Isolation and Characterization of a Sulfur-Oxidizing Chemolithotroph Growing on Crude Oil under Anaerobic Conditions

ABSTRACT Molecular approaches have shown that a group of bacteria (called cluster 1 bacteria) affiliated with the ε subclass of the class Proteobacteria constituted major populations in underground crude-oil storage cavities. In order to unveil their physiology and ecological niche, this study isolated bacterial strains (exemplified by strain YK-1) affiliated with the cluster 1 bacteria from an oil storage cavity at Kuji in Iwate, Japan. 16S rRNA gene sequence analysis indicated that its closest relative was Thiomicrospira denitrificans (90% identity). Growth experiments under anaerobic conditions showed that strain YK-1 was a sulfur-oxidizing obligate chemolithotroph utilizing sulfide, elemental sulfur, thiosulfate, and hydrogen as electron donors and nitrate as an electron acceptor. Oxygen also supported its growth only under microaerobic conditions. Strain YK-1 could not grow on nitrite, and nitrite was the final product of nitrate reduction. Neither sugars, organic acids (including acetate), nor hydrocarbons could serve as carbon and energy sources. A typical stoichiometry of its energy metabolism followed an equation: S2− + 4NO3 − → SO4 2− + 4NO2 − (ΔG 0 = −534 kJ mol−1). In a difference from other anaerobic sulfur-oxidizing bacteria, this bacterium was sensitive to NaCl; growth in medium containing more than 1% NaCl was negligible. When YK-1 was grown anaerobically in a sulfur-depleted inorganic medium overlaid with crude oil, sulfate was produced, corresponding to its growth. On the contrary, YK-1 could not utilize crude oil as a carbon source. These results suggest that the cluster 1 bacteria yielded energy for growth in oil storage cavities by oxidizing petroleum sulfur compounds. Based on its physiology, ecological interactions with other members of the groundwater community are discussed.

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Sulfuricurvum kujiense gen. nov., sp. nov., a facultatively anaerobic, chemolithoautotrophic, sulfur-oxidizing bacterium isolated from an underground crude-oil storage cavity

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63243-0 ◽

2004 ◽

Vol 54 (6) ◽

pp. 2297-2300 ◽

Cited By ~ 168

Author(s):

Yumiko Kodama ◽

Kazuya Watanabe

Keyword(s):

Crude Oil ◽

Electron Acceptor ◽

Rrna Gene ◽

Microaerobic Condition ◽

Facultatively Anaerobic ◽

Oil Storage ◽

Novel Genus And Species ◽

Thiomicrospira Denitrificans ◽

Sulfur Oxidizing ◽

Bacterium Strain

A facultatively anaerobic, chemolithoautotrophic, sulfur-oxidizing bacterium, strain YK-1T, was isolated from an underground crude-oil storage cavity at Kuji in Iwate, Japan. The cells were motile, curved rods and had a single polar flagellum. Optimum growth occurred in a low-strength salt medium at pH 7·0 and 25 °C. It utilized sulfide, elemental sulfur, thiosulfate and hydrogen as the electron donors and nitrate as the electron acceptor under anaerobic conditions, but it did not use nitrite. Oxygen also served as the electron acceptor under the microaerobic condition (O2 in the head space 1 %). It did not grow on sugars, organic acids or hydrocarbons as carbon and energy sources. The DNA G+C content of strain YK-1T was 45 mol%. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that its closest relative was Thiomicrospira denitrificans in the ‘Epsilonproteobacteria’, albeit with low homology (90 %). On the basis of physiological and phylogenetic data, strain YK-1T should be classified into a novel genus and species, for which the name Sulfuricurvum kujiense gen. nov., sp. nov. is proposed. The type strain is YK-1T (=JCM 11577T=MBIC 06352T=ATCC BAA-921T).

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Isolation and Characterization of Facultative-Anaerobic Antimonate-Reducing Bacteria

Microorganisms ◽

10.3390/microorganisms8091435 ◽

2020 ◽

Vol 8 (9) ◽

pp. 1435

Author(s):

Ziran Yang ◽

Hisaaki Hosokawa ◽

Takuya Sadakane ◽

Masashi Kuroda ◽

Daisuke Inoue ◽

...

Keyword(s):

Wastewater Treatment ◽

Current Knowledge ◽

Strictly Anaerobic ◽

Bacterial Strains ◽

Anaerobic Conditions ◽

Practical Applications ◽

Isolation And Characterization ◽

Facultative Anaerobic ◽

Microaerobic Conditions ◽

A Minor

Microbial antimonate (Sb(V)) reduction is a promising approach to remove Sb(V) from wastewater. However, current knowledge regarding microbial Sb(V) reduction is limited to strictly anaerobic conditions. This study was the first to isolate three facultative-anaerobic Sb(V)-reducing bacterial strains from the sludge collected from a wastewater treatment facility in an antimony products plant. Two of the isolated strains, designated Dechloromonas sp. AR-2 and Propionivibrio sp. AR-3, were characterized based on their Sb(V)-reducing abilities. When cultivated under anaerobic conditions with Sb(V) and acetate as the electron acceptor and donor, respectively, both strains could efficiently reduce 5.0 mM Sb(V), removing most of it from the water phase within 7 d. Along with Sb(V) reduction by the strains, white precipitates, which were likely amorphous Sb(OH)3 solids, were formed with a minor generation of soluble antimonite. Additionally, respiratory Sb(V) reduction by both strains occurred not only under anaerobic but also microaerobic conditions. It was suggested that Sb(V) reduction and the growth abilities of the strains under microaerobic conditions presented a substantial advantage of the use of strains AR-2 and AR-3 for practical applications to Sb(V)-containing wastewater treatment.

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Predominant Effect of Host Genetics on Levels of Lactobacillus johnsonii Bacteria in the Mouse Gut

Applied and Environmental Microbiology ◽

10.1128/aem.00324-11 ◽

2011 ◽

Vol 77 (18) ◽

pp. 6531-6538 ◽

Cited By ~ 24

Author(s):

Keren Buhnik-Rosenblau ◽

Yael Danin-Poleg ◽

Yechezkel Kashi

Keyword(s):

Genetic Background ◽

Well Being ◽

Probiotic Bacterium ◽

Mouse Genetics ◽

Rrna Gene ◽

Bacterial Strains ◽

Lactobacillus Johnsonii ◽

Content Type ◽

Isolation And Characterization ◽

Mouse Lines

ABSTRACTThe gut microbiota is strongly associated with the well-being of the host. Its composition is affected by environmental factors, such as food and maternal inoculation, while the relative impact of the host's genetics have been recently uncovered. Here, we studied the effect of the host genetic background on the composition of intestinal bacteria in a murine model, focusing on lactic acid bacteria (LAB) as an important group that includes many probiotic strains. Based on 16S rRNA gene genotyping, variation was observed in fecal LAB populations of BALB/c and C57BL/6J mouse lines.Lactobacillus johnsonii, a potentially probiotic bacterium, appeared at significantly higher levels in C57BL/6J versus BALB/c mouse feces. In the BALB/c gut, theL. johnsoniilevel decreased rapidly after oral administration, suggesting that some selective force does not allow its persistence at higher levels. The genetic inheritance ofL. johnsoniilevels was further tested in reciprocal crosses between the two mouse lines. The resultant F1 offspring presented similarL. johnsoniilevels, confirming that mouse genetics plays a major role in determining these levels compared to the smaller maternal effect. Our findings suggest that mouse genetics has a major effect on the composition of the LAB population in general and on the persistence ofL. johnsoniiin the gut in particular. Concentrating on a narrow spectrum of culturable LAB enables the isolation and characterization of such potentially probiotic bacterial strains, which might be specifically oriented to the genetic background of the host as part of a personalized-medicine approach.

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Sulfurospirillum cavolei sp. nov., a facultatively anaerobic sulfur-reducing bacterium isolated from an underground crude oil storage cavity

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64823-0 ◽

2007 ◽

Vol 57 (4) ◽

pp. 827-831 ◽

Cited By ~ 53

Author(s):

Yumiko Kodama ◽

Le Thu Ha ◽

Kazuya Watanabe

Keyword(s):

Carbon Source ◽

Crude Oil ◽

Dna Hybridization ◽

Gene Sequence ◽

Sequence Similarity ◽

Rrna Gene ◽

The Novel ◽

Facultatively Anaerobic ◽

Oil Storage ◽

Curved Rods

A novel facultatively anaerobic sulfur-reducing bacterium, designated strain Phe91T, was isolated from petroleum-contaminated groundwater in an underground crude oil storage cavity at Kuji in Iwate, Japan. Cells of strain Phe91T were slightly curved rods with single polar flagella. Optimum growth was observed at pH 7.0 and 30 °C. The novel strain utilized elemental sulfur, thiosulfate, sulfite, dithionite, arsenate, nitrate and DMSO as electron acceptors with lactate as an energy and carbon source, but nitrite was not utilized. Microaerophilic growth was also observed. Fumarate, pyruvate, lactate, malate, succinate, hydrogen (with acetate as a carbon source) and formate (with acetate) could serve as electron donors. Fumarate, pyruvate and malate were fermented. The DNA G+C content was 42.7 mol%. On the basis of 16S rRNA gene sequence phylogeny, strain Phe91T was affiliated with the genus Sulfurospirillum in the class Epsilonproteobacteria and was most closely related to Sulfurospirillum deleyianum (sequence similarity 97 %). However, the DNA–DNA hybridization value between strain Phe91T and S. deleyianum was only 14 %. Based on the physiological and phylogenetic data, Phe91T should be classified as a representative of a novel species in the genus Sulfurospirillum; the name Sulfurospirillum cavolei sp. nov. is proposed, with Phe91T (=JCM 13918T=DSM 18149T) as the type strain.

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Isolation and characterization of glycerol-fermenting bacteria from the rumen of red deer

Canadian Journal of Microbiology ◽

10.1139/m97-158 ◽

1997 ◽

Vol 43 (12) ◽

pp. 1102-1110 ◽

Cited By ~ 3

Author(s):

Graeme N. Jarvis ◽

Jürgen H. Thiele ◽

Carsten Strömpl ◽

Edward R. B. Moore

Keyword(s):

16S Rrna ◽

Cervus Elaphus ◽

Red Deer ◽

Rrna Gene ◽

Bacterial Strains ◽

Glycerol Fermentation ◽

Sequence Comparisons ◽

Fermentation Products ◽

Isolation And Characterization ◽

Fermenting Bacteria

The rumen contents of juvenile red deer (Cervus elaphus) were used as a source for the enrichment of obligately anaerobic glycerol-fermenting bacteria. Three bacterial strains were isolated from the 10−4 dilution (isolates DR6A and DR6B) and 10−9 dilution (isolate DR7) of the deer rumen contents. The isolates DR6A, DR6B, and DR7 produced ethanol (42 mM) and acetate (5 mM), propionate (31 mM) and acetate (42 mM), and formate (25 mM) and ethanol (38 mM), respectively, as the major glycerol fermentation products. Interestingly, acetate, propionate, and formate were observed to be the major glycerol fermentation products in mixed cultures obtained from the deer rumen. The three isolates were all shown to be related phylogenetically to the ruminal species Clostridium clostridiiforme, Clostridium celerecrescens, and Clostridium aerotolerans within the clostridial taxonomic cluster XIVa, on the basis of 16S rRNA gene sequence comparisons. But, because of phenotypic differences, each isolate is considered to be a new species within the genus Clostridium, which has not been previously described or isolated from the rumen ecosystem.Key words: red deer, ecology, glycerol fermentation, Clostridium, rumen, 16S rRNA.

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Isolation and characterization of bacteria associated with silkworm gut under antibiotic-treated larval feeding

Brazilian Journal of Biology ◽

10.1590/1519-6984.249664 ◽

2024 ◽

Vol 84 ◽

Author(s):

A. Javaid ◽

M. Hussain ◽

K. Aftab ◽

M. F. Malik ◽

M. Umar ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Close Relation ◽

Rrna Gene ◽

Bacterial Strains ◽

Larval Weight ◽

Silkworm Larvae ◽

Cocoon Production ◽

Isolation And Characterization

Abstract The impact of antibiotics on growth, cocoon production was assessed in addition to isolation and characterization of bacteria associated with silkworm gut of infected larvae. Larval rearing was maintained at recommended conditions of temperature and humidity. Silkworm larvae showing abnormal symptoms were collected from the control group and dissected for gut collection. Bacteria were isolated from the gut content by spreading on agar plates and incubated at 37 °C for 48 hrs. Bacterial identification and phylogenetic analysis were carried out by 16S rRNA gene sequencing. The isolated bacteria were subjected to antimicrobial susceptibility test (disc diffusion methods) by using Penicillin (10 µg/mL), Tetracycline (30 µg/mL), Amoxicillin (25 µg/mL), Ampicillin (10 µg/mL), and Erythromycin (15 µg/mL). All isolated strains showed positive results for the catalase test. We isolated and identified bacterial strains (n = 06) from the gut of healthy and diseased silkworm larvae. Based on the 16S rRNA gene sequence, isolated bacteria showed close relation with Serratia, Bacillus, and Pseudomonas spp. Notably, 83.3% of strains were resistant to Penicillin, Tetracycline, Amoxicillin, Ampicillin, and Erythromycin but 16.6% showed antibiotic susceptibility to the above-mentioned commonly used antibiotics. Silkworm larvae fed on penicillin-treated leaves showed significant improvement in larval weight, larval length, and cocoon production. Significantly higher larval weight (6.88g), larval length (5.84cm), and cocoon weight (1.33g) were recorded for larvae fed on leaves treated with penicillin as compared to other antibiotics. Isolated bacterial strains showed close relation with Serratia spp., Bacillus spp. and Pseudomonas spp.

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Isolation and Characterization of Metal-Reducing Thermoanaerobacter Strains from Deep Subsurface Environments of the Piceance Basin, Colorado

Applied and Environmental Microbiology ◽

10.1128/aem.68.12.6013-6020.2002 ◽

2002 ◽

Vol 68 (12) ◽

pp. 6013-6020 ◽

Cited By ~ 105

Author(s):

Yul Roh ◽

Shi V. Liu ◽

Guangshan Li ◽

Heshu Huang ◽

Tommy J. Phelps ◽

...

Keyword(s):

Iron Reduction ◽

Thermophilic Bacteria ◽

Ionic Composition ◽

Metabolic Inhibitors ◽

Rrna Gene ◽

Piceance Basin ◽

Bacterial Strains ◽

Deep Subsurface ◽

Isolation And Characterization ◽

Subsurface Environments

ABSTRACT Five bacterial strains were isolated from anaerobic enrichment cultures that had originated from inoculations with samples collected from the deep subsurface environments of the millions-of-years-old, geologically and hydrologically isolated Piceance Basin in Colorado. Small-subunit rRNA gene-based analyses indicated that all of these bacteria were closely related to Thermoanaerobacter ethanolicus, with similarities of 99.4 to 99.5%. Three isolates (X513, X514, and X561) from the five bacterial strains were used to examine physiological characteristics. These thermophilic bacteria were able to use acetate, glucose, hydrogen, lactate, pyruvate, succinate, and xylose as electron donors while reducing Fe(III), cobalt(III), chromium(VI), manganese(IV), and uranium(VI) at 60°C. One of the isolates (X514) was also able to utilize hydrogen as an electron donor for Fe(III) reduction. These bacteria exhibited diverse mineral precipitation capabilities, including the formation of magnetite (Fe3O4), siderite (FeCO3), rhodochrosite (MnCO3), and uraninite (UO2). The gas composition of the incubation headspace and the ionic composition of the incubation medium exerted profound influences on the types of minerals formed. The susceptibility of the thermophilic Fe(III)-reducing cultures to metabolic inhibitors specific for ferric reductase, hydrogenase, and electron transport indicated that iron reduction by these bacteria is an enzymatic process.

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Isolation and Characterization of Burkholderia gladioli from Orchids in Hawaii

Plant Disease ◽

10.1094/pd-89-1273 ◽

2005 ◽

Vol 89 (12) ◽

pp. 1273-1278 ◽

Cited By ~ 18

Author(s):

Lisa M. Keith ◽

Kelvin T. Sewake ◽

Francis T. Zee

Keyword(s):

Laboratory Data ◽

Molecular Characteristics ◽

Rrna Gene ◽

Cupric Sulfate ◽

Bacterial Strains ◽

Biochemical Tests ◽

Leaf Spots ◽

Gene Testing ◽

Isolation And Characterization ◽

Burkholderia Gladioli

Bacterial diseases of orchids continue to be serious problems. Bacterial strains were isolated from orchid plants exhibiting disease symptoms in Hawaii. Small to large leaf spots with or without water-soaking or soft rots were observed on various orchid genera, including Dendrobium, Oncidium, and Miltonia spp. and hybrids. Bacteria isolated and cultured from the lesions were tentatively identified using analytical profile index (API) strips and standard physiological and biochemical tests, and confirmed by species-specific polymerase chain reaction and sequencing of the 16S rRNA gene. The variation in pathogenic, morphological, cultural, and molecular characteristics of the orchid isolates also was evaluated. In our studies, a gramnegative, aerobic, rod-shaped bacterium that produced pale yellow, opaque, round colonies with entire margins on nutrient broth yeast extract agar (NBY) was isolated consistently from diseased orchid plants. On yeast dextrose calcium carbonate agar, the isolates produced brownishyellow, nonmucoid colonies, with the majority of the strains secreting a diffusible yellow or tan pigment into the media. The bacterium was identified as Burkholderia gladioli. Molecular analysis indicated very little diversity in the 16S rDNA gene. Testing B. gladioli isolates using media containing copper or streptomycin indicated varying levels of resistance (copper resistant = Cur; streptomycin resistant, Smr), with approximately 75% of the strains resistant to copper and 94% of the strains resistant to streptomycin. The minimum inhibitory concentration (MIC) of cupric sulfate among Cur strains ranged from 50 to 1,000 μg/ml and the MIC of streptomycin was 50 to 100 μg/ml for all Smr B. gladioli strains tested. Field and laboratory data suggest the frequent use of these chemicals in nurseries may have inadvertently resulted in the development of copper and streptomycin resistance in B. gladioli from orchids.

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Iron-Corroding Methanogen Isolated from a Crude-Oil Storage Tank

Applied and Environmental Microbiology ◽

10.1128/aem.00668-09 ◽

2010 ◽

Vol 76 (6) ◽

pp. 1783-1788 ◽

Cited By ~ 114

Author(s):

Taku Uchiyama ◽

Kimio Ito ◽

Koji Mori ◽

Hirohito Tsurumaru ◽

Shigeaki Harayama

Keyword(s):

Crude Oil ◽

Storage Tank ◽

Enrichment Culture ◽

Sole Source ◽

Microbiologically Influenced Corrosion ◽

Bottom Plate ◽

Rrna Gene ◽

Scanning Electron Micrographs ◽

Oil Storage ◽

Oil Storage Tank

ABSTRACT Microbiologically influenced corrosion of steel in anaerobic environments has been attributed to hydrogenotrophic microorganisms. A sludge sample collected from the bottom plate of a crude-oil storage tank was used to inoculate a medium containing iron (Fe0) granules, which was then incubated anaerobically at 37°C under an N2-CO2 atmosphere to enrich for microorganisms capable of using iron as the sole source of electrons. A methanogen, designated strain KA1, was isolated from the enrichment culture. An analysis of its 16S rRNA gene sequence revealed that strain KA1 is a Methanococcus maripaludis strain. Strain KA1 produced methane and oxidized iron much faster than did the type strain of M. maripaludis, strain JJT, which produced methane at a rate expected from the abiotic H2 production rate from iron. Scanning electron micrographs of iron coupons that had been immersed in either a KA1 culture, a JJT culture, or an aseptic medium showed that only coupons from the KA1 culture had corroded substantially, and these were covered with crystalline deposits that consisted mainly of FeCO3.

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Effective Removal of Alkanes and Polycyclic Aromatic Hydrocarbons by Bacteria from Soil Chronically Exposed to Crude Petroleum Oil

10.21203/rs.3.rs-207407/v1 ◽

2021 ◽

Author(s):

Eman Afkar ◽

Aly M. Hafez ◽

Rashid I.H. Ibrahim ◽

Munirah Aldayel

Keyword(s):

Polycyclic Aromatic Hydrocarbons ◽

Crude Oil ◽

Aromatic Hydrocarbons ◽

Oil Spills ◽

Practical Significance ◽

Gas Chromatography Mass Spectrometry ◽

Rrna Gene ◽

Bacterial Strains ◽

Polycyclic Aromatic ◽

Long Chain

Abstract In this study, two bacterial strains isolated from an oil-contaminated soil, designated as AramcoS2 and AramcoS4 were able to degrade crude oil, long-chain n-alkanes of C10 to C20; (n-decane, n-undecane, n-dodecane, n-tridecane, n-tetradecane, n-pentadecane, n-hexadecane, n-heptadecane, n-octadecane n-nonadecane, and n-eicosane) and polycyclic aromatic hydrocarbons (PAHs) including biphenyl, naphthalene, and anthracene. Gas chromatography-mass spectrometry (GC-MS) technique was conducted to analyze and identify the crude oil residues after biodegradation. AramcoS2 and AramcoS4 were able to reduce the concentration of long-chain n-alkanes of C10-C20 efficiently on average by 77% of the original concentration. Both isolates could also degrade PAHs on average by 67% of the original concentration within 7 and 14 days of incubation at 30ºC, pH=6.8±0.2. The 16S rRNA gene sequences of AramcoS2 and S4 classified these isolates as Actinobacteria; well-known alkanes and PAHs degraders. The nucleotide sequences of AramcoS2 and AramcoS4 were submitted to the GenBank database under the accession numbers MN142506 and MN142551, respectively. Both isolates can be used to restore the environments contaminated with crude oil components. They should be of great practical significance both in bioremediation of soil contaminated with crude oil and bio-treatment of oil spills on surface water.

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