scholarly journals Microbial Lithotrophic Oxidation of Structural Fe(II) in Biotite

2012 ◽  
Vol 78 (16) ◽  
pp. 5746-5752 ◽  
Author(s):  
Evgenya Shelobolina ◽  
Huifang Xu ◽  
Hiromi Konishi ◽  
Ravi Kukkadapu ◽  
Tao Wu ◽  
...  
Keyword(s):  
Nitrate Reduction ◽  
Enrichment Culture ◽  
Growth Yield ◽  
Initial Step ◽  
Organic Ligands ◽  
Granitic Rocks ◽  
Enzymatic Oxidation ◽  
Microbial Oxidation ◽  
Trioctahedral Mica ◽  
K Release

ABSTRACTMicroorganisms are known to participate in the weathering of primary phyllosilicate minerals through the production of organic ligands and acids and through the uptake of products of weathering. Here we show that the lithotrophic Fe(II)-oxidizing, nitrate-reducing enrichment culture described by Straub et al. (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl. Environ. Microbiol. 62:1458–1460, 1996) can grow via oxidation of structural Fe(II) in biotite, a Fe(II)-rich trioctahedral mica found in granitic rocks. Oxidation of silt/clay-sized biotite particles was detected by a decrease in extractable Fe(II) content and simultaneous nitrate reduction. Mössbauer spectroscopy confirmed structural Fe(II) oxidation. Approximately 1.5 × 107cells were produced per μmol of Fe(II) oxidized, in agreement with previous estimates of the growth yield of lithoautotrophic circumneutral-pH Fe(II)-oxidizing bacteria. Microbial oxidation of structural Fe(II) resulted in biotite alterations similar to those found in nature, including a decrease in the unit cell b dimension toward dioctahedral levels and Fe and K release. Structural Fe(II) oxidation may involve either direct enzymatic oxidation, followed by solid-state mineral transformation, or indirect oxidation as a result of the formation of aqueous Fe, followed by electron transfer from Fe(II) in the mineral to Fe(III) in solution. Although it is not possible to distinguish between these two mechanisms with available data, the complete absence of aqueous Fe in oxidation experiments favors the former alternative. The demonstration of microbial oxidation of structural Fe(II) suggests that microorganisms are directly responsible for the initial step in the weathering of biotite in granitic aquifers and the plant rhizosphere.

Denitrification with isopropanol as a carbon source in a biofilm system

1994 ◽  
Vol 30 (11) ◽  
pp. 69-78 ◽  
Author(s):  
Yongwoo Hwang ◽  
Hiroshi Sakuma ◽  
Toshihiro Tanaka
Keyword(s):  
Carbon Source ◽  
Nitrate Removal ◽  
Growth Yield ◽  
Pilot Scale ◽  
Denitrification Rate ◽  
Hydrogen Donor ◽  
Microbial Oxidation ◽  
Biological Denitrification ◽  
Batch Tests

Several batch tests and pilot-scale investigations on biological denitrification with isopropanol were performed. Isopropanol was converted to acetone by microbial oxidation during denitrification. Isopropanol itself little contributed to denitrification in practice while the converted acetone played a role of a main hydrogen donor. A larger quantity of nitrite intermediate was formed by using methanol compared to the case of isopropanol. The measured requirement of isopropanol was 2.0 mg mg−1 NO3-N, and was 2/3 of methanol. The oxygen equivalent of isopropanol for nitrate removal was almost the same as that of methanol. The denitrifier net growth yield for isopropanol was greater than for methanol. In order to maximize the denitrification rate, it is essential to convert isopropanol to acetone rapidly by accurate dosing for nitrogen load because the denitrification rate was accelerated by using acetone only. Excessive dose of isopropanol can cause a decrease in the denitrification rate as well as an increase of BOD in the effluent.

scholarly journals Life at the Energetic Edge: Kinetics of Circumneutral Iron Oxidation by Lithotrophic Iron-Oxidizing Bacteria Isolated from the Wetland-Plant Rhizosphere

2002 ◽  
Vol 68 (8) ◽  
pp. 3988-3995 ◽  
Author(s):  
Scott C. Neubauer ◽  
David Emerson ◽  
J. Patrick Megonigal
Keyword(s):  
Iron Oxidation ◽  
Growth Yield ◽  
Chemical Oxidation ◽  
Total Iron ◽  
Cellular Growth ◽  
Live Cells ◽  
Wetland Plant ◽  
Microbial Oxidation ◽  
Total Oxidation ◽  
Oxidation Rates

ABSTRACT Batch cultures of a lithotrophic Fe(II)-oxidizing bacterium, strain BrT, isolated from the rhizosphere of a wetland plant, were grown in bioreactors and used to determine the significance of microbial Fe(II) oxidation at circumneutral pH and to identify abiotic variables that affect the partitioning between microbial oxidation and chemical oxidation. Strain BrT grew only in the presence of an Fe(II) source, with an average doubling time of 25 h. In one set of experiments, Fe(II) oxidation rates were measured before and after the cells were poisoned with sodium azide. These experiments indicated that strain BrT accounted for 18 to 53% of the total iron oxidation, and the average cellular growth yield was 0.70 g of CH2O per mol of Fe(II) oxidized. In a second set of experiments, Fe(II) was constantly added to bioreactors inoculated with live cells, killed cells, or no cells. A statistical model fitted to the experimental data demonstrated that metabolic Fe(II) oxidation accounted for up to 62% of the total oxidation. The total Fe(II) oxidation rates in these experiments were strongly limited by the rate of Fe(II) delivery to the system and were also influenced by O2 and total iron concentrations. Additionally, the model suggested that the microbes inhibited rates of abiotic Fe(II) oxidation, perhaps by binding Fe(II) to bacterial exopolymers. The net effect of strain BrT was to accelerate total oxidation rates by up to 18% compared to rates obtained with cell-free treatments. The results suggest that neutrophilic Fe(II)-oxidizing bacteria may compete for limited O2 in the rhizosphere and therefore influence other wetland biogeochemical cycles.

Oxidation of inorganic sulfur compounds: Chemical and enzymatic reactions

1999 ◽  
Vol 45 (2) ◽  
pp. 97-105 ◽  
Author(s):  
Isamu Suzuki
Keyword(s):  
Sulfur Oxidation ◽  
Chemical Oxidation ◽  
Sulfur Compounds ◽  
Enzymatic Oxidation ◽  
Enzymatic Reactions ◽  
Oxidation Reactions ◽  
Microbial Oxidation ◽  
Inorganic Sulfur ◽  
Nucleophilic Cleavage ◽  
Oxidation Of Sulfur Compounds

Microbial oxidation of inorganic sulfur compounds is governed by both chemical and enzymatic reactions. It is therefore essential to understand reactions possible in chemistry when we consider enzymatic reactions. Various oxidation states of sulfur atoms in inorganic sulfur compounds and chemical oxidation reactions as well as nucleophilic cleavage of sulfur-sulfur bonds are discussed. The scheme of enzymatic oxidation of sulfur compounds with S2-→> S0→> SO32-→> SO42-as the main oxidation pathway is discussed with thiosulfate and polythionates leading into the main pathway for complete oxidation to sulfate. Enzymatic reactions are related to chemical reactions and the use of inhibitors for S0→> SO32-and SO32-→> SO42-is discussed for analyzing and establishing reaction stoichiometries. The proposed pathway is supported by a variety of evidence in many different microorganisms including some genetic evidence if the oxidation steps include all the systems irrespective of oxidizing agents (O2, Fe3+, cytochromes etc.).Key words: sulfur, oxidation, chemical, enzymatic, reactions.

Multidimensional Reveal of Nitrogen Regulation on Comammox

2020 ◽  
Author(s):  
Yuxiang Zhao ◽  
Jiajie Hu ◽  
Weiling Yang ◽  
Jiaqi Wang ◽  
Zhongjun Jia ◽  
...  
Keyword(s):  
Nitrogen Source ◽  
Nitrate Reduction ◽  
Ammonia Oxidation ◽  
Enrichment Culture ◽  
Ammonia Oxidizer ◽  
Nitrification Rate ◽  
Ammonia Oxidizing Bacteria ◽  
Metagenomic Sequencing ◽  
Sole Nitrogen Source ◽  
Total Bacteria

Abstract Background The discovery of complete ammonia oxidizer (comammox) was groundbreaking. Comammox can use ammonia as the sole nitrogen source and turn it to nitrate. Moreover, genomic data indicated that comammox contained genes which can metabolize urea and nitrite. However, the feasibility of enriching comammox with urea and nitrite in long term has not been proved. This study enriched comammox’s culture by using nitrite in reactor SA and urea in reactor SB. Results The nitrification rate of reactor SB (1.29 mg N·g -1 biofilm · d -1 ) was higher than that in reactor SA (0.6 mg N · g -1 biofilm · d -1 ) at the 390 th day. Comammox outnumbered ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in both reactor SA (9.04 × 10 9 copies / g biofilm) and reactor SB (5.34×10 10 copies/ g biofilm). In reactor SA, comammox’s amoA accounted for 92% of the total amoA, which was higher than that in reactor SB (85%). However, the percentage of comammox (4%) in total bacteria was much lower than reactor SB (14%). The results of metagenomic sequencing showed that all the pathways of nitrogen cycle including nitrification, nitrogen fixation, denitrification, assimilation nitrate reduction, and dissimilation nitrate reduction can be detected in both reactor SA and reactor SB except the anammox pathway. The genes related to nitrite oxidation and nitrate reduction in reactor SA (TPM = 5099; TPM = 3329) was higher than that of in reactor SB (TPM = 4071; TPM = 2984), presumably due to the demand of turning nitrite to nitrate and turning nitrate to ammonia. While genes related to ammonia oxidation and urea metabolism in reactor SB (TPM = 3915; TPM = 3638) was higher than that in reactor SA (TPM = 2708; TPM = 3002). Conclusion Nitrite and urea can regulate the enrichment culture of comammox by converting its metabolic pathway. Using nitrite as sole nitrogen source can improve the proportion comammox’s amoA in total amoA while using urea as the sole nitrogen source may increase comammox’s proportion in total bacteria. These results can accelerate the enrichment of comammox and facilitate the promotion of comammox’s engineering operation.

scholarly journals Biodegradation of cis-Dichloroethene as the Sole Carbon Source by a β-Proteobacterium

2002 ◽  
Vol 68 (6) ◽  
pp. 2726-2730 ◽  
Author(s):  
Nicholas V. Coleman ◽  
Timothy E. Mattes ◽  
James M. Gossett ◽  
Jim C. Spain
Keyword(s):  
Enrichment Culture ◽  
Growth Yield ◽  
Utilization Rate ◽  
Specific Substrate ◽  
Resting Cells ◽  
Aerobic Bacterium ◽  
16S Ribosomal Dna ◽  
Epoxidation Reaction ◽  
Specific Substrate Utilization Rate ◽  
Ribosomal Dna Sequence

ABSTRACT An aerobic bacterium capable of growth on cis-dichloroethene (cDCE) as a sole carbon and energy source was isolated by enrichment culture. The 16S ribosomal DNA sequence of the isolate (strain JS666) had 97.9% identity to the sequence from Polaromonas vacuolata, indicating that the isolate was a β-proteobacterium. At 20°C, strain JS666 grew on cDCE with a minimum doubling time of 73 ± 7 h and a growth yield of 6.1 g of protein/mol of cDCE. Chloride analysis indicated that complete dechlorination of cDCE occurred during growth. The half-velocity constant for cDCE transformation was 1.6 ± 0.2 μM, and the maximum specific substrate utilization rate ranged from 12.6 to 16.8 nmol/min/mg of protein. Resting cells grown on cDCE could transform cDCE, ethene, vinyl chloride, trans-dichloroethene, trichloroethene, and 1,2-dichloroethane. Epoxyethane was produced from ethene by cDCE-grown cells, suggesting that an epoxidation reaction is the first step in cDCE degradation.

scholarly journals Insights into Nitrate-Reducing Fe(II) Oxidation Mechanisms through Analysis of Cell-Mineral Associations, Cell Encrustation, and Mineralogy in the Chemolithoautotrophic Enrichment Culture KS

2017 ◽  
Vol 83 (13) ◽  
Author(s):  
M. Nordhoff ◽  
C. Tominski ◽  
M. Halama ◽  
J. M. Byrne ◽  
M. Obst ◽  
...  
Keyword(s):  
Nitrate Reduction ◽  
Reactive Nitrogen Species ◽  
Enrichment Culture ◽  
Green Rust ◽  
Reactive Nitrogen ◽  
Nitrogen Species ◽  
Content Type ◽  
Nitrate Reducers ◽  
Mineral Associations ◽  
Mixotrophic Conditions

ABSTRACT Most described nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOB) are mixotrophic and depend on organic cosubstrates for growth. Encrustation of cells in Fe(III) minerals has been observed for mixotrophic NRFeOB but not for autotrophic phototrophic and microaerophilic Fe(II) oxidizers. So far, little is known about cell-mineral associations in the few existing autotrophic NRFeOB. Here, we investigate whether the designated autotrophic Fe(II)-oxidizing strain (closely related to Gallionella and Sideroxydans) or the heterotrophic nitrate reducers that are present in the autotrophic nitrate-reducing Fe(II)-oxidizing enrichment culture KS form mineral crusts during Fe(II) oxidation under autotrophic and mixotrophic conditions. In the mixed culture, we found no significant encrustation of any of the cells both during autotrophic oxidation of 8 to 10 mM Fe(II) coupled to nitrate reduction and during cultivation under mixotrophic conditions with 8 to 10 mM Fe(II), 5 mM acetate, and 4 mM nitrate, where higher numbers of heterotrophic nitrate reducers were present. Two pure cultures of heterotrophic nitrate reducers (Nocardioides and Rhodanobacter) isolated from culture KS were analyzed under mixotrophic growth conditions. We found green rust formation, no cell encrustation, and only a few mineral particles on some cell surfaces with 5 mM Fe(II) and some encrustation with 10 mM Fe(II). Our findings suggest that enzymatic, autotrophic Fe(II) oxidation coupled to nitrate reduction forms poorly crystalline Fe(III) oxyhydroxides and proceeds without cellular encrustation while indirect Fe(II) oxidation via heterotrophic nitrate-reduction-derived nitrite can lead to green rust as an intermediate mineral and significant cell encrustation. The extent of encrustation caused by indirect Fe(II) oxidation by reactive nitrogen species depends on Fe(II) concentrations and is probably negligible under environmental conditions in most habitats. IMPORTANCE Most described nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOB) are mixotrophic (their growth depends on organic cosubstrates) and can become encrusted in Fe(III) minerals. Encrustation is expected to be harmful and poses a threat to cells if it also occurs under environmentally relevant conditions. Nitrite produced during heterotrophic denitrification reacts with Fe(II) abiotically and is probably the reason for encrustation in mixotrophic NRFeOB. Little is known about cell-mineral associations in autotrophic NRFeOB such as the enrichment culture KS. Here, we show that no encrustation occurs in culture KS under autotrophic and mixotrophic conditions while heterotrophic nitrate-reducing isolates from culture KS become encrusted. These findings support the hypothesis that encrustation in mixotrophic cultures is caused by the abiotic reaction of Fe(II) with nitrite and provide evidence that Fe(II) oxidation in culture KS is enzymatic. Furthermore, we show that the extent of encrustation caused by indirect Fe(II) oxidation by reactive nitrogen species depends on Fe(II) concentrations and is probably negligible in most environmental habitats.

Nitrate reduction coupled with microbial oxidation of sulfide in river sediment

2012 ◽  
Vol 12 (9) ◽  
pp. 1435-1444 ◽  
Author(s):  
Xunan Yang ◽  
Shan Huang ◽  
Qunhe Wu ◽  
Renduo Zhang
Keyword(s):  
Nitrate Reduction ◽  
River Sediment ◽  
Microbial Oxidation

scholarly journals Characterization of an Isolate That Uses Vinyl Chloride as a Growth Substrate under Aerobic Conditions

2000 ◽  
Vol 66 (8) ◽  
pp. 3535-3542 ◽  
Author(s):  
Matthew F. Verce ◽  
Ricky L. Ulrich ◽  
David L. Freedman
Keyword(s):  
Vinyl Chloride ◽  
Suspended Solids ◽  
Specific Growth ◽  
Enrichment Culture ◽  
Initial Step ◽  
Aerobic Biodegradation ◽  
Utilization Rate ◽  
Rrna Gene ◽  
Donor Source

ABSTRACT An aerobic enrichment culture was developed by using vinyl chloride (VC) as the sole organic carbon and electron donor source. VC concentrations as high as 7.3 mM were biodegraded without apparent inhibition. VC use did not occur when nitrate was provided as the electron acceptor. A gram-negative, rod-shaped, motile isolate was obtained from the enrichment culture and identified based on biochemical characteristics and the sequence of its 16S rRNA gene asPseudomonas aeruginosa, designated strain MF1. The observed yield of MF1 when it was grown on VC was 0.20 mg of total suspended solids (TSS)/mg of VC. Ethene, acetate, glyoxylate, and glycolate also served as growth substrates, while ethane, chloroacetate, glycolaldehyde, and phenol did not. Stoichiometric release of chloride and minimal accumulation of soluble metabolites following VC consumption indicated that the predominant fate for VC is mineralization and incorporation into cell material. MF1 resumed consumption of VC after at least 24 days when none was provided, unlike various mycobacteria that lost their VC-degrading ability after brief periods in the absence of VC. When deprived of oxygen for 2.5 days, MF1 did not regain the ability to grow on VC, and a portion of the VC was transformed into VC-epoxide. Acetylene inhibited VC consumption by MF1, suggesting the involvement of a monooxygenase in the initial step of VC metabolism. The maximum specific VC utilization rate for MF1 was 0.41 μmol of VC/mg of TSS/day, the maximum specific growth rate was 0.0048/day, and the Monod half-saturation coefficient was 0.26 μM. A higher yield and faster kinetics occurred when MF1 grew on ethene. When grown on ethene, MF1 was able to switch to VC as a substrate without a lag. It therefore appears feasible to grow MF1 on a nontoxic substrate and then apply it to environments that do not exhibit a capacity for aerobic biodegradation of VC.

scholarly journals Stable Isotopic Studies of n-Alkane Metabolism by a Sulfate-Reducing Bacterial Enrichment Culture

2005 ◽  
Vol 71 (12) ◽  
pp. 8174-8182 ◽  
Author(s):  
Irene A. Davidova ◽  
Lisa M. Gieg ◽  
Mark Nanny ◽  
Kevin G. Kropp ◽  
Joseph M. Suflita
Keyword(s):  
Enrichment Culture ◽  
Initial Step ◽  
Gas Chromatography Mass Spectrometry ◽  
Resonance Spectroscopy ◽  
Sulfate Reducing ◽  
Cell Extracts ◽  
Stable Isotopic ◽  
Isotopic Studies ◽  
Fumarate Addition ◽  
Metabolism Analysis

ABSTRACT Gas chromatography-mass spectrometry and nuclear magnetic resonance spectroscopy were used to study the metabolism of deuterated n-alkanes (C6 to C12) and 1-13C-labeled n-hexane by a highly enriched sulfate-reducing bacterial culture. All substrates were activated via fumarate addition to form the corresponding alkylsuccinic acid derivatives as transient metabolites. Formation of d 14-hexylsuccinic acid in cell extracts from exogenously added, fully deuterated n-hexane confirmed that this reaction was the initial step in anaerobic alkane metabolism. Analysis of resting cell suspensions amended with 1-13C-labeled n-hexane confirmed that addition of the fumarate occurred at the C-2 carbon of the parent substrate. Subsequent metabolism of hexylsuccinic acid resulted in the formation of 4-methyloctanoic acid, and 3-hydroxy-4-methyloctanoic acid was tentatively identified. We also found that 13C nuclei from 1-13C-labeled n-hexane became incorporated into the succinyl portion of the initial metabolite in a manner that indicated that 13C-labeled fumarate was formed and recycled during alkane metabolism. Collectively, the findings obtained with a sulfate-reducing culture using isotopically labeled alkanes augment and support the previously proposed pathway (H. Wilkes, R. Rabus, T. Fischer, A. Armstroff, A. Behrends, and F. Widdel, Arch. Microbiol. 177:235-243, 2002) for metabolism of deuterated n-hexane by a denitrifying bacterium.

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