the genus Bacillus was 96.83 % with Bacillus cellulosilyticus JCM 9156 T . A polyphasic taxonomic study based on morphological, physiological, biochemical and phylogenetic data indicated that strain EGI 80668 T represents a novel species of the genus Bacillus, for which the name Bacillus tamaricis sp. nov. (type strain EGI 80668 T =KCTC 33703 T =CGMCC 1.15917 T ) is proposed.

Genome Sequence of Carbon Dioxide-Sequestering Serratia sp. Strain ISTD04 Isolated from Marble Mining Rocks.

Science.gov (United States)

Kumar, Manish; Gazara, Rajesh Kumar; Verma, Sandhya; Kumar, Madan; Verma, Praveen Kumar; Thakur, Indu Shekhar

2016-10-20

The Serratia sp. strain ISTD04 has been identified as a carbon dioxide (CO 2 )-sequestering bacterium isolated from marble mining rocks in the Umra area, Rajasthan, India. This strain grows chemolithotrophically on media that contain sodium bicarbonate (NaHCO 3 ) as the sole carbon source. Here, we report the genome sequence of 5.07 Mb Serratia sp. ISTD04. Copyright © 2016 Kumar et al.

Microwhip scorpions (Palpigradi) feed on heterotrophic cyanobacteria in Slovak caves - a curiosity among Arachnida

Czech Academy of Sciences Publication Activity Database

Smrž, J.; Kováč, L.; Mikeš, J.; Lukešová, Alena

2013-01-01

Roč. 8, č. 10 (2013), e75989 E-ISSN 1932-6203 Institutional support: RVO:60077344 Keywords : microwhip scorpions * heterotrophic cyanobacteria * Slovak caves Subject RIV: EG - Zoology Impact factor: 3.534, year: 2013

Draft genome sequence of Pseudomonas sp. strain M47T1, carried by Bursaphelenchus xylophilus isolated from Pinus pinaster.

Science.gov (United States)

Proença, Diogo Neves; Espírito Santo, Christophe; Grass, Gregor; Morais, Paula V

2012-09-01

The draft genome sequence of Pseudomonas sp. strain M47T1, carried by the Bursaphelenchus xylophilus pinewood nematode, the causative agent of pine wilt disease, is presented. In Pseudomonas sp. strain M47T1, genes that make this a plant growth-promoting bacterium, as well as genes potentially involved in nematotoxicity, were identified.

Improvement of biological nitrogen removal with nitrate-dependent Fe(II) oxidation bacterium Aquabacterium parvum B6 in an up-flow bioreactor for wastewater treatment.

Science.gov (United States)

Zhang, Xiaoxin; Li, Ang; Szewzyk, Ulrich; Ma, Fang

2016-11-01

Aquabacterium parvum strain B6 exhibited efficient nitrate-dependent Fe(II) oxidation ability using nitrate as an electron acceptor. A continuous up-flow bioreactor that included an aerobic and an anoxic section was constructed, and strain B6 was added to the bioreactor as inocula to explore the application of microbial nitrate-dependent Fe(II) oxidizing (NDFO) efficiency in wastewater treatment. The maximum NRE (anoxic section) and TNRE of 46.9% and 79.7%, respectively, could be obtained at a C/N ratio of 5.3:1 in the influent with HRT of 17. Meanwhile, the taxonomy composition of the reactor was assessed, as well. The NDFO metabolism of strain B6 could be expected because of its relatively dominant position in the anoxic section, whereas potential heterotrophic nitrification and aerobic denitrification developed into the prevailing status in the aerobic section after 50days of continuous operation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Heterotrophic denitrification vs. autotrophic anammox – quantifying collateral effects on the oceanic carbon cycle

Directory of Open Access Journals (Sweden)

W. Koeve

2010-08-01

Full Text Available The conversion of fixed nitrogen to N₂ in suboxic waters is estimated to contribute roughly a third to total oceanic losses of fixed nitrogen and is hence understood to be of major importance to global oceanic production and, therefore, to the role of the ocean as a sink of atmospheric CO₂. At present heterotrophic denitrification and autotrophic anammox are considered the dominant sinks of fixed nitrogen. Recently, it has been suggested that the trophic nature of pelagic N₂-production may have additional, "collateral" effects on the carbon cycle, where heterotrophic denitrification provides a shallow source of CO₂ and autotrophic anammox a shallow sink. Here, we analyse the stoichiometries of nitrogen and associated carbon conversions in marine oxygen minimum zones (OMZ focusing on heterotrophic denitrification, autotrophic anammox, and dissimilatory nitrate reduction to nitrite and ammonium in order to test this hypothesis quantitatively. For open ocean OMZs the combined effects of these processes turn out to be clearly heterotrophic, even with high shares of the autotrophic anammox reaction in total N₂-production and including various combinations of dissimilatory processes which provide the substrates to anammox. In such systems, the degree of heterotrophy (ΔCO₂:ΔN₂, varying between 1.7 and 6.5, is a function of the efficiency of nitrogen conversion. On the contrary, in systems like the Black Sea, where suboxic N-conversions are supported by diffusive fluxes of NH₄⁺ originating from neighbouring waters with sulphate reduction, much lower values of ΔCO₂:ΔN₂ can be found. However, accounting for concomitant diffusive fluxes of CO₂, the ratio approaches higher values similar to those computed for open ocean OMZs. Based on this analysis, we question the significance of collateral effects concerning the trophic

Bacillus endozanthoxylicus sp. nov., an endophytic bacterium isolated from Zanthoxylum bungeanum Maxim leaves.

Science.gov (United States)

Ma, Li; Xi, Jia-Qin; Cao, Yong-Hong; Wang, Xiao-Yan; Zheng, Shuai-Chao; Yang, Cheng-Gang; Yang, Ling-Ling; Mi, Qi-Li; Li, Xue-Mei; Zhu, Ming-Liang; Mo, Ming-He

2017-10-01

A Gram-stain-positive, rod-shaped, motile bacterium, designated as 1404 T , was isolated from leaves of Chinese red pepper (Huajiao) (Zanthoxylum bungeanum Maxim) collected from Gansu, north-west China. Spores were not observed under a range of conditions. Strain 1404 T was observed to grow at 15-45 °C and pH 6.0-10.0 and in presence of 0-5 % (w/v) NaCl concentration. The cell wall of strain 1404 T was found to contain meso-diaminopimelic acid, and the predominant respiratory quinone was identified as MK-7. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as well as three unidentified polar lipids. The major fatty acids profile of strain 1404 T consisted of iso-C15 : 0 (25.6 %), anteiso-C15 : 0 (18.4 %) and iso-C14 : 0 (12.1 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 1404 T was affiliated to the genus Bacillus and was closely related to Bacillusoryzisoli 1DS3-10 T , Bacillusbenzoevorans DSM 5391 T and Bacilluscirculans DSM 11 T with sequence similarity of 98.3, 98.2 and 96.9 %, respectively. The G+C content of the genomic DNA was determined to be 39.4 mol%. DNA-DNA hybridization values indicated that relatedness between strain 1404 T and the type strains of closely related species of the genus Bacillus was below 41 %. Therefore, on the basis of the data from the polyphasic taxonomic study presented, strain 1404 T represents a novel species of the genus Bacillus, for which the name proposed is Bacillus endozanthoxylicus sp. nov. The type strain is 1404 T (=CCTCC AB 2017021 T =KCTC 33827 T ).

Isolation and characterization of a furfural-degrading bacterium Bacillus cereus sp. strain DS1.

Science.gov (United States)

Zheng, Dan; Bao, Jianguo; Lu, Jueming; Gao, Chunlei

2015-02-01

Furfural was found to be the main organic pollutant in the wastewater coming from the Diosgenin factory. This substance is derived from acidic pentosan in Dioscorea zingiberensis and is also found in a variety of agricultural byproducts, including corncobs, oat, wheat bran, and sawdust. It is regarded as a toxicant and an inhibitor to the growth of microorganism in both sewage disposal and biological fermentation. A furfural-degrading strain (DS1) was isolated from activated sludge of wastewater treatment plant in a diosgenin factory by continuous enrichment culture. The strain was identified as Bacillus cereus based on morphological, physiological tests, as well as on 16S rDNA sequence and Biolog analyses. The capacity of this strain to grow on a mineral salt medium, utilizing furfural as the sole carbon and energy source to degrade furfural, was investigated in this study. Under the condition of pH 9.0, temperature 35 °C, with rotating speed of 150 rpm, and an inoculum of 6 %, the strain showed that the furfural degradation capacity reaches 35 % in 7 days, as measured by high-performance liquid chromatography. The addition of inorganic carbon sources could bring down the biodegradation efficiency of the furfural. The strain DS1 showed better furfural removal capacity, as compared to other inorganic carbon sources in the media. Furthermore, a furfural concentration of as high as 4,000 mg L(-1) was tolerated by the culture. The capacity to degrade furfural was demonstrated for the first time by using the genus B. cereus. This study suggests the possible application in biodegradation strategies.

A "footprint" of plant carbon fixation cycle functions during the development of a heterotrophic fungus.

Science.gov (United States)

Lyu, Xueliang; Shen, Cuicui; Xie, Jiatao; Fu, Yanping; Jiang, Daohong; Hu, Zijin; Tang, Lihua; Tang, Liguang; Ding, Feng; Li, Kunfei; Wu, Song; Hu, Yanping; Luo, Lilian; Li, Yuanhao; Wang, Qihua; Li, Guoqing; Cheng, Jiasen

2015-08-11

Carbon fixation pathway of plants (CFPP) in photosynthesis converts solar energy to biomass, bio-products and biofuel. Intriguingly, a large number of heterotrophic fungi also possess enzymes functionally associated with CFPP, raising the questions about their roles in fungal development and in evolution. Here, we report on the presence of 17 CFPP associated enzymes (ten in Calvin-Benson-Basham reductive pentose phosphate pathway and seven in C4-dicarboxylic acid cycle) in the genome of Sclerotinia sclerotiorum, a heterotrophic phytopathogenic fungus, and only two unique enzymes: ribulose-1, 5-bisphosphate carboxylase-oxygenase (Rubisco) and phosphoribulokinase (PRK) were absent. This data suggested an incomplete CFPP-like pathway (CLP) in fungi. Functional profile analysis demonstrated that the activity of the incomplete CLP was dramatically regulated during different developmental stages of S. sclerotiorum. Subsequent experiments confirmed that many of them were essential to the virulence and/or sclerotial formation. Most of the CLP associated genes are conserved in fungi. Phylogenetic analysis showed that many of them have undergone gene duplication, gene acquisition or loss and functional diversification in evolutionary history. These findings showed an evolutionary links in the carbon fixation processes of autotrophs and heterotrophs and implicated the functions of related genes were in course of continuous change in different organisms in evolution.

Draft genome sequence of the arsenite-oxidizing strain Aliihoeflea sp. 2WW, isolated from arsenic-contaminated groundwater

NARCIS (Netherlands)

Cavalca, L.; Corsini, A.; Andreoni, V.; Muyzer, G.

2013-01-01

Here, we report the draft genome sequence of the arsenite-oxidizing bacterium Aliihoeflea sp. strain 2WW, which consists of a 4.15-Mb chromosome and contains different genes that are involved in arsenic transformations.

Natural Competence of Xylella fastidiosa Occurs at a High Frequency Inside Microfluidic Chambers Mimicking the Bacterium's Natural Habitats.

Science.gov (United States)

Kandel, Prem P; Lopez, Samantha M; Almeida, Rodrigo P P; De La Fuente, Leonardo

2016-09-01

Xylella fastidiosa is a xylem-limited bacterium that is the causal agent of emerging diseases in a number of economically important crops. Genetic diversity studies have demonstrated homologous recombination occurring among X. fastidiosa strains, which has been proposed to contribute to host plant shifts. Moreover, experimental evidence confirmed that X. fastidiosa is naturally competent for recombination in vitro Here, as an approximation of natural habitats (plant xylem vessels and insect mouthparts), recombination was studied in microfluidic chambers (MCs) filled with media amended with grapevine xylem sap. First, different media were screened for recombination in solid agar plates using a pair of X. fastidiosa strains that were previously reported to recombine in coculture. The highest frequency of recombination was obtained with PD3 medium, compared to those with the other two media (X. fastidiosa medium [XFM] and periwinkle wilt [PW] medium) used in previous studies. Dissection of the media components led to the identification of bovine serum albumin as an inhibitor of recombination that was correlated to its previously known effect on inhibition of twitching motility. When recombination was performed in liquid culture, the frequencies were significantly higher under flow conditions (MCs) than under batch conditions (test tubes). The recombination frequencies in MCs and agar plates were not significantly different from each other. Grapevine xylem sap from both susceptible and tolerant varieties allowed high recombination frequency in MCs when mixed with PD3. These results suggest that X. fastidiosa has the ability to be naturally competent in the natural growth environment of liquid flow, and this phenomenon could have implications in X. fastidiosa environmental adaptation. Xylella fastidiosa is a plant pathogen that lives inside xylem vessels (where water and nutrients are transported inside the plant) and the mouthparts of insect vectors. This bacterium

Feeding, growth and metabolism of the marine heterotrophic dinoflagellate Gyrodinium dominans

DEFF Research Database (Denmark)

Schmoker, Claire; Thor, Peter; Hernández-león, Santiago

2011-01-01

may inflict high metabolic costs. Gross growth efficiencies (GGEs), determined for G. dominans in both food availability conditions, were within the range of values reported for other heterotrophic protozoans, and while GGE decreased when concentrations of food were high in organisms fed a single...... pulse of food, the opposite was observed in organisms acclimatized to a constant level of food....

Methylobacterium pseudosasae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the bamboo phyllosphere.

Science.gov (United States)

Madhaiyan, Munusamy; Poonguzhali, Selvaraj

2014-02-01

A pink-pigmented, Gram negative, aerobic, facultatively methylotrophic bacterium, strain BL44(T), was isolated from bamboo leaves and identified as a member of the genus Methylobacterium. Phylogenetic analysis based on 16S rRNA gene sequences showed similarity values of 98.7-97.0 % with closely related type strains and showed highest similarity to Methylobacterium zatmanii DSM 5688(T) (98.7 %) and Methylobacterium thiocyanatum DSM 11490(T) (98.7 %). Methylotrophic metabolism in this strain was confirmed by PCR amplification and sequencing of the mxaF gene coding for the α-subunit of methanol dehydrogenase. Strain BL44(T) produced three known quorum sensing signal molecules with similar retention time to C8, C10 and C12-HSLs when characterized by GC-MS. The fatty acid profiles contained major amounts of C18:1 ω7c, iso-3OH C17:0 and summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH), which supported the grouping of the isolate in the genus Methylobacterium. The DNA G+C content was 66.9 mol%. DNA relatedness of the strain BL44(T) to its most closely related strains ranged from 12-43.3 %. On the basis of the phenotypic, phylogenetic and DNA-DNA hybridization data, strain BL44(T) is assigned to a novel species of the genus Methylobacterium for which the name Methylobacterium pseudosasae sp. nov. is proposed (type strain BL44(T) = NBRC 105205(T) = ICMP 17622(T)).

Salinicola tamaricis sp. nov., a heavy-metal-tolerant, endophytic bacterium isolated from the halophyte Tamarix chinensis Lour.

Science.gov (United States)

Zhao, Guo-Yan; Zhao, Li-Ya; Xia, Zhi-Jie; Zhu, Jin-Lei; Liu, Di; Liu, Chun-Yue; Chen, Xiu-Lan; Zhang, Yu-Zhong; Zhang, Xi-Ying; Dai, Mei-Xue

2017-06-01

A Gram-stain-negative, rod-shaped bacterium, strain F01T, was isolated from leaves of Tamarix chinensis Lour. The isolate grew optimally at 30 °C, at pH 7.0 and with 5.0 % (w/v) NaCl, and showed a high tolerance to manganese, lead, nickel, ferrous ions and copper ions. The major fatty acids were C18 : 1ω7c and C16 : 0, and the predominant respiratory quinone was Q-9. Polar lipids were dominated by diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, unidentified aminoglycolipids and phospholipids. The DNA G+C content was 65.8 %. Based on multilocus phylogenetic analysis, strain F01T belonged to the genus Salinicola, with highest 16S rRNA gene sequence similarity to Salinicola peritrichatus CGMCC 1.12381T (97.7 %). The level of DNA-DNA hybridization between strain F01T and closely related Salinicola strains was well below 70 %. According to the phenotypic, genetic and chemotaxonomic data, strain F01T is considered to represent a novel species in the genus Salinicola, for which the name Salinicola tamaricis sp. nov. is proposed. The type strain is F01T (=CCTCC AB 2015304T=KCTC 42855T).

Engineering a wild fast-growing Mycoplasma bacterium to generate ...

International Development Research Centre (IDRC) Digital Library (Canada)

2018-01-12

Jan 12, 2018 ... The CCPP bacterium causes sick animals to experience severe symptoms ... because antibiotic treatment does not eliminate the responsible bacterium. ... To develop a fast growing CCPP vaccine for cheaper production and ...

Draft Genome Sequence of the Plant Growth–Promoting Rhizobacterium Acinetobacter radioresistens Strain SA188 Isolated from the Desert Plant Indigofera argentea

KAUST Repository

Lafi, Feras Fawzi; Alam, Intikhab; Bisseling, Ton; Geurts, Rene; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged

2017-01-01

Acinetobacter radioresistens strain SA188 is a plant endophytic bacterium, isolated from root nodules of the desert plants Indigofera spp., collected in Jizan, Saudi Arabia. Here, we report the 3.2-Mb draft genome sequence of strain SA188, highlighting characteristic pathways for plant growth–promoting activity and environmental adaptation.

Draft Genome Sequence of the Plant Growth–Promoting Rhizobacterium Acinetobacter radioresistens Strain SA188 Isolated from the Desert Plant Indigofera argentea

KAUST Repository

Lafi, Feras Fawzi

2017-03-03

Acinetobacter radioresistens strain SA188 is a plant endophytic bacterium, isolated from root nodules of the desert plants Indigofera spp., collected in Jizan, Saudi Arabia. Here, we report the 3.2-Mb draft genome sequence of strain SA188, highlighting characteristic pathways for plant growth–promoting activity and environmental adaptation.

Heterotrophic cultivation of Chlorella pyrenoidosa using sucrose as the sole carbon source by co-culture with Rhodotorula glutinis.

Science.gov (United States)

Wang, Shikai; Wu, Yong; Wang, Xu

2016-11-01

Heterotrophic cultivation of microalgae is a feasible alternative strategy to avoid the light limitation of photoautotrophic culture, but the heterotrophic utilization of disaccharides is difficult for microalgae. Aimed at this problem, a co-culture system was developed by mix culture of C. pyrenoidosa and R. glutinis using sucrose as the sole carbon source. In this system, C. pyrenoidosa could utilize glucose and fructose which were hydrolyzed from sucrose by R. glutinis. The highest specific growth rate and final cell number proportion of algae was 1.02day(-1) and 45%, respectively, when cultured at the initial algal cell number proportion of 95.24% and the final algal cell density was 111.48×10(6)cells/mL. In addition, the lipid content was also promoted due to the synergistic effects in mix culture. This study provides a novel approach using sucrose-riched wastes for the heterotrophic culture of microalgae and may effectively decrease the cost of carbon source. Copyright © 2016 Elsevier Ltd. All rights reserved.

Helicobacter Catalase Devoid of Catalytic Activity Protects the Bacterium against Oxidative Stress.

Science.gov (United States)

Benoit, Stéphane L; Maier, Robert J

2016-11-04

Catalase, a conserved and abundant enzyme found in all domains of life, dissipates the oxidant hydrogen peroxide (H 2 O 2 ). The gastric pathogen Helicobacter pylori undergoes host-mediated oxidant stress exposure, and its catalase contains oxidizable methionine (Met) residues. We hypothesized catalase may play a large stress-combating role independent of its classical catalytic one, namely quenching harmful oxidants through its recyclable Met residues, resulting in oxidant protection to the bacterium. Two Helicobacter mutant strains ( katA H56A and katA Y339A ) containing catalase without enzyme activity but that retain all Met residues were created. These strains were much more resistant to oxidants than a catalase-deletion mutant strain. The quenching ability of the altered versions was shown, whereby oxidant-stressed (HOCl-exposed) Helicobacter retained viability even upon extracellular addition of the inactive versions of catalase, in contrast to cells receiving HOCl alone. The importance of the methionine-mediated quenching to the pathogen residing in the oxidant-rich gastric mucus was studied. In contrast to a catalase-null strain, both site-change mutants proficiently colonized the murine gastric mucosa, suggesting that the amino acid composition-dependent oxidant-quenching role of catalase is more important than the well described H 2 O 2 -dissipating catalytic role. Over 100 years after the discovery of catalase, these findings reveal a new non-enzymatic protective mechanism of action for the ubiquitous enzyme. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Dynamics of pollution-indicator and heterotrophic bacteria in sewage treatment lagoons.

Science.gov (United States)

Legendre, P; Baleux, B; Troussellier, M

1984-09-01

The spatio-temporal dynamics of pollution-indicator bacteria and aerobic heterotrophic bacteria were studied in the sewage treatment lagoons of an urban wastewater center after 26 months of biweekly sampling at eight stations in these lagoons. Robust statistical methods of time-series analysis were used to study successional steps (through chronological clustering) and rhythmic behavior through time (through contingency periodogram). The aerobic heterotrophic bacterial community showed two types of temporal evolution: in the first four stations, it seems mainly controlled by the nutrient support capacity of the sewage input, whereas in the remaining part of the lagoon, it seems likely that the pollution-indicator bacteria are gradually replaced by other bacterial types that are better adapted to this environment. On the other hand, the pollution-indicator bacteria showed an annual cycle which increased in amplitude at distances further from the wastewater source. The main events in this cycle were produced simultaneously at all stations, indicating control of these bacterial populations by climatic factors, which act through physical and chemical factors, and also through other biological components of this ecosystem (phytoplankton and zooplankton). Finally, we use results from this study to suggest a modified design for a future study program.

Fermentation of glycolate by a pure culture of a strictly anaerobic gram-positive bacterium belonging to the family Lachnospiraceae.

Science.gov (United States)

Janssen, Peter H; Hugenholtz, Philip

2003-05-01

The component bacteria of a three-membered mixed culture able to ferment glycolate to acetate, propionate and CO(2) were isolated in pure culture. All three strains were strict anaerobes that, on the basis of comparative 16S rRNA gene sequence analysis, belonged to the order Clostridiales in the phylum Firmicutes (low G+C gram-positive bacteria). Two of the strains were not involved in glycolate metabolism. The third, the glycolate-fermenting strain 19gly4 (DSM 11261), was related to members of the family Lachnospiraceae. The cells of strain 19gly4 were oval- to lemon-shaped, 0.85 microm long and 0.65 microm in diameter, occurring singly, in pairs, or in chains of up to 30 cells. Strain 19gly4 fermented glycolate or fumarate to acetate, succinate, and CO(2). Hydrogen was not formed, and strain 19gly4 was able to grow on glycolate in pure culture without any syntrophic hydrogen transfer and without the use of an external electron acceptor. There was no evidence for homoacetogenic metabolism. This bacterium therefore differs in metabolism from previously reported glycolate-utilising anaerobes.

Marinospirillum insulare sp. nov., a novel halophilic helical bacterium isolated from kusaya gravy.

Science.gov (United States)

Satomi, M; Kimura, B; Hayashi, M; Okuzumi, M; Fujii, T

2004-01-01

A novel species that belongs to the genus Marinospirillum is described on the basis of phenotypic characteristics, phylogenetic analysis of 16S rRNA and gyrB gene sequences and DNA-DNA hybridization. Four strains of helical, halophilic, Gram-negative, heterotrophic bacteria were isolated from kusaya gravy, which is fermented brine that is used for the production of traditional dried fish in the Izu Islands of Japan. All of the new isolates were motile by means of bipolar tuft flagella, of small cell size, coccoid-body-forming and aerophilic; it was concluded that they belong to the same bacterial species, based on DNA-DNA hybridization values (>70% DNA relatedness). DNA G+C contents of the new strains were 42-43 mol% and they had isoprenoid quinone Q-8 as the major component. Phylogenetic analysis of 16S rRNA gene sequences indicated that the new isolates were members of the genus Marinospirillum; sequence similarity of the new isolates to Marinospirillum minutulum, Marinospirillum megaterium and Marinospirillum alkaliphilum was 98.5, 98.2 and 95.2%, respectively. Phylogenetic analysis based on the gyrB gene indicated that the new isolates had enough phylogenetic distance from M. minutulum and M. megaterium to be regarded as different species, with 84.7 and 78.7% sequence similarity, respectively. DNA-DNA hybridization showed that the new isolates had <36% DNA relatedness to M. minutulum and M. megaterium, supporting the phylogenetic conclusion. Thus, a novel species is proposed: Marinospirillum insulare sp. nov. (type strain, KT=LMG 21802T=NBRC 100033T).

Zymomonas mobilis: a bacterium for ethanol production

Energy Technology Data Exchange (ETDEWEB)

Baratti, J.C.; Bu' Lock, J.D.

1986-01-01

Zymomonas mobilis is a facultative anaerobic gram negative bacterium first isolated in tropical countries from alcoholic beverages like the African palm wine, the Mexican pulque and also as a contaminant of cider (cider sickness) or beer in the European countries. It is one of the few facultative anaerobic bacteria degrading glucose by the Entner-Doudoroff pathway usually found in strictly aerobic microorganisms. Some work was devoted to this bacterium in the 50s and 60s and was reviewed by Swings and De Ley in their classical paper published in 1977. During the 70s there was very little work on the bacterium until 1979 and the first report by the Australian group of P.L. Rogers on the great potentialities of Z. mobilis for ethanol production. At that time the petroleum crisis had led the developed countries to search for alternative fuel from renewable resources. The Australian group clearly demonstrated the advantages of the bacterium compared to the yeasts traditionally used for the alcoholic fermentation. As a result, there was a considerable burst in the Zymomonas literature which started from nearly zero in the late 70s to attain 70 papers published in the field in 1984. In this article, papers published from 1982 to 1986 are reviewed.

Taxonomic characterization of the cellulose-degrading bacterium NCIB 10462

Energy Technology Data Exchange (ETDEWEB)

Dees, C.; Ringleberg, D.; Scott, T.C. [Oak Ridge National Lab., TN (United States); Phelps, T. [Univ. of Tennessee, Knoxville, TN (United States)

1994-06-01

The gram negative cellulase-producing bacterium NCIB 10462 has been previously named Pseudomonas fluorescens subsp. or var. cellulosa. Since there is renewed interest in cellulose-degrading bacteria for use in bioconversion of cellulose to chemical feed stocks and fuels, we re-examined the characteristics of this microorganism to determine its proper taxonomic characterization and to further define it`s true metabolic potential. Metabolic and physical characterization of NCIB 10462 revealed that this was an alkalophilic, non-fermentative, gram negative, oxidase positive, motile, cellulose-degrading bacterium. The aerobic substrate utilization profile of this bacterium was found to have few characteristics consistent with a classification of P. fluorescens with a very low probability match with the genus Sphingomonas. Total lipid analysis did not reveal that any sphingolipid bases are produced by this bacterium. NCIB 10462 was found to grow best aerobically but also grows well in complex media under reducing conditions. NCIB 10462 grew slowly under full anaerobic conditions on complex media but growth on cellulosic media was found only under aerobic conditions. Total fatty acid analysis (MIDI) of NCIB 10462 failed to group this bacterium with a known pseudomonas species. However, fatty acid analysis of the bacteria when grown at temperatures below 37{degrees}C suggest that the organism is a pseudomonad. Since a predominant characteristic of this bacterium is it`s ability to degrade cellulose, we suggest it be called Pseudomonas cellulosa.

Best practices in heterotrophic high-cell-density microalgal processes: achievements, potential and possible limitations

Czech Academy of Sciences Publication Activity Database

Bumbak, F.; Cook, S.; Zachleder, Vilém; Hauser, S.; Kovar, K.

2011-01-01

Roč. 91, č. 1 (2011), 31-46 ISSN 0175-7598 Institutional research plan: CEZ:AV0Z50200510 Keywords : Heterotrophic growth * Microalgae * High-celldensity culture Subject RIV: EE - Microbiology, Virology Impact factor: 3.425, year: 2011

Lipid transfer proteins and protease inhibitors as key factors in the priming of barley responses to Fusarium head blight disease by a biocontrol strain of Pseudomonas fluorescens.

Science.gov (United States)

Petti, Carloalberto; Khan, Mojibur; Doohan, Fiona

2010-11-01

Strains of non-pathogenic pseudomonad bacteria, can elicit host defence responses against pathogenic microorganisms. Pseudomonas fluorescens strain MKB158 can protect cereals from pathogenesis by Fusarium fungi, including Fusarium head blight which is an economically important disease due to its association with both yield loss and mycotoxin contamination of grain. Using the 22 K barley Affymetrix chip, trancriptome studies were undertaken to determine the local effect of P. fluorescens strain MKB158 on the transcriptome of barley head tissue, and to discriminate transcripts primed by the bacterium to respond to challenge by Fusarium culmorum, a causal agent of the economically important Fusarium head blight disease of cereals. The bacterium significantly affected the accumulation of 1203 transcripts and primed 74 to positively, and 14 to negatively, respond to the pathogen (P = 0.05). This is the first study to give insights into bacterium priming in the Triticeae tribe of grasses and associated transcripts were classified into 13 functional classes, associated with diverse functions, including detoxification, cell wall biosynthesis and the amplification of host defence responses. In silico analysis of Arabidopsis homologs of bacterium-primed barley genes indicated that, as is the case in dicots, jasmonic acid plays a role in pseudomonad priming of host responses. Additionally, the transcriptome studies described herein also reveal new insights into bacterium-mediated priming of host defences against necrotrophs, including the positive effects on grain filling, lignin deposition, oxidative stress responses, and the inhibition of protease inhibitors and proteins that play a key role in programmed cell death.

Sepsis and Hemocyte Loss in Honey Bees (Apis mellifera) Infected with Serratia marcescens Strain Sicaria.

Science.gov (United States)

Burritt, Nancy L; Foss, Nicole J; Neeno-Eckwall, Eric C; Church, James O; Hilger, Anna M; Hildebrand, Jacob A; Warshauer, David M; Perna, Nicole T; Burritt, James B

2016-01-01

Global loss of honey bee colonies is threatening the human food supply. Diverse pathogens reduce honey bee hardiness needed to sustain colonies, especially in winter. We isolated a free-living Gram negative bacillus from hemolymph of worker honey bees (Apis mellifera) found separated from winter clusters. In some hives, greater than 90% of the dying bees detached from the winter cluster were found to contain this bacterium in their hemolymph. Throughout the year, the same organism was rarely found in bees engaged in normal hive activities, but was detected in about half of Varroa destructor mites obtained from colonies that housed the septic bees. Flow cytometry of hemolymph from septic bees showed a significant reduction of plasmatocytes and other types of hemocytes. Interpretation of the16S rRNA sequence of the bacterium indicated that it belongs to the Serratia genus of Gram-negative Gammaproteobacteria, which has not previously been implicated as a pathogen of adult honey bees. Complete genome sequence analysis of the bacterium supported its classification as a novel strain of Serratia marcescens, which was designated as S. marcescens strain sicaria (Ss1). When compared with other strains of S. marcescens, Ss1 demonstrated several phenotypic and genetic differences, including 65 genes not previously found in other Serratia genomes. Some of the unique genes we identified in Ss1 were related to those from bacterial insect pathogens and commensals. Recovery of this organism extends a complex pathosphere of agents which may contribute to failure of honey bee colonies.

Sepsis and Hemocyte Loss in Honey Bees (Apis mellifera) Infected with Serratia marcescens Strain Sicaria

Science.gov (United States)

Burritt, Nancy L.; Foss, Nicole J.; Neeno-Eckwall, Eric C.; Church, James O.; Hildebrand, Jacob A.; Warshauer, David M.; Perna, Nicole T.; Burritt, James B.

2016-01-01

Global loss of honey bee colonies is threatening the human food supply. Diverse pathogens reduce honey bee hardiness needed to sustain colonies, especially in winter. We isolated a free-living Gram negative bacillus from hemolymph of worker honey bees (Apis mellifera) found separated from winter clusters. In some hives, greater than 90% of the dying bees detached from the winter cluster were found to contain this bacterium in their hemolymph. Throughout the year, the same organism was rarely found in bees engaged in normal hive activities, but was detected in about half of Varroa destructor mites obtained from colonies that housed the septic bees. Flow cytometry of hemolymph from septic bees showed a significant reduction of plasmatocytes and other types of hemocytes. Interpretation of the16S rRNA sequence of the bacterium indicated that it belongs to the Serratia genus of Gram-negative Gammaproteobacteria, which has not previously been implicated as a pathogen of adult honey bees. Complete genome sequence analysis of the bacterium supported its classification as a novel strain of Serratia marcescens, which was designated as S. marcescens strain sicaria (Ss1). When compared with other strains of S. marcescens, Ss1 demonstrated several phenotypic and genetic differences, including 65 genes not previously found in other Serratia genomes. Some of the unique genes we identified in Ss1 were related to those from bacterial insect pathogens and commensals. Recovery of this organism extends a complex pathosphere of agents which may contribute to failure of honey bee colonies. PMID:28002470

Microflora of urogenital tract in pregnancy with asymptomatic bacterium

International Nuclear Information System (INIS)

Abdullaeva, R.A.

2006-01-01

The article contains results of research interrelationship from colonization of vagina and urinary tract diseases. E.coli one of the main factors in development asymptomatic bacterium. Presented high effects of penicillin medicaments and nitrofurans in treatment of asymptomatic bacterium

Heterotrophic compensation: a possible mechanism for resilience of coral reefs to global warming or a sign of prolonged stress?

Directory of Open Access Journals (Sweden)

Adam D Hughes

Full Text Available Thermally induced bleaching has caused a global decline in corals and the frequency of such bleaching events will increase. Thermal bleaching severely disrupts the trophic behaviour of the coral holobiont, reducing the photosynthetically derived energy available to the coral host. In the short term this reduction in energy transfer from endosymbiotic algae results in an energy deficit for the coral host. If the bleaching event is short-lived then the coral may survive this energy deficit by depleting its lipid reserves, or by increasing heterotrophic energy acquisition. We show for the first time that the coral animal is capable of increasing the amount of heterotrophic carbon incorporated into its tissues for almost a year following bleaching. This prolonged heterotrophic compensation could be a sign of resilience or prolonged stress. If the heterotrophic compensation is in fact an acclimatization response, then this physiological response could act as a buffer from future bleaching by providing sufficient heterotrophic energy to compensate for photoautotrophic energy losses during bleaching, and potentially minimizing the effect of subsequent elevated temperature stresses. However, if the elevated incorporation of zooplankton is a sign that the effects of bleaching continue to be stressful on the holobiont, even after 11 months of recovery, then this physiological response would indicate that complete coral recovery requires more than 11 months to achieve. If coral bleaching becomes an annual global phenomenon by mid-century, then present temporal refugia will not be sufficient to allow coral colonies to recover between bleaching events and coral reefs will become increasingly less resilient to future climate change. If, however, increasing their sequestration of zooplankton-derived nutrition into their tissues over prolonged periods of time is a compensating mechanism, the impacts of annual bleaching may be reduced. Thus, some coral species

The Ssr protein (T1E_1405) from Pseudomonas putida DOT-T1E enables oligonucleotide-based recombineering in platform strain P. putida EM42

DEFF Research Database (Denmark)

Aparicio, Tomás; Ingemann Jensen, Sheila; Nielsen, Alex Toftgaard

2016-01-01

Some strains of the soil bacterium Pseudomonas putida have become in recent years platforms of choice for hosting biotransformations of industrial interest. Despite availability of many genetic tools for this microorganism, genomic editing of the cell factory P. putida EM42 (a derivative of refer......Some strains of the soil bacterium Pseudomonas putida have become in recent years platforms of choice for hosting biotransformations of industrial interest. Despite availability of many genetic tools for this microorganism, genomic editing of the cell factory P. putida EM42 (a derivative...

Membrane biofouling in a wastewater nitrification reactor: microbial succession from autotrophic colonization to heterotrophic domination

KAUST Repository

Lu, Huijie; Xue, Zheng; Saikaly, Pascal; Nunes, Suzana Pereira; Bluver, Ted R.; Liu, Wen-Tso

2015-01-01

through significant changes. Initial colonizers were replaced by fast-growing and metabolically versatile heterotrophs (e.g., unclassified Sphingobacteria). The declining EPS polysaccharide to protein (PS:PN) ratios could be correlated well

First report of a cross-kingdom pathogenic bacterium, Achromobacter xylosoxidans isolated from stipe-rot Coprinus comatus.

Science.gov (United States)

Ye, Luona; Guo, Mengpei; Ren, Pengfei; Wang, Gangzheng; Bian, Yinbing; Xiao, Yang; Zhou, Yan

2018-03-01

Coprinus comatus is an edible mushroom widely cultivated in China as a delicious food. Various diseases have occurred on C. comatus with the cultivated area increasing. In this study, the pathogenic bacterium JTG-B1, identified as Achromobacter xylosoxidans by 16S rDNA and nrdA gene sequencing, was isolated from edible mushroom Coprinus comatus with serious rot disease on its stipe. A. xylosoxidans has been confirmed as an important opportunistic human pathogenic bacterium and has been isolated from respiratory samples from cystic fibrosis. It is widely distributed in the environment. Here, we first report that fungi can also serve as a host for A. xylosoxidans. We confirmed that it can cross-kingdom infect between animals (mice) and fungi (C. comatus). The results of pathogenicity tests, physiological, biochemical and genotyping analysis of A. xylosoxidans from different hosts suggested that different strain of A. xylosoxidans may have pathogenicity differentiation. A. xylosoxidans not only is pathogenic to C. comatus but also may threaten human health. Copyright © 2017 Elsevier GmbH. All rights reserved.

Study on human intestinal bacterium Blautia sp. AUH-JLD56 for the conversion of arctigenin to (-)-3'-desmethylarctigenin.

Science.gov (United States)

Liu, Ming-Yue; Li, Meng; Wang, Xiu-Ling; Liu, Peng; Hao, Qing-Hong; Yu, Xiu-Mei

2013-12-11

Arctium lappa L. (A. lappa) is a popularly used vegetable as well as herbal medicine. Human intestinal microflora was reported to convert arctiin, the lignan compound with highest content in the dried fruits of Arctium lappa, to a series of metabolites. However, the specific bacterium responsible for the formation of 3'-desmethylarctigenin (3'-DMAG), the most predominant metabolite of arctiin by rat or human intestinal microflora, has not been isolated yet. In the present study, we isolated one single bacterium, which we named Blautia sp. AUH-JLD56, capable of solely biotransforming arctiin or arctigenin to (-)-3'-DMAG. The structure of the metabolite 3'-DMAG was elucidated by electrospray ionization mass spectrometry (ESI-MS) and (1)H and (13)C nuclear magnetic resonance spectroscopy. The biotransforming kinetics and maximum biotransforming capacity of strain AUH-JLD56 was investigated. In addition, the metabolite 3'-DMAG showed significantly higher 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity than that of the substrate arctigenin at the concentrations tested.

Biochemical System Analysis of Lutein Production by Heterotrophic Chlorella pyrenoidosa in a Fermentor

Directory of Open Access Journals (Sweden)

Zheng-Yun Wu

2009-01-01

Full Text Available Chlorella is a promising alternative source of lutein, as it can be cultivated heterotrophically with high efficiency. In this study, the carotenoids in Chlorella pyrenoidosa heterotrophically cultivated in a 19-litre fermentor have been analyzed and determined by using HPLC and HPLC-MS. A biochemical system theory (BST model was developed for understanding the regulatory features of carotenoid metabolism during the batch cultivation. Factors that influence lutein production by C. pyrenoidosa were discussed based on the model. It shows that low flux for lycopene formation is the major bottleneck for lutein production, while by-product syntheses and inhibitions affect the cellular lutein content much less. However, with further increase of the cellular lutein content, the inhibition on lycopene formation by lutein may become a limiting factor. Although speculative, these results may provide useful information for further elucidation of the regulatory mechanisms of carotenoid biosynthesis in Chlorella and modifying its metabolic network to enhance lutein production.

Low nitrogen stress stimulating the indole-3-acetic acid biosynthesis of Serratia sp. ZM is vital for the survival of the bacterium and its plant growth-promoting characteristic.

Science.gov (United States)

Ouyang, Liming; Pei, Haiyan; Xu, Zhaohui

2017-04-01

Serratia sp. ZM is a plant growth-promoting (PGP) bacterial strain isolated from the rhizospheric soil of Populus euphratica in northwestern China. In this study, low nitrogen supply significantly stimulated the production of indole-3-acetic acid (IAA) in Serratia sp.ZM. The inoculation of the bacterium to wheat seedlings improved plant growth compared with the uninoculated group, and the stimulating effect was more prominent under low nitrogen stress. Inactivation of the predicted key gene in the IAA biosynthesis pathway impaired IAA production and significantly hampered mutant growth in poor medium. Furthermore, the IAA-deficient mutant lost the PGP effect under either normal or low nitrogen conditions in plant experiments. This study revealed the significant impact of environmental nitrogen levels on IAA production in the PGP strain and the vital effect of IAA on resistance physiology of both the bacterium and host plant. The characteristics of Serratia sp. ZM also indicated its application potential as a biofertilizer for plants, especially those suffering from poor nitrogen soil.

Comparison of heterotrophic and autotrophic denitrification processes for nitrate removal from phosphorus-limited surface water.

Science.gov (United States)

Wang, Zheng; He, Shengbing; Huang, Jungchen; Zhou, Weili; Chen, Wanning

2018-03-29

Phosphorus (P) limitation has been demonstrated for micro-polluted surface water denitrification treatment in previous study. In this paper, a lab-scale comparative study of autotrophic denitrification (ADN) and heterotrophic denitrification (HDN) in phosphorus-limited surface water was investigated, aiming to find out the optimal nitrogen/phosphorus (N/P) ratio and the mechanism of the effect of P limitation on ADN and HDN. Furthermore, the optimal denitrification process was applied to the West Lake denitrification project, aiming to improve the water quality of the West Lake from worse than grade V to grade IV (GB3838-2006). The lab-scale study showed that the lack of P indeed inhibited HDN more greatly than ADN. The optimal N/P ratio for ADN and HDN was 25 and a 0.15 mg PO 4 3- -P L -1 of microbial available phosphorus (MAP) was observed. P additions could greatly enhance the resistance of ADN and HDN to hydraulic loading shock. Besides, The P addition could effectively stimulate the HDN performance via enriching the heterotrophic denitrifiers and the denitrifying phosphate-accumulating organisms (DNPAOs). Additionally, HDN was more effective and cost-effective than ADN for treating P-limited surface water. The study of the full-scale HDBF (heterotrophic denitrification biofilter) indicated that the denitrification performance was periodically impacted by P limitation, particularly at low water temperatures. Copyright © 2018 Elsevier Ltd. All rights reserved.

Nitrogen uptake by heterotrophic bacteria and phytoplankton in the nitrate-rich Thames estuary

NARCIS (Netherlands)

Middelburg, J.J.; Nieuwenhuize, J.

2000-01-01

The uptake of ammonium, nitrate, amino acids and urea was examined in the nitrate-rich Thames estuary and adjacent area in the North Sea during February 1999. The majority of uptake was by heterotrophic bacteria, as demonstrated by addition of a prokaryotic inhibitor that lowered uptake rates by 82,

Hydrogen production by recombinant Escherichia coli strains

Science.gov (United States)

Maeda, Toshinari; Sanchez‐Torres, Viviana; Wood, Thomas K.

2012-01-01

Summary The production of hydrogen via microbial biotechnology is an active field of research. Given its ease of manipulation, the best‐studied bacterium Escherichia coli has become a workhorse for enhanced hydrogen production through metabolic engineering, heterologous gene expression, adaptive evolution, and protein engineering. Herein, the utility of E. coli strains to produce hydrogen, via native hydrogenases or heterologous ones, is reviewed. In addition, potential strategies for increasing hydrogen production are outlined and whole‐cell systems and cell‐free systems are compared. PMID:21895995

Reduction of nitric oxide catalyzed by hydroxylamine oxidoreductase from an anammox bacterium.

Science.gov (United States)

Irisa, Tatsuya; Hira, Daisuke; Furukawa, Kenji; Fujii, Takao

2014-12-01

The hydroxylamine oxidoreductase (HAO) from the anammox bacterium, Candidatus Kuenenia stuttgartiensis has been reported to catalyze the oxidation of hydroxylamine (NH2OH) to nitric oxide (NO) by using bovine cytochrome c as an oxidant. In contrast, we investigated whether the HAO from anammox bacterium strain KSU-1 could catalyze the reduction of NO with reduced benzyl viologen (BVred) and the NO-releasing reagent, NOC 7. The reduction proceeded, resulting in the formation of NH2OH as a product. The oxidation rate of BVred was proportional to the concentration of BVred itself for a short period in each experiment, a situation that was termed quasi-steady state. The analyses of the states at various concentrations of HAO allowed us to determine the rate constant for the catalytic reaction, (2.85 ± 0.19) × 10(5) M(-1) s(-1), governing NO reduction by BVred and HAO, which was comparable to that reported for the HAO from the ammonium oxidizer, Nitrosomonas with reduced methyl viologen. These results suggest that the anammox HAO functions to adjust anammox by inter-conversion of NO and NH2OH depending on the redox potential of the physiological electron transfer protein in anammox bacteria. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Mechanisms of tolerance and high degradation capacity of the herbicide mesotrione by Escherichia coli strain DH5-α.

Directory of Open Access Journals (Sweden)

Luiz R Olchanheski

Full Text Available The intensive use of agrochemicals has played an important role in increasing agricultural production. One of the impacts of agrochemical use has been changes in population structure of soil microbiota. The aim of this work was to analyze the adaptive strategies that bacteria use to overcome oxidative stress caused by mesotrione, which inhibits 4-hydroxyphenylpyruvate dioxygenase. We also examined antioxidative stress systems, saturation changes of lipid membranes, and the capacity of bacteria to degrade mesotrione. Escherichia coli DH5-á was chosen as a non-environmental strain, which is already a model bacterium for studying metabolism and adaptation. The results showed that this bacterium was able to tolerate high doses of the herbicide (10× field rate, and completely degraded mesotrione after 3 h of exposure, as determined by a High Performance Liquid Chromatography. Growth rates in the presence of mesotrione were lower than in the control, prior to the period of degradation, showing toxic effects of this herbicide on bacterial cells. Changes in the saturation of the membrane lipids reduced the damage caused by reactive oxygen species and possibly hindered the entry of xenobiotics in the cell, while activating glutathione-S-transferase enzyme in the antioxidant system and in the metabolizing process of the herbicide. Considering that E. coli DH5-α is a non-environmental strain and it had no previous contact with mesotrione, the defense system found in this strain could be considered non-specific. This bacterium system response may be a general adaptation mechanism by which bacterial strains resist to damage from the presence of herbicides in agricultural soils.

A novel radio-tolerant astaxanthin-producing bacterium reveals a new astaxanthin derivative: astaxanthin dirhamnoside.

Science.gov (United States)

Asker, Dalal; Awad, Tarek S; Beppu, Teruhiko; Ueda, Kenji

2012-01-01

Astaxanthin is a red ketocarotenoid that exhibits extraordinary health-promoting activities such as antioxidant, anti-inflammatory, antitumor, and immune booster. The recent discovery of the beneficial roles of astaxanthin against many degenerative diseases such as cancers, heart diseases, and exercise-induced fatigue has raised its market demand as a nutraceutical and medicinal ingredient in aquaculture, food, and pharmaceutical industries. To satisfy the growing demand for this high-value nutraceuticals ingredient and consumer interest in natural products, many research efforts are being made to discover novel microbial producers with effective biotechnological production of astaxanthin. Using a rapid screening method based on 16S rRNA gene, and effective HPLC-Diodearray-MS methods for carotenoids analysis, we succeeded to isolate a unique astaxanthin-producing bacterium (strain TDMA-17(T)) that belongs to the family Sphingomonadaceae (Asker et al., Appl Microbiol Biotechnol 77: 383-392, 2007). In this chapter, we provide a detailed description of effective HPLC-Diodearray-MS methods for rapid analysis and identification of the carotenoids produced by strain TDMA-17(T). We also describe the methods of isolation and identification for a novel bacterial carotenoid (astaxanthin derivative), a major carotenoid that is produced by strain TDMA-17(T). Finally, we describe the polyphasic taxonomic analysis of strain TDMA-17(T) and the description of a novel species belonging to genus Sphingomonas.

Identification of a 4-Deoxy-l-erythro-5-hexoseulose Uronic Acid Reductase, FlRed, in an Alginolytic Bacterium Flavobacterium sp. Strain UMI-01

Directory of Open Access Journals (Sweden)

Akira Inoue

2015-01-01

Full Text Available In alginate-assimilating bacteria, alginate is depolymerized to unsaturated monosaccharide by the actions of endolytic and exolytic alginate lyases (EC 4.2.2.3 and EC 4.2.2.11. The monosaccharide is non-enzymatically converted to 4-deoxy-l-ery thro-5-hexoseulose uronic acid (DEH, then reduced to 2-keto-3-deoxy-d-gluconate (KDG by a specific reductase, and metabolized through the Entner–Doudoroff pathway. Recently, the NADPH-dependent reductase A1-R that belongs to short-chain dehydrogenases/reductases (SDR superfamily was identified as the DEH-reductase in Sphingomonas sp. A1. We have subsequently noticed that an SDR-like enzyme gene, flred, occurred in the genome of an alginolytic bacterium Flavobacterium sp. strain UMI-01. In the present study, we report on the deduced amino-acid sequence of flred and DEH-reducing activity of recombinant FlRed. The deduced amino-acid sequence of flred comprised 254 residues and showed 34% amino-acid identities to that of A1-R from Sphingomonas sp. A1 and 80%–88% to those of SDR-like enzymes from several alginolytic bacteria. Common sequence motifs of SDR-superfamily enzymes, e.g., the catalytic tetrad Asn-Lys-Tyr-Ser and the cofactor-binding sequence Thr-Gly-x-x-x-Gly-x-Gly in Rossmann fold, were completely conserved in FlRed. On the other hand, an Arg residue that determined the NADPH-specificity of Sphingomonas A1-R was replaced by Glu in FlRed. Thus, we investigated cofactor-preference of FlRed using a recombinant enzyme. As a result, the recombinant FlRed (recFlRed was found to show high specificity to NADH. recFlRed exhibited practically no activity toward variety of aldehyde, ketone, keto ester, keto acid and aldose substrates except for DEH. On the basis of these results, we conclude that FlRed is the NADH-dependent DEH-specific SDR of Flavobacterium sp. strain UMI-01.

Decadal warming causes a consistent and persistent shift from heterotrophic to autotrophic respiration in contrasting permafrost ecosystems.

Science.gov (United States)

Hicks Pries, Caitlin E; van Logtestijn, Richard S P; Schuur, Edward A G; Natali, Susan M; Cornelissen, Johannes H C; Aerts, Rien; Dorrepaal, Ellen

2015-12-01

Soil carbon in permafrost ecosystems has the potential to become a major positive feedback to climate change if permafrost thaw increases heterotrophic decomposition. However, warming can also stimulate autotrophic production leading to increased ecosystem carbon storage-a negative climate change feedback. Few studies partitioning ecosystem respiration examine decadal warming effects or compare responses among ecosystems. Here, we first examined how 11 years of warming during different seasons affected autotrophic and heterotrophic respiration in a bryophyte-dominated peatland in Abisko, Sweden. We used natural abundance radiocarbon to partition ecosystem respiration into autotrophic respiration, associated with production, and heterotrophic decomposition. Summertime warming decreased the age of carbon respired by the ecosystem due to increased proportional contributions from autotrophic and young soil respiration and decreased proportional contributions from old soil. Summertime warming's large effect was due to not only warmer air temperatures during the growing season, but also to warmer deep soils year-round. Second, we compared ecosystem respiration responses between two contrasting ecosystems, the Abisko peatland and a tussock-dominated tundra in Healy, Alaska. Each ecosystem had two different timescales of warming (permafrost ecosystems. © 2015 John Wiley & Sons Ltd.

Plant growth-promoting bacterium Acinetobacter calcoaceticus P23 increases the chlorophyll content of the monocot Lemna minor (duckweed) and the dicot Lactuca sativa (lettuce).

Science.gov (United States)

Suzuki, Wakako; Sugawara, Masayuki; Miwa, Kyoko; Morikawa, Masaaki

2014-07-01

Acinetobacter calcoaceticus P23 is a plant growth-promoting bacterium that was isolated from the surface of duckweed (Lemna aoukikusa). The bacterium was observed to colonize on the plant surfaces and increase the chlorophyll content of not only the monocotyledon Lemna minor but also the dicotyledon Lactuca sativa in a hydroponic culture. This effect on the Lactuca sativa was significant in nutrient-poor (×1/100 dilution of H2 medium) and not nutrient-rich (×1 or ×1/10 dilutions of H2 medium) conditions. Strain P23 has the potential to play a part in the future development of fertilizers and energy-saving hydroponic agricultural technologies. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Jeotgalibacillus soli sp. nov., a Gram-stain-positive bacterium isolated from soil.

Science.gov (United States)

Cunha, Sofia; Tiago, Igor; Paiva, Gabriel; Nobre, Fernanda; da Costa, Milton S; Veríssimo, António

2012-03-01

A Gram-staining-positive, motile, rod-shaped, spore-forming bacterium, designated P9(T), was isolated from soil in Portugal. This organism was aerobic and catalase- and oxidase-positive. It had an optimum growth temperature of about 35 °C and an optimum growth pH of about 8.0-8.5, and grew in medium with 0-9% (w/v) NaCl. The cell-wall peptidoglycan was of the A1α type, with L-lysine as the diagnostic diamino acid. The major respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids were anteiso-C(15:0) (45.4%), iso-C(15:0) (22.0%) and anteiso-C(17:0) (11.2%). The genomic DNA G+C content was about 39.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain P9(T) was most closely related to Jeotgalibacillus campisalis DSM 18983(T) (96.8%) and Jeotgalibacillus marinus DSM 1297(T) (96.5%). These two recognized species formed a coherent cluster with strain P9(T) that was supported by a bootstrap value of 99%. On the basis of the phylogenetic analysis and physiological and biochemical characteristics, strain P9(T) (=DSM 23228(T)=LMG 25523(T)) represents a novel species of the genus Jeotgalibacillus, for which the name Jeotgalibacillus soli sp. nov. is proposed.

Draft Genome Sequence of Sphingopyxis sp. Strain MWB1, a Crude-Oil-Degrading Marine Bacterium

Science.gov (United States)

Kim, Jonghyun; Kim, Soo Jung; Kim, Seon Hee; Kim, Seung Il; Moon, Yoon-Jung; Park, Sung-Joon

2014-01-01

Sphingopyxis sp. strain MWB1, which is capable of degrading crude oil, diesel, and kerosene, was isolated from crude oil–contaminated seashore in Tae-an, South Korea. Here, we report the draft genome sequence of this strain, which comprises 3,118,428 bp with a G+C content of 62.85 mol%. PMID:25477411

Draft Genome Sequence of an Active Heterotrophic Nitrifier-Denitrifier, Cupriavidus pauculus UM1

OpenAIRE

Putonti, Catherine; Polley, Nathaniel; Castignetti, Domenic

2018-01-01

ABSTRACT Here, we present the draft genome sequence of Cupriavidus pauculus UM1, a metal-resistant heterotrophic nitrifier-denitrifier capable of synthesizing nitrite from pyruvic oxime. The size of the genome is 7,402,815 bp with a GC content of 64.8%. This draft assembly consists of 38 scaffolds.

Synechococcus growth in the ocean may depend on the lysis of heterotrophic bacteria

Czech Academy of Sciences Publication Activity Database

Weinbauer, M.G.; Bonilla-Findji, O.; Chan, A.M.; Dolan, J. R.; Short, S.M.; Šimek, Karel; Wilhelm, S. W.; Suttle, C.A.

2011-01-01

Roč. 33, č. 10 (2011), s. 1465-1476 ISSN 0142-7873 R&D Projects: GA ČR(CZ) GA206/08/0015 Institutional research plan: CEZ:AV0Z60170517 Keywords : viruses * growth control of cyanobacteria * heterotrophic bacterioplankton Subject RIV: EE - Microbiology, Virology Impact factor: 2.079, year: 2011

Methylobacterium marchantiae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the thallus of a liverwort.

Science.gov (United States)

Schauer, S; Kämpfer, P; Wellner, S; Spröer, C; Kutschera, U

2011-04-01

A pink-pigmented, facultatively methylotrophic bacterium, designated strain JT1(T), was isolated from a thallus of the liverwort Marchantia polymorpha L. and was analysed by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis placed the strain in a clade with Methylobacterium adhaesivum AR27(T), Methylobacterium fujisawaense DSM 5686(T), Methylobacterium radiotolerans JCM 2831(T) and Methylobacterium jeotgali S2R03-9(T), with which it showed sequence similarities of 97.8, 97.7, 97.2 and 97.4 %, respectively. However, levels of DNA-DNA relatedness between strain JT1(T) and these and the type strains of other closely related species were lower than 70 %. Cells of JT1(T) stained Gram-negative and were motile, rod-shaped and characterized by numerous fimbriae-like appendages on the outer surface of their wall (density up to 200 µm(-2)). Major fatty acids were C(18 : 1)ω7c and C(16 : 0). Based on the morphological, physiological and biochemical data presented, strain JT1(T) is considered to represent a novel species of the genus Methylobacterium, for which the name Methylobacterium marchantiae sp. nov. is proposed. The type strain is JT1(T) ( = DSM 21328(T)  = CCUG 56108(T)).

Helicobacter Catalase Devoid of Catalytic Activity Protects the Bacterium against Oxidative Stress*♦

Science.gov (United States)

Benoit, Stéphane L.; Maier, Robert J.

2016-01-01

Catalase, a conserved and abundant enzyme found in all domains of life, dissipates the oxidant hydrogen peroxide (H2O2). The gastric pathogen Helicobacter pylori undergoes host-mediated oxidant stress exposure, and its catalase contains oxidizable methionine (Met) residues. We hypothesized catalase may play a large stress-combating role independent of its classical catalytic one, namely quenching harmful oxidants through its recyclable Met residues, resulting in oxidant protection to the bacterium. Two Helicobacter mutant strains (katAH56A and katAY339A) containing catalase without enzyme activity but that retain all Met residues were created. These strains were much more resistant to oxidants than a catalase-deletion mutant strain. The quenching ability of the altered versions was shown, whereby oxidant-stressed (HOCl-exposed) Helicobacter retained viability even upon extracellular addition of the inactive versions of catalase, in contrast to cells receiving HOCl alone. The importance of the methionine-mediated quenching to the pathogen residing in the oxidant-rich gastric mucus was studied. In contrast to a catalase-null strain, both site-change mutants proficiently colonized the murine gastric mucosa, suggesting that the amino acid composition-dependent oxidant-quenching role of catalase is more important than the well described H2O2-dissipating catalytic role. Over 100 years after the discovery of catalase, these findings reveal a new non-enzymatic protective mechanism of action for the ubiquitous enzyme. PMID:27605666

Survival of diverse bacillus thuringiensis strains in gypsy moth (Lepidotera: Lymantriidae) is correlated with urease production

Science.gov (United States)

Bacillus thuringiensis is an entomopathogenic bacterium that can kill a variety of pest insects, but seldom causes epizootics because it replicates poorly in insects. By attempting to repeatedly pass lepidopteran-active B. thuringiensis strains through gypsy moth larvae, we found that only those str...

Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome.

Science.gov (United States)

Hahn, Martin W; Schmidt, Johanna; Taipale, Sami J; Doolittle, W Ford; Koll, Ulrike

2014-09-01

A pure culture of an actinobacterium previously described as 'Candidatus Rhodoluna lacicola' strain MWH-Ta8 was established and deposited in two public culture collections. Strain MWH-Ta8(T) represents a free-living planktonic freshwater bacterium obtained from hypertrophic Meiliang Bay, Lake Taihu, PR China. The strain was characterized by phylogenetic and taxonomic investigations, as well as by determination of its complete genome sequence. Strain MWH-Ta8(T) is noticeable due to its unusually low values of cell size (0.05 µm(3)), genome size (1.43 Mbp), and DNA G+C content (51.5 mol%). Phylogenetic analyses based on 16S rRNA gene and RpoB sequences suggested that strain MWH-Ta8(T) is affiliated with the family Microbacteriaceae with Pontimonas salivibrio being its closest relative among the currently described species within this family. Strain MWH-Ta8(T) and the type strain of Pontimonas salivibrio shared a 16S rRNA gene sequence similarity of 94.3 %. The cell-wall peptidoglycan of strain MWH-Ta8(T) was of type B2β (B10), containing 2,4-diaminobutyric acid as the diamino acid. The predominant cellular fatty acids were anteiso-C15 : 0 (36.5 %), iso-C16 : 0 (16.5 %), iso-C15 : 0 (15.6 %) and iso-C14 : 0 (8.9 %), and the major (>10 %) menaquinones were MK-11 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The combined phylogenetic, phenotypic and chemotaxonomic data clearly suggest that strain MWH-Ta8(T) represents a novel species of a new genus in the family Microbacteriaceae, for which the name Rhodoluna lacicola gen. nov., sp. nov. is proposed. The type strain of the type species is MWH-Ta8(T) ( = DSM 23834(T) = LMG 26932(T)). © 2014 IUMS.

Regulation of annual variation in heterotrophic bacterial production in the Schelde estuary (SW Netherlands)

NARCIS (Netherlands)

Goosen, N.K.; Van Rijswijk, P.; Kromkamp, J.C.; Peene, J.

1997-01-01

Heterotrophic bacterioplankton production (H-3-thymidine incorporation rate) and abundance in the surface water of the Schelde estuary (The Netherlands) were studied during an annual cycle in 1991 along the salinity gradient (0.8 to 33 psu). Bacterial production and numbers increased from the lower

Salt-inducible promoter derivable from a lactic acid bacterium, and its use in a lactic acid bacterium for production of a desired protein

NARCIS (Netherlands)

Sanders, Jan Willem; Kok, Jan; Venema, Gerard; Ledeboer, Adrianus Marinus

1998-01-01

The invention provides a salt-inducible promoter present in SEQ ID NO: 10 and derivable from a lactic acid bacterium in isolation from the coding sequence normally controlled by said promoter in a wild-type lactic acid bacterium, with modifications and important parts thereof. Also provided are a

Dehalogenimonas formicexedens sp. nov., a chlorinated alkane-respiring bacterium isolated from contaminated groundwater.

Science.gov (United States)

Key, Trent A; Bowman, Kimberly S; Lee, Imchang; Chun, Jongsik; Albuquerque, Luciana; da Costa, Milton S; Rainey, Fred A; Moe, William M

2017-05-01

A strictly anaerobic, Gram-stain-negative, non-spore-forming bacterium designated NSZ-14T, isolated from contaminated groundwater in Louisiana (USA), was characterized using a polyphasic approach. Strain NSZ-14T reductively dehalogenated a variety of polychlorinated aliphatic alkanes, producing ethene from 1,2-dichloroethane, propene from 1,2-dichloropropane, a mixture of cis- and trans-1,2-dichloroethene from 1,1,2,2-tetrachloroethane, vinyl chloride from 1,1,2-trichloroethane and allyl chloride (3-chloro-1-propene) from 1,2,3-trichloropropane. Formate or hydrogen could both serve as electron donors. Dechlorination occurred between pH 5.5 and 7.5 and over a temperature range of 20-37 °C. Major cellular fatty acids included C18 : 1ω9c, C14 : 0 and C16 : 0. 16S rRNA gene sequence-based phylogenetic analysis indicated that the strain clusters within the class Dehalococcoidia of the phylum Chloroflexi, most closely related to but distinct from type strains of the species Dehalogenimonas alkenigignens (97.63 % similarity) and Dehalogenimonas lykanthroporepellens (95.05 %). A complete genome sequence determined for strain NSZ-14T revealed a DNA G+C content of 53.96 mol%, which was corroborated by HPLC (54.1±0.2 mol% G+C). Genome-wide comparisons based on average nucleotide identity by orthology and estimated DNA-DNA hybridization values combined with phenotypic and chemotaxonomic traits and phylogenetic analysis indicate that strain NSZ-14T represents a novel species within the genus Dehalogenimonas, for which the name Dehalogenimonas formicexedens sp. nov. is proposed. The type strain is NSZ-14T (=HAMBI 3672T=JCM 19277T=VKM B-3058T). An emended description of Dehalogenimonas alkenigignens is also provided.

Screening of Mutation High-Yielding Biocontrol Bacterium BJ1 by Ion Beam Irradiation and Effect of Controlling Fusarium oxysporum cucunerinum Disease

International Nuclear Information System (INIS)

Ma Shuang; Dong Xicun; Li Wenjian; Wang Jufang; Yu Lixia; Liu Jing

2010-01-01

BJ1 of Bacillus subtilis is an important biocontrol factor in control of fungus disease. In order to improve the antagonistic ability of the strain,and obtain high-efficiency strains, 12 C 6+ of different doses and linear energy transfer (LET) was used to irradiate the biocontrol bacterium BJ1. The optimum dose and LET of ion beam irradiation for the BJ1 are 200-400 Gy and 60 keV/μm,respectively. The antagonistic ability is increased by 2%-21%. The control effect of mutation to Fusarium oxysporum f. sp. cucunerinum is increased by 17.48% over that of BJ1, and mutation also has better plant growth-promoting effect. (authors)

Advenella alkanexedens sp. nov., an alkane-degrading bacterium isolated from biogas slurry samples.

Science.gov (United States)

Wang, Huimin; Zhou, Shan; Wang, Yanwei; Kong, Delong; Guo, Xiang; Zhu, Jie; Dong, Weiwei; Ruan, Zhiyong

2016-02-01

A novel aerobic bacterium, designated strain LAM0050 T , was isolated from a biogas slurry sample, which had been enriched with diesel oil for 30 days. Cells of strain LAM0050 T were gram-stain-negative, non-motile, non-spore-forming and coccoid-shaped. The optimal temperature and pH for growth were 30-35 °C and 8.5, respectively. The strain did not require NaCl for growth, but tolerated up to 5.3 % (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain LAM0050 T was a member of the genus Advenella , and was most closely related to Advenella faeciporci KCTC 23732 T , Advenella incenata CCUG 45225 T , Advenella kashmirensis DSM 17095 T and Advenella mimigardefordensis DSM 17166 T , with 98.1, 96.6, 96.6 and 96.3 % sequence similarity, respectively. The DNA-DNA hybridization relatedness between strain LAM0050 T and A. faeciporci KCTC 23732 T was 41.7 ± 2.4 %. The genomic DNA G+C content was 51.2 mol%, as determined by the T m method. The major fatty acids of strain LAM0050 T were C 16 : 0 , C 17 : 0 cyclo, summed feature 3 (C 16 : 1 ω7 c and/or C 16 : 1 ω6 c ) and summed feature 8 (C 18 : 1 ω7 c and/or C 18 : 1 ω6 c ). The predominant ubiquinone was Q-8. The main polar lipids were diphosphatidyglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine and four unidentified phospholipids. Based on the phenotypic and genotypic properties, strain LAM0050 T is suggested to represent a novel species of the genus Advenella , for which the name Advenella alkanexedens sp. nov., is proposed, the type strain is LAM0050 T ( = ACCC 06485 T  = JCM 30465 T ).

Compared microbiology of granular sludge under autotrophic, mixotrophic and heterotrophic denitrification conditions.

Science.gov (United States)

Fernández, N; Sierra-Alvarez, R; Amils, R; Field, J A; Sanz, J L

2009-01-01

Water contamination by nitrate is a wideworld extended phenomena. Biological autotrophic denitrification has a real potential to face this problem and presents less drawbacks than the most extended heterotrophic denitrification. Three bench-scale UASB reactors were operated under autotrophic (R1, H2S as electron donor), mixotrophic (R2, H2S plus p-cresol as electron donors) and heterotrophic (R3, p-cresol as electron donor) conditions using nitrate as terminal electron acceptor. 16S rDNA genetic libraries were built up to compare their microbial biodiversity. Six different bacteria phyla and three archaeal classes were observed. Proteobacteria was the main phyla in all reactors standing out the presence of denitrifiers. Microorganisms similar to Thiobacillus denitrificans and Acidovorax sp. performed the autotrophic denitification. These OTUs were displaced by chemoheterotrophic denitrifiers, especially by Limnobacter-like and Ottowia-like OTUs. Other phyla were Bacteroidetes, Chloroflexi, Firmicutes and Actinobacteria that--as well as Archaea members--were implicated in the degradation of organic matter, as substrate added as coming from endogenous sludge decay under autotrophic conditions. Archaea diversity remained low in all the reactors being Methanosaeta concilii the most abundant one.

Metabolic Engineering of the Actinomycete Amycolatopsis sp. Strain ATCC 39116 towards Enhanced Production of Natural Vanillin

OpenAIRE

Fleige, Christian; Meyer, Florian; Steinbüchel, Alexander

2016-01-01

The Gram-positive bacterium Amycolatopsis sp. ATCC 39116 is used for the fermentative production of natural vanillin from ferulic acid on an industrial scale. The strain is known for its outstanding tolerance to this toxic product. In order to improve the productivity of the fermentation process, the strain's metabolism was engineered for higher final concentrations and molar yields. Degradation of vanillin could be decreased by more than 90% through deletion of the vdh gene, which codes for ...

Natranaerobaculum magadiense gen. nov., sp. nov., an anaerobic, alkalithermophilic bacterium from soda lake sediment.

Science.gov (United States)

Zavarzina, Daria G; Zhilina, Tatyana N; Kuznetsov, Boris B; Kolganova, Tatyana V; Osipov, Georgy A; Kotelev, Mikhail S; Zavarzin, Georgy A

2013-12-01

An obligately alkaliphilic, anaerobic, thermo- and halotolerant, spore-forming bacterium was isolated from sediments of soda lake Magadi (Kenya) and designated strain Z-1001(T). Cells of strain Z-1001(T) were straight, Gram-positive rods, slowly motile. Strain Z-1001(T) was found to be an obligate anaerobe. It grew within a pH range from 7.5 to 10.7 with an optimum at 9.25-9.5 (at 40 °C), a temperature range from 20 to 57 °C with an optimum at 45-50 °C, and a NaCl concentration range from 0 to 1.55 M with an optimum at 1.2-1.4 M. Peptides, such as meat and yeast extracts, peptone and tryptone, were fermented by Z-1001(T). Carbohydrates did not support growth. With yeast extract as an electron donor, strain Z-1001(T) reduced S(2)O(3)(2-), NO(-)(3), AsO(3-)(4), Fe(III) citrate and anthraquinone-2,6-disulfonate (AQDS) as electron acceptors. The isolate was able to grow oligotrophically with a very small amount of yeast extract: 0.03 g l(-1). The main fatty acids were C16 : 0, C16 : 1ω7c, C18 : 0 and C18 : 1ω9. The DNA G+C content of the isolate was 35.6 mol%. 16S rRNA gene sequence analysis showed that strain Z-1001(T) is a member of family Natranaerobiaceae, clustering with the type strain of Natranaerobius thermophilus (95.8-96.0 % sequence similarity). On the basis of physiological and phylogenetic data it is proposed that strain Z-1001(T) ( = DSM 24923(T) = VKM B-2666(T)) represents a novel genus and species, Natranaerobaculum magadiense gen. nov., sp. nov.

The efficiency of gamma irradiation on the bacterium pseudomonas fluorescence (Migh) against the mediterranean fruit fly ceratitis capitata (wiedemann)

International Nuclear Information System (INIS)

Fadel, A.M.

2002-01-01

The efficiency of the bacterium pseudomonas fluorescence against the mediterranean fruit fly ceratitis capitata (Wied.) was investigated. Adult emergence was significantly reduced by applying the wild and gamma irradiated strain (150 and 300 Gy). The highest reduction occurred by the mutant P1 and the highest concentration (10 8 ). The activity of this bacteria increased by gamma irradiation compared to that of the wild isolate. The reduction in adult survival of both males and females was highly significant by applying the irradiated bacteria with the two doses of gamma radiation and different concentration (10 8 , 10 6 and 10 4 ) of bacterial suspension. Applying the bacteria as a culture filtrate reduced adult survival of wild strain significantly, while the irradiated strain recorded a significant reduction in males and females with the highest concentration (100 %) and by applying the two doses of gamma radiation (150 and 300 Gy) and in females only at the concentration 50% by using the dose of 150 Gy

Characterization and Potential Applications of a Selenium Nanoparticle Producing and Nitrate Reducing Bacterium Bacillus oryziterrae sp. nov.

Science.gov (United States)

Bao, Peng; Xiao, Ke-Qing; Wang, Hui-Jiao; Xu, Hao; Xu, Peng-Peng; Jia, Yan; Häggblom, Max M.; Zhu, Yong-Guan

2016-09-01

A novel nitrate- and selenite reducing bacterium strain ZYKT was isolated from a rice paddy soil in Dehong, Yunnan, China. Strain ZYKT is a facultative anaerobe and grows in up to 150, 000 ppm O2. The comparative genomics analysis of strain ZYKT implies that it shares more orthologues with B. subtilis subsp. subtilis NCIB 3610T (ANIm values, 85.4-86.7%) than with B. azotoformans NBRC 15712T (ANIm values, 84.4-84.7%), although B. azotoformans NBRC 15712T (96.3% 16S rRNA gene sequence similarity) is the closest Bacillus species according to 16S rRNA gene comparison. The major cellular fatty acids of strain ZYKT were iso-C14:0 (17.8%), iso-C15:0 (17.8%), and C16:0 (32.0%). The polar lipid profile consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminophospholipid. Based on physiological, biochemical and genotypic properties, the strain was considered to represent a novel species of the genus Bacillus, for which the name Bacillus oryziterrae sp. nov. is proposed. The type strain is ZYKT (=DSM 26460T =CGMCC 1.5179T). Strain ZYKT can reduce nitrate to nitrite and ammonium and possesses metabolic genes for nitrate reduction including nar, nap and nrf. Biogenic selenium nanoparticles of strain ZYKT show a narrow size distribution and agree with the gaussian distribution. These selenium nanoparticles show significant dose-dependent inhibition of the lung cancer cell line H157, which suggests potential for application in cancer therapy.

Properties of hydrogenase from Megasphaera elsdenii

NARCIS (Netherlands)

Dijk, van C.

1980-01-01

This thesis is concerned with the purification and properties of hydrogenase from the obligate anaerobic rumen bacterium Megasphaera elsdenii. In chapter 1 the motives underlying this thesis, the physiological role of hydrogenase in some heterotrophs, including

Draft Genome Sequence of the Biocontrol Strain Serratia plymuthica A30, Isolated from Rotting Potato Tuber Tissue

NARCIS (Netherlands)

Czajkowski, R.L.; Wolf, van der J.M.

2012-01-01

Serratia plymuthica A30 is a Gram-negative bacterium expressing antagonistic activity toward blackleg- and soft rot-causing Dickeya sp. biovar 3 (“Dickeya solani”). Here, we present the draft genome sequence of strain A30, which has been isolated from rotten potato tuber tissue

Influence of river discharge on abundance and dissemination of heterotrophic, indicator and pathogenic bacteria along the East Coast of India.

Science.gov (United States)

Prasad, V R; Srinivas, T N R; Sarma, V V S S

2015-06-15

In order to examine the influence of discharge from different rivers from peninsular India and urban sewage on intensity and dissemination of heterotrophic, indicator and pathogenic bacteria, a study was carried out during peak discharge period along coastal Bay of Bengal. The coastal Bay received freshwater inputs from the river Ganges while Godavari and Krishna contributed to the south. Contrasting difference in salinity, temperature, nutrients and organic matter was observed between north and south east coast of India. The highest heterotrophic, indicator and pathogenic bacterial abundance was observed in the central coastal Bay that received urban sewage from the major city. Intensity and dissemination of heterotrophic, indicator and pathogenic bacteria displayed linear relation with magnitude of discharge. The coliform load was observed up to 100km from the coast suggesting that marine waters were polluted during the monsoon season and its impact on the ecosystem needs further studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effects of substrate concentrations on the growth of heterotrophic bacteria and algae in secondary facultative ponds.

Science.gov (United States)

Kayombo, S; Mbwette, T S A; Katima, J H Y; Jorgensen, S E

2003-07-01

This paper presents the effect of substrate concentration on the growth of a mixed culture of algae and heterotrophic bacteria in secondary facultative ponds (SFPs) utilizing settled domestic sewage as a sole source of organic carbon. The growth of the mixed culture was studied at the concentrations ranging between 200 and 800 mg COD/l in a series of batch chemostat reactors. From the laboratory data, the specific growth rate (micro) was determined using the modified Gompertz model. The maximum specific growth rate ( micro(max)) and half saturation coefficients (K(s)) were calculated using the Monod kinetic equation. The maximum observed growth rate ( micro(max)) for heterotrophic bacteria was 3.8 day(-1) with K(s) of 200 mg COD/l. The micro(max) for algal biomass based on suspended volatile solids was 2.7 day(-1) with K(s) of 110 mg COD/l. The micro(max) of algae based on the chlorophyll-a was 3.5 day(-1) at K(s) of 50mg COD/l. The observed specific substrate removal by heterotrophic bacteria varied between the concentrations of substrate used and the average value was 0.82 (mg COD/mg biomass). The specific substrate utilization rate in the bioreactors was direct proportional to the specific growth rate. Hence, the determined Monod kinetic parameters are useful for the definition of the operation of SFPs.

Factor driving heterotrophic dinoflagellate in relation to environment conditions in Kerkennah Islands (eastern coast of Tunisa

Directory of Open Access Journals (Sweden)

Mounir Ben Brahim

2015-09-01

Full Text Available Objective: To study the seasonal variability of heterotrophic dinoflagellate in the station of Cercina (southern coast of Tunisia. Methods: Sampling was done in 2007 in Cercina station located in the western coast of Kerkennah (34°41'27'' N; 11°07'45'' E (Southern Tunisia. Three replicates of water samples were taken during 10 days of each month. Environmental variables and nutrients were measured in situ. Results: A significant seasonal difference was observed for temperature and water salinity. The highest values were observed in spring and summer. No significant seasonal difference was, however, detected for nitrite, nitrate, ammonia, silica and phosphate. Sixty-five species of dinoflagellate were identified in the station of Cercina. Abundance of dinoflagellates fluctuated between seasons with values showing a significant seasonal and monthly difference. The highest mean abundance was recorded in spring in April, while the lowest abundance was detected in December in winter. Protoperidinium granii was the main species contributing to the dissimilarity between spring and winter with 13.98% followed by Peridinium sp. with 12.5% of dissimilarity and by Polykrikos sp. with 10.58%. Conclusions: Heterotrophic dinoflagellates proliferate in spring and summer. This increase was justified by the nutrient availability. Protoperidinium granii and Polykrikos kofoidii were the main heterotrophic dinoflagellate making difference between seasons and their densities were positively correlated with both temperature and salinity.

Methylobacterium populi sp. nov., a novel aerobic, pink-pigmented, facultatively methylotrophic, methane-utilizing bacterium isolated from poplar trees (Populus deltoides x nigra DN34).

Science.gov (United States)

Van Aken, Benoit; Peres, Caroline M; Doty, Sharon Lafferty; Yoon, Jong Moon; Schnoor, Jerald L

2004-07-01

A pink-pigmented, aerobic, facultatively methylotrophic bacterium, strain BJ001T, was isolated from internal poplar tissues (Populus deltoidesxnigra DN34) and identified as a member of the genus Methylobacterium. Phylogenetic analyses showed that strain BJ001T is related to Methylobacterium thiocyanatum, Methylobacterium extorquens, Methylobacterium zatmanii and Methylobacterium rhodesianum. However, strain BJ001T differed from these species in its carbon-source utilization pattern, particularly its use of methane as the sole source of carbon and energy, an ability that is shared with only one other member of the genus, Methylobacterium organophilum. In addition, strain BJ001T is the only member of the genus Methylobacterium to be described as an endophyte of poplar trees. On the basis of its physiological, genotypic and ecological properties, the isolate is proposed as a member of a novel species of the genus Methylobacterium, Methylobacterium populi sp. nov. (type strain, BJ001T=ATCC BAA-705T=NCIMB 13946T).

An efficient thermotolerant and halophilic biosurfactant-producing bacterium isolated from Dagang oil field for MEOR application

Science.gov (United States)

Wu, Langping; Richnow, Hans; Yao, Jun; Jain, Anil

2014-05-01

Dagang Oil field (Petro China Company Limited) is one of the most productive oil fields in China. In this study, 34 biosurfactant-producing strains were isolated and cultured from petroleum reservoir of Dagang oil field, using haemolytic assay and the qualitative oil-displacement test. On the basis of 16S rDNA analysis, the isolates were closely related to the species in genus Pseudomonas, Staphylococcus and Bacillus. One of the isolates identified as Bacillus subtilis BS2 were selected for further study. This bacterium was able to produce a type of biosurfactant with excessive foam-forming properties at 37ºC as well as at higher temperature of 55ºC. The biosurfactant produced by the strain BS2 could reduce the surface tension of the culture broth from 70.87 mN/m to 28.97 mN/m after 8 days of incubation at 37ºC and to 36.15 mN/m after 20 days of incubation at 55ºC, respectively. The biosurfactant showed stability at high temperature (up to 120ºC), a wide range of pH (2 to 12) and salt concentrations (up to 12%) offering potential for biotechnology. Fourier transform infrared (FT-IR) spectrum of extracted biosurfactant tentatively characterized the produced biosurfactant as glycolipid derivative. Elemental analysis of the biosurfactant by energy dispersive X-ray spectroscopy (EDS) reveals that the biosurfactant was anionic in nature. 15 days of biodegradation of crude oil suggested a preferential usage of n-alkane upon microbial metabolism of BS2 as a carbon substrate and consequently also for the synthesis of biosurfactants. Core flood studies for oil release indicated 9.6% of additional oil recovery over water flooding at 37ºC and 7.2% of additional oil recovery at 55 ºC. Strain BS2 was characterized as an efficient biosurfactant-producing, thermotolerant and halophillic bacterium and has the potential for application for microbial enhanced oil recovery (MEOR) through water flooding in China's oil fields even in situ as adapted to reservoir chemistry and

Temperature regulation of marine heterotrophic prokaryotes increases latitudinally as a breach between bottom-up and top-down controls

KAUST Repository

Moran, Xose Anxelu G.

2017-04-19

Planktonic heterotrophic prokaryotes make up the largest living biomass and process most organic matter in the ocean. Determining when and where the biomass and activity of heterotrophic prokaryotes are controlled by resource availability (bottom-up), predation and viral lysis (top-down) or temperature will help in future carbon cycling predictions. We conducted an extensive survey across subtropical and tropical waters of the Atlantic, Indian and Pacific Oceans during the Malaspina 2010 Global Circumnavigation Expedition and assessed indices for these three types of controls at 109 stations (mostly from the surface to 4000 m depth). Temperature control was approached by the apparent activation energy in eV (ranging from 0.46 to 3.41), bottom-up control by the slope of the log-log relationship between biomass and production rate (ranging from -0.12 to 1.09) and top-down control by an index that considers the relative abundances of heterotrophic nanoflagellates and viruses (ranging from 0.82 to 4.83). We conclude that temperature becomes dominant (i.e. activation energy >1.5 eV) within a narrow window of intermediate values of bottom-up (0.3-0.6) and top-down 0.8-1.2) controls. A pervasive latitudinal pattern of decreasing temperature regulation towards the Equator, regardless of the oceanic basin, suggests that the impact of global warming on marine microbes and their biogeochemical function will be more intense at higher latitudes. Our analysis predicts that 1°C ocean warming will result in increased biomass of heterotrophic prokaryoplankton only in waters with <26°C of mean annual surface temperature. This article is protected by copyright. All rights reserved.

Draft Genome Sequence of an Active Heterotrophic Nitrifier-Denitrifier, Cupriavidus pauculus UM1.

Science.gov (United States)

Putonti, Catherine; Polley, Nathaniel; Castignetti, Domenic

2018-02-08

Here, we present the draft genome sequence of Cupriavidus pauculus UM1, a metal-resistant heterotrophic nitrifier-denitrifier capable of synthesizing nitrite from pyruvic oxime. The size of the genome is 7,402,815 bp with a GC content of 64.8%. This draft assembly consists of 38 scaffolds. Copyright © 2018 Putonti et al.

Differential gene expression in Xylella fastidiosa 9a5c during co-cultivation with the endophytic bacterium Methylobacterium mesophilicum SR1.6/6.

Science.gov (United States)

Dourado, Manuella Nóbrega; Santos, Daiene Souza; Nunes, Luiz Roberto; Costa de Oliveira, Regina Lúcia Batista da; de Oliveira, Marcus Vinicius; Araújo, Welington Luiz

2015-12-01

Xylella fastidiosa, the causal agent of citrus variegated chlorosis (CVC), colonizes plant xylem, reducing sap flow, and inducing internerval chlorosis, leaf size reduction, necrosis, and harder and smaller fruits. This bacterium may be transmitted from plant to plant by sharpshooter insects, including Bucephalogonia xanthopis. The citrus endophytic bacterium Methylobacterium mesophilicum SR1.6/6 colonizes citrus xylem and previous studies showed that this strain is also transferred from plant to plant by B. xanthopis (Insecta), suggesting that this endophytic bacterium may interact with X. fastidiosa in planta and inside the insect vector during co-transmission by the same insect vector. To better understand the X. fastidiosa behavior in the presence of M. mesophilicum, we evaluated the X. fastidiosa transcriptional profile during in vitro interaction with M. mesophilicum SR1.6/6. The results showed that during co-cultivation, X. fastidiosa down-regulated genes related to growth and up-regulated genes related to energy production, stress, transport, and motility, suggesting the existence of a specific adaptive response to the presence of M. mesophilicum in the culture medium. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Noncontiguous finished genome sequence and description of Paenibacillus ihumii sp. nov. strain AT5

Directory of Open Access Journals (Sweden)

A.H. Togo

2016-03-01

Full Text Available Paenibacillus ihumii sp. nov. strain AT5 (= CSUR 1981 = DSM 100664 is the type strain of P. ihumii. This bacterium was isolated from a stool sample from a morbidly obese French patient using the culturomics approach. The genome of this Gram-negative, facultative anaerobic, motile and spore-forming bacillus is 5 924 686 bp long. Genomic analysis identified 253 (5% of 3812 genes as ORFans and at least 2599 (50.03% of 5194 orthologous proteins not shared with the closest phylogenetic species.

A method for measuring losses of soil carbon by heterotrophic respiration from peat soils under oil palms

Science.gov (United States)

Farmer, Jenny; Manning, Frances; Smith, Jo; Arn Teh, Yit

2017-04-01

The effects of drainage and deforestation of South East Asian peat swamp forests for the development of oil palm plantations has received considerable attention in both mainstream media and academia, and is the source of significant discussion and debate. However, data on the long-term carbon losses from these peat soils as a result of this land use change is still limited and the methods with which to collect this data are still developing. Here we present the ongoing evolution and implementation of a method for separating autotrophic and heterotrophic respiration by sampling carbon dioxide emissions at increasing distance from palm trees. We present the limitations of the method, modelling approaches and results from our studies. In 2011 we trialled this method in Sumatra, Indonesia and collected rate measurements over a six day period in three ages of oil palm. In the four year oil palm site there were thirteen collars that had no roots present and from these the peat based carbon losses were recorded to be 0.44 g CO2 m2 hr-1 [0.34; 0.57] (equivalent to 39 t CO2 ha-1 yr-1 [30; 50]) with a mean water table depth of 0.40 m, or 63% of the measured total respiration across the plot. In the two older palm sites of six and seven years, only one collar out of 100 had no roots present, and thus a linear random effects model was developed to calculate heterotrophic emissions for different distances from the palm tree. This model suggested that heterotrophic respiration was between 37 - 59% of total respiration in the six year old plantation and 39 - 56% in the seven year old plantation. We applied this method in 2014 to a seven year old plantation, in Sarawak, Malaysia, modifying the method to include the heterotrophic contribution from beneath frond piles and weed covered areas. These results indicated peat based carbon losses to be 0.42 g CO2 m2 hr-1 [0.27;0.59] (equivalent to 37 t CO2 ha-1 yr-1 [24; 52]) at an average water table depth of 0.35 m, 47% of the measured

Primary Isolation Strain Determines Both Phage Type and Receptors Recognised by Campylobacter jejuni Bacteriophages

DEFF Research Database (Denmark)

Sørensen, Martine C. Holst; Gencay, Yilmaz Emre; Birk, Tina

2015-01-01

were identified based on host range analysis and genome restriction profiles. Most phages were isolated using C. jejuni strains NCTC12662 and RM1221 and interestingly phage genome size (140 kb vs. 190 kb), host range and morphological appearance correlated with the isolation strain. Thus, according......In this study we isolated novel bacteriophages, infecting the zoonotic bacterium Campylobacter jejuni. These phages may be used in phage therapy of C. jejuni colonized poultry to prevent spreading of the bacteria to meat products causing disease in humans. Many C. jejuni phages have been isolated...... therefore chose seven C. jejuni strains each expressing different CPS structures as indicator strains in a large screening for phages in samples collected from free-range poultry farms. Forty-three phages were isolated using C. jejuni NCTC12658, NCTC12662 and RM1221 as host strains and 20 distinct phages...

Desulfohalophilus alkaliarsenatis gen. nov., sp. nov., an extremely halophilic sulfate- and arsenate-respiring bacterium from Searles Lake, California

Science.gov (United States)

Blum, Jodi Switzer; Kulp, Thomas R.; Han, Sukkyun; Lanoil, Brian; Saltikov, Chad W.; Stolz, John F.; Miller, Laurence G.; Oremland, Ronald S.

2012-01-01

A haloalkaliphilic sulfate-respiring bacterium, strain SLSR-1, was isolated from a lactate-fed stable enrichment culture originally obtained from the extreme environment of Searles Lake, California. The isolate proved capable of growth via sulfate-reduction over a broad range of salinities (125–330 g/L), although growth was slowest at salt-saturation. Strain SLSR-1 was also capable of growth via dissimilatory arsenate-reduction and displayed an even broader range of salinity tolerance (50–330 g/L) when grown under these conditions. Strain SLSR-1 could also grow via dissimilatory nitrate reduction to ammonia. Growth experiments in the presence of high borate concentrations indicated a greater sensitivity of sulfate-reduction than arsenate-respiration to this naturally abundant anion in Searles Lake. Strain SLSR-1 contained genes involved in both sulfate-reduction (dsrAB) and arsenate respiration (arrA). Amplicons of 16S rRNA gene sequences obtained from DNA extracted from Searles Lake sediment revealed the presence of close relatives of strain SLSR-1 as part of the flora of this ecosystem despite the fact that sulfate-reduction activity could not be detected in situ. We conclude that strain SLSR-1 can only achieve growth via arsenate-reduction under the current chemical conditions prevalent at Searles Lake. Strain SLSR-1 is a deltaproteobacterium in the family Desulfohalobiacea of anaerobic, haloalkaliphilic bacteria, for which we propose the name Desulfohalophilus alkaliarsenatis gen. nov., sp. nov.

Draft Genome Sequence of the Biocontrol Strain Serratia plymuthica A30, Isolated from Rotting Potato Tuber Tissue

NARCIS (Netherlands)

Czajkowski, R.L.; Van der Wolf, J.M.

2012-01-01

Serratia plymuthica A30 is a Gram-negative bacterium expressing antagonistic activity toward blackleg- and soft rot-causing Dickeya sp. biovar 3 ("Dickeya solani"). Here, we present the draft genome sequence of strain A30, which has been isolated from rotten potato tuber tissue. [KEYWORDS: biovar 3

Roseimarinus sediminis gen. nov., sp. nov., a facultatively anaerobic bacterium isolated from coastal sediment.

Science.gov (United States)

Wu, Wen-Jie; Liu, Qian-Qian; Chen, Guan-Jun; Du, Zong-Jun

2015-07-01

A Gram-stain-negative, facultatively anaerobic, non-motile and pink-pigmented bacterium, designated strain HF08(T), was isolated from marine sediment of the coast of Weihai, China. Cells were rod-shaped, and oxidase- and catalase-positive. The isolate grew optimally at 33 °C, at pH 7.5-8.0 and with 2-3% (w/v) NaCl. The dominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C14 : 0. Menaquinone 7 (MK-7) was the major respiratory quinone and the DNA G+C content was 44.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of the class Bacteroidia, and shared 88-90% sequence similarity with the closest genera Sunxiuqinia, Prolixibacter, Draconibacterium, Mariniphaga and Meniscus. Based on the phylogenetic and phenotypic evidence presented, a novel species in a new genus of the family Prolixibacteraceae is proposed, with the name Roseimarinus sediminis gen. nov., sp. nov. The type strain of Roseimarinus sediminis is HF08(T) ( = KCTC 42261(T) = CICC 10901(T)).

Genome Sequence of Anoxybacillus geothermalis Strain GSsed3, a Novel Thermophilic Endospore-Forming Species

Science.gov (United States)

Filippidou, Sevasti; Jaussi, Marion; Junier, Thomas; Wunderlin, Tina; Roussel-Delif, Ludovic; Jeanneret, Nicole; Vieth-Hillebrand, Andrea; Vetter, Alexandra; Regenspurg, Simona; McMurry, Kim; Gleasner, Cheryl D.; Lo, Chien-Chi; Li, Paul; Vuyisich, Momchilo; Chain, Patrick S.

2015-01-01

Anoxybacillus geothermalis strain GSsed3 is an endospore-forming thermophilic bacterium isolated from filter deposits in a geothermal site. This novel species has a larger genome size (7.2 Mb) than that of any other Anoxybacillus species, and it possesses genes that support its phenotypic metabolic characterization and suggest an intriguing link to metals. PMID:26067952

Degradation of pyrene in soil and in vitro by a Bacillus lentus strain ...

African Journals Online (AJOL)

A bacterium isolated from an asphalt plant soil and identified as a strain of Bacillus lentus was tested in vitro and in sterilized and native soils for ability to survive and sustain pyrene degradation over a period of 63 days. The exponential growth rate in vitro was 0.049 d-1 and the doubling time 2.65 d. In the control flask ...

Curiously modern DNA for a "250 million-year-old" bacterium.

Science.gov (United States)

Nickle, David C; Learn, Gerald H; Rain, Matthew W; Mullins, James I; Mittler, John E

2002-01-01

Studies of ancient DNA have attracted considerable attention in scientific journals and the popular press. Several of the more extreme claims for ancient DNA have been questioned on biochemical grounds (i.e., DNA surviving longer than expected) and evolutionary grounds (i.e., nucleotide substitution patterns not matching theoretical expectations for ancient DNA). A recent letter to Nature from Vreeland et al. (2000), however, tops all others with respect to age and condition of the specimen. These researchers extracted and cultured a bacterium from an inclusion body from what they claim is a 250 million-year (Myr)-old salt crystal. If substantiated, this observation could fundamentally alter views about bacterial physiology, ecology and evolution. Here we report on molecular evolutionary analyses of the 16S rDNA from this specimen. We find that 2-9-3 differs from a modern halophile, Salibacillus marismortui, by just 3 unambiguous bp in 16S rDNA, versus the approximately 59 bp that would be expected if these bacteria evolved at the same rate as other bacteria. We show, using a Poisson distribution, that unless it can be shown that S. marismortui evolves 5 to 10 times more slowly than other bacteria for which 16S rDNA substitution rates have been established, Vreeland et al.'s claim would be rejected at the 0.05 level. Also, a molecular clock test and a relative rates test fail to substantiate Vreeland et al.'s claim that strain 2-9-3 is a 250-Myr-old bacterium. The report of Vreeland et al. thus falls into a long series of suspect ancient DNA studies.

Lethal Effect on Bacterium of Decay of Incorporated Radioactive Atoms (3H, 14C, 32P)

International Nuclear Information System (INIS)

Apelgot, Sonia

1968-01-01

The biological effect of decay of 3 H, 14 C and 32 P incorporated into a bacterium depends on the nature of the organic molecule labelled, on the position of the isotope within it and on the isotope itself. In sum, results obtained to date show that: The decay of 3 H atoms incorporated into certain macromolecules of a bacterium causes sterilization through ionization by the ß - particle emitted; transmutation is of negligible importance. This self-irradiation is comparable in effect with X-rays and is affected in a similar manner by the same factors: temperature, presence of a radioprotector, radiosensitivity of the strain. Decay of 14 C or 32 P atoms incorporated into bacterial DNA is lethal because of the transmutation effect; ionizations produced by emitted ß - particles may be disregarded. Survival curves for 32 P transmutations depend on the experimental conditions. Some of the results obtained with 32 P are similar to those obtained with X-rays, e.g. effects of temperature, radical capture and oxygen, while others are similar to those of u.v. light, e.g., effect of growth conditions. Comparative tests made with 32 P indicate that the recoil energy of transmutation is not the phenomenon responsible for the lethal effect observed. Comparison of the results obtained after X-irradiation or decay of 3 H or 32 P incorporated into the DNA of bacteria of the same strain of E. coli shows that the efficiency of a 32 P transmutation is about four times greater than that of an ionization produced at random within the same DNA. (author) [fr

ISOLATION AND CHARACTERIZATION OF A MOLYBDENUM-REDUCING AND AZO-DYE DECOLORIZING SERRATIA MARCESCENS STRAIN NENI-1 FROM INDONESIAN SOIL

Directory of Open Access Journals (Sweden)

Neni Gusmanizar

2016-01-01

Full Text Available Heavy metals and organic xenobiotics including dyes are important industrial components with their usage amounting to the millions of tonnes yearly. Their presence in the environment is a serious pollution issue globally. Bioremediation of these pollutants using microbes with multiple detoxification capacity is constantly being sought. In this work we screen the ability of a molybdenum-reducing bacterium isolated from contaminated soil to decolorize various azo and triphenyl methane dyes. The bacterium reduces molybdate to molybdenum blue (Mo-blue optimally at pH 6.0, and temperatures of between 25 and 40oC. Glucose was the best electron donor for supporting molybdate reduction followed by sucrose, trehalose, maltose, d-sorbitol, dmannitol, d-mannose, myo-inositol, glycerol and salicin in descending order. Other requirements include a phosphate concentration of between 5.0 and 7.5 mM and a molybdate concentration between 10 and 20 mM. The absorption spectrum of the Moblue produced was similar to previous Mo-reducing bacterium, and closely resembles a reduced phosphomolybdate. Molybdenum reduction was inhibited by copper, silver and mercury at 2 ppm by 43.8%, 42.3% and 41.7%, respectively. We screen for the ability of the bacterium to decolorize various dyes. The bacterium was able to decolorize the dye Congo Red. Biochemical analysis resulted in a tentative identification of the bacterium as Serratia marcescens strain Neni-1. The ability of this bacterium to detoxify molybdenum and decolorize azo dye makes this bacterium an important tool for bioremediation.

Isolation and characterization of Ethanologenbacterium HitB49 gen. nov. sp. nov., an anaerobic, high hydrogen-producing bacterium with a special ethanol-type-fermentation

Energy Technology Data Exchange (ETDEWEB)

Lin, M. [Harbin Inst. of Technology, Harbin, HL (China). School of Municipal and Environmental Engineering]|[Nanyang Technological Univ., Singapore (Singapore). Inst. of Environmental Science and Engineering; Ren, N.Q.; Wang, A.J. [Harbin Inst. of Technology, Harbin, HL (China). School of Municipal and Environmental Engineering; Liang, D.T.; Tay, J.H. [Nanyang Technological Univ., Singapore (Singapore). Inst. of Environmental Science and Engineering

2004-07-01

Hydrogen, an important future energy source, can be produced by several fermentative microorganisms. The factor that prevents widespread biohydrogen production is the difficulty in isolating the ideal high hydrogen-producing bacterium (HPB). In this study, the Hungate technology was used to isolate and cultivate 210 strains of dominant fermentative bacteria. They were isolated from 6 sludges with ethanol-type fermentation (ETF) bioreactors. The study examined the production of hydrogen in pH 4, very low pH in ETF. The maximum rate in the biohydrogen-producing reactor was promising under continuous flow condition. The novel genus of HPB was Ethanologenbacterium Hit, of which strain B49 belonged to the ETF bacteria.

Atomic force microscopy study of the structure function relationships of the biofilm-forming bacterium Streptococcus mutans

Science.gov (United States)

Cross, Sarah E.; Kreth, Jens; Zhu, Lin; Qi, Fengxia; Pelling, Andrew E.; Shi, Wenyuan; Gimzewski, James K.

2006-02-01

Atomic force microscopy (AFM) has garnered much interest in recent years for its ability to probe the structure, function and cellular nanomechanics inherent to specific biological cells. In particular, we have used AFM to probe the important structure-function relationships of the bacterium Streptococcus mutans. S. mutans is the primary aetiological agent in human dental caries (tooth decay), and is of medical importance due to the virulence properties of these cells in biofilm initiation and formation, leading to increased tolerance to antibiotics. We have used AFM to characterize the unique surface structures of distinct mutants of S. mutans. These mutations are located in specific genes that encode surface proteins, thus using AFM we have resolved characteristic surface features for mutant strains compared to the wild type. Ultimately, our characterization of surface morphology has shown distinct differences in the local properties displayed by various S. mutans strains on the nanoscale, which is imperative for understanding the collective properties of these cells in biofilm formation.

Nitrate removal from groundwater by cooperating heterotrophic with autotrophic denitrification in a biofilm-electrode reactor

Energy Technology Data Exchange (ETDEWEB)

Zhao, Yingxin [School of Water Resources and Environment, China University of Geosciences, Beijing 100083 (China); Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 3058572 (Japan); Feng, Chuanping, E-mail: fengchuangping@gmail.com [School of Water Resources and Environment, China University of Geosciences, Beijing 100083 (China); Wang, Qinghong; Yang, Yingnan; Zhang, Zhenya; Sugiura, Norio [Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 3058572 (Japan)

2011-09-15

Highlights: {yields} Intensified biofilm-electrode reactor using cooperative denitrification is developed. {yields} IBER combines heterotrophic and autotrophic denitrification. {yields} CO{sub 2} formed by heterotrophic denitrification is used by autotrophic bacteria. {yields} Optimum running conditions are C/N = 0.75, HRT = 8 h, and I = 40 mA. {yields} A novel degradation mechanism for cooperating denitrification process is proposed. - Abstract: An intensified biofilm-electrode reactor (IBER) combining heterotrophic and autotrophic denitrification was developed for treatment of nitrate contaminated groundwater. The reactor was evaluated with synthetic groundwater (NO{sub 3}{sup -}N50 mg L{sup -1}) under different hydraulic retention times (HRTs), carbon to nitrogen ratios (C/N) and electric currents (I). The experimental results demonstrate that high nitrate and nitrite removal efficiency (100%) were achieved at C/N = 1, HRT = 8 h, and I = 10 mA. C/N ratios were reduced from 1 to 0.5 and the applied electric current was changed from 10 to 100 mA, showing that the optimum running condition was C/N = 0.75 and I = 40 mA, under which over 97% of NO{sub 3}{sup -}N was removed and organic carbon (methanol) was completely consumed in treated water. Simultaneously, the denitrification mechanism in this system was analyzed through pH variation in effluent. The CO{sub 2} produced from the anode acted as a good pH buffer, automatically controlling pH in the reaction zone. The intensified biofilm-electrode reactor developed in the study was effective for the treatment of groundwater polluted by nitrate.

Anoxybacillus vitaminiphilus sp. nov., a strictly aerobic and moderately thermophilic bacterium isolated from a hot spring.

Science.gov (United States)

Zhang, Xin-Qi; Zhang, Zhen-Li; Wu, Nan; Zhu, Xu-Fen; Wu, Min

2013-11-01

A strictly aerobic, Gram-stain-positive, motile and spore-forming bacterium, strain 3nP4(T), was isolated from the Puge hot spring located in the south-western geothermal area of China. Strain 3nP4(T) grew at 38-66 °C (optimum 57-60 °C), at pH 6.0-9.3 (optimum 7.0-7.5) and with 0-4 % (w/v) NaCl (optimum 0-0.5 %). Phylogenetic analysis of 16S rRNA gene sequences, as well as DNA-DNA relatedness values, indicated that the isolate represents a novel species of the genus Anoxybacillus, related most closely to Anoxybacillus voinovskiensis DSM 12111(T). Strain 3nP4(T) had diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid as major polar lipids and iso-C15 : 0 and iso-C17 : 0 as major fatty acids, which are both typical chemotaxonomic characteristics of the genus Anoxybacillus. The mean DNA G+C content of strain 3nP4(T) was 39.2±0.95 mol% (HPLC). A distinctive characteristic of the novel isolate was its extreme reliance on vitamin mixture or yeast extract for growth. Based on data from this taxonomic study using a polyphasic approach, strain 3nP4(T) is considered to represent a novel species of the genus Anoxybacillus, for which the name Anoxybacillus vitaminiphilus sp. nov. is proposed. The type strain is 3nP4(T) ( = CGMCC 1.8979(T) = JCM 16594(T)).

Lactic acid production from xylose by Geobacillus stearothermophilus strain 15

Science.gov (United States)

Kunasundari, B.; Naresh, S.; Chu, J. E.

2017-09-01

Lactic acid is an important compound with a wide range of industrial applications. The present study tested the efficiency of xylose, as a sole carbon source to be converted to lactic acid by Geobacillus stearothermophilus strain 15. To the best of our knowledge, limited information is available on the directed fermentation of xylose to lactic acid by this bacterium. The effects of different parameters such as temperature, pH, incubation time, agitation speed, concentrations of nitrogen and carbon sources on the lactic acid production were investigated statistically. It was found that the bacterium exhibited poor assimilation of xylose to lactic acid. Temperature, agitation rate and incubation time were determined to improve the lactic acid production slightly. The highest lactic acid yield obtained was 8.9% at 45°C, 300 RPM, 96 h, pH of 6.0 with carbon and nitrogen source concentrations were fixed at 5% w/v.

Clostridium thiosulfatireducens sp. nov., a proteolytic, thiosulfate- and sulfur-reducing bacterium isolated from an upflow anaerobic sludge blanket (UASB) reactor.

Science.gov (United States)

Hernández-Eugenio, Guadalupe; Fardeau, Marie-Laure; Cayol, Jean-Luc; Patel, Bharat K C; Thomas, Pierre; Macarie, Hervé; Garcia, Jean-Louis; Ollivier, Bernard

2002-09-01

A strictly anaerobic, gram-positive, sporulating rod (0.5-0.6 x 2.0-4.0 microm), designated strain Lup 21T, was isolated from an upflow anaerobic sludge blanket (UASB) reactor treating cheese-factory wastewater. Strain Lup 21T was motile by means of peritrichous flagella, had a G+C content of 31.4 mol% and grew optimally at 37 degrees C, pH 7.4, in the absence of NaCl. It is a heterotrophic micro-organism, utilizing proteinaceous compounds (gelatin, peptides, Casamino acids and various single amino acids) but unable to use any of the carbohydrates tested as a carbon and energy source. It reduced thiosulfate and elemental sulfur to sulfide in the presence of Casamino acids as carbon and energy sources. Acetate, butyrate, isobutyrate, isovalerate, CO2 and sulfide were end products from oxidation of gelatin and Casamino acids in the presence of thiosulfate as an electron acceptor. In the absence of thiosulfate, serine, lysine, methionine and histidine were fermented. On the basis of 16S rRNA similarity, strain Lup 21T was related to members of the low-G+C Clostridiales group, Clostridium subterminale DSM 6970T being the closest relative (with a sequence similarity of 99.4%). DNA-DNA hybridization was 56% with this species. On the basis of phenotypic, genotypic and phylogenetic characteristics, the isolate was designated as a novel species of the genus Clostridium, Clostridium thiosulfatireducens sp. nov. The type strain is strain Lup 21T (= DSM 13105T = CIP 106908T).

Brockia lithotrophica gen. nov., sp. nov., an anaerobic thermophilic bacterium from a terrestrial hot spring.

Science.gov (United States)

Perevalova, Anna A; Kublanov, Ilya V; Baslerov, R V; Zhang, Gengxin; Bonch-Osmolovskaya, Elizaveta A

2013-02-01

A novel thermophilic bacterium, strain Kam1851(T), was isolated from a terrestrial hot spring of the Uzon Caldera, Kamchatka Peninsula, Russia. Cells of strain Kam1851(T) were spore-forming rods with a gram-positive type of cell wall. Growth was observed between 46 and 78 °C, and pH 5.5-8.5. The optimal growth (doubling time, 6.0 h) was at 60-65 °C and pH 6.5. The isolate was an obligate anaerobe growing in pre-reduced medium only. It grew on mineral medium with molecular hydrogen or formate as electron donors, and elemental sulfur, thiosulfate or polysulfide as electron acceptors. The main cellular fatty acids were C(16 : 0) (34.2 %), iso-C(16 : 0) (18 %), C(18 : 0) (12.8 %) and iso-C(17 : 0) (11.1 %). The G+C content of the genomic DNA of strain Kam1851(T) was 63 mol%. 16S rRNA gene sequence analysis showed that strain Kam1851(T) belonged to the order Thermoanaerobacterales, but it was not closely related to representatives of any genera with validly published names. The most closely related strains, which had no more than 89.2 % sequence similarity, were members of the genera Ammonifex and Caldanaerobacter. On the basis of its phylogenetic position and novel phenotypic features, isolate Kam1851(T) is proposed to represent a novel species in a new genus, Brockia lithotrophica gen. nov., sp. nov.; the type strain of Brockia lithotrophica is Kam1851(T) ( = DSM 22653(T) = VKM B-2685(T)).

Metabolic engineering of a diazotrophic bacterium improves ammonium release and biofertilization of plants and microalgae.

Science.gov (United States)

Ambrosio, Rafael; Ortiz-Marquez, Juan Cesar Federico; Curatti, Leonardo

2017-03-01

The biological nitrogen fixation carried out by some Bacteria and Archaea is one of the most attractive alternatives to synthetic nitrogen fertilizers. However, with the exception of the symbiotic rhizobia-legumes system, progress towards a more extensive realization of this goal has been slow. In this study we manipulated the endogenous regulation of both nitrogen fixation and assimilation in the aerobic bacterium Azotobacter vinelandii. Substituting an exogenously inducible promoter for the native promoter of glutamine synthetase produced conditional lethal mutant strains unable to grow diazotrophically in the absence of the inducer. This mutant phenotype could be reverted in a double mutant strain bearing a deletion in the nifL gene that resulted in constitutive expression of nif genes and increased production of ammonium. Under GS non-inducing conditions both the single and the double mutant strains consistently released very high levels of ammonium (>20mM) into the growth medium. The double mutant strain grew and excreted high levels of ammonium under a wider range of concentrations of the inducer than the single mutant strain. Induced mutant cells could be loaded with glutamine synthetase at different levels, which resulted in different patterns of extracellular ammonium accumulation afterwards. Inoculation of the engineered bacteria into a microalgal culture in the absence of sources of C and N other than N 2 and CO 2 from the air, resulted in a strong proliferation of microalgae that was suppressed upon addition of the inducer. Both single and double mutant strains also promoted growth of cucumber plants in the absence of added N-fertilizer, while this property was only marginal in the parental strain. This study provides a simple synthetic genetic circuit that might inspire engineering of optimized inoculants that efficiently channel N 2 from the air into crops. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All

Limnobacter humi sp. nov., a thiosulfate-oxidizing, heterotrophic bacterium isolated from humus soil, and emended description of the genus Limnobacter Spring et al. 2001.

Science.gov (United States)

Nguyen, Tuan Manh; Kim, Jaisoo

2017-07-01

Three Gram-negative, strictly aerobic, chemolithoheterotrophic bacterial strains, designated UCM-30, UCM-33, and UCM-39 T , were isolated in South Korea. Based on their 16S rRNA gene sequences, the three isolated strains were found to be similar to Limnobacter thiooxidans CS-K2 T (97.41-97.68%), Limnobacter litoralis KP1-19 T (95.55-95.76%), and various genera belonging to the class Betaproteobacteria (90.34-93.34%). DNA-DNA hybridization showed 79.3-83.9% similarity between the genomic DNA of UCM-39 T , UCM-30, and UCM-33, while the sequence similarity between UCM-39 T and L. thiooxidans KACC 13837T or L. litoralis LMG 24869T was 23.7% and 18.6%, respectively. The DNA G+C content of UCM 39T was 59.7 mol%, the major ubiquinone was Q-8, and the optimal oxidation rate was observed at 10 mM thiosulfate. The major fatty acids (≥ 10%) were summed features 3 (C 16:1 ω7c and/or C 16:1 ω6c) and 8 (C 18:1 ω7c and/or C 18:1 ω6c), and C 16:0 . The major polar lipids (diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol) were found in all members of genus Limnobacter. Based on phenotypic, physiological, and phylogenetic analyses, the UCM-39T strain was found to be significantly distinct to represent a novel species affiliated to the genus Limnobacter. We propose to name it Limnobacter humi sp. nov. with the type strain UCM-39 T (=KACC 18574 T =NBRC 111650 T ).

Production and characterization of bioemulsifier from a marine bacterium, Acinetobacter calcoaceticus subsp. anitratus SM7

Directory of Open Access Journals (Sweden)

Kulnaree Phetrong

2008-05-01

Full Text Available Marine bacterium strain SM7 was isolated as a bioemulsifier-producing bacterium from oil-spilled seawater in Songkhla lagoon, Thailand. It was identified as Acinetobacter calcoaceticus subsp. anitratus based on morphology, biochemicalcharacteristics and 16S rRNA sequence. A. calcoaceticus subsp. anitratus SM7 produced an extracellular emulsifying agent when grown in a minimal salt medium (pH 7.0 containing 0.3% (v/v n-heptadecane and 0.1% (w/v ammoniumhydrogen carbonate as carbon source and nitrogen source, respectively, at 30oC with agitation rate of 200 rpm. Crude bioemulsifier was recovered from the culture supernatant by ethanol precipitation with a yield of 2.94 g/l and had a criticalemulsifier concentration of 0.04 g/ml. The crude bioemulsifier was capable of emulsifying n-hexadecane in a broad pH range (6-12, temperatures (30-121oC and in the presence of NaCl up to 12% (w/v. The bioemulsifier was stable in saltsolution ranging from 0 to 0.1% (w/v of MgCl2 and CaCl2. The broad range of pH stability, thermostability and salt tolerance suggested that the bioemulsifier from A. calcoaceticus subsp. anitratus SM7 could be useful in environmentalapplication, especially bioremediation of oil-polluted seawater.

Prior Inoculation with Type B Strains of Francisella tularensis Provides Partial Protection against Virulent Type A Strains in Cottontail Rabbits.

Directory of Open Access Journals (Sweden)

Vienna R Brown

Full Text Available Francisella tularensis is a highly virulent bacterium that is capable of causing severe disease (tularemia in a wide range of species. This organism is characterized into two distinct subspecies: tularensis (type A and holarctica (type B which vary in several crucial ways, with some type A strains having been found to be considerably more virulent in humans and laboratory animals. Cottontail rabbits have been widely implicated as a reservoir species for this subspecies; however, experimental inoculation in our laboratory revealed type A organisms to be highly virulent, resulting in 100% mortality following challenge with 50-100 organisms. Inoculation of cottontail rabbits with the same number of organisms from type B strains of bacteria was found to be rarely lethal and to result in a robust humoral immune response. The objective of this study was to characterize the protection afforded by a prior challenge with type B strains against a later inoculation with a type A strain in North American cottontail rabbits (Sylvilagus spp. Previous infection with a type B strain of organism was found to lengthen survival time and in some cases prevent death following inoculation with a type A2 strain of F. tularensis. In contrast, inoculation of a type A1b strain was uniformly lethal in cottontail rabbits irrespective of a prior type B inoculation. These findings provide important insight about the role cottontail rabbits may play in environmental maintenance and transmission of this organism.

[Screening and optimization of cholesterol conversion strain].

Science.gov (United States)

Fan, Dan; Xiong, Bingjian; Pang, Cuiping; Zhu, Xiangdong

2014-10-04

Bacterial strain SE-1 capable of transforming cholesterol was isolated from soil and characterized. The transformation products were identified. Fermentation conditions were optimized for conversion. Cholesterol was used as sole carbon source to isolate strain SE-1. Morphology, physiological and biochemical characteristics of strain SE-1 were studied. 16S rRNA gene was sequenced and subjected to phylogenetic analysis. Fermentation supernatants were extracted with chloroform, the transformation products were analyzed by silica gel thin layer chromatography and Sephadex LH20. Their structures were identified by 1H-NMR and 13C-NMR. Fermentation medium including carbon and nitrogen, methods of adding substrates and fermentation conditions for Strain SE-1 were optimized. Strain SE-1 was a Gram-negative bacterium, exhibiting the highest homologs to Burkholderia cepacia based on the physiological analysis. The sequence analysis of 16S rRNA gene of SE-1 strain and comparison with related Burkholderia show that SE-1 strain was very close to B. cepacia (Genbank No. U96927). The similarity was 99%. The result of silica gel thin layer chromatography shows that strain SE-1 transformed cholesterol to two products, 7beta-hydroxycholesterol and the minor product was 7-oxocholesterol. The optimum culture conditions were: molasses 5%, (NH4 )2SO4 0.3%, 4% of inoculation, pH 7.5 and 36 degrees C. Under the optimum culture condition, the conversion rate reached 34.4% when concentration of cholesterol-Tween 80 was 1 g/L. Cholesterol 7beta-hydroxylation conversion rate under optimal conditions was improved by 20.8%. Strain SE-1 isolated from soil is capable of converting cholesterol at lab-scale.

Gellertiella hungarica gen. nov., sp. nov., a novel bacterium of the family Rhizobiaceae isolated from a spa in Budapest.

Science.gov (United States)

Tóth, Erika; Szuróczki, Sára; Kéki, Zsuzsa; Bóka, Károly; Szili-Kovács, Tibor; Schumann, Peter

2017-11-01

A novel alphaproteobacterium, strain RAM11 T , belonging to the family Rhizobiaceae was isolated from the pool water of a thermal bath in Budapest, Hungary. Based on the 16S rRNA gene sequence strain RAM11 T shows the highest sequence similarity values to Ensifer adhaerens Casida A (97.44 %), to Ensifer (syn. Sinorhizobium) americanus CFNEI 156 T (96.87 %) and to Rhizobium azooxidifex Po 20/26 T (96.76 %). The new bacterium is strictly aerobic, its optimum growth occurs at 20-37 °C, between pH 7 and 9 and without NaCl. It is motile due to a single polar flagellum, capable of budding and forms rosettes in liquid culture. The major isoprenoid quinone of strain RAM11 T is Q-10, the major cellular fatty acids are C18 : 1ω7c and 11-MeC18 : 1ω7c. The polar lipid profile contains phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, an unidentified aminolipid and an unidentified phospholipid. The G+C content of DNA of the type strain is 62.9 mol%. Strain RAM11 T (=DSM 29853 T =NCAIM B.02618 T ) is proposed as type strain of a new genus and species with the proposed name Gellertiella hungarica gen. nov., sp. nov.

Rhodonellum psychrophilum gen. nov., sp. nov., a novel psychrophilic and alkaliphilic bacterium of the phylum Bacteroidetes isolated from Greenland.

Science.gov (United States)

Schmidt, Mariane; Priemé, Anders; Stougaard, Peter

2006-12-01

A novel alkaliphilic and psychrophilic bacterium was isolated from the cold and alkaline ikaite tufa columns of the Ikka Fjord in south-west Greenland. According to 16S rRNA gene sequence analysis, strain GCM71(T) belonged to the family 'Flexibacteraceae' in the phylum Bacteroidetes. Strain GCM71(T), together with five related isolates from ikaite columns, formed a separate cluster with 86-93 % gene sequence similarity to their closest relative, Belliella baltica. The G+C content of the DNA from strain GCM71(T) was 43.1 mol%, whereas that of B. baltica was reported to be 35 mol%. DNA-DNA hybridization between strain GCM71(T) and B. baltica was 9.5 %. The strain was red pigmented, Gram-negative, strictly aerobic with non-motile, rod-shaped cells. The optimal growth conditions for strain GCM71(T) were pH 9.2-10.0, 5 degrees C and 0.6 % NaCl. The fatty acid profile of the novel strain was dominated by branched and unsaturated fatty acids (90-97 %), with a high abundance of iso-C(17 : 1)omega9c (17.5 %), iso-C(17 : 0) 3-OH (17.5 %) and summed feature 3, comprising iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c (12.6 %). Phylogenetic, chemotaxonomic and physiological characteristics showed that the novel strain could not be affiliated to any known genus. A new genus, Rhodonellum gen. nov., is proposed to accommodate the novel strain. Strain GCM71(T) (=DSM 17998(T)=LMG 23454(T)) is proposed as the type strain of the type species, Rhodonellum psychrophilum sp. nov.

Draft Genome Sequence of a Kale (Brassica oleracea L.) Root Endophyte, Pseudomonas sp. Strain C9.

Science.gov (United States)

Laugraud, Aurelie; Young, Sandra; Gerard, Emily; O'Callaghan, Maureen; Wakelin, Steven

2017-04-13

Pseudomonas sp. strain C9 is a plant growth-promoting bacterium isolated from the root tissue of Brassica oleracea L. grown in soil from Marlborough, New Zealand. Its draft genome of 6,350,161 bp contains genes associated with plant growth promotion and biological control. Copyright © 2017 Laugraud et al.

Haloalkane-utilizing Rhodococcus strains isolated from geographically distinct locations possess a highly conserved gene cluster encoding haloalkane catabolism

NARCIS (Netherlands)

Poelarends, GJ; Bosma, T; Kulakov, LA; Larkin, MJ; Marchesi, [No Value; Weightman, AJ; Janssen, DB; Kulakov, Leonid A.; Larkin, Michael J.; Marchesi, Julian R.; Weightman, Andrew J.

The sequences of the 16S rRNA and haloalkane dehalogenase (dhaA) genes of five gram-positive haloalkane-utilizing bacteria isolated from contaminated sites in Europe, Japan, and the United States and of the archetypal haloalkane-degrading bacterium Rhodococcus sp. strain NCIMB13064 were compared.

Massive occurrence of heterotrophic filaments in acidified lakes: seasonal dynamics and composition

Czech Academy of Sciences Publication Activity Database

Vrba, Jaroslav; Nedoma, Jiří; Kohout, L.; Kopáček, Jiří; Nedbalová, L.; Ráčková, P.; Šimek, Karel

2003-01-01

Roč. 46, č. 3 (2003), s. 281-294 ISSN 0168-6496 R&D Projects: GA ČR GA206/97/0072; GA ČR GA206/00/0063; GA ČR GA206/03/1583; GA AV ČR IAA6017202; GA AV ČR IPP1011802 Institutional research plan: CEZ:AV0Z6017912 Keywords : bacterioplankton * phylogenetic identification * heterotrophic filaments Subject RIV: EE - Microbiology, Virology Impact factor: 2.947, year: 2003

Genome Sequence of Aeribacillus pallidus Strain GS3372, an Endospore-Forming Bacterium Isolated in a Deep Geothermal Reservoir

OpenAIRE

Sevasti Filippidou; Marion Jaussi; Thomas Junier; Tina Wunderlin; Nicole Jeanneret; Simona Regenspurg; Po-E Li; Chien-Chi Lo; Shannon Johnson; Kim McMurry; Cheryl D. Gleasner; Momchilo Vuyisich; Patrick S. Chain; Pilar Junier

2015-01-01

The genome of strain GS3372 is the first publicly available strain of Aeribacillus pallidus. This endospore-forming thermophilic strain was isolated from a deep geothermal reservoir. The availability of this genome can contribute to the clarification of the taxonomy of the closely related Anoxybacillus, Geobacillus, and Aeribacillus genera.

Biodiversity of culturable heterotrophic bacteria in the Southern Adriatic Sea Italian coastal waters

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Loredana Stabili

2004-04-01

Full Text Available The qualitative and quantitative composition of culturable heterotrophic bacteria in water samples from the Southern Adriatic Sea of Italy was examined. Water samples were collected monthly, for a year, at 16 stations along the coast line between Brindisi and Santa Maria di Leuca. The results obtained described the heterotrophic bacterial community over an annual cycle. Mean values of bacterial densities were 5.3 x 104 CFUml-1 in Brindisi, 5.8 x 104 CFUml-1 in S. Cataldo, 4.3 x 104 CFUml-1 in Otranto and 6.7 x 104 CFUml-1 in S. M. di Leuca. The differences in bacterial densities between the sites considered were estimated. The hydrodynamic circulation, the trophism and the geographical position of the examined sites contribute to justify the different bacterial density trends. The bacterial community consisted mainly of the genera Aeromonas, Pseudomonas, Photobacterium and Flavobacterium. The Enterobacteriaceae represented a considerable fraction of the bacterial community in the Southern Adriatic Sea. Bacilli were predominant among the Gram positive bacteria. The enzymatic versatility of the observed genera suggest their importance in organic matter turnover of this oligotrophic ecosystem.

Photosynthetic and Heterotrophic Ferredoxin Isoproteins Are Colocalized in Fruit Plastids of Tomato1

Science.gov (United States)

Aoki, Koh; Yamamoto, Miyuki; Wada, Keishiro

1998-01-01

Fruit tissues of tomato (Lycopersicon esculentum Mill.) contain both photosynthetic and heterotrophic ferredoxin (FdA and FdE, respectively) isoproteins, irrespective of their photosynthetic competence, but we did not previously determine whether these proteins were colocalized in the same plastids. In isolated fruit chloroplasts and chromoplasts, both FdA and FdE were detected by immunoblotting. Colocalization of FdA and FdE in the same plastids was demonstrated using double-staining immunofluorescence microscopy. We also found that FdA and FdE were colocalized in fruit chloroplasts and chloroamyloplasts irrespective of sink status of the plastid. Immunoelectron microscopy demonstrated that FdA and FdE were randomly distributed within the plastid stroma. To investigate the significance of the heterotrophic Fd in fruit plastids, Glucose 6-phosphate dehydrogenase (G6PDH) activity was measured in isolated fruit and leaf plastids. Fruit chloroplasts and chromoplasts showed much higher G6PDH activity than did leaf chloroplasts, suggesting that high G6PDH activity is linked with FdE to maintain nonphotosynthetic production of reducing power. This result suggested that, despite their morphological resemblance, fruit chloroplasts are functionally different from their leaf counterparts. PMID:9765529

Diffusive fractionation complicates isotopic partitioning of autotrophic and heterotrophic sources of soil respiration.

Science.gov (United States)

Moyes, Andrew B; Gaines, Sarah J; Siegwolf, Rolf T W; Bowling, David R

2010-11-01

Carbon isotope ratios (δ¹³C) of heterotrophic and rhizospheric sources of soil respiration under deciduous trees were evaluated over two growing seasons. Fluxes and δ¹³C of soil respiratory CO₂ on trenched and untrenched plots were calculated from closed chambers, profiles of soil CO₂ mole fraction and δ¹³C and continuous open chambers. δ¹³C of respired CO₂ and bulk carbon were measured from excised leaves and roots and sieved soil cores. Large diel variations (>5‰) in δ¹³C of soil respiration were observed when diel flux variability was large relative to average daily fluxes, independent of trenching. Soil gas transport modelling supported the conclusion that diel surface flux δ¹³C variation was driven by non-steady state gas transport effects. Active roots were associated with high summertime soil respiration rates and around 1‰ enrichment in the daily average δ¹³C of the soil surface CO₂ flux. Seasonal δ¹³C variability of about 4‰ (most enriched in summer) was observed on all plots and attributed to the heterotrophic CO₂ source. © 2010 Blackwell Publishing Ltd.

Genomics and ecophysiology of heterotrophic nitrogen fixing bacteria isolated from estuarine surface water

DEFF Research Database (Denmark)

Bentzon-Tilia, Mikkel; Severin, Ina; Hansen, Lars H.

2015-01-01

The ability to reduce atmospheric nitrogen (N2) to ammonia, known as N2 fixation, is a widely distributed trait among prokaryotes that accounts for an essential input of new N to a multitude of environments. Nitrogenase reductase gene (nifH) composition suggests that putative N2-fixing heterotrop......The ability to reduce atmospheric nitrogen (N2) to ammonia, known as N2 fixation, is a widely distributed trait among prokaryotes that accounts for an essential input of new N to a multitude of environments. Nitrogenase reductase gene (nifH) composition suggests that putative N2-fixing...... heterotrophic organisms are widespread in marine bacterioplankton, but their autecology and ecological significance are unknown. Here, we report genomic and ecophysiology data in relation to N2 fixation by three environmentally relevant heterotrophic bacteria isolated from Baltic Sea surface water: Pseudomonas...... liter-1, presumably accommodated through aggregate formation. Glucose stimulated N2 fixation in general, and reactive N repressed N2 fixation, except that ammonium (NH4 ) stimulated N2 fixation in R. palustris BAL398, indicating the use of nitrogenase as an electron sink. The lack of correlations...

New Insights on the Ecology of Free-living, Heterotrophic Nanoflagellates Based on the Use of Molecular Biological Approaches

National Research Council Canada - National Science Library

Lim, Lin

1997-01-01

.... Restriction fragment length polymorphism (RFLP) analysis of small subunit rDNA differentiated cultures of heterotrophic nanoflagellates according to established taxonomic classification at the generic and species level...

Enhanced lipid accumulation and biodiesel production by oleaginous Chlorella protothecoides under a structured heterotrophic-iron (II) induction strategy.

Science.gov (United States)

Li, Yuqin; Mu, Jinxiu; Chen, Di; Xu, Hua; Han, Fangxin

2015-05-01

A structured heterotrophic-iron (II) induction (HII) strategy was proposed to enhance lipid accumulation in oleaginous Chlorella protothecoides. C. protothecoides subjected to heterotrophic-iron (II) induction achieved a favorable lipid accumulation up to 62 % and a maximum lipid productivity of 820.17 mg/day, representing 2.78-fold and 3.64-fold increase respectively over heterotrophic cultivation alone. HII-induced cells produced significantly elevated levels of 16:0, 18:1(Δ9), and 18:2(Δ9,12) fatty acids (over 90 %). The lipid contents and plant lipid-like fatty acid compositions exhibit the potential of HII-induced C. protothecoides as biodiesel feedstock. Furthermore, 31 altered proteins in HII-induced algal cells were successfully identified. These differentially expressed proteins were assigned into nine molecular function categories, including carbohydrate metabolism, lipid biosynthesis, Calvin cycle, cellular respiration, photosynthesis, energy and transport, protein biosynthesis, regulate and defense, and unclassified. Analysis using the Kyoto encyclopedia of genes and genomes and gene ontology annotation showed that malic enzyme, acyltransferase, and ACP were key metabolic checkpoints found to modulate lipid accumulation in C. protothecoides. The results provided possible applications of HII cultivation strategy in other microalgal species and new possibilities in developing genetic and metabolic engineering microalgae for desirable lipid productivity.

Genome Sequence of Streptomyces viridosporus Strain T7A ATCC 39115, a Lignin-Degrading Actinomycete

Energy Technology Data Exchange (ETDEWEB)

Davis, Jennifer R. [Brown University; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Teshima, Hazuki [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Wei, Chia-Lin [Los Alamos National Laboratory (LANL); Han, James [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Szeto, Ernest [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Peters, Lin [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Sello, Jason K. [Brown University

2013-01-01

We announce the availability of the genome sequence of Streptomyces viridosporus strain T7A ATCC 39115, a plant biomass- degrading actinomycete. This bacterium is of special interest because of its capacity to degrade lignin, an underutilized compo- nent of plants in the context of bioenergy. It has a full complement of genes for plant biomass catabolism.

Genome sequence of the agar-degrading marine bacterium Alteromonadaceae sp. strain G7.

Science.gov (United States)

Kwak, Min-Jung; Song, Ju Yeon; Kim, Byung Kwon; Chi, Won-Jae; Kwon, Soon-Kyeong; Choi, Soobeom; Chang, Yong-Keun; Hong, Soon-Kwang; Kim, Jihyun F

2012-12-01

Here, we present the high-quality draft genome sequence of the agar-degrading marine gammaproteobacterium Alteromonadaceae sp. strain G7, which was isolated from coastal seawater to be utilized as a bioresource for production of agar-derived biofuels. The 3.91-Mb genome contains a number of genes encoding algal polysaccharide-degrading enzymes such as agarases and sulfatases.

Genome Sequence of the Agar-Degrading Marine Bacterium Alteromonadaceae sp. Strain G7

OpenAIRE

Kwak, Min-Jung; Song, Ju Yeon; Kim, Byung Kwon; Chi, Won-Jae; Kwon, Soon-Kyeong; Choi, Soobeom; Chang, Yong-Keun; Hong, Soon-Kwang; Kim, Jihyun F.

2012-01-01

Here, we present the high-quality draft genome sequence of the agar-degrading marine gammaproteobacterium Alteromonadaceae sp. strain G7, which was isolated from coastal seawater to be utilized as a bioresource for production of agar-derived biofuels. The 3.91-Mb genome contains a number of genes encoding algal polysaccharide-degrading enzymes such as agarases and sulfatases.

Colwellia psychrerythraea strains from distant deep sea basins show adaptation to local conditions

Directory of Open Access Journals (Sweden)

Stephen M Techtmann

2016-05-01

Full Text Available Many studies have shown that microbes, which share nearly identical 16S rRNA genes, can have highly divergent genomes. Microbes from distinct parts of the ocean also exhibit biogeographic patterning. Here we seek to better understand how certain microbes from the same species have adapted for growth under local conditions. The phenotypic and genomic heterogeneity of three strains of Colwellia psychrerythraea was investigated in order to understand adaptions to local environments. Colwellia are psychrophilic heterotrophic marine bacteria ubiquitous in cold marine ecosystems. We have recently isolated two Colwellia strains: ND2E from the Eastern Mediterranean and GAB14E from the Great Australian Bight. The 16S rRNA sequence of these two strains were greater than 98.2% identical to the well-characterized C. psychrerythraea 34H, which was isolated from arctic sediments. Salt tolerance, and carbon source utilization profiles for these strains were determined using Biolog Phenotype Microarrays’. These strains exhibited distinct salt tolerance, which was not associated with the salinity of sites of isolation. The carbon source utilization profiles were distinct with less than half of the tested carbon sources being metabolized by all three strains. Whole genome sequencing revealed that the genomes of these three strains were quite diverse with some genomes having up to 1600 strain-specific genes. Many genes involved in degrading strain-specific carbon sources were identified. There appears to be a link between carbon source utilization and location of isolation with distinctions observed between the Colwellia isolate recovered from sediment compared to water column isolates.

First report of a lipopeptide biosurfactant from thermophilic bacterium Aneurinibacillus thermoaerophilus MK01 newly isolated from municipal landfill site.

Science.gov (United States)

Sharafi, Hakimeh; Abdoli, Mahya; Hajfarajollah, Hamidreza; Samie, Nima; Alidoust, Leila; Abbasi, Habib; Fooladi, Jamshid; Zahiri, Hossein Shahbani; Noghabi, Kambiz Akbari

2014-07-01

A biosurfactant-producing thermophile was isolated from the Kahrizak landfill of Tehran and identified as a bacterium belonging to the genus Aneurinibacillus. A thermostable lipopeptide-type biosurfactant was purified from the culture medium of this bacterium and showed stability in the temperature range of 20-90 °C and pH range of 5-10. The produced biosurfactant could reduce the surface tension of water from 72 to 43 mN/m with a CMC of 1.21 mg/mL. The strain growing at a temperature of 45 °C produces a substantial amount of 5 g/L of biosurfactant in the medium supplemented with sunflower oil as the sole carbon source. Response surface methodology was employed to optimize the biosurfactant production using sunflower oil, sodium nitrate, and yeast extract as variables. The optimization resulted in 6.75 g/L biosurfactant production, i.e., 35% improved as compared to the unoptimized condition. Thin-layer chromatography, FTIR spectroscopy, 1H-NMR spectroscopy, and biochemical composition analysis confirmed the lipopeptide structure of the biosurfactant.

The impact of strain-specific immunity on Lyme disease incidence is spatially heterogeneous.

Science.gov (United States)

Khatchikian, Camilo E; Nadelman, Robert B; Nowakowski, John; Schwartz, Ira; Wormser, Gary P; Brisson, Dustin

2017-12-01

Lyme disease, caused by the bacterium Borrelia burgdorferi, is the most common tick-borne infection in the US. Recent studies have demonstrated that the incidence of human Lyme disease would have been even greater were it not for the presence of strain-specific immunity, which protects previously infected patients against subsequent infections by the same B. burgdorferi strain. Here, spatial heterogeneity is incorporated into epidemiological models to accurately estimate the impact of strain-specific immunity on human Lyme disease incidence. The estimated reduction in the number of Lyme disease cases is greater in epidemiologic models that explicitly include the spatial distribution of Lyme disease cases reported at the county level than those that utilize nationwide data. strain-specific immunity has the greatest epidemiologic impact in geographic areas with the highest Lyme disease incidence due to the greater proportion of people that have been previously infected and have developed strain-specific immunity. Copyright © 2017 Elsevier Inc. All rights reserved.

Whole-Genome Sequence of Chlamydia abortus Strain GN6 Isolated from Aborted Yak Fetus

OpenAIRE

Li, Zhaocai; Cai, Jinshan; Cao, Xiaoan; Lou, Zhongzi; Chao, Yilin; Kan, Wei; Zhou, Jizhang

2017-01-01

ABSTRACT The obligate intracellular Gram-negative bacterium Chlamydia abortus is one of the causative agents of abortion and fetal loss in sheep, goats, and cattle in many countries. It also affects the reproductivity of yaks (Bos grunniens). This study reports the whole-genome sequence of Chlamydia abortus strain GN6, which was isolated from aborted yak fetus in Qinghai-Tibetan Plateau, China.

Draft Genome Sequences of Two Propionibacterium acnes Strains Isolated from Progressive Macular Hypomelanosis Lesions of Human Skin

DEFF Research Database (Denmark)

Petersen, Rolf; Lomholt, Hans B.; Scholz, Christian F. P.

2015-01-01

Propionibacterium acnes is a Gram-positive bacterium that is prevalent on human skin. It has been associated with skin disorders such as acne vulgaris and progressive macular hypomelanosis (PMH). Here, we report draft genome sequences of two type III P. acnes strains, PMH5 and PMH7, isolated from...

Draft Genome Sequence of Cupriavidus pauculus Strain KF709, a Biphenyl-Utilizing Bacterium Isolated from Biphenyl-Contaminated Soil

OpenAIRE

Watanabe, Takahito; Yamazoe, Atsushi; Hosoyama, Akira; Fujihara, Hidehiko; Suenaga, Hikaru; Hirose, Jun; Futagami, Taiki; Goto, Masatoshi; Kimura, Nobutada; Furukawa, Kensuke

2015-01-01

We report the draft genome sequence of Cupriavidus pauculus strain KF709, which comprises 6,826,799 bp with 6,272 coding sequences. The strain KF709 utilizes biphenyl and degrades low-chlorinated biphenyls; however, it possesses fewer coding sequences involved in the degradation of aromatic compounds than other strains belonging to the Betaproteobacteria.

Genome Sequence of Aeribacillus pallidus Strain GS3372, an Endospore-Forming Bacterium Isolated in a Deep Geothermal Reservoir.

Science.gov (United States)

Filippidou, Sevasti; Jaussi, Marion; Junier, Thomas; Wunderlin, Tina; Jeanneret, Nicole; Regenspurg, Simona; Li, Po-E; Lo, Chien-Chi; Johnson, Shannon; McMurry, Kim; Gleasner, Cheryl D; Vuyisich, Momchilo; Chain, Patrick S; Junier, Pilar

2015-08-27

The genome of strain GS3372 is the first publicly available strain of Aeribacillus pallidus. This endospore-forming thermophilic strain was isolated from a deep geothermal reservoir. The availability of this genome can contribute to the clarification of the taxonomy of the closely related Anoxybacillus, Geobacillus, and Aeribacillus genera. Copyright © 2015 Filippidou et al.

Photobacterium kishitanii sp. nov., a luminous marine bacterium symbiotic with deep-sea fishes.

Science.gov (United States)

Ast, Jennifer C; Cleenwerck, Ilse; Engelbeen, Katrien; Urbanczyk, Henryk; Thompson, Fabiano L; De Vos, Paul; Dunlap, Paul V

2007-09-01

Six representatives of a luminous bacterium commonly found in association with deep, cold-dwelling marine fishes were isolated from the light organs and skin of different fish species. These bacteria were Gram-negative, catalase-positive, and weakly oxidase-positive or oxidase-negative. Morphologically, cells of these strains were coccoid or coccoid-rods, occurring singly or in pairs, and motile by means of polar flagellation. After growth on seawater-based agar medium at 22 degrees C for 18 h, colonies were small, round and white, with an intense cerulean blue luminescence. Analysis of 16S rRNA gene sequence similarity placed these bacteria in the genus Photobacterium. Phylogenetic analysis based on seven housekeeping gene sequences (16S rRNA gene, gapA, gyrB, pyrH, recA, rpoA and rpoD), seven gene sequences of the lux operon (luxC, luxD, luxA, luxB, luxF, luxE and luxG) and four gene sequences of the rib operon (ribE, ribB, ribH and ribA), resolved the six strains as members of the genus Photobacterium and as a clade distinct from other species of Photobacterium. These strains were most closely related to Photobacterium phosphoreum and Photobacterium iliopiscarium. DNA-DNA hybridization values between the designated type strain, Photobacterium kishitanii pjapo.1.1(T), and P. phosphoreum LMG 4233(T), P. iliopiscarium LMG 19543(T) and Photobacterium indicum LMG 22857(T) were 51, 43 and 19 %, respectively. In AFLP analysis, the six strains clustered together, forming a group distinct from other analysed species. The fatty acid C(17 : 0) cyclo was present in these bacteria, but not in P. phosphoreum, P. iliopiscarium or P. indicum. A combination of biochemical tests (arginine dihydrolase and lysine decarboxylase) differentiates these strains from P. phosphoreum and P. indicum. The DNA G+C content of P. kishitanii pjapo.1.1(T) is 40.2 %, and the genome size is approximately 4.2 Mbp, in the form of two circular chromosomes. These strains represent a novel species, for

Ponticoccus marisrubri sp. nov., a moderately halophilic marine bacterium of the family Rhodobacteraceae

KAUST Repository

Zhang, Guishan

2017-10-06

Strain SJ5A-1T, a Gram-stain-negative, coccus-shaped, non-motile, aerobic bacterium, was isolated from the brine-seawater interface of the Erba Deep in the Red Sea, Saudi Arabia. The colonies of strain SJ5A-1T have a beige to pale-brown pigmentation, are approximately 0.5-0.7 µm in diameter, and are catalase and oxidase positive. Growth occurred optimally at 30-33 °C, pH 7.0-7.5, and in the presence of 9.0-12.0 % NaCl (w/v). Phylogenetic analysis of the 16S rRNA gene indicates that strain SJ5A-1T is a member of the genus Ponticoccus within the family Rhodobacteraceae. Ponticoccus litoralis DSM 18986T is the most closely related described species based on 16S rRNA gene sequence identity (96.7 %). The DNA-DNA hybridization value between strain SJ5A-1T and P. litoralis DSM 18986T was 36.7 %. The major respiratory quinone of strain SJ5A-1T is Q-10; it predominantly uses the fatty acids C18 : 1 (54.2 %), C18 : 0 (11.2 %), C16 : 0 (8.6 %), 11-methyl C18 : 1ω7c (7.7 %), C19 : 0cyclo ω8c (3.3 %), and C12 : 1 3-OH (3.5 %), and its major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, phosphocholine, an unknown aminolipid, an unknown phospholipid and two unknown lipids. The genome draft of strain SJ5A-1T as presented here is 4 562 830 bp in size and the DNA G+C content is 68.0 mol %. Based on phenotypic, phylogenetic and genotypic data, strain SJ5A-1T represents a novel species in the genus Ponticoccus, for which we propose the name Ponticoccus marisrubri sp. nov. The type strain of P. marisrubri is SJ5A-1T (=JCM 19520T=ACCC19863T).

ANALYSIS OF IMMUNE RESPONSES ON TRANSGENIC TIGER SHRIMP (Penaeus monodon AGAINST PATHOGENIC BACTERIUM Vibrio harveyi

Directory of Open Access Journals (Sweden)

Andi Parenrengi

2014-06-01

Full Text Available Vibriosis is one of main diseases of the black tiger shrimp Penaeus monodon infected by pathogenic bioluminous bacterium Vibrio harveyi that can cause mass mortalities in shrimp culture. The bacteria can also trigger the disease white spot syndrome virus (WSSV. An effort to produce shrimp disease-resistant strains has been done through transgenesis technology with antiviral gene transfection. By this technology, it is expected an increase in the immune response of shrimp in a variety of diseasecausing pathogens. This study aimed to determine the immune responses (total haemocytes, haemocyte differentiation, and phenoloxydase activity of transgenic tiger shrimp against pathogenic bacterium V. harveyi. Research using completely randomized design, which consists of two treatments and three replications. Test animals being used were transgenic and non-transgenic shrimp with size, weight 3.93±1.25 g and a total length of 7.59±0.87 cm. Treatments being tested were the injection of bacterium V. harveyi (density of 5x106 cfu/mL of 0.1 mL/individual on transgenic (A and non-transgenic shrimp (B. Immune response parameters such as total haemocytes, haemocyte differentiation, and phenoloxydase activity were observed on day 1, 3, and 6 days after challenging. Data were analyzed using t-test by SPSS software. The results showed that the total haemocyte of transgenic shrimp was not significantly different (P>0.05 from non-transgenic shrimp, but haemocyte differentiation and phenoloxydase activity were significantly different (P<0.05 especially on sixth days after being exposed to the bioluminescent bacteria. The study results implied that transgenic shrimp has a better immune response compared than non-transgenic shrimp.

Deterioration study of a material for encapsulation of radioactive wastes, the Portland cement, by heterotrophic microorganisms isolated from natural media

International Nuclear Information System (INIS)

Perfettini, J.

1989-01-01

Soils and geologic formations selected for storage of radioactive waste storage contain microflora (nitrifying and sulfoxidizing bacteria, heterotrophic microorganisms) that can corrode cement through acidic metabolism products. Nutriments required for their development are also found in these biotopes. Corrosine effects of organic acids produced by heterotrophic microorganisms are: mass decrease, leaching (especially Ca), dissolution of portlandite crystals Ca (OH) 2 , increase of porosity and decrease of flexural strength. Excretion of corrosive organic acids by bacteria is promoted by high temperature and basic pH. Acidification by fungi requires also a high temperature but an acidic pH [fr

Development of plasmid vector and electroporation condition for gene transfer in sporogenic lactic acid bacterium, Bacillus coagulans.

Science.gov (United States)

Rhee, Mun Su; Kim, Jin-Woo; Qian, Yilei; Ingram, L O; Shanmugam, K T

2007-07-01

Bacillus coagulans is a sporogenic lactic acid bacterium that ferments glucose and xylose, major components of plant biomass, a potential feedstock for cellulosic ethanol. The temperature and pH for optimum rate of growth of B. coagulans (50 to 55 degrees C, pH 5.0) are very similar to that of commercially developed fungal cellulases (50 degrees C; pH 4.8). Due to this match, simultaneous saccharification and fermentation (SSF) of cellulose to products by B. coagulans is expected to require less cellulase than needed if the SSF is conducted at a sub-optimal temperature, such as 30 degrees C, the optimum for yeast, the main biocatalyst used by the ethanol industry. To fully exploit B. coagulans as a platform organism, we have developed an electroporation method to transfer plasmid DNA into this genetically recalcitrant bacterium. We also constructed a B. coagulans/E. coli shuttle vector, plasmid pMSR10 that contains the rep region from a native plasmid (pMSR0) present in B. coagulans strain P4-102B. The native plasmid, pMSR0 (6823bp), has 9 ORFs, and replicates by rolling-circle mode of replication. Plasmid pNW33N, developed for Geobacillus stearothermophilus, was also transformed into this host and stably maintained while several other Bacillus/Escherichia coli shuttle vector plasmids were not transformed into B. coagulans. The transformation efficiency of B. coagulans strain P4-102B using the plasmids pNW33N or pMSR10 was about 1.5x10(16) per mole of DNA. The availability of shuttle vectors and an electroporation method is expected to aid in genetic and metabolic engineering of B. coagulans.

Genetic characterization, nickel tolerance, biosorption, kinetics, and uptake mechanism of a bacterium isolated from electroplating industrial effluent.

Science.gov (United States)

Nagarajan, N; Gunasekaran, P; Rajendran, P

2015-04-01

Electroplating industries in Madurai city produce approximately 49,000 L of wastewater and 1200 L of sludge every day revealing 687-5569 ppm of nickel (Ni) with other contaminants. Seventeen Ni-tolerant bacterial strains were isolated from nutrient-enriched effluents. Among them one hyper Ni accumulating strain was scored and identified as Bacillus cereus VP17 on the basis of morphology, biochemical tests, 16S rDNA gene sequencing, and phylogenetic analysis. Equilibrium data of Ni(II) ions using the bacterium as sorbent at isothermal conditions (37 °C) and pH 6 were best adjusted by Langmuir (R(2) = 0.6268) and Freundlich models (R(2) = 0.9505). Experimental validation reveals Ni sorption takes place on a heterogeneous surface of the biosorbent, and predicted metal sorption capacity is 434 ppm. The pseudo-second-order kinetic model fitted the biosorption kinetic data better than the pseudo-first-order kinetic model (R(2) = 0.9963 and 0.3625). Scanning electron microscopy, energy dispersive X-ray, and Fourier transform infrared spectroscopy studies of the bacterial strain with and without Ni(II) ion reveals the biosorption mechanism. The results conclude possibilities of using B. cereus VP17 for Ni bioremediation.

Photobacterium galatheae sp. nov., a bioactive bacterium isolated from a mussel in the Solomon Sea

DEFF Research Database (Denmark)

Machado, Henrique; Giubergia, Sonia; Mateiu, Ramona Valentina

2015-01-01

A novel, Gram-negative marine bacterium, S2753T, was isolated from a mussel of the Solomon Sea, Solomon Islands. Analysis of the 16S rRNA gene sequence and whole genome sequence data placed strain S2753T in the genus Photobacterium with the closest relative being Photobacterium halotolerans DSM...... 18316T (97.7 % 16S rRNA gene similarity). Strain S2753T was able to grow from 15 to 40 °C and in NaCl concentrations of 0.5 to 9 % (w/v). The predominant fatty acids were 16 : 1ω7c/16 : 1ω6c (27.9 %), 16 : 0 (22.1 %) and 18 : 1ω7c/8 : 1ω6c (21.4 %). The genomic DNA G+C mol content was 49.5 mol%. Based...... is genomically distinct enough to be considered a novel species. The name Photobacterium galatheae is proposed and the type-strain is S2753T( = LMG 28894T = DSM 100496T)....

O-heterocyclic derivatives with antibacterial properties from marine bacterium Bacillus subtilis associated with seaweed, Sargassum myriocystum.

Science.gov (United States)

Chakraborty, Kajal; Thilakan, Bini; Chakraborty, Rekha Devi; Raola, Vamshi Krishna; Joy, Minju

2017-01-01

The brown seaweed, Sargassum myriocystum associated with heterotrophic bacterium, Bacillus subtilis MTCC 10407 (JF834075) exhibited broad-spectra of potent antibacterial activities against pathogenic bacteria Aeromonas hydrophila, Vibrio vulnificus, and Vibrio parahaemolyticus. B. subtilis MTCC 10407 was found to be positive for polyketide synthetase (pks) gene, and therefore, was considered to characterize secondary metabolites bearing polyketide backbone. Using bioassay-guided fractionation, two new antibacterial O-heterocyclic compounds belonging to pyranyl benzoate analogs of polyketide origin, with activity against pathogenic bacteria, have been isolated from the ethyl acetate extract of B. subtilis MTCC 10407. In the present study, the secondary metabolites of B. subtilis MTCC 10407 with potent antibacterial action against bacterial pathogens was recognized to represent the platform of pks-1 gene-encoded products. Two homologous compounds 3 (3-(methoxycarbonyl)-4-(5-(2-ethylbutyl)-5,6-dihydro-3-methyl-2H-pyran-2-yl)-butyl benzoate) and 4 [2-(8-butyl-3-ethyl-3,4,4a,5,6,8a-hexahydro-2H-chromen-6-yl)-ethyl benzoate] also have been isolated from the ethyl acetate extract of host seaweed S. myriocystum. The two compounds isolated from ethyl acetate extract of S. myriocystum with lesser antibacterial properties shared similar structures with the compounds purified from B. subtilis that suggested the ecological and metabolic relationship between these compounds in seaweed-bacterial relationship. Tetrahydropyran-2-one moiety of the tetrahydropyrano-[3,2b]-pyran-2(3H)-one system of 1 might be cleaved by the metabolic pool of seaweeds to afford methyl 3-(dihydro-3-methyl-2H-pyranyl)-propanoate moiety of 3, which was found to have no significant antibacterial activity. It is therefore imperative that the presence of dihydro-methyl-2H-pyran-2-yl propanoate system is essentially required to impart the greater activity. The direct involvement of polarisability (Pl) with