Transcriptome of a
            <i>Nitrosomonas europaea</i>
            Mutant with a Disrupted Nitrite Reductase Gene (
            <i>nirK</i>
            )

Cho, Catherine Mee-Hie; Tao, Yan; Liu, Xueduan; Wu, Liyou; Zhou, Jizhong; Stein, Lisa Y.

doi:10.1128/aem.02958-05

Cited by 40 publications

(30 citation statements)

References 29 publications

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“…gene cluster was up-regulated in a nitrite reductase-deficient mutant of Nitrosomonas europaea, indicating involvement of sNOR in the nitrosative stress response (10).…”

Section: Vol 74 2008mentioning

confidence: 94%

Complete Genome Sequence of Nitrobacter hamburgensis X14 and Comparative Genomic Analysis of Species within the Genus Nitrobacter

Starkenburg

Larimer

Stein

et al. 2008

Appl Environ Microbiol

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105

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The alphaproteobacterium Nitrobacter hamburgensis X14 is a gram-negative facultative chemolithoautotroph that conserves energy from the oxidation of nitrite to nitrate. Sequencing and analysis of the Nitrobacter hamburgensis X14 genome revealed four replicons comprised of one chromosome (4.4 Mbp) and three plasmids (294, 188, and 121 kbp). Over 20% of the genome is composed of pseudogenes and paralogs. Whole-genome comparisons were conducted between N. hamburgensis and the finished and draft genome sequences of Nitrobacter winogradskyi and Nitrobacter sp. strain Nb-311A, respectively. Most of the plasmid-borne genes were unique to N. hamburgensis and encode a variety of functions (central metabolism, energy conservation, conjugation, and heavy metal resistance), yet ϳ21 kb of a ϳ28-kb "autotrophic" island on the largest plasmid was conserved in the chromosomes of Nitrobacter winogradskyi Nb-255 and Nitrobacter sp. strain Nb-311A. The N. hamburgensis chromosome also harbors many unique genes, including those for heme-copper oxidases, cytochrome b 561 , and putative pathways for the catabolism of aromatic, organic, and one-carbon compounds, which help verify and extend its mixotrophic potential. A Nitrobacter "subcore" genome was also constructed by removing homologs found in strains of the closest evolutionary relatives, Bradyrhizobium japonicum and Rhodopseudomonas palustris. Among the Nitrobacter subcore inventory (116 genes), copies of genes or gene clusters for nitrite oxidoreductase (NXR), cytochromes associated with a dissimilatory nitrite reductase (NirK), PII-like regulators, and polysaccharide formation were identified. Many of the subcore genes have diverged significantly from, or have origins outside, the alphaproteobacterial lineage and may indicate some of the unique genetic requirements for nitrite oxidation in Nitrobacter.Nitrification is a two-step process by which ammonia is converted to nitrate via nitrite. Nitrification plays a key role in transformation of fertilizer nitrogen in agricultural systems and is a key component of nitrogen removal in wastewater treatment. Production of soluble inorganic nitrogen by nitrification can lead to the contamination and eutrophication of terrestrial and aquatic ecosystems, while the gaseous products of nitrifier denitrification, nitric oxide (NO) and nitrous oxide (N 2 O), destroy stratospheric ozone and greatly contribute to global warming (26, 54, 61). Nitrite-oxidizing bacteria (NOB) participate in the process of nitrification by converting nitrite (NO 2 Ϫ ), the end product of ammonia oxidation, into nitrate (NO 3 Ϫ ) according to the following reaction; NO 2Nitrite also functions as an electron donor for the reduction of NAD ϩ via reverse electron flow as well as for the generation of ATP by oxidative phosphorylation (17).Although several phylogenetically distinct genera (Nitrospira, Nitrobacter, Nitrococcus, and Nitrospina) carry out NO 2 Ϫ oxidation, most of what is known about the physiology and biochemistry of NOB has been derived from studies of t...

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“…gene cluster was up-regulated in a nitrite reductase-deficient mutant of Nitrosomonas europaea, indicating involvement of sNOR in the nitrosative stress response (10).…”

Section: Vol 74 2008mentioning

confidence: 94%

Complete Genome Sequence of Nitrobacter hamburgensis X14 and Comparative Genomic Analysis of Species within the Genus Nitrobacter

Starkenburg

Larimer

Stein

et al. 2008

Appl Environ Microbiol

Self Cite

105

View full text Add to dashboard Cite

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“…Standards for qPCR were generated by PCR amplifying the amoA gene from the genomic DNA of Nitrosomonas europaea [43]. The PCR products were confirmed on an agarose gel and then cloned into a pGEM-T Easy vector following the manufacturer's instructions (Promega, Madison, Wis, USA).…”

Section: Microbial Community Composition and Dynamicsmentioning

confidence: 99%

Impact of Indian Mustard (Brassica juncea) and Flax (Linum usitatissimum) Seed Meal Applications on Soil Carbon, Nitrogen, and Microbial Dynamics

Wang

Hollister

et al. 2012

Applied and Environmental Soil Science

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There is a critical need to investigate how land application of dedicated biofuel oilseed meals affects soil ecosystems. In this study, mustard (Brassica juncea) and flax (Linum usitatissimum) seed meals and sorghum-sudangrass (Sorghum bicolor) were added to soil at levels of 0, 1, 2.5, and 5% (w/w). Both the type of amendment and application rate affected soil organic C, total C & N, and C & N mineralization. Mustard meal amendment initially inhibited C mineralization as compared to flax, but >50% of mustard and flax organic C was mineralized within 51 d. Nitrogen mineralization was similar for flax and mustard, except for the 2.5% rate for which a lower proportion of mustard N was converted to nitrate. The mustard meal greatly impacted microbial community composition, appearing to select for specific fungal populations. The potential varying impacts of different oilseed meals on soil ecosystems should be considered when developing recommendations for land application.

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“…These studies have mainly utilized Nitrosomonas europaea or Nitrosomonas eutropha, two relatively fast-growing AOB often found in nutrientrich environments (29,(39)(40)(41)(42)(43). The AOB proteome analyses have focused on the effect of variable environmental or physiologic growth conditions, such as starvation (42), heavy-metal contamination (41), biofilm formation (43), and the effect of nitrogen dioxide (NO 2 ) or anoxia (40).…”

mentioning

confidence: 99%

Effects of Bacterial Community Members on the Proteome of the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain Is79

Sedlacek

Nielsen

Greis

et al. 2016

Appl Environ Microbiol

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Microorganisms in the environment do not exist as the often-studied pure cultures but as members of complex microbial communities. Characterizing the interactions within microbial communities is essential to understand their function in both natural and engineered environments. In this study, we investigated how the presence of a nitrite-oxidizing bacterium (NOB) and heterotrophic bacteria affect the growth and proteome of the chemolithoautotrophic ammonia-oxidizing bacterium (AOB) Nitrosomonas sp. strain Is79. We investigated Nitrosomonas sp. Is79 in co-culture with Nitrobacter winogradskyi, in co-cultures with selected heterotrophic bacteria, and as a member of the nitrifying enrichment culture G5-7. In batch culture, N. winogradskyi and heterotrophic bacteria had positive effects on the growth of Nitrosomonas sp. Is79. An isobaric tag for relative and absolute quantification (iTRAQ) liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was used to investigate the effect of N. winogradskyi and the co-cultured heterotrophic bacteria from G5-7 on the proteome of Nitrosomonas sp. Is79. In co-culture with N. winogradskyi, several Nitrosomonas sp. Is79 oxidative stress response proteins changed in abundance, with periplasmic proteins increasing and cytoplasmic proteins decreasing in abundance. In the presence of heterotrophic bacteria, the abundance of proteins directly related to the ammonia oxidation pathway increased, while the abundance of proteins related to amino acid synthesis and metabolism decreased. In summary, the proteome of Nitrosomonas sp. Is79 was differentially influenced by the presence of either N. winogradskyi or heterotrophic bacteria. Together, N. winogradskyi and heterotrophic bacteria reduced the oxidative stress for Nitrosomonas sp. Is79, which resulted in more efficient metabolism. IMPORTANCEAerobic ammonia-oxidizing microorganisms play an important role in the global nitrogen cycle, converting ammonia to nitrite. In their natural environment, they coexist and interact with nitrite oxidizers, which convert nitrite to nitrate, and with heterotrophic microorganisms. The presence of nitrite oxidizers and heterotrophic bacteria has a positive influence on the growth of the ammonia oxidizers. Here, we present a study investigating the effect of nitrite oxidizers and heterotrophic bacteria on the proteome of a selected ammonia oxidizer in a defined culture to elucidate how these two groups improve the performance of the ammonia oxidizer. The results show that the presence of a nitrite oxidizer and heterotrophic bacteria reduced the stress for the ammonia oxidizer and resulted in more efficient energy generation. This study contributes to our understanding of microbemicrobe interactions, in particular between ammonia oxidizers and their neighboring microbial community.

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Transcriptome of a Nitrosomonas europaea Mutant with a Disrupted Nitrite Reductase Gene ( nirK )

Cited by 40 publications

References 29 publications

Complete Genome Sequence of Nitrobacter hamburgensis X14 and Comparative Genomic Analysis of Species within the Genus Nitrobacter

Complete Genome Sequence of Nitrobacter hamburgensis X14 and Comparative Genomic Analysis of Species within the Genus Nitrobacter

Impact of Indian Mustard (Brassica juncea) and Flax (Linum usitatissimum) Seed Meal Applications on Soil Carbon, Nitrogen, and Microbial Dynamics

Effects of Bacterial Community Members on the Proteome of the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain Is79

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