d-Lactate metabolism and the obligate requirement for CO2 during growth on nitrite by the facultative lithoautotroph Nitrobacter hamburgensis

Starkenburg, Shawn R.; Arp, Daniel J.; Bottomley, Peter J.

doi:10.1099/mic.0.2008/018085-0

Cited by 11 publications

(8 citation statements)

References 28 publications

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“…It is possible that some NOB tended to use the simple organic carbon from the organic fertilizer or the organic products decomposed by fungi. Previous studies have shown that facultative/mixotrophic NOB were found to assimilate a narrow range of simple organic carbon compounds (e.g., acetate, D -lactate, pyruvate and glycerol) ( Bock, 1976 ; Starkenburg et al, 2008 ). Fertilizer-induced shifts in nitrifier community composition may be explained by the direct/indirect effects of selective feeding on certain nutrient substance types as a result of the general effect of fertilizer on environmental conditions.…”

Section: Discussionmentioning

confidence: 99%

Nitrite-Oxidizing Bacteria Community Composition and Diversity Are Influenced by Fertilizer Regimes, but Are Independent of the Soil Aggregate in Acidic Subtropical Red Soil

Han

Luo

et al. 2018

Front. Microbiol.

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Nitrification is the two-step aerobic oxidation of ammonia to nitrate via nitrite in the nitrogen-cycle on earth. However, very limited information is available on how fertilizer regimes affect the distribution of nitrite oxidizers, which are involved in the second step of nitrification, across aggregate size classes in soil. In this study, the community compositions of nitrite oxidizers (Nitrobacter and Nitrospira) were characterized from a red soil amended with four types of fertilizer regimes over a 26-year fertilization experiment, including control without fertilizer (CK), swine manure (M), chemical fertilization (NPK), and chemical/organic combined fertilization (MNPK). Our results showed that the addition of M and NPK significantly decreased Nitrobacter Shannon and Chao1 index, while M and MNPK remarkably increased Nitrospira Shannon and Chao1 index, and NPK considerably decreased Nitrospira Shannon and Chao1 index, with the greatest diversity achieved in soils amended with MNPK. However, the soil aggregate fractions had no impact on that alpha-diversity of Nitrobacter and Nitrospira under the fertilizer treatment. Soil carbon, nitrogen and phosphorus in the soil had a significant correlation with Nitrospira Shannon and Chao1 diversity index, while total potassium only had a significant correlation with Nitrospira Shannon diversity index. However, all of them had no significant correlation with Nitrobacter Shannon and Chao1 diversity index. The resistance indices for alpha-diversity indexes (Shannon and Chao1) of Nitrobacter were higher than those of Nitrospira in response to the fertilization regimes. Manure fertilizer is important in enhancing the Nitrospira Shannon and Chao1 index resistance. Principal co-ordinate analysis revealed that Nitrobacter- and Nitrospira-like NOB communities under four fertilizer regimes were differentiated from each other, but soil aggregate fractions had less effect on the nitrite oxidizers community. Redundancy analysis and Mantel test indicated that soil nitrogen, carbon, phosphorus, and available potassium content were important environmental attributes that control the Nitrobacter- and Nitrospira-like NOB community structure across different fertilization treatments under aggregate levels in the red soil. In general, nitrite-oxidizing bacteria community composition and alpha-diversity are depending on fertilizer regimes, but independent of the soil aggregate.

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Section: Discussionmentioning

confidence: 99%

Nitrite-Oxidizing Bacteria Community Composition and Diversity Are Influenced by Fertilizer Regimes, but Are Independent of the Soil Aggregate in Acidic Subtropical Red Soil

Han

Luo

et al. 2018

Front. Microbiol.

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“…The growth rate of N. europaea under such conditions was lower than the growth rate on CO 2 , but a high growth yield was observed (17). Enhanced growth yield and rate have also been reported for Nitrobacter hamburgensis (NOB) when D-lactate and NO 2 Ϫ were supplied as the sole carbon source and as energy source, respectively (52). Similarly, Nitrospira appeared to simultaneously assimilate inorganic and organic carbon (e.g., pyruvate), but it is still unclear whether Nitrospira spp.…”

mentioning

confidence: 89%

“…A likely explanation for this discrepancy is that the AOB were utilizing organic compounds as a carbon source in the low-DO systems, decreasing the need for an energetically expensive reductive process to convert CO 2 to cellular carbon inherent in autotrophic metabolism. In contrast, mixotrophic metabolism reduces the energy requirement for cell synthesis as organic carbon is used, thereby increasing the cell yield (17,43,52,62). Chemolithoorganotrophic growth of AOB has been demonstrated under anoxic conditions where molecular oxygen is replaced with nitrogen dioxide or nitrogen tetroxide as electron acceptor and pyruvate or lactate is replaced with CO 2 as carbon source (24,48).…”

Section: Vol 77 2011 High Yield Of Aob In Low-do Systems 7791mentioning

confidence: 99%

Low-Dissolved-Oxygen Nitrifying Systems Exploit Ammonia-Oxidizing Bacteria with Unusually High Yields

Bellucci

Ofiţeru

Graham

et al. 2011

Appl Environ Microbiol

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In wastewater treatment plants, nitrifying systems are usually operated with elevated levels of aeration to avoid nitrification failures. This approach contributes significantly to operational costs and the carbon footprint of nitrifying wastewater treatment processes. In this study, we tested the effect of aeration rate on nitrification by correlating ammonia oxidation rates with the structure of the ammonia-oxidizing bacterial (AOB) community and AOB abundance in four parallel continuous-flow reactors operated for 43 days. Two of the reactors were supplied with a constant airflow rate of 0.1 liter/min, while in the other two units the airflow rate was fixed at 4 liters/min. Complete nitrification was achieved in all configurations, though the dissolved oxygen (DO) concentration was only 0.5 ؎ 0.3 mg/liter in the low-aeration units. The data suggest that efficient performance in the low-DO units resulted from elevated AOB levels in the reactors and/or putative development of a mixotrophic AOB community. Denaturing gel electrophoresis and cloning of AOB 16S rRNA gene fragments followed by sequencing revealed that the AOB community in the low-DO systems was a subset of the community in the high-DO systems. However, in both configurations the dominant species belonged to the Nitrosomonas oligotropha lineage. Overall, the results demonstrated that complete nitrification can be achieved at low aeration in lab-scale reactors. If these findings could be extended to full-scale plants, it would be possible to minimize the operational costs and greenhouse gas emissions without risk of nitrification failure.The water industry is energy intensive. In the United Kingdom, the water industry uses 9 TWh, releasing 5 million tonnes (carbon dioxide equivalent) of greenhouse gases (GHGs) to the atmosphere per year (61). Driven by increasing operational power costs and the need to abate anthropogenic GHG release, the water industry is being forced to develop new lowenergy and cost-effective technologies. In activated sludge systems, particular regard should be given to nitrification, the two-step biological oxidation of ammonia to nitrate via nitrite. This process prevents excessive hazardous discharges of nitrogen into receiving waters. Conventional nitrification is carried out by the ammonia-oxidizing bacteria (AOB) and the nitriteoxidizing bacteria (NOB). The AOB, responsible for the first and often limiting step of nitrification (39), are generally considered to have a strictly chemolithoautotrophic aerobic metabolism, to grow slowly, and to be poor competitors for oxygen (22, 60). Consequently, nitrifying systems are usually operated at a solid retention time (SRT) longer than 5 days and dissolved oxygen (DO) concentration above 2 mg/liter to satisfy both carbon and nitrogen removal requirements and to overcome diffusional resistance in the flocs (59).However, there is evidence that complete nitrification can also occur at low DO levels (Ͻ0.5 mg/liter) (35) or with intermittent aeration (30). Also, a recent theoretical study ...

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“…The Nitrobacter hamburgensis X14 strain oxidizes nitrite to conserve energy and is commonly used in nitrification research [8]. Although the strain was isolated more than 100 years ago [9], limited research on this strain has been published due to the lack of genetic manipulation tools.…”

Section: Introductionmentioning

confidence: 99%

A Mimicking-of-DNA-Methylation-Patterns Pipeline for Overcoming the Restriction Barrier of Bacteria

et al. 2012

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Genetic transformation of bacteria harboring multiple Restriction-Modification (R-M) systems is often difficult using conventional methods. Here, we describe a mimicking-of-DNA-methylation-patterns (MoDMP) pipeline to address this problem in three difficult-to-transform bacterial strains. Twenty-four putative DNA methyltransferases (MTases) from these difficult-to-transform strains were cloned and expressed in an Escherichia coli strain lacking all of the known R-M systems and orphan MTases. Thirteen of these MTases exhibited DNA modification activity in Southwestern dot blot or Liquid Chromatography–Mass Spectrometry (LC–MS) assays. The active MTase genes were assembled into three operons using the Saccharomyces cerevisiae DNA assembler and were co-expressed in the E. coli strain lacking known R-M systems and orphan MTases. Thereafter, results from the dot blot and restriction enzyme digestion assays indicated that the DNA methylation patterns of the difficult-to-transform strains are mimicked in these E. coli hosts. The transformation of the Gram-positive Bacillus amyloliquefaciens TA208 and B. cereus ATCC 10987 strains with the shuttle plasmids prepared from MoDMP hosts showed increased efficiencies (up to four orders of magnitude) compared to those using the plasmids prepared from the E. coli strain lacking known R-M systems and orphan MTases or its parental strain. Additionally, the gene coding for uracil phosphoribosyltransferase (upp) was directly inactivated using non-replicative plasmids prepared from the MoDMP host in B. amyloliquefaciens TA208. Moreover, the Gram-negative chemoautotrophic Nitrobacter hamburgensis strain X14 was transformed and expressed Green Fluorescent Protein (GFP). Finally, the sequence specificities of active MTases were identified by restriction enzyme digestion, making the MoDMP system potentially useful for other strains. The effectiveness of the MoDMP pipeline in different bacterial groups suggests a universal potential. This pipeline could facilitate the functional genomics of the strains that are difficult to transform.

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d-Lactate metabolism and the obligate requirement for CO2 during growth on nitrite by the facultative lithoautotroph Nitrobacter hamburgensis

Cited by 11 publications

References 28 publications

Nitrite-Oxidizing Bacteria Community Composition and Diversity Are Influenced by Fertilizer Regimes, but Are Independent of the Soil Aggregate in Acidic Subtropical Red Soil

Nitrite-Oxidizing Bacteria Community Composition and Diversity Are Influenced by Fertilizer Regimes, but Are Independent of the Soil Aggregate in Acidic Subtropical Red Soil

Low-Dissolved-Oxygen Nitrifying Systems Exploit Ammonia-Oxidizing Bacteria with Unusually High Yields

A Mimicking-of-DNA-Methylation-Patterns Pipeline for Overcoming the Restriction Barrier of Bacteria

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