Molecular analysis of ammonia oxidation and denitrification in natural environments

Bothe, Hermann; Jost, Günter; Schloter, Michael; Ward, Bettie; Witzel, Karl-Paul

doi:10.1111/j.1574-6976.2000.tb00566.x

Cited by 248 publications

(88 citation statements)

References 186 publications

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“…within the tissues of Pacific corals (13). Ralstonia is a broad genus of symbiotic bacteria; phylotypes belonging to this genus are capable of denitrification (48) and can be plant pathogens (49) and could therefore serve diverse roles within corals.…”

Section: Discussionmentioning

confidence: 99%

Distinguishing between Microbial Habitats Unravels Ecological Complexity in Coral Microbiomes

2016

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This study demonstrates that coral tissue or mucus habitats structure the microbiome of corals and that separation of these habitats facilitates identification of consistent microbial associates. Using this approach, we demonstrated that sequences related to “Candidatus Amoebophilus,” recognized intracellular symbionts of amoebae, were highly associated with the tissues of Caribbean corals and possibly endosymbionts of a protistan host within corals, adding a further degree of intricacy to coral holobiont symbioses. Examining specific habitats within complex hosts such as corals is useful for targeting important microbial associations that may otherwise be masked by the sheer microbial diversity associated with all host habitats.

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Section: Discussionmentioning

confidence: 99%

Distinguishing between Microbial Habitats Unravels Ecological Complexity in Coral Microbiomes

2016

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“…Often used as a molecular probe for microbial denitrification, nir-encoded enzymes are responsible for reducing a mineralized form of nitrogen to a gaseous form (27)(28)(29)(30). Though previous studies have identified denitrification genes at hydrothermal vents (34,55,56), they were only recently detected at Lo 'ihi and in at least some Zetaproteobacteria as well via an annotated metagenomic assembly of a fosmid library (57).…”

Section: Discussionmentioning

confidence: 99%

“…The enzyme products (e.g., the product of nirK) are responsible for the conversion of nitrite to nitric oxide (or nitrous oxide). This is a key step in denitrification because it reduces mineralized nitrogen and helps differentiate denitrifiers from nitrate respirers (27)(28)(29)(30). Finally, the detection of arsenic resistance genes (arsC) in our metagenomic assembly from Pohaku Vents represents an exciting opportunity to investigate arsenic detoxification in microbial mat communities at Lo 'ihi.…”

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confidence: 99%

Quantitative PCR Analysis of Functional Genes in Iron-Rich Microbial Mats at an Active Hydrothermal Vent System (Lō'ihi Seamount, Hawai'i)

Jesser

Fullerton

Hager

et al. 2015

Appl Environ Microbiol

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The chemolithotrophic Zetaproteobacteria represent a novel class of Proteobacteria which oxidize Fe(II) to Fe(III) and are the dominant bacterial population in iron-rich microbial mats. Zetaproteobacteria were first discovered at Lo 'ihi Seamount, located 35 km southeast off the big island of Hawai'i, which is characterized by low-temperature diffuse hydrothermal venting. Novel nondegenerate quantitative PCR (qPCR) assays for genes associated with microbial nitrogen fixation, denitrification, arsenic detoxification, Calvin-Benson-Bassham (CBB), and reductive tricarboxylic acid (rTCA) cycles were developed using selected microbial mat community-derived metagenomes. Nitrogen fixation genes were not detected, but all other functional genes were present. This suggests that arsenic detoxification and denitrification processes are likely cooccurring in addition to two modes of carbon fixation. Two groups of microbial mat community types were identified by terminal restriction fragment length polymorphism (T-RFLP) and were further described based on qPCR data for zetaproteobacterial abundance and carbon fixation mode preference. qPCR variance was associated with mat morphology but not with temperature or sample site. Geochemistry data were significantly associated with sample site and mat morphology. Together, these qPCR assays constitute a functional gene signature for iron microbial mat communities across a broad array of temperatures, mat types, chemistries, and sampling sites at Lo 'ihi Seamount. Deep-sea hydrothermal vents are dynamic and extremely productive biological ecosystems supported by chemosynthetic microbial primary production. In the absence of photosynthesis, microorganisms derive energy via the oxidation of reduced chemicals [e.g., H 2 , H 2 S, Fe(II), and CH 4 ] emitted in hydrothermal fluids (1). In contrast to other strategies for microbial chemosynthesis at hydrothermal vents, iron oxidation has only more recently been studied (2). By weight, iron is the most abundant element in the earth, and it has vast potential as an energy source for microbes via chemolithoautotrophy coupled to Fe(II) oxidation (3). However, iron's ability to act as an electron donor for the biotic fixation of CO 2 in neutrophilic environments is limited by the rapid abiotic oxidation of Fe(II) to Fe(III) in the presence of oxygen (4, 5). Despite the ephemeral nature of iron as an energy source, iron-oxidizing bacteria (FeOB) have been identified in a wide array of freshwater and marine habitats and can flourish at circumneutral deep-sea vents with sharp redox gradients and hydrothermal fluids high in CO 2 and reduced iron (6-9). The recently described Zetaproteobacteria represent a novel class of marine Proteobacteria that are diverse and abundant contributors to deep-sea FeOB communities (10).Zetaproteobacteria were first discovered at iron-rich, low-temperature hydrothermal vents at Lo 'ihi Seamount, HI (2, 11), and have been demonstrated to be significant microbial colonizers of seamounts (10, 12). Lo 'ihi Seamount is a s...

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“…faecalis could aerobically reduce nitrite, and the nitrite reduction ability originated from the copper-containing nitrite reductase coded for by nirK (33,34). In the BES with an electrode as the sole electron donor, the reduction rates increased to 1.98, 4.37, and 3.91 mg/liter/h for Ϫ0.06, Ϫ0.15, and Ϫ0.30 V, respectively.…”

Section: Nitrate and Nitrite Reduction Enhanced By Cathode In Besmentioning

confidence: 99%

Enhanced Alcaligenes faecalis Denitrification Rate with Electrodes as the Electron Donor

Wang

Zeng

et al. 2015

Appl Environ Microbiol

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bThe utilization by Alcaligenes faecalis of electrodes as the electron donor for denitrification was investigated in this study. The denitrification rate of A. faecalis with a poised potential was greatly enhanced compared with that of the controls without poised potentials. For nitrate reduction, although A. faecalis could not reduce nitrate, at three poised potentials of ؉0.06, ؊0.06, and ؊0.15 V (versus normal hydrogen electrode [NHE]), the nitrate was partially reduced with ؊0.15-and ؊0.06-V potentials at rates of 17.3 and 28.5 mg/liter/day, respectively. The percentages of reduction for ؊0.15 and ؊0.06 V were 52.4 and 30.4%, respectively. Meanwhile, for nitrite reduction, the poised potentials greatly enhanced the nitrite reduction. The nitrite reduction rates for three poised potentials (؊0.06, ؊0.15, and ؊0.30 V) were 1.98, 4.37, and 3.91 mg/liter/h, respectively. When the potentials were cut off, the nitrite reduction rate was maintained for 1.5 h (from 2.3 to 2.25 mg/liter/h) and then greatly decreased, and the reduction rate (0.38 mg/liter/h) was about 1/6 compared with the rate (2.3 mg/liter/h) when potential was on. Then the potentials resumed, but the reduction rate did not resume and was only 2 times higher than the rate when the potential was off.A lcaligenes faecalis is a Gram-negative heterotrophic bacterium that is common in soil (1). A. faecalis was reported to aerobically produce nitrite (NO 2 Ϫ ), nitrate, nitric oxide (NO), and nitrous oxide in both peptone-meat extract and defined media with ammonium and citrate as the sole nitrogen and carbon sources (2). Nevertheless, A. faecalis also had denitrification ability as the bacterium had a copper-containing nitrite reductase that catalyzes the reduction of nitrite (NO 2 Ϫ ) to nitric oxide (NO) (3). Recent research by Lu et al. revealed that A. faecalis might be able to use extracellular electrons from semiconducting mineral photocatalysis for metabolism (4). In their study, with photoelectrons A. faecalis gradually became the dominant species in the soil microbial community, indicating this bacterium might have a potential to utilize photoelectrons (4).The interaction between microbes and solid minerals is becoming a worldwide hot spot in the field of geomicrobiology, an interdisciplinary field involving geology and microbiology. Especially, the electron flows between microbes and minerals (or electrodes) are a major research interest in this field. Currently, the models of microbes donating electrons to minerals (or electrodes) are categorized into three types: direct contact, electron shuttle, and microbial extracellular appendages (5). Direct contact between cells and the electrode surface will no doubt facilitate the electron exchanges (6). Under some circumstances, the environmental chemicals or microbially secreted chemicals could act as an electron shuttle, transferring electrons via redox reactions (7,8). Besides secreting chemical compounds, some bacteria have evolved extracellular structures, the conductive flagella called "nanowir...

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Molecular analysis of ammonia oxidation and denitrification in natural environments

Cited by 248 publications

References 186 publications

Distinguishing between Microbial Habitats Unravels Ecological Complexity in Coral Microbiomes

Distinguishing between Microbial Habitats Unravels Ecological Complexity in Coral Microbiomes

Quantitative PCR Analysis of Functional Genes in Iron-Rich Microbial Mats at an Active Hydrothermal Vent System (Lō'ihi Seamount, Hawai'i)

Enhanced Alcaligenes faecalis Denitrification Rate with Electrodes as the Electron Donor

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